STUDY OF ANTIBIOTIC RESISTANCE OF PENICILLIN

BINDING PROTEIN IN Clostridium perfrigens

A PROJECT SUBMITTED TO
SHIVAJI UNIVERSITY, KOLHAPUR

FOR THE DEGREE 0F

MASTER OF SCIENCE
IN
MICROBIOLOGY

UNDER THE FACULTY

OF SCIENCE BY
ANJUM MESTRI
PRIYA PARMANANDANI
PRIYANKA TIWARI
SAVITA BHOSALE
UNDER THE GUIDANCE OF

Dr. S. R. WAGHMARE Dr. K. D. SONAWANE

Co-Guide Guide

DEPARTMENT OF MICROBIOLOGY,
SHIVAJI UNIVERSITY, KOLHAPUR
2020-2021
 Department of Microbiology,
Shivaji University, Kolhapur

CERTIFICATE

This is to certify that the thesis entitled ― STUDY OF ANTIBIOTIC

RESISTANCE OF PENICILLIN BINDING PROTEIN IN Clostridium perfrigens” is

being submitted here with for the award of the Degree of M. Sc. in
Microbiology of Shivaji University, Kolhapur. The work reported in this Project
is based upon the results of the original work carried out Ms. ANJUM MESTRI,
Ms. PRIYA PARMANANDANI, Ms. PRIYANKA TIWARI, Ms. SAVITA BHOSALE
under my supervision and guidance. To the best of my knowledge and belief the
work embodied in this Project has not formed earlier the basis for the award of
any Degree or Diploma or similar title of this or any other University or
examining body.

Place: Kolhapur

Date:

Dr. S. R. Waghmare Prof. K. D. Sonawane Prof. K. D.Sonawane

(Co-Guide) (Guide) Coordinator
 DECLARATION

We hereby declare that the thesis ―STUDY OF ANTIBIOTIC

RESISTANCE OF PENICILLIN BINDING PROTEIN” completed and written by
us has not previously formed the basis for the award of any Degree or
Diploma or other similar title of this or any other University or examining
body.

Place: Kolhapur

Date:

Ms. ANJUM MESTRI

Ms. PRIYA PARMANANDANI
Ms. PRIYANKA TIWARI
Ms. SAVITA BHOSALE
 ACKNOWLEDGEMENT

We take this opportunity to express our sincere thanks towards the

Department of Microbiology, Shivaji University, Kolhapur for
providing us opportunity to work under this project. Our special
thanks to Prof. K. D. Sonawane, Co-ordinator, Department of
microbiology for providing us opportunity to do project work, and
also giving us permission to use materials and media from laboratory.
Also our sincere thanks to Dr. Shailesh R. Waghmare for his
valuable guidance and help throughout our project work and also
thankful to Dr.Naiem H. Nadaf, Ms. Snehal Paymal for their help and
guidance in project work. Thanks to all my classmates who are
directly or indirectly helped in project.
 INDEX

Sr. no. Title

1. Introduction

2. Review Of Literature

3. Aim and Objectives

4. Materials and Methods

5. Results and Discussion

6. Summary and Conclusion

7. References
 INTRODUCTION

Penicillin an bactericidal antibiotic , acts on bacterial cell wall and its synthesis . It act at
different stages of cell wall synthesis and inhibits the multiplication of organism. It‘s possible
for the drug due to the structural similarities with substrate. Penicillin Binding Protein are the
group of proteins characterize by having affinity to bind with penicillin. As its normal
constituent in some bacteria leads to resistance in species. The penicillin binding protein are
of different types based on molecular weight as High Molecular Mass and Low Molecular
Mass . The number of PBPs vary in different organisms which acts differently. But basically
by means of functions they are glycosyl transferases, Transpeptidases and corboxyl
peptidases which are responsible for connecting two sugar moieties together (NaGlu and
NaMur),to cross link the bridge of side chain and to remove terminal amino acid of
pentapeptide side chain respectively.
Penicillin binds to the penicillin binding protein with it‘s beta lactum bond positioned at
active sites, and the acylation of active site nucleophile involved in acyl enzyme formation
which is responsible for opening of beta lactum ring i e resistance to the antibiotic. This can
be achieved by means of mutation, changing affinity and alterations of active site residues
To overcome this problem it‘s important to study resistance of antibiotics . And the
problem can be controlled by altering the drug molecules with respect to resistant enzyme
which makes it enable to act with highest efficiency at lower concentration.
The Penicillin binding proteins are ectoproteins (membrane proteins) which maintains the
flexibility of enzymatic domain. Such PBP are isolated from membrane using fluorescent
penicillin Bocillin. For isolation of PBP from cell membrane potassium phosphate buffer is
used. For purification of PBP the conventional method of solubilization by using detergents
is used , but it causes denaturation of proteins. Hence, the advanced technique like Affinity
Chromatography is widely used. The PBP can bind to Ampicillin, so ampicillin affinity
chromatography is suitable method, along with immobilised metal affinity (Ni-NRA)
chromatography also used. The binding efficiency of PBPs with penicillin is determined by
calculating their acylation and deacylation rates upon interaction with Bocillin.
As pbs are normal constituent of some bacteria we are glancing it for pbps in clostridium
species.
Clostridium perfringens are gram positive, rod shaped, anaerobic,spore forming
bacteria,present in decaying matter,marin sediments,soil as well as intestinal tract of human
and insect. food poisoning in human is caused by type A strain which produces CPE
i.e.C.perfringens Enterotoxins,coaded by cpe gene.it generally occurs due to improper
handeling or poorly prepared meat and poultry it is common bacterial agent for gas
gangrene.So its necessary to study the resistance in Clostridium
There are 6 pbp studied, having molecular weight 42200 and also relative affinities of
pbp for 16 beta lactam antibiotics were determined . they contain multiple binding proteins in
there cytoplasmic membrane, these proteins have enzymatic activity which is important in
peptidoglycan synthesis. The interaction between drug and receptor is helpful in
understanding the mechanism of action of beta lactam antibiotics and principal of bacterial
growth and division. Pbp of various bacteria were studied but yet an aerobic species were not
studied. To identify binding patterns they are subjected to gel electrophoresis and
autoradiography for isolation so different strains are compared to know about binding
patterns.
the cytoplasmic membrane of C. perfringens contains multiple PBPs. The concentrations at
which beta-lactams saturate PBP 3 and 4 correlate well with the MICs of the agents,
suggesting that these proteins are the lethal targets. Further investigation of the PBPs of C.
perfringens will be interesting to identify specific functions of individual PBPs and to assess
the role of PBPs in the recent observation of decreasing susceptibility of this species to
penicillin.
Bioinformatics tools are used to study pbps are
PDB
Protein databank is a structural database which stores and deposit 3D structure of
biomolecules such as enzyme, nucleic acid and drug molecules while protein databases gives
information about primary sequence of the protein.(1)
Uniprot
Uniprot (Universal Protein Resource ) is a comprehensive resource for protein sequence and
annotation data . The databases are the UniProt Knowledgebase (UniProtKB) , UniProt
Refrence Clusters (UniRef), UniProt Archive (uniParc) Here one can search, download
protein sequence and also structure can be seen if it is available(2)
BLAST
Basic Alignment Search Tool (BLAST) is a program used to perform or to identify the
similar sequences from the database. (3)
Prosa
The protein structure analysis (prosa) used for the refinement and validation of experimental
protein.(4)
Rasmol
Rasmol is a visualising software having molecular graphics used to visualise 3D structure of
protein, nucleic acid and drug molecule Also from 3D structure of protein one can determine
no. Of Alpha helices, beta sheets and loops(5)
Chimera
Chimera is used for drug discovery, many methods of molecule modeling have been
employed to study complex biological and chemical systems. Experimental strategies are
integrated with computational approaches for identification, characterization and
development of novel drug or compound(6)
Ramchandran plot:
One is to show in theory which values, or conformations, of the ψ and φ angles are possible
for an amino-acid residue in a protein .(7)
Chou Fasman method
The Chou Fasman method is an empirical technique for the prediction of secondary structure
of proteins(8)
SWISS Model
SWISS Model is a fully automated protein structure homolgy modeling server which is used
to make protein modeling it gives 3D structure of protein(9)
Molecular Docking
It is used to model or mimic the behaviour of molecules or molecular system.(10)
 AIMS AND OBJECTIVES.

Aim:
To construct the three dimensional model of penicillin binding protein from Clostridium
perfrigens using homology modelling techniques and study of interaction between PBP and
penicillin.

Objectives
1. Extraction of amino acid sequence of penicillin binding protein from Clostridium
perfrigens from protein sequence database.
2. Secondary structure analysis using bioinformatics methods like CFSSP
3. Model building study of PBP using homology-modelling techniques.
4. Validation of predicted 3D model using online bioinformatics servers.
 REVIEW OF PROJECT

ANTIBIOTIC

Antibiotic is a secondary metabolite produced by one organism which acts on other

organism at low concentrations.
They are either bactericidal or bacteriostatic. Classified on basis of mechanism of action are
Action on Cell wall synthesis
Action on cell membrane
Action on protein synthesis
Action on nucleic acid
PENICILLIN
Penicillin is an example of inhibiting by acting on cell wall synthesis.
Penicillin are a group of antibiotic originally obtained from Penicillin moulds Alexander
Fleming was the first who discovered Penicillin in 1928 from P.rubens (11). Howard Florey
and Ernst Boris Chain at University of Oxford were successfully isolated and purified
Penicillin F.
Penicillins are among the most heavily used antibacterials in medicine. Their efficacy against
susceptible organisms and large margin of safety make them nearly ideal antibacterials.
Classes of Penicillins

 Natural Penicillins
o Penicillin G (same as Benzylpenicillin)
o Penicillin V (same as Phenoxymethylpenicillin)
 Aminopenicillins
o Ampicillin
o Amoxicillin
o Hetacillin
 Penicillinase-resistant Penicillins (Antistaphylococcal Penicillins)
o Methicillin (prototype)
o Cloxacillin
o Dicloxacillin
o Nafcillin
o Oxacillin
  Extended Spectrum Penicillins (Antipseudomonal Penicilllins)
o Azlocillin
o Carbenicillin
o Mezlocillin
o Piperacillin
o Ticarcillin
 Beta-lactamase Inhibitors
o Clavulanic acid

Natural penicillins

Natural penicillins include penicillin G for parenteral use and penicillin V for oral use only.
These drugs are primarily indicated for infections caused by gram-positive organisms
including anaerobes. Spirochetes and some gram-negative organisms are susceptible, so
require higher concentrations. The Enterobacteriaceae and Pseudomonas aeruginosa are
resistant.

Aminopenicillins

Aminopenicillins have a relatively broad spectrum of activity, for penicillins, which includes
many gram-positive and gram-negative bacteria. Ampicillin can be used both orally (acid
stable) and parenterally, whereas amoxicillin is used orally. These drugs are beta-lactamase
sensitive. The oral bioavailability of ampicillin (35-50%) is lower and more variable than that
of amoxicillin ( 70-90%). These drugs are not very active against Bacteroides fragilis despite
being effective against other anaerobes. Inhibited by b-lactamase activity.

Antistaphylococcal penicillins

All antistaphylococcal penicillins have oral dose forms. Some have IV/IM and intramammary
(VM) forms. Penicillinase-resistant penicillins include the classical compound methicillin,
widely used in senstivity testing for this group, and nafcillin. The isoxazolyl
penicillins constitute an important subgroup that includes the closely
related oxacillin, cloxacillin, and dicloxacillin. None of these drugs has outstanding
bioavailability when given orally, but all of the isoxazolyls have oral dose forms. Only
oxacillin and nafcillin have a parenteral (IV/IM) dose form. This group includes the only
penicillin derivatives that have significant beta-lactamase resistance. The trade name of
methicillin, Staphcillin, betrays its primary therapeutic application. Resistance to methicillin
is growing among staphylococci and one should use vancomycin as a substitute when
necessary. Penicillin G is much more effective against non-beta-lactamase producing
staphylococci and is preferred over the antistaphylococcal derivatives. Members of this class
are preferred for treatment of Staphylococcus aureus infections of the skin and soft tissues.
Parenterally administered nafcillin should be used for serious infections and orally
administered dicloxacillin should be used for the remainder.

Antipseudomonal penicillins

Only the indanyl carbenicillin has an oral dose form. Other antipseudomonal penicillins are
given IV/IM. Antipseudomonal penicillins include the carboxypenicillins
(carbenicillin and ticarcillin), acylureidopenicillins (azlocillin and mezlocillin), and one
piperazine penicillin derivative (piperacillin). With the exception of the indanyl derivative of
carbenicillin, which is an oral dose form, all are for parenteral use (IM or IV). Except for
carbencillin, the reason most of these drugs are used parenterally is that they are poorly
absorbed orally rather than because they are destroyed by gastric acidity. All of these drugs
are sensitive to beta-lactamase destruction. Piperacillin is more active than the others
against Pseudomonas aeruginosa in vitro and has activity that corresponds to gentamicin, an
aminoglycoside. Although carbenicillin and others in this group are active against many
gram-positive organisms, they are generally less effective than penicillin G and ampicillin.

Amidino penicillins

Amidino penicillins are the final group and include only one member, amidinocillin. The
major accepted use of this drug is for urinary tract infections caused by gram-negative
organisms.

PROPERTIES
PBPs are defined as those bacterial proteins that bind penicillins and other β-lactam
antibiotics covalently. PBPs are readily detected and their relative amounts quantitated by
incubation of bacterial membranes with [ 14C] Penicillin G, followed by sodiumdodecylsulfate
(SDS) gel electrophoresis and fluorography. Use of [ 3H] Penicillin G of high specific activity
permits labeling of PBPs in vivo. In a organism, PBPs are numbered in order of decreasing
apparent molecular weight, which usually ranges from Mr ~ 140,000-40,000 (although PBPs
as small as M r ~25000 have also been detected.
There is no necessary relationship between equivalently numbered PBPs of two unrelated
organisms e.g. PBP-2 of E. coli and PBP-2 of Bacillus subtilis, although taxonomically
related bacteria have similar PBP patterns. Although most investigators use [ 14C] Penicillin G
to detect PBPs, additional binding proteins are, in general, not detected using other
radioactively labeled β-Iactams including 14C-labeled mecillinam, cefoxitin, PC-904,
furazlocillin, and moxalactam or 3H-Iabeled propionyl ampicillin. Using [125I] an additional
PBP (PBP-IC) is detected in E. coli membranes.
Most bacteria contain between 1000 and 10,000 total PBP molecules per cell, with the PBPs
comprising approximately 1% of the total membrane protein.(16) Particular PBPs vary
greatly in their relative abundance: E. coli PBP-2 accounts for approximately 1% of the
organism's penicillin-binding activity, estimated to correspond to 0.01% of total membrane
protein and only 15-20 molecules of PBP-2 per cell as compared to ~ 90% of the total
penicillin binding activity for Bacillus stearothermophilus PBP-5.
The affinity of a PBP for a given β-lactam is usually expressed as the concentration of
antibiotic required to reduce [14C] Penicillin G binding to the PBP by 50% and is determined
after preincubation with the unlabeled βLlactam under given conditions of time, temperature,
etc. However, quantitative measurements of a PBP's sensitivity to β-Lactams determined can
vary, depending on both the time of incubation with the β-Lactam and on the concentration of
membrane suspensions used as source of PBP, with lower inhibitory concentrations often
obtained using more dilute membrane suspensions. For these reasons, affinities of PBPs for
β-Lactams are probably more meaningful when determined in vivo.
 PBPs of a given organism exhibit widely varying sensitivities to, β-Lactams. Examination of
the sensitivity of PBPs from several organisms to a wide variety of β-Lactam antibiotics
suggests two general categories of PBPs,
1. Low molecular weight (M r ",40,000-50,000), which are somewhat less sensitive to
many penicillins and highly insensitive to most cephalosporins, and
2. High molecular weight (Mr ",6,0,000-140,000), which are generally more sensitive to
both penicillins and cephalosporins.
This dichotomy, based on sensitivity to β- lactam antibiotics, extends to several other
properties of the PBPs, including their relative abundance, in vitro activities, and importance
for cell growth and viability. Thus, in general, the low-molecular-weight PBPs are relatively
abundant, catalyze efficient penicillin-sensitive D,D-alanine carboxypeptidase (CPase)
reactions in vitro and appear to be unnecessary for cell viability. By contrast, high-molecular-
weight PBPs are usually minor components, do not catalyze CPase or transpeptidation
reactions using model substrates, and are often essential for cell viability. Most PBPs are
integral membrane proteins [found in the inner (cytoplasmic) membrane in gram-negative
bacteria] and thus require treatment with nonionic or mild anionic detergents for
solubilization in active form.
PBPs in peptidoglycan
Bacteria have multiple PBPs, some of which have started to reveal their clear roles during
the cell division cycle. High molecular mass (HMM) PBPs are classified according to the
number of reactions a single polypeptide is able to catalyze:
1. bifunctional (class A) enzymes catalyze both the polymerization of the GlcNAc-MurNAc
chains (glycosyltransfer, GT) and cross-linking of adjacent stem peptide (transpeptidation,
TP) reactions, while
2. monofunctional (class B) proteins present only transpeptidase activity .
The glycosyltransferase reaction catalyzes the association between MurNAc and GlcNAc
groups, employing Lipid II as a substrate. While the saccharidic chain grows by two sugar
units, each reaction generates free undecaprenyl pyrophosphate, which is again ‗flipped‘ back
towards the cytosolic side of the membrane where it is hydrolyzed to undecaprenyl phosphate
and is recycled in a new reaction.
Transpeptidation, on the other hand, generally re quires that the enzyme recognize the
terminal D-alanine, D- alanine moiety of the stem peptide and catalyze the attack of the
carbonyl group of the penultimate D-alanine by the lateral amino group at position of an
adjacent chain . The acceptor involved in enzyme deacylation is the amino group of a glycine
residue (as in Staphylococcus aureus), that of a lysine residue (as in Streptococcus
pneumoniae), or of a diaminopimelate group (as in Escherichia coli).
While in most bacteria, structural variations are possible, and may range from acetylation
and phosphorylation of the sugar units, to addition of extra residues onto the penta-peptides.
Thus mechanism generates a branched peptidoglycan, a common structural feature in Gram-
positive organisms as .
1. streptococci, for example, MurM and MurN catalyze the addition of short dipeptides
(serine-alanine or di-alanine) onto the amino group of the stem peptide lysine;
2. staphylococci, the same residue is bound with a pentaglycine group, reactions catalyzed
by the FemX, FemA and FemB enzymes; and
3. enterococci, the stem peptide lysine harbors either an asparagine or an aspartic acid side
chain. These features seem to be linked to an increased level of drug resistance. In
streptococci, many penicillin-resistant strains carry branched muropeptides, and inactivation
of the murM and murN genes reverts the drug resistance phenotype and supports synthesis of
unbranched peptidoglycan.
In addition, the acceptor in the transpeptidation reaction can also be a water molecule,which
will thus finalize a D- alanine, D-alanine (or D, D-) carboxypeptidation reaction, catalyzed by
low molecular mass (LMM) PBPs. In this case, stem pentapeptides are hydrolyzed into
tetrapeptides (with D-alanine being released), preventing further peptidoglycan crosslinking.
Thus, LMM PBPs are involved in the regulation of the level of peptidoglycan .
Blocking of either the transpeptidation or carboxypeptidation reactions by b-lactam
antibiotics, which structurally resemble the D, D- stem peptide moiety, weakens the
peptidoglycan and may engender cell death.
This powerful mechanism, which has made penicillin and its analogs the most widely
employed antibiotics for any infectious malady worldwide for the past 70 years, has been
challenged by the propagation of drug-resistant strains, underlining the need for novel
antibiotic therapies(17)
Types
There are a large number of PBPs, usually several in each organism, and they are found as
both membrane-bound and cytoplasmic proteins. The different PBPs occur in different
numbers per cell and have varied affinities for penicillin. The PBPs are usually broadly
classified into high-molecular-weight (HMW) and low-molecular-weight (LMW)
Altered PBPs associated with b-lactam resistance are more commonly found in gram-positive
than in gram-negative bacteria (Table 1). In laboratory strains, high-level, PBP-mediated
resistance occurs in several steps rather than as a single-step mutation. Possibly, the steric
similarity of b-lactams to the natural substrate makes difficult decreased affinity for the
former with full retention of catalytic activity toward the latter by the target enzymes. By
inference, clinical resistance may require the introduction of multiple amino acid
substitutions in the target enzyme, in effect, resculpturing the active site. Nevertheless, once
present in a strain, resistance may rapidly spread along with the resistant strain.
Analysis of 213 unique eubacterial genomes revealed more than 430 class A and 350 class B
PBPs, as well as 250 low molecular mass D, D- carboxypeptidases. Since PBPs are
membrane-associated molecules, most of the HMM enzymes display a short cytoplasmic
region at the N-terminus, followed by a single transmembrane region; class A molecules then
carry sequences coding for both GT and TP domains, while class B molecules display only a
TP domain preceded by an N-terminal unit of unknown function.(17)
High molecular mass PBPs -- class A and class B enzyme
Class A
Class A PBPs can be found in two main forms: the most common arrangement displays GT
and TP domains interconnected by a linker of variable length, followed by a short C-terminal
sequence. In a second group, the C- terminal region is followed by different structural
elements, such as a fibronectin type 3 domain. In general, there are two class A PBPs per
genome, reflecting the importance of these enzymes in bacterial metabolism. Bacteria may
also carry monofunctional GT enzymes which are characterized by a unique GT unit
associated to the trans- membrane region.
Class B
Class B PBPs can be divided into four main groups.
1. The largest and by far most representative one harbors the simplest arrangement, which
involves an N-terminal unit followed by the transpeptidase domain; this group includes well-
studied proteins such as PBP3 from E. coli.
2. Two other groups are represented by approximately 60 PBPs which display either one or
two short sequences corresponding to an a/b unit positioned after the TP domain;
streptococcal PBP2x harbors two of these a/b units at its C- terminus. In several databases
this a/b unit is identified as a PASTA (‗PBP and Ser/Thr kinase attached‘) domain, since its
homologs are harbored by over 100 PBP and kinase sequences. Although the PASTA domain
has been suggested as being a b-lactam binding, peptidoglycan-sensing unit).
3. The last group of class B enzymes harbors an NTF2 (‗nuclear transport factor 2‘)- like
domain upstream from the N-terminal domain; although the function of this insertion is
unclear, this group of enzymes is represented by the well-studied staphylococcal PBP2a.
 There are approximately 1.7 class B PBPs per eubacterial genome. LMM PBPs, namely D,
D-carboxypeptidases, are unusual in the sense that the TP domain is encoded after a signal
peptide and their membrane association is accomplished by either a transmembrane or an
amphipathic helix, both C-terminally located. D, D- endopeptidases are also present within
some genomes, but at 0.07 examples per genome they are far less statistically representative
of classical PBPs than the ones.
Low molecular mass PBPs
The penicilloyl serine transferase fold is also shared by the LMM PBPs (such as PBP3 from
Streptococcus pneumoniae, PBP5 from E. coli and PBP4 from Staphylococcus aureus, which
are D, D- carboxypeptidases and, albeit able to recognize the C-terminal end of stem peptides
as substrates, do not catalyze a transpeptidation reaction. Interestingly, these molecules
possess an elongated, b-strand rich C- terminal domain which separates the catalytic region
from the amphipathic helix (the latter not included in the crystal structures. This domain has
been proposed to act as a pedestal which could position the catalytic region of LMM PBPs in
close apposition to the peptidoglycan. If this were the case, the amphipathic helix could
permit the enzymes to skid on the membrane surface without being associated within it, while
the pedestal could place the catalytic domain at the required height for optimal substrate
recognition.(18)
Gram positive organisms
MRSA
The most common example of PBP-mediated clinical resistance is MRSA, a major pathogen
of increasing importance. MRSA isolates show high-level resistance to all ,b-lactams. They
may be homogeneously or heterogeneously resistant; in the latter case, cells with increased
levels of resistance may be present at low frequency (typically, 10-4 to 10-7) in the form of
one or more subpopulations. A reduction in the growth temperature (from 37 to 30°C) or an
increase in the osmolality of the growth medium can increase the proportion of the resistant
cells modestly (e.g., to 10-3), dramatically (e.g., to 10-1) (99), or not at all
MRSA strains first appeared in 1961 but became a serious threat in the 1980s. Since then,
MRSA strains have caused hospital outbreaks of colonization and infection throughout the
world. The coexistence of multiple antibiotic resistance, particularly quinolone resistance, in
MRSA is an alarming recent development. Multiply resistant strains of MRSA have so far
remained susceptible to vancomycin, currently the single reserve antibiotic for the treatment
of MRSA infections, S. aureus has five PBPs with molecular sizes of 87 (PBP 1), 80 (PBP 2),
75 (PBP 3), 70 (PBP3'), and 41 (PBP 4) k Da. Of these, PBPs 1, 2, and 3 are essential and
have high affinities for 1-lactam antibiotics. PBP 1 may be the primary peptidoglycan
transpeptidase, PBP 2 is a transpeptidase functioning in nongrowing cells, PBP 3 is a
septation-associated transpeptidase , and PBP 4 is a DD-carboxypeptidase and transpeptidase
involved in secondary cross-linking of the peptidoglycan. In MRSA, an additional 78-kDa
PBP, 2a or 2' , is invariably found and has provided new insights into the mechanism of
resistance. PBP 2a has a low affinity for 1-lactams and may catalyse a penicillin insensitive
transpeptidation . It is encoded by a chromosomal gene (mec A), which is located on a 30-kb
DNA segment (mec determinant) of unknown source. Transformation of methicillin-
susceptible S. aureus with a mec A- containing plasmid converts it to MRSA. However,
cellular levels of PBP 2a do not correlate with levels of methicillin resistance. The expression
of PBP 2a is affected by growth conditions such as pH and temperature, the presence of a
penicillinase plasmid, and a regulatory region (mecR) on the mec determinant. The presence
of NaCl in the growth medium also affects the phenotypic expression of methicillin
resistance, but through inhibition of autolysis. An insertion element, IS431, on mec may be
responsible for deletion of mecA and reversion to the susceptibility phenotype on sub
cloning. The DNA region between mecA and IS431 varies in length among strains, the
variability being due to a 40-bp repeat. In addition to mecA, another chromosomal gene,
femA (factor essential for methicillin resistance) has been implicated in methicillin
resistance. It encodes a 48-kDa protein which does not affect expression of PBP 2a but
affects the glycine content of peptidoglycan, cell wall turnover, and susceptibility to β-
lactams.
PBP 2a has been proposed to have evolved from the fusion of a regulatory region for 3-
lactamase and a PBP structural gene of unknown origin since it is induced by β-lactams.
There is some evidence for differential induction of PBP 2a by different β-lactams, and
claims have been made that some, β lactams have activity against MRSA. However, to date
no, lactam has been proven to be clinically useful against MRSA, although new 1-lactams
that bind to PBP 2a and that are active against MRSA may emerge in the future. In this
context, the recent cloning of PBP 2a and the expression of a truncated (22 amino acids
deleted from the N terminus), water-soluble form in E. coli are hopeful developments.
Fosfomycin, a structural analog of phosphoenolpyruvate which inhibits the condensation of
PEP and UDP-GlcNAc to form UDP-MurNAc , decreases PBP 2a expression and acts
synergistically with 3-lactams against MRSA . It also increases PBP 2 expression and weakly
antagonizes 3-lactams against methicillin-susceptible S. aureus. The clinical implications of
these findings are unclear. Staphylococcus epidennidis, the most common coagulase-
negative Staphylococcus spp., has a PBP pattern and a methicillin resistance mode similar to
those of S. aureus. The organism is commonly found in prosthetic devices and is thus a
nosocomial pathogen of increasing importance. In both S. epidernidis and Staphylococcus
haemolyticus, another coagulase-negative Staphylococcus spp., PBP 2a (mecA gene) is
homologous to the PBP 2a of S. aureus. Polymerase chain reaction has recently been used for
the genotypic identification of methicillin- resistant, coagulase-negative staphylococci.
enterococcus
Enterococcus faecalis and Enterococcus faecium are naturally resistant to most, β-lactams.
The two organisms have similar PBP patterns: five PBPs, of which 1 (105 kDa) and 3 (79
kDa) are associated with resistance. PBP 3 has a low affinity and acylation rate for 3-lactams
and is overproduced in resistant strains(17).
GRAM NEGATIVE
Clinical resistance to, β-lactams in gram-negative bacteria is not commonly associated with
altered PBPs. This is probably due to the effectiveness of b-lactamases, coupled with reduced
outer membrane permeability, in producing resistance. Some examples are mentioned.
There are seven PBPs in E. coli, of which 1 (90 kDa), 2 (66 kDa), and 3 (60 kDa) are
essential and are involved, respectively, in elongation, shape, and septation. All three are
bifunctional enzymes with transpeptidase and transglycosylase activities that probably reside
in the amino- and carboxy-terminal halves of the protein, respectively. b-Lactam antibiotics
that bind to PBP 1 (cephaloridine) cause lysis, while those that bind to PBP 2 (amdinocillin)
produce giant spherical cells and those that bind to PBP 3 (aztreonam, carumonam) result in
filamentation.
Enterobacter, Klebsiella and Salmonella spp. have PBP profiles very similar to that of E.
coli, while Proteus and Serratia PBPs are somewhat different, although they are still
correlatable with E. coli PBPs. So far, PBP-mediated clinical resistance has not been found in
these organisms. The PBP pattern of, P. aeruginosa is also correlatable with that of E. coli,
and binding of, β-lactam antibiotics generally results in morphological changes similar to
those observed in E. coli. Interestingly, fosfomycin decreases PBP β expression and
antagonizes b-lactams, although the latter effect may be secondary to β-lactamase induction.
Non-p-lactamase-mediated resistance to b-lactams in clinical isolates and laboratory mutants
has been reported and is associated with reduction in PBP 3 binding.
In Haemophilus influenzae, eight PBPs with molecular sizes of 27 to 90 kDa have been
detected. PBP 2(80 kDa) and PBP 3 (75 kDa) correspond, on the basis of their sensitivities to,
β-lactam antibiotics, to PBPs la and 2 of E. coli, while PBPs 4 (68 kDa) and 5 (64 kDa) have
transpeptidase activity in permeabilized cells. Haemophilus spp. (and Neisseria spp.) have
relatively permeable outer membranes, as evidenced by their susceptibilities to the
hydrophobic Penicillin G and erythromycin. Non-b- lactamase-mediated resistance to P-
lactams in clinical isolates is associated with decreased binding to PBPs 3 (75 kDa), 4 (68
kDa), and 5 (64 kDa). In N. gonorrhoeae, three major PBPs with molecular sizes of 90 (PBP
1), 63 (PBP 2) and 48 (PBP 3) kDa have been detected (17)
Some More Examples
In Acinetobacter calcoaceticus, an emerging pathogen, six PBPs have been detected of which
PBPs 1 (94 kDa), 2 (92 kDa), and 5 (59 kDa) are implicated in resistance to, β-lactam
antibiotics. The PBP pattern of Acinetobacter baumannii is markedly different, and in
laboratory mutants resistant to imipenem, binding to all PBPs was reduced, possibly
reflecting, β-lactamase interference. The clinical implications of these laboratory findings are
not yet clear. In the anaerobe Bacteroides fragilis, a major pathogen naturally resistant to
most 1-lactams by virtue of its P-lactamases and outer membrane permeability, four PBPs
have been detected. Of these, PBP 1 (100 kDa) may be the major peptidoglycan
transpeptidase and PBP 2 (86 kDa) may be involved in septation. PBP 2 is the target for most
P-lactam antibiotics. Cefoxitin resistance in laboratory mutants has been associated with
reduced binding to PBP 1, while in clinical isolates cefoxitin resistance has been associated
with reduced binding to both PBPs 1 and 2. Resistance to cephalothin and other
cephalosporins is associated with reduced binding to PBP 3 (65 kDa). Other Bacteroides spp.
have PBP patterns similar to that of B. fragilis, but their resistance to 1-lactams has not yet
been examined.
Penicillin-Binding Protein 7/8 (PBP7/8) and β-Lactamase PER-1 Although PBPs are
commonly involved in resistance to β- lactam antibiotics, PBP7/8 encoded by the pbpG gene
is a virulence factor in A. baumannii. The pbpG mutant strain grows similar to its wild-type
strain in Luria-Bertani medium, but the mutant shows reduced growth in human serum and its
survival significantly decreases in rat soft-tissue infection and pneumonia models. An
investigation of bacterial morphology using electron microscopy suggested that loss of
PBP7/8 may have affected peptidoglycan structure, which may affect susceptibility to host
defense factors. Interestingly, β-lactamase PER-1 has been suggested to be an A. baumannii
virulence factor. PER-1 is an extended-spectrum- β-lactamase (ESBL), but this gene is
associated with cell adhesion. Nine PER-1-producing strains adhere to the Caco2 cell lines,
whereas all PER-1-negative strains are negative for cell adhesion. Notably, many β-
lactamases are associated with virulence in various pathogenic bacteria, such as E. coli, P.
aeruginosa, and K. pneumoniae. However, no general mechanisms have been proposed.(19)
Bacterial resistance to them is generally driven either by the production of enzymes that
inactivate them (b-lactamases), or by the modification of their targets in the cell wall
(penicillin-binding Proteins, PBPs), sometimes in conjunction with mechanisms leading to
diminished permeability or active efflux . While the acquisition of modified PBPs showing
low affinity for b-lactams is well known to be a major resistance mechanism in Gram-
positive cocci, such as penicillin-resistant Streptococcus pneumoniae or the much-feared
methicillin-resistant Staphylococcus aureus, this mechanism has not been thought to be
important for most species of Gram-negative rods. The production of intrinsic or horizontally
acquired b-lactamases is undoubtedly the predominant resistance mechanism in the latter
organisms. Among GNRs, the most widely distributed b-lactamases are chromosomally-
encoded AmpC variants, produced by most Enterobacteriaceae and Pseudomonas aeruginosa,
high up the list of pathogens causing life-threatening infections in hospitalized patients
world-wide.
Although AmpC is produced at very low basal levels in wild- type strains, its expression is
highly inducible in the presence of certain b-lactams (b-lactamase inducers) such as cefoxitin
or imipenem. In fact, the efficacy of the widely-used broad spectrum penicillins (such as
piperacillin) and cephalosporins (such as ceftazidime) relies on the fact that they are very
weak AmpC inducers, even though they are efficiently hydrolyzed by this enzyme.
Unfortunately, mutants showing constitutive high level AmpC production (AmpC
derepressed mutants) are frequently selected during treatment with these b-lactams, leading to
the failure of antimicrobial therapy . In some natural strains of Enterobacteriaceae and P.
aeruginosa , the inactivation of AmpD (cytosolic N-acetyl-anhydromuramyl-L-alanine
amidase involved in peptidoglycan recycling, and point mutations in AmpR (LysR-type
transcriptional regulator required for ampC induction have been found to lead to AmpC
overexpres- sion, and thus to b-lactam resistance.
DRUG RESISTANCE
Drug resistance is the reduction in effectiveness of medication such as antimicrobial or
antineoplastic in treating a disease or condition.(12) The main mechanism of resistance are,
limiting uptake of a drug, modification of a drug target, inactivation of a drug, and active
efflux of a drug. These mechanisms may be native to the microorganisms or acquired from
other microorganism.
Some low-molecular-weight PBPs associate with the MreB cytoskeleton and follow its
rotation around the cell, inserting peptidoglycans in an oriented manner during cell
growth.[13] In contrast, high- molecular-weight PBPs are independent from MreB and
maintain cell wall integrity by detecting and repairing defects in the peptidoglycan.(14)
ANTIBIOTICS PBPs bind to β-lactam antibiotics because they are similar in chemical
structure to the modular pieces that form the peptidoglycan.(15) they bind to penicillin, the β-
lactam amide bond is ruptured to form a covalent bond with the catalytic serine residue at the
PBPs active site. This is an irreversible reaction and inactivates the enzyme.
Mechanism, active sites and β-lactam action
According to the substrate analog hypothesis the penicillin binds and inactivates
peptidoglycan transpeptidase by virtue of its structural similarities to at least some of the
possible conformations of the acyl-D alanyl-n-alanine termini of nascent peptidoglycan
strands . These structural similarities are most evident when the free carboxyl groups and the
terminal asymmetric centers which is necessary for activity of both (penicillin and peptide
susubstrate )are aligned and resulting in the similar positioning of highly reactive CO-NH β-
lactam bond and the peptide bond cleaved during a transpeptidase or carboxypeptidase
reaction. The transpeptidase was react with its peptide substrate to form an acyl-enzyme
intermediate, with the elimination of n-alanine. Subsequent reaction with the free amino
group of a second cross-bridge would lead to formation of a cross-link and regeneration of
the enzyme. Alternatively, hydrolysis of the acyl-enzyme intermediate would effect a D-
alanine carboxypeptidase reaction. As a substrate analog, penicillin would bind to the enzyme
as transpeptidase or carboxypeptidase with its β-Iactam bond positioned at the active site. A
relatively facile acylation of the same active site nucleophile involved in acyl-enzyme
formation would then occur with the opening of the b-Iactam ring, forming an inactive
penicilloyl-enzyme. This proposal for the mechanism of action of penicillin predicts:
(a) The existence of a covalent penicilloyl-enzyme as the inactive form of peptidoglycan
transpeptidase it means penicillin-sensitive enzymes are the proteins that bind penicillin
covalently
(b) Occurrence of acyl enzymes as catalytic intermediates in the uninhibited reaction
(c) The substitution of both a penicilloyl moiety and an acyl-D-alanyl moiety derived from
substrate on the same amino acid residue after reaction of enzyme with penicillin or with
substrate.
Also, it was hypothesized that b-Iactamases might have evolved from penicillin-sensitive
enzymes by developing an efficient catalytic mechanism for hydrolysis of the penicilloyl
enzyme. Many of the studies described in the previous sections support the first two
predictions of this model. that are The ability to trap near-stoichiometric acyl-enzyme
intermediate using the dep si peptide substrate diacetyl-L-Lys-D-Ala-D-Iactate made it
feasible to test directly the third prediction that a penicilloyl moiety and an acyl moiety both
bind to the same active-site amino acid residue using CPases from Bacillus sp. as model
penicillin-sensitive enzymes. Radiolabeled peptides were purified from chemical or
enzymatic digests of CPase labeled at the antibiotic binding site with [14C] Penicillin G or,
alternatively, labeled at the catalytic site by rapid denaturation of an acyl enzyme formed
using the depsipeptide[14C] -diacetyl-L-lys-D-ala-D-lactate and their amino acid sequences
determined. Penicillin- and substrate-labeled peptides were shown to have identical primary
structures, with acyl moieties derived from antibiotic and from substrate bound in ester
linkage to the identical residue, serine 36, in both CPases. Further studies demonstrated that
cefoxitin, a 7α-methoxycephalosporin, also binds to serine 36 of the B. subtilis CPase . These
findings provide strong evidence that β-Iactam antibiotics are active site-directed acylating
agents, as predicted by the substrate analog hypothesis . This important conclusion was later
extended to include E. coli PBP-6 and Streptomyces R61 exocellular CPase [for which it had
been suggested that penicillin binds at an allosteric site] by comparison of the two sets (i.e. b
lactam- and substrate-labeled) of peptides after partial proteolysis using several cleavage
methods . The unavailability of near-stoichiometric acyl-enzymes derived from any high-
molecular-weight PBPs precludes comparison of substrate and antibiotic binding sites of
these PBPs using these methods.
PBPs are serine acyltransferases whose TP-associated catalytic activity catalyzing the
formation of cross- linked peptidoglycan, is also the target of b-lactam antibiotics. The
binding of PBP catalytic cleft to b-lactams at active site of serine resulting into acyl-enzyme
can only be hydrolyzed at a very slow rate, thus reducing the amount of peptidoglycan cross-
linking. b-lactamases, however, are able to hydrolyze the β- lactam ring with extremely high
turnover rates
Escherichia coli PBP1b is the enzyme of choice for the study of transpeptidation and
glycosyltransfer reactions catalyzed by PBPs. In a recent article, Vollmer and colleagues
have shown that the full-length E. coli PBP1b (thus containing the transmembrane segment)
is a dimer, and catalyzes both reactions on the Lipid II substrate and transpeptidation activity
could also be identified, confirming the delayed transpeptidation event for this enzyme .
Although these studies prove that the TP domain of PBPs is capable of transpeptidation,
crystal structures of PBPs complexed to substrates, products or catalysis intermediates are
still not available.
PBPs and drug resistance
Once a PBP is acylated by a β-lactam antibiotic, it is unable to catalyze hydrolysis of the
covalent acyl-enzyme intermediate and is inactivated and peptidoglycan transpeptidation
cannot occur, and the cell wall is weakened. Although the emergence of drug-resistant strains
has proven to be a worldwide problem. Gram- negative pathogens such as Pseudomonas
aeruginosa and E. coli evade β-lactam action by excreting β-lactamases into the periplasm. In
other word‘s the antibiotic cannot access its macromolecular target due to its forced efflux
from the bacterium via an antibiotic efflux pump, such as the MexA ,B-OprM pump in
Pseudomonas strains .on other hand Gram-positive bacteria, such as streptococci, which do
not secrete β- lactamases, produce highly mutated, drug-insensitive PBPs. Staphylococcus
aureus strains circumvent β-lactam action by acquiring a novel, highly drug resistant class B
PBP (PBP2a) through horizontal transfer of the mecA gene from a yet unidentified species
Enterococci, some of which are major nosocomial pathogens, are naturally resistant to β-
lactams due to the presence of one PBP (PBP5fm in E. faecium) with low level affinity for
penicillin and its analogs; point mutations in or overproduction of PBP5fm can lead to very
high levels of resistance Interestingly, albeit the incorporation of these key PBP mutations,
resistant bacteria still seem to divide and turn over peptidoglycan at comparable rates; the
complex mechanisms underlining this enduring catalytic efficiency are unknown.
Other Active-Site Residues
The demonstration of serine 36 as a catalytic inter mediate for CPase does not preclude
covalent intermediates involving other residues (e.g. histidine, cysteine). A role for cysteines
in the catalytic mechanism can be suggested by the following experiments.
1 agents inhibit release of the bound penicilloyl moiety by E. coli PBPs-5 and -6 without
significantly affecting their penicillin-binding activity .
 2 Inhibition of penicillin release is paralleled by inhibition of deacylation of a substrate-
derived acyl moiety, such that an acyl-enzyme intermediate accumulates and CPase activity
is lost .
3 A mutant of E. coli PBP-5 (dac A) has biochemical properties similar to that of the
sulfhydryl-inhibited wild-type form pbp, suggesting that the mutation might involve an
active-site ccystein
4. In the case of the CPases from Bacillus sp. and from S.jaecalis, sulfhydryl reagents inhibit
penicillin binding and CPase activity .
5 Enzymatic release of the bound penicilloyl moiety (either after fragmentation or in the
presence of hydroxylamine) is, however, insensitive to sulfhydryl reagents with the CPases
from Bacillus sp.
6 Thus sulfhydryl alkylation interferes with the binding and/or acylation by penicillin and
substrate of the CPases from Bacillus sp., but not with deacylation either in the presence of
hydroxylamine or following fragmentation. A possible role for an active-site arginine in
stabilizing the anionic substrates of the R61 CPase has been proposed based on chemical
modification studies using 1X, b-dicarbonyl compounds .
High Resolution Structural Analysis
A)X-ray structural analysis of crystalline PBPs complexed either with b- lactams or with
suitable cell wall peptides should help in further understanding of the mechanism of action
as :
(a) enzymatic mechanisms for processing R-D-Ala-D-Ala substrates
(b) whether b- lactams are recognized as substrate analogs?
c) the structural relationships among PBPs and between CPases and b Iactamases
(d) the rational design of new β-lactam antibiotics.
Most of the PBPs are dissolved in detergent micelles are often insoluble in aqueous media,
thus produces difficulty in crystallization . So proteolytically cleved membrane-derived
CPases can be yield active, water-soluble fragments which are suitable for crystallization are
described below.
1 By using the exocellular (water-soluble) CPases from Streptomyces sp., such complications
are avoided, and crystalline complexes suitable for structural analysis cab be obtained .
2The three-dimensional structure of the Streptomyces R61 exocellular CPase has recently
been determined to 2.8-A resolution .
3The electron -density difference maps were obtained by Fourier difference synthesis by
comparing crystals of the native enzyme with a crystalline cephalosporin C-, o-
iodophenylpenicillin- and R-L-Lys-D-Glu-D-Ala-CPase complexes, and suggested the
binding of all three ligands in the same region of the molecule And consistent with the
prediction of the substrate analog hypothesis .
4 Studies on the primary structure of this CPase begun recently should be helpful in further
defining molecular structure at the active site.
X-ray emission study in StreptomycesProton-induced X-ray emission studies of the
Streptomyces albus G exocellular CPase have led to the discovery of a previously undetected
enzyme-bound zinc atom essential for catalysis and the results showed are as follows:
1The activity lost upon its removal by dialysis and is restored with its stoichiometric
readdition.
2 The three dimensional structure of this zinc CPase has recently determined
3 The primary structure , implicate three histidine residues located in a cleft in the carboxyl-
terminal domain as ligands for the active-site zinc.
4Fourier synthesis at A resolution of a zinc CPase-p iodopeniciIIanate complex suggested the
possibility of acylation of yet another histidine (His 191) as the cause of inhibition by the b-
Iactam.
5 The additional roles for either Arg 137 in charge-pairing the substrate's carboxyl group and
His 191 as a proton donor were proposed.
6 This penicillin-resistant zinc enzyme is most likely not related to penicillin sensitive CPases
detected as PBPs
β-LACTAMS AS SUBSTRATE ANALOGS
Evaluation of the structural features that confer on b-lactam antibiotics their potent and
specific inhibitory properties. It is seen that b-lactams that are effective active-site inhibitors
of cell wall biosynthesis require: (a) sufficient structural similarity to physiological substrates
to permit recognition by essential cell-wall enzymes
(b) a highly reactive b-lactam bond to facilitate rapid acylation of the enzyme's active site
(c) structural features that effectively minimize transfer of the covalently bound penicilloyl
moiety to solvent or to cell wall amino aacceptor
It means the inhibition is slowly reversible or irreversible. And Steric hindrance of incoming
nucleophiles by the antibiotic's thiazolidine ring (still bound covalently via the C5-C6 bond
after cleavage of the β-Iactam) probably is an important factor contributing to stability of the
penicilloyl enzyme. Although important differences in bond angles and bond distances
between effective b-lactam antibiotics and peptide substrates exist some can be understood in
terms of the proposed structural analogy between penicillin and a possible transition state
structure formed during the enzyme-mediated cleavage of the o-Ala-o-Ala peptide bond
A possibility supported by molecular orbital calculations is:
1 The enzyme for such a transition state would facilitate compression of the peptide dihedral
angle resulting in the loss of double-bond character and a weakening of the peptide bond.
2 Energy required for this distortion would reduce the net energy of binding substrate to
enzyme
3 In contrast, the nonplanarity of the bicyclic ring system of penicillins (and cephalosporins)
already imparts significant single-bond character to the corresponding b lactam bond, thus
favoring binding and acylation by β-Iactams.
4 The question as to whether penicillin-sensitive enzymes bind β-Iactams more tightly than
normal substrates can be examined by comparing constants for binding (Ko= L tiki) and
acylation (k2)
5 By various β-Iactam antibiotics to the analogous KM and kcat values for CPase substrates
6 The comparisons suggest that CPases do not bind β-Iactams with significantly higher
affinity (lower Ko) than peptide substrates. Thus, if certain structural features of b-Iactams
favor binding by mimicking the tetrahedral transition state of a dipeptide undergoing
cleavage
7 The features, including portions of the thiazolidine (dihydro thiazine) ring with no analogy
in the dipeptide, might decrease enzyme recognition such that, overall, substrate and
antibiotic bind with similar affinity.
8 The side chains of effective b-lactams and active peptide substrates are structurally
unrelated points to the complexity of their interactions with penicillin-sensitive enzymes .
9 High-resolution X-ray diffraction studies in progress should help resolve these and related
questions.
10The highly reactive b-lactam bond essential for the rapid acylation of target PBPs by many
penicillins and cephalosporins largely reflects the b- lactam's strained four-membered ring
resulting, in part, from the loss of normal amide resonance due to steric constraints that
prevent coplanarity of the three substituents of the p-Iactam nitrogen.
11This is seen as a greater C=O stretching frequency, shorter C=O bond length and longer
CO-N bond length in active penicillins and cephalosporins when compared to unstrained b-
lactams .
12 In Δ3 -cephalosporins amide resonance is further decreased by the enamine contribution .
13Substitution of a good leaving group at the C-3 methylene of cephalosporins permits
expulsion of the methylene substituent with formation of an exocyclic double bond upon
cleavage of the β-Iactam thereby increasing both the β-Iactam's reactivity and biological
activity significantly .
14 The low chemical reactivity and reduced biological activity of Δ2-cephalosporin
derivatives [which appear more closely isosteric to penicillin than the active Δ3-
cephalosporins ] further support the importance of a reactive b-lactam bond for the efficient
acylation of essential PBPs. 15 Thus β-Iactams such as penicillin G are good inhibitors of
CPase as a consequence of their rapid acylation of the enzyme [k2 = 20-6000 times greater
than k2 for the usual CPase substrates, in the case of Streptomyces R61 CPase ] and not
because of a particularly high affinity for the enzyme (as reflected by a KD value comparable
to other CPase substrates).
16. Thus, the high potency and specific inhibitory properties of b-lactam antibiotics reflect a
relatively favorable recognition by the target PBPs coupled with their strong acylating
capability.
17. These properties impart a high k2/KD ratio which, when coupled with the stability of the
covalent β- Iactam-enzyme complex (small k3), enables these antibiotics to inactivate
sensitive enzymes of cell wall biosynthesis with high efficiency (20)
RESISTANCE OF PBP
Resistance in Enterococcus faecium
Enterococci are generally 10 to 1000-fold less susceptible to b-lactams than streptococci .
Such natural resistance is linked to production of a class B PBP with low affinity for b-
lactams, PBP5fm is responsible for the resistance as it takes over the catalytic role of other
PBPs when these are inhibited by antibiotics. The overproduction of PBP5fm is linked to an
initial, low level of resistance . However, acquisition of mutations within the PBP5fm
sequence are responsible for the development of even higher levels of resistance which may
reach MIC values of 512mgmL1 . The crystal structure of PBP5fm reveals that it contains a
classical transpeptidase domain preceded by an elongated N-terminal region In its active site,
Met485 is located three residues after the Ser480-X-Asn482 catalytic triad, and its mutation
into Thr or Ala is responsible for MIC values which are 16-fold higher than for wild type. It
can be concluded that the absence of the large Met side chain allows the catalytic Lys425
which is present nearby and having more degrees of freedom that‘s why it‘s participating less
efficiently in the acylation mechanism. Also in certain resistant enterococcal strains, a single
serine residue (Ser4660) is introduced in the PBP5fm sequence (thus in between residues 466
and 467 )in the left side of the cavity of PBP5fm is already stabilized by a salt bridge between
Arg464 and Asp481, and Val465 which plays a key role in b-lactam recognition and the
insertion of a residue at position 4660 could affect this recognition pattern, and thus b-lactam
binding .
b-LACTAM RESISTANCE BY S. pneumoniae
S. pneumoniae is a human commensal of the nasopharyngeal microbiota . The infection of
S. pneumoniae in a immunocompromised person is mainly responsible here , the first
appearance of b-lactam resistance in S. pneumoniae, this bacterium has responded quickly to
clinical interventions by recombination with other streptococci . S.pneumoniae achieves b-
lactam resistance through ex- tensive and complementary ―mosaic‖ mutation of three key
PBP target enzymes with minimal fitness cost
b-LACTAM RESISTANCE BY M.tuberculosis
The presence of cell envelope is responsible for impermeability to antibiotic . Important
additional factors contributing toward the b-lactam insensitivity of M. tuberculosis (in
addition to impermeability) are the expression of efflux transporters, the versatility of this
bacterium with respect to the synthesis of alternate peptidoglycan structures, and expression
of a robust—sufficiently so, as to represent a possible means of detection of M. tuberculosis
infection b-lactamase Due to this reasons, the b-lactams are not used to control M.
tuberculosis infection. The multiple drug treatment is required
b-LACTAM RESISTANCE BY S. aureus
S. aureus is a Gram-positive coccus and commensal produces invasive infection by b-lactam-
resistant S. aureus following surgery and increasingly within the community to the soft tissue
remains as difficult a challenge for chemotherapeutic Control today . The mechanism
correspond to a complexity of regulatory mechanisms and center on an acquired PBP known
as PBP2a. This acquired PBP2a completes the synthesis of the peptidoglycan of S. aureus
following incapacitation of its other PBPs by a b-lactam. The cell wall of S. aureus is thicker
than many other Gram-positive bacteria, and, indeed, increased cell-wall thickness gives
resistance .At the molecular level, a distinctive feature of the peptidoglycan of b-lactam-
resistant S. aureus is the presence of a pentaglycine cross-bridge extension to lysine of the
peptidoglycan stem. Addition to this pentaglycine extension involves catalysis by the
enzymes of the Fem (―factors enhancing methicillin‖ resistance) pathway. A comparison of
the mature cell wall of S. aureus and the cell wall made by S. aureus having disruptions in the
Fem pathway shows distinct differences in the polymeric structure . This bacterium acquired
two resistance mechanisms, with each acquisition occurring early in the 50-year history of
this resistance. Following the clinical introduction of the earliest penicillins, penicillin-
resistant S.aureus appeared as a result of expression of a penicillin-specific b-lactamase. This
b-lactamase was, and remains today, a ―penicillinase‖ of modest catalytic ability by
comparison to the b-lactam capability of the b-lactamases now endemic among the Gram-
negative bacteria. This penicillinase nonetheless provided resistance to S. aureus against
these early penicillin structures. In response, medicinal chemists discovered that penicillins
substituted with sterically large aryl groups, exemplified by methicillin, were poor substrates
of the penicillinase. The therapeutic value of methicillin was not long-lived. S. aureus, in
short order, acquired methicillin resistance by acquisition from environmental cocci of a new
PBP This acquired transpeptidase (PBP2a) integrates into the enzyme assembly for
peptidoglycan synthesis as a b-lactam-insensitive catalyst. PBP2a distinguishes between the
peptidoglycan as a substrate and against the b-lactam as an inactivator. As this ability extends
to all structural classes of b-lactams (not just methicillin), this second resistance mechanism
has persevered as a powerful resistance mechanism against all but the newest guises of b-
lactam structure. The empirically derived structures of the anti- MRSA (methicillin-resistant
S. aureus) cephalosporins, exemplified by ceftobiprole and ceftarolineare successful
antibiotics against S. aureus (and other Gram-positive bacteria) as a direct result of their
ability to evade this structural discrimination by PBP2a. How- ever, although the framework
for our discussion is PBP2a, we also provide a perspective on the role of the auxiliary
mechanisms
The central question is the uniqueness of PBP2a. Methicillin-sensitive S. aureus encodes
eight enzymes for peptidoglycan synthesis. MRSA has nine (now including PBP2a). The core
eight enzymes arePBP1(a mono functional transpeptidase, active in cell division and
separation), PBP2 (a bifunctional transglycosylase and transpeptidase), PBP3 (a
transpeptidase), PBP4 (a low-molecular-mass transpeptidase), two monofunctional
transglycosylases, and two ―auxiliary‖ transpeptidases (FmtA and FmtB). Genetic deletion of
these activities, most recently using a MRSA strain, shows that only two—PBP1 and PBP2—
are required for the normal growth and normal shape of S. aureus, albeit with loss of b-lactam
resistance, in- creased lysozyme susceptibility, and decreased virulence . Assembly of the
MRSA peptidoglycan in the presence of the b-lactam challenge requires cooperative PBP2-
dependent transglycosylation and PBP2a-dependent transpeptidation .The presumption that
the peptidoglycan benefits from cross-linking by a second transpeptidase is supported by
evidence implicating both PBP4 and FmtA. PBP4 is involved in peripheral wall
peptidoglycan remodeling. PBP4 is essential for b-lactam resistance in the community strains
of MRSA. A b-lactam (cefoxitin) with high PBP4 affinity is synergistic with oxacillin .
Although the catalytic role of FmtA remains to be fully clarified, its presumed function is
transpeptidation under conditions of cell-wall stres.
Peptidoglycan biosynthesis is highly regulated at numerous levels, including by kinase
phosphorylation, stress-response pathways, and the transmembrane delivery of lipid II as the
substrate for its PBPs . Notwithstanding the catalytic competence of PBP2a in MRSA, PBP2a
expression is induced following the irreversible acylation of the ex- posed cell-surface
domain of the transmembrane sensor protein MecR by a b-lactam anti- biotic. PBP2a is made
only when circumstances demand its presence. The MecR protein is structurally and
functionally homologous to a BlaR sensor protein, which itself controls expression of the S.
aureus penicillinase. Cross talk between the two pathways adds additional complexity to the
poorly understood and multi-event cascades ultimately inducing PBP2a (and/or penicillinase)
expression. A molecular-level understanding of these pathways is anticipated to identify new
targets for antibiotic synergy with b-lactams. An important advance with respect to PBP2a is
the discovery that its active site is under allosteric control with respect to two loop motions
that open the active site in response to its peptidoglycan substrate . b-Lactams that
appropriately mimic peptidoglycan structure, such as ceftaroline, have good MRSA activity
by their ability to effect this allosteric opening. The appreciable distance between the newly
discovered allosteric site and transpeptidase active site is evident from the crystal structure of
the non-b-lactam bound to PBP2a . As a consequence of their allosteric-induced opening of
the active site, the concentrations achieved by these b-lac- tams in vivo coincide with the
concentration required for PBP2a inactivation . Subversion of the allosteric mechanism also
has been achieved in vitro using a threefold b-lactam combination . Non-b-lactam allosteric
effectors capable of b-lactam synergy have also been identified .
Genomic technologies identify additional loci that synergize with b-lactams , including
within the peptidoglycan biosynthesis pathway , the FtsZ-dependent organization of the
peptidoglycan biosynthetic machinery , and the coordination of the synthesis of the wall
teichoic acids with that of the peptidoglycan .The targets identified within the wall teichoic
acid pathway may have special significance as the synergistic pairing of intervention against
both biosynthetic pathways may extend to other Gram-positive bacteria . The translation of
successful in vitro combination therapy into successful clinical therapy is never
straightforward . Nonetheless, intervention at coupled binding sites (such as by simultaneous
occupancy of the allosteric site and active site of PBP2a by two b-lactams) and at intersecting
pathways (such as synergy between simultaneous disruption of peptidoglycan and teichoic
acid biosynthesis by two separate inhibitors) is emerging as a credible (if not yet viable, apart
from b-lactam b-lactamase pairs) strategy to control resistant bacterial pathogens.(21)

Resistance by Mutation
Mutation of P.aerugenosa PBP4 is the main driver of the one -step high level b lactam
resistance in vitro and in Vivo.
The mechanism of b lactam resistance were studied in previously described collection of 36
independent Ceftazidime resistant mutants.These mutants were obtained in vitro (one step
spontaneous)or in Vivo (after 3 days of treatment with humanised Ceftazidime regimen in
mouse model of lung infection)at two Ceftazidime concentrations are 4 and 16 mg/ ml,and
select the wild type strain PAO1 having normal mutation rate supply or it‘s mutS deficient
hypermutable PAODmutS having high mutation rate supply.In the previous study ,all
mutants were shown to be highly resistant to all tested penicillins, cephalosporins,and
monobactams.They found that , there is overexpression of the chromosomal cephalosporinase
Amp C responsible for the b lactam resistance in all cases.Hence,to find out genetic
mechanism m. Leading to AmpC hyperproduction ,they sequenced,and quantified the
expression of all genes,so known to be involved in amp C regulation and overexpression
(ampD,ampE,ampDh2,ampDh3 and ampR)in 36 mutants.For that performed coplementation
experiments with plasmids harbouring the wild type amp D gene(pUCPAD ) or the complete
amp DE operon (pUCPAGE). In contrast to present method, almost none of the mutants
showed mutations in any of the loci examined. But the only exception were 4 mutants
obtained in Vivo from PAODmutS (high mutation rate supply)at the low Ceftazidime
concentrations (4mg/ml),showing different mutation in ampD. Only the four ampD mutants
showed positive complementation with pUCPAD,but all 36 mutants showed positive
complementation with pUCPAGE. Furthermore,the positive complementation required the
simultaneous presence of both amp D and amp E , since plasmids harbouring ampDE operon
with a non functional ampD and wild type amp E also failed to complement the resistance
phenotype.These findings suggested that , mutation in ampD or ampR are not at all the most
common in vitro and in Vivo, leading to Amp C overexpression and high level b lactam
resistance in the P.aerogenosa.The results suggest that one step high level Ceftazidime
resistance in P.aerogenosa, mainly occur through the single mutation in gene or genes
previously unknown to be involved in b lactam resistance or AmpC regulation.For resistance
phenotype, single mutation has to be responsible is shown by Ceftazidime resistance
mutations rates.At two different Ceftazidime concentrations are 4 and 16 mg/ml, spontaneous
resistant mutants were obtained with state of 10-8 mutations per cell division for wild type
PAO1 and 10-5,10-6 for PAODmutS,from that they rule out there should be involvement of
more than one mutation in resistance phenotype.Hence,to detect mutation in gene ,yet
unknown to be involved in the b lactam resistance they followed whole genome analysis
approach.Four of the PAO1 Ceftazidime resistant in vitro mutants were analysed by
comparative hybridisation on recently described microarray for the discovery of single
nucleotide polymorphisms in P.aerogenosa using parental PAO1 strain as reference. Major
decrease in hybridisation ratio (indicating deletions of 500-1000bade pairs) were detectable
for two of the mutants in gene PA3047,the E.colidac B orthilog, encoding nonessential low
molecular mass PBP4.PCR and sequencing confirmed the presence of deletions in this genes
.The two remaining mutants 1A1 and ID4 shows pronounced decrease of hybridisation ratio
at a single position in gene PA3047 ,PCR and sequencing identified as well the mutations,a G
to A Change in nt 819 leading to premature stop codon for 1A1 and ATO C Change in nt
235 leading to missense mutation for ID4. The PBP has been characterised in E.coli,which is
nonessential low molecular mass class C PBP with DD carboxypeptidase and DD
endopeptidase activity,play important role in morphology ma
intenance,peptidoglycan maturation and recycling and cell separation during division.The
PBP4 of P.aerogenosa show 27% identity with that of E.coli and contains all conserved
motifs. The alignment of E. coli and P.aeruginosa PBP4 sequences is included in. Following
the discovery of mutations within the ortholog, they sequenced this gene in the rest of the
collection of the 36 ceftazidime resistant mutants. All but 2 of the 32 mutants not having
mutations in ampD had mutations in dacB.A total of 28 different mutations were detected,
and included deletions/insertions , nonsense mutations , and missense mutations Many of the
missense mutationsoccurred in sequences encoding highly conserved motifs, including the
catalytic serine, at position 72 in P. aeruginosa.
In order to further confirm the role of dacB mutations in b- lactam resistance, they
constructed the dacB knockout mutant of PAO1 (PADdacB). The inactivation of dacB in
PAO1 yielded an almost identical phenotype to that documented in the ceftazidime-resistant
dacB spontaneous mutants, with high level b-lactam resistance and ampC overexpression.

Mutation of P.aerugenosa PBP4 determines an AmpR dependent overexpression of b

lactamase AmpC
To study the role Of PBP4 mutation in b lactam resistance and pregulation of Amp C
expression ,AmpC and AmpR (transcriptional regulator of AmpC),AmpD+negative regulator
of AmpC),and amp E(second component of bicistronic ampDE operon are constructed,which
encodes Ann Inner membrane bound sensory transducer that modulates AmpD activity). For
that they knockout mutants of strain 1A1(spontaneous mutant of PAO1) and strain PAZO1 as
control.If there is inactivation of ampC ,then completely restored ceftazidime succeptibility in
1A1 observed,and showed that overexpression of b lactamase is essential for resistance
phenotype.Also,the inactivation of ampR restored ceftazidime succeptibility and basal ampC
expression levels,thus showing that the effect of PBP4 mutation requires a functional ampR
Therefore considering that PBP4 has been involved in peptidoglycan recycling,it seems
reasonable to believe that amp C overexpression driven by dac B inactivation as occurs in the
classical ampD mutation pathway.. should be consequences of qualitative and quantitative
modification of muropeptides,that are the effector molecules for smpC induction through
their interaction with ampR.
Additionally, they show that the AmpDE pathway of AmpC repression is functional in the
PBP4 mutants, since the inactivation of ampD dramatically increased further ampC
expression and ceftazidime resistance in 1A1. Furthermore, while the inactivation of ampE in
PAO1 (or in its ampD mutant) did not produce significant effects, it also determined a
marked increase of ampC expression and ceftazidime resistance in the dacB mutant. These
results suggest that both genes of the ampDE operon play a major role in the dacB mutant
background. This conclusion is further supported by the positive complementation of the
PBP4 mutants with the complete ampDE operon expressed from a multicopy plasmid.
Moreover, the expression of dacB from a multicopy plasmid (pUCPdB) also complemented
both, the dacB and the ampD mutants. Therefore, these results show that PBP4 and AmpDE
are parallel synergic ampC regulatory pathways (a defect in one of them can be
complemented by increasing the amount of the other), both ultimately relying on a functional
AmpR. While both pathways have a very similar effect on ampC expression, PBP4 mutation
confers high level (clinical) b-lactam resistance (i.e. resistant according to current
breakpoints), while ampD inactivation confers only moderate resistance (i.e. still susceptible
according to current resistance breakpoints). In fact, the resistance level conferred by PBP4
mutation is more similar to that conferred by the simultaneous inactivation of the three ampD
genes of P. Aeruginosa, that produces a much higher increase in ampC expression.
Nevertheless, this mechanism of high-level resistance is not found among clinical strains,
because it requires the acquisition of several mutations and because it causes a marked
reduction of fitness and virulence .Here we show that in vivo (murine systemic infection
model) fitness is not affected in the PAO1 dacB mutant, as shown by the competition index
of 0.92, in sharp contrast to the previously documented CIs of less than 0.01 for the double
and triple ampD mutants . Therefore, in contrast to the ampD inactivation pathway, PBP4
mutation in P. aeruginosa is a very efficient one-step trigger of high level b-lactam resistance
mechanism of potentially enormous clinical relevance.

To explore the effect of PBP4 mutation , they performed whole genome analysis of gene
expression in two selected mutant strains (1A1 and 2A2) compared to wild type PAO1.(22)
.
ISOLATION, EXTRACTION AND PURIFICATION
PBPs are ectoproteins tethered to the outer facet of the cytoplasmic membrane with a C-
terminal amphipathic membrane anchor that maintains the flexibility of the enzymatic
domain while working on the PG layer placed just above. As PBPs are membrane proteins,
we have described the process of membrane isolation and detection of PBPs using the
fluorescent penicillin BOCILLIN [5]. However, being a membrane protein, it is difficult to
purify these proteins in their active form. The conventional method of solubilization for such
proteins is to use different deter- gents, but in most of the cases, PBPs undergo denaturation
upon detergent treatment. Renaturation of the protein is not guaranteed and might result in
loss of activity. As PBPs can bind to ampicillin, ampicillin-affinity chromatography is a
suitable and convenient procedure for their purification [6]. PBPs can also be purified using
immobilized metal-affinity (Ni-NTA) chromatography. Both the methods have been
described in this chapter. The binding efficiency of PBPs with penicillin is determined by
calculating their acylation and deacylation rates upon interaction with BOCILLIN. The
related protocols are discussed here, and we have also explained the methodology of the DD-
carboxypeptidase assay that is helpful to determine the kinetic parameters of the interaction
of the PBP with its peptide substrates.
Isolation of Membrane- Anchored PBPs from the Cell Membrane
1. 10 mM potassium phosphate buffer, pH 7.4: 1MK 2HPO4: Dissolve 1.74 g dipotassium
phosphate (K2HPO4) in 10 mL water
1 M KH 2PO4: Dissolve 1.36 g potassium diphosphate (KH2PO4) in 10 mL water. To
prepare 100 mM phosphate buffer, pH 7.4, mix 8.02 mL of 1MK 2HPO4 and 1.98 mL of 1 M
KH2PO4, and adjust the volume to 100 mL with water. Finally, dilute 100 mM phosphate
buffer with water to prepare 10 mM phosphate buffer
Cloning of Soluble Form of PBPs
1. pT7-7K and pET28a(+) plasmids.
2. E. coli BL21(DE3) strain
Expression of Soluble PBPs
1. Inducer: 100 mM IPTG. Dissolve 238 mg IPTG (isopropyl-1- thio-β-D-galactopyranoside)
in 8 mL of water. Make up the volume to 10 mL. Filter the solution through a 0.22 μm
syringe-driven filter and store at 20 C. (Protect from light.) 2. Lysis buffer: 10 mM Tris–HCl,
300 mM NaCl, 0.2 mM PMSF, pH 8.0:
1 M Tris–HCl, pH 8.0, stock solution. To prepare a 1 M stock solution of Tris–HCl, dissolve
121.14 g Tris base in 800 mL of water. Adjust the pH to 8.0 by adding concentrated HCl, and
make up the volume to 1000 mL.
1 M NaCl stock solution: Dissolve 58.44 g sodium chloride in 1000 mL water.
100 mM PMSF stock solution: Dissolve 1.74 mg PMSF (phenylmethylsulfonyl
fluoride) in 10 mL isopropanol. Store at 20 C.
 To prepare 100 mL of lysis buffer, mix 1 mL of 1 M Tris–HCl, pH 8, and 30 mL of 1 M
NaCl. Finally, make up the volume to 100 mL with water. Add PMSF to the buffer just
before sonication such that the final concentration is 0.2 mM
Purification of Soluble PBPs
Affinity chromatography is popularly used for protein purification. It exploits the biological
function of the biomolecules to separate them. The process involves a specific and reversible
interaction of a protein or peptide (mobile phase) with a ligand which has been immobilized
on a solid support (stationary phase).
Coupling of Ampicillin into Activated CH-Sepharose 4B

Ampicillin-coupled CH-Sepharose 4B is used for purification of PBPs. Activated CH-

Sepharose 4B is synthesized in several steps. Firstly, aminocaproic acid is immobilized to
cyanogen bromide- activated Sepharose 4B to form CH-Sepharose 4B, which is further
activated by esterification of its carboxyl group with N-hydroxysuccinimide (Fig. 1). As
ampicillin [6-(D()-alpha-aminophenylacetamido) penicillanic acid] contains a primary amino
group, it can easily be coupled with the activated CH-Sepharose 4B.
1. Affinity resin: Use activated CH-Sepharose 4B.
2. HCl (0.001 N): Dilute 1 N HCl 1000 times in water. Be careful while handling
concentrated HCl.
3. Coupling buffer: 100 mM NaHCO3, 500 mM NaCl, pH 8.0. Dissolve 4.2 g sodium
bicarbonate (NaHCO3) in 200 mL of water. Add 250 mL of 1 M NaCl to it. Adjust the pH to
8.0. Make up the volume to 500 mL with water.
4. Blocking buffer: 100 mM Tris–HCl, pH 8.0. Add 25 mL of 1 M Tris–HCl, pH 8.0, to
water, and make up the volume to 250 ml.
5. Wash buffer A: 100 mM acetate buffer, 500 mM NaCl, pH 4.0. Dissolve 3.4 g sodium
acetate (C2H3NaO2) in 100 mL of water. Add 125 mL of 1 M NaCl to it. Adjust the pH to 4
using glacial acetic acid. Finally, make up the volume to 250 mL with water.
 6. Wash buffer B: 100 mM Tris–HCl, 500 mM NaCl, pH 8.0. Mix 25 mL of 1 M Tris–HCl,
pH 8.0, and 125 mL of 1 M NaCl to water, and make up the volume to 250 mL.
Purification Through Ampicillin-Affinity Chromatography
1. Wash buffer C: 50 mM Tris–HCl, 1 M NaCl, pH 7.5. Dissolve 29.22 g NaCl in 300 mL
water. To this, add 25 mL of 1 M Tris–HCl, pH 8.0. Adjust the pH to 7.5 with concentrated
HCl, and make up the volume to 500 mL with water.
2. Wash buffer D: 50 mM Tris–HCl, pH 7.5. Add 25 mL of 1 M Tris–HCl, pH 8.0–400 mL
water. Adjust the pH to 7.5 with concentrated HCl. Finally, make up the volume to 500 mL
with water.
3. Elution buffer: 1 M NH2OH, 500 mM Tris–HCl, pH 7.0. Dissolve 20.8 ghydroxylamine
(NH2OH) in100mL water. To this, add 150 mL of 1 M Tris–HCl, pH 8.0. Adjust the pH to
7.0 with concentrated HCl. Finally, make up the volume to 300 mL with water.
4. Dialysis buffer: 20 mM Tris–HCl, 150 mM NaCl, pH 7.5. Mix 20 mL of 1 M Tris–HCl,
pH 8.0, and 150 mL of 1 M NaCl with 700 mL water. Adjust the pH to 7.5 with concentrated
HCl. Finally, make up the volume to 1 L with water.

Ni-NTA Affinity Chromatography

Immobilized metal-affinity chromatography is widely used for the purification of histidine-
tagged proteins. The (histidine)6 tag is one of the most common tags used to facilitate the
purification of recombinant proteins. It binds to Ni-NTA and is eluted with high
concentrations of imidazole. Nitrilotriacetic acid (NTA) is a tetra- dentate chelating adsorbent
that engages four of the six ligand binding sites in the coordination sphere of the nickel ion,
and the remaining two sites interact with the His tag. NTA binds metal ions in a stable
condition and inhibits the loss under strict washing conditions [7]. The optimal placement of
the tag can be either at the C- or the N-terminus and is protein specific. At pH 8.0 the tagging
is small and uncharged and does not affect the folding of the protein of interest. If necessary,
the tag can be removed.
1. Binding buffer: 10 mM Tris–HCl, 300 mM NaCl, 25 mM imidazole, pH 8.0, 1 M
imidazole. Dissolve 6.808 g imidazole in 100 mL water. Mix 2.5 mL of 1 M Tris–HCl, pH
8.0, 75 mL of 1 M NaCl, and 6.25 mL of1 M imidazole. Make up the volume to 250 mL with
water.
2. Elution buffer: 10 mM Tris–HCl, 300 mM NaCl, 500 mM imidazole, pH 8.0. Mix 2.5 mL
of 1 M Tris–HCl, pH 8.0, 75 mL of 1 M NaCl, and 125 mL of 1 M imidazole. Make up the
volume to 250 mL with water.
BOCILLIN Binding Assay
BOCILLIN FL penicillin is a fluorescent penicillin and is used to determine penicillin-
binding protein profiles of a number of bacteria [5]. It is synthesized from penicillin V and
BODIPY FL dye (which is spectrally similar to fluorescein). The excitation and emission
wavelengths are 488 and 526 nm, respectively.
1. 10 mM potassium phosphate buffer, pH 7.4
2. 5 mM BOCILLIN stock solution: To prepare a solution of 5 mg/mL (7.5 mM), add 1 mg
of BOCILLIN FL penicillin and sodium salt (mol. wt. 661.46) to 200 μL of water. From this,
dilute 133.3–200 μL to get 5 mM BOCILLIN. (Protect from light.)
Kinetic Analysis of the Interaction of PBPs with BOCILLIN
Determination of the Acylation Rate Constant
1. 10 mM potassium phosphate buffer, pH 7.4
2. 5 mM BOCILLIN. Denaturing buffer: 250 mM Tris–HCl, pH 6.8, 10% SDS, 0.02%
bromophenol blue. The SDS-PAGE gel loading dye is used as the denaturing buffer. For 10
mL buffer, mix 2.5 mL of 1 M Tris–HCl with 6.5 mL water. Adjust the pH to 6.8. To this add
1 g SDS (sodium dodecyl sulfate) and 2 mg bromophenol blue, and let it dissolve. Finally,
make up the solution to 10 mL with water.
Determination of the Deacylation Rate Constant
1. 10 mM potassium phosphate buffer, pH 7.4
2. 5 mM BOCILLIN.
3. Penicillin G (sodium salt).
4. Denaturing buffer .
Kinetic Analysis of DD- Carboxypeptidase Activity of PBP
1. 50 mM Tris–HCl, pH 8.5: Add 5 mL of 1 M Tris–HCl to 70 mL water. Adjust the pH to
8.5 with concentrated HCl. Finally, make up the volume to 100 mL with water.
2. 1 mg/mL flavin adenine dinucleotide (FAD) stock solution: Weigh 1 mg FAD and dissolve
in 1 mL water. Store the stock solution at 20 C. (Protect from light.)
3. 0.3 mg/mL FAD working solution: Dilute 300 μL of 1 mg/ mL FAD with water to prepare
1 mL of 0.3 mg/mL FAD solution. Prepare freshly before use. (Protect from light.)
4. 5 mg/mL D-amino acid oxidase: Weigh 5 mg of D-amino acid oxidase and dissolve in 1
mL water. Store the solution at 20 C. (Protect from light.)
5. 10 μg/mL horseradish peroxidase: Dissolve 5000 units of horseradish peroxidase in 3.2 M
ammonium sulfate suspension containing potassium phosphate buffer of pH 6.0. The protein
concentration in this suspension is 13 mg/mL. Dilute 0.77 μL of the horseradish peroxidase
solution to 1 mL with water to form peroxidase solution of the desired concentration.
6. Enzyme-coenzyme mixture: Prepare a mixture containing horseradish peroxidase, D-
amino acid oxidase, and FAD in the following ratio: 50 mM Tris–HCl, pH 8.5; 0.3 mg/mL
FAD; 10 μg/mL horseradish peroxidase; 5 mg/mL D-amino acid oxidase ¼ 20:10:5:1.
(Prepare freshly before use.)
7. 10 mg/mL o-dianisidine dihydrochloride: Weigh 10 mg o- dianisidine dihydrochloride and
dissolve in 1 mL water. (Pre- pare freshly before use.)
8. Artificial tripeptide substrate: Nα,Nε-diacetyl-Lys-D-Ala-D-Ala.
Prepareastocksolutionof50mMofthepeptide,anddiluteitto the desired concentration
required.(Prepare freshly before use.)
9. Peptidoglycan mimetic pentapeptide substrate: L-Ala-γ-D-Glu- L-Lys-D-Ala-D-Ala
(custom synthesized). Prepare a stock solution of 50 mM of the peptide, and dilute it to the
desired concentration required. (Prepare freshly before use.)
Detection of Membrane- Anchored PBPs in the Cell Membrane
1. Inoculate 500 mL of LB with 1% of an overnight bacterial culture, and incubate at 37C
with shaking until it reaches an OD600 ~ 0.4.
2. Harvest the cells by centrifugation (5000 g for 10 min).
3. Wash the pellet twice, and finally resuspend it in 100 mM phosphate buffer, pH 7.0.
4. Lyse the homogenous suspension of cells by sonication.
5. Centrifuge the lysate at 5000 g for 10 min to remove the cellular debris, and transfer the
supernatant to a fresh tube.
6. Centrifuge the supernatant at 100,000 g for 60 min at 4 C to precipitate the membranes by
using an ultracentrifuge.
7. Resuspend the pelleted membranes in the same buffer, and estimate the total protein by
Bradford protein estimation kit. Plot a standard curve of the amount of BSA (μg) versus
absorbance at 595 nm, and determine the concentration of the protein from this standard
curve.
Cloning of Soluble Form of PBPs
pT7-7K and pET28a(+) Expression Systems
When ampicillin-affinity chromatography is used for purifying PBPs, the plasmid pT7-7K is
used as the expression vector, whereas the pET28a(+) expression system is used for
purification using Ni-NTA chromatography. Both the vectors have the T7 promoter. T7 RNA
polymerase is very active and is used for high-level transcription of the gene of interest. The
expression of the PBP gene is induced by providing a source of T7 RNA polymerase which is
provided by using a host that contains a chromosomal copy of the T7 RNA polymerase gene.
There are many such host strains.
However, the use of E. coli BL21 (DE3) as the host is specified here. It contains the λDE3
lysogen that carries the gene for T7 RNA polymerase under control of the lacUV5 promoter,
which can be induced by IPTG [8].
Detection of Sequences for N-Terminal Signal Peptide and C-Terminal Amphipathic
Helix
PBPs are membrane-anchored proteins which make their purification difficult.
Conventionally membrane proteins are solubilized using detergents, but PBPs get denatured
upon detergent treatment. However, for the ease of purification and subsequent
characterization, the PBPs can be genetically engineered to express them in their soluble
forms within the cytoplasm. For this, the nucleotide sequences corresponding to the amino
acids at the N-terminal signal peptide and C-terminal amphipathic regions have to be
removed. The presence and location of the signal peptide cleavage site in the amino acid
sequence of the gene are detected by using the ―SignalP 4.1‖ server [9]. Signal peptides range
from 21 to 29 amino acids. A representative image of a typical prediction result from the
SignalP server is shown in Fig. 2. Here, the first 21 amino acids from the N-terminal are
detected as the signal peptide sequence. The C-terminal amphipathic regions can be detected
using different servers, e.g., ―HELIQUEST‖ [10]. These regions can also be detected by
three-dimensional modelling of protein.
Construction of the Clones and Transformation
1. Design the primers such that the resultant gene would express in its soluble form, devoid of
the aforementioned terminal sequences.
2. Amplify the gene encoding the soluble form of the PBP, and clone it in the vector. The
choice of vector depends on the method of purification to be used. Confirm the sequence of
the gene by sequencing.
3. Prepare chemical competent cells of E. coli BL21 (DE3) by following the standard
protocol.
4. Transform BL21 (DE3) chemical competent cells with the cloned constructs, through the
heat-shock method. Select the recombinant clones against 50 μg/mL kanamycin. (The
expression vectors pT7-7K and pET28a (+) have the kanamycin resistance gene.)
5. Make sure the transformants are correct by digesting with the restriction enzymes that are
used for cloning and subsequently confirm by DNA sequencing.
6. Inoculate the freshly transformed BL21 (DE3) strain harboring the desired construct for
further expression studies.
Expression of Soluble PBPs
Before purification of any protein in its active form, it is necessary to optimize its expression.
In the afore mentioned expression systems, very high levels of gene expression can be
achieved by increasing the concentration of IPTG and increasing the post-induction period.
However, sometimes a majority of the protein might remain as inclusion bodies. Moreover,
IPTG is toxic to cells and is expensive too. So, to achieve a balance between cell survival and
protein production, we have to optimize several parameters such as the IPTG concentration,
the growth phase at which IPTG is to be added, the post-induction temperature, and the
period of post–induction. For expression optimization:
1. Allow the culture to grow overnight in a kanamycin- supplemented LB broth. 2. Next
morning, inoculate 10 mL of kanamycin-supplemented LB broth with 0.1% inoculum from
the overnight culture.
3. Express the gene by varying any one of the four parameters at a time, i.e., IPTG
concentration, incubation temperature, phase of induction, and period of post–induction.
4. To check the expression levels, harvest the cells by centrifuging at 5000 g at 4 ˚C for 10
min.
5. Resuspend the cell pellets in 200 μL lysis buffer, and sonicate the above mixture
6. Centrifuge the sonicated samples at 10,000 g at 4 ˚C for 30 min. Insoluble cell components
(membranes and cell debris) will be pelleted at the bottom of the tube.
7. Collect the supernatants containing the soluble proteins and transfer into a fresh tube.
Estimate the protein concentration by Bradford protein estimation kit using BSA as the
standard.
8. Run a 15% SDS-PAGE following the standard protocol, to determine the expression
levels.
9. After finalizing the optimum expression conditions, scale up the volume depending on the
yield obtained and the concentration of protein desired.
Purification of Soluble PBPs
Coupling of Ampicillin into Activated CH-Sepharose 4B
1. Suspend 2 g of freeze-dried activated CH-Sepharose 4B in 0.001 N HCl, and wash it with
the same.
2. Dissolve 90 mg ampicillin in the coupling buffer, and allow it to mix with the resin for 2 h
at room temperature with gentle shaking.
3. Wash away the excess ampicillin with 500 mL of coupling buffer.
4. Block the remaining active site groups by incubating the ampicillin-coupled resin in the
blocking buffer for 1 h.
5. Finally, wash the ampicillin-coupled resin thrice alternatively, with wash buffer A and
buffer B.
Purification Through Ampicillin-Affinity Chromatography
1. Mix the cell lysate with ampicillin-coupled activated CH-Sepharose 4B, and incubate for 1
h at 30 ˚C.
2. Wash the resin with 1 L of wash buffer C followed by 1 L of wash buffer D, using a
sintered glass funnel.
3. Elute the PBPs bound to the resin with the elution buffer with a flow rate of 1 mL/min.
Monitor the elution profile by measuring the absorbance of the eluents at 280 nm [11].
4. Immediately pool the purified protein fractions, and dialyze for 12 h with three changes
against dialysis buffer.
5. Estimate the concentration of the purified protein using Brad- ford assay. 6. Store the
protein on ice at 0 ˚C for immediate use or at80 C (with 50% glycerol) for long-term storage
Ni-NTA Affinity Chromatography
1. In a chromatography system, wash the His Trap affinity (Ni-NTA) column with degassed
Milli-Q water to remove the ethanol. The washing is complete after the conductivity and the
protein concentration levels reach zero. The purification can also be done without a
chromatography sytem. In that case, one has to use a glass column with Ni-NTA resin and
follow the protocol from above step.
2. Equilibrate the column with the five column volumes (CV) of binding buffer. Stop the
equilibration process once the conductivity becomes constant.
3. Load the cell lysate onto the pre-equilibrated column. Choose the sample loop according
to the volume of your cell lysate.
4. Wash the column with five CV of the binding buffer.
5. Elute the proteins from the column with the elution buffer after making a gradient between
25 and 500 mM imidazole.
6. Dialyze the fractions collected with three changes of the dialysis buffer for a duration of 12
h.
7. Estimate the concentration of the purified protein, and store the protein properly.

BOCILLIN Binding Assay

This assay is done to confirm whether the purified soluble proteins are enzymatically active.
The PBPs are allowed to bind to its substrate, BOCILLIN.
A distinct band of BOCILLIN-bound PBP at 488 nm reveals that the purified protein is
active.
1. Dissolve the purified PBP (5 μg) in 10 mM potassium phosphate buffer, pH 7.4, and label
it with 50 μg/mL of BOCILLIN.
2. Incubate the mixture in the dark at 35 ˚C for 30 min.
3. Run the samples through SDS-PAGE following the standard protocol.
4. To visualize the labelled PBPs, wash the gel twice with deionized water, and scan
immediately through a Typhoon imager at the excitation and emission wavelengths of 488
and 526 nm, respectively. The gel can also be visualized using a UV transilluminator, though
a Gel Doc system having a 470 nm filter would be preferred.
5. After staining and destaining the gel, visualize the purified protein bands, and document
the gel image.
Representative images of SDS-PAGE and BOCILLIN binding of a purified PBP are shown in
Fig. 4.

Isolation and Sequence Analysis of dacB, which encodes a Sporulation Specific PBPs in
Bacillus subtilis.
Kinetic Analysis of the Interaction of PBPs with BOCILLIN
When a PBP enzyme (E) interacts with its substrate (S) (either peptide or beta-lactam), the
kinetic parameters of the interaction are calculated based on the following reaction:
k1 k2 k3
E+S E.S E-S E+P
where ―E S‖ is the covalent acyl-enzyme complex, ―P‖ denotes the product released, and K
¼ (k1 + k2)/k1,―E·S‖ is the non-covalent Michaelis complex.
Determination of the Acylation Rate Constant
The efficiency of PBP binding to penicillin is determined by the rate of acyl-enzyme complex
formation. It is determined by the second- order rate constant k2/K at subsaturating
concentrations of the substrate (beta-lactam antibiotics) [12]. The acylation rate k2/K is
obtained from the time course study of the enzyme-substrate complex formation with
BOCILLIN [13].
1. Prepare four different concentrations of the BOCILLIN substrate (25, 50, 75, and 100 μM)
in 10 mM potassium phosphate buffer, pH 7.4, in separate vials.
2. Preincubate the vials at 35 ˚C for 10 min.
3. Add the purified PBP to the BOCILLIN substrate and incubate in the dark.
4. Aliquot the samples (15 μL) at specific time intervals.
5. Immediately after aliquoting the sample, stop the reaction by adding it to the denaturing
buffer. Keep collecting samples at specific time intervals till the last time point.
6. Run the BOCILLIN-labelled PBP samples and analyze through SDS-PAGE. The sequence
in which the samples are loaded should match the sequence in which they are collected.
7. Quantify the band intensities of the BOCILLIN-bound proteins by densitometric scanning
using a Typhoon.
8. Analyze the data to determine the acylation rate constant (k2/ K) of the PBP.
Determination of the Deacylation Rate Constant
The deacylation of the BOCILLIN-PBP complex leads to the release of free PBP and the
cleaved BOCILLIN. The deacylation reaction is described by the first-order rate constant k3,
which is determined from the following equation:

( )

In this equation, PBPt is the residual acyl-enzyme concentration at time t, and PBP0 is the
initial concentration of acyl-enzyme complex. The deacylation rate constant (k3) of the
soluble PBP is determined by quantifying the fluorescence of enzyme-bound BOCILLIN (the
acyl-enzyme complex) that decreases over time and is determined using the above equation
[12, 14].
1. Incubate the PBP with BOCILLIN (50 μM) at 35 ˚C for 30 min in 10 mM potassium
phosphate buffer, pH 7.4.
2. At t0, add an excess of penicillin G (3 mM), and immediately aliquot out 15 μL and mix it
with a denaturing buffer to stop the reaction.
3. Similarly, keep aliquoting 15 μL samples at various time intervals.
4. Run all the collected samples in a sequence through SDS-PAGE.
5. Measure the fluorescent intensity of the BOCILLIN remained bound to the PBP, at
different time points by densitometric scanning.
6. Analyze the data to determine the deacylation rate constant (k3) of the PBP.
Kinetic Analysis of DD- Carboxypeptidase Activity of PBP
The DD-CPase activity of the soluble PBP is determined using the artificial peptide, Nα, Nε-
diacetyl-L-Lys-D-Ala-D-Ala, and the peptidoglycan-mimetic pentapeptide substrate, L-Ala-
γ-D-Glu-L- Lys-D-Ala-D-Ala. The kinetic parameters for the DD-CPase assay are deduced
from the linear regression of the double reciprocal plot (Lineweaver-Burk plot):
 [ ]
where reaction velocity (the reaction rate) is denoted by ―V,‖ Michaelis-Menten constant by
―Km,‖ maximum reaction velocity by ―Vmax,‖ and substrate concentration by ―[S].‖ Km
(mM) is the concentration of substrate at which the half-maximal velocity is achieved. The
kinetic data can be analyzed through the ―Enzyme Kinetic Module‖ of SigmaPlot (Systat
Software, San Jose, CA) to determine ―Km‖ and ―kcat‖ values [12].
1. In a 96-well plate, mix 1μg of PBP with varying concentrations (2–10 mM) of the
respective peptides, and adjust the reaction volume to 60 μL with 50 mM Tris–HCl, pH 8.5.
2. Incubate the reaction mixture for 30 min at 37 ˚C.
3. Add 10 μL o-dianisidine dihydrochloride and 140 μL of the enzyme-coenzyme mixture to
it. (Perform this step in the dark.)
4. Incubate in dark conditions at 37 ˚C.
5. Stop the reaction by adding 40 μL of 0.005 N HCl.
6. Estimate the free D-alanine generated, and compare against the standard D-alanine (1
mg/mL) solution by measuring the absorbance at 460 nm.
7. Analyze the data to determine the kinetic parameters, turnover number (kcat), and substrate
concentration at half the maxi- mum velocity (Km).
The reaction mechanism of the amount of free D-alanine estimation after DD-
carboxypeptidation. A representative image of a typical DD-CPase assay result is shown in
Fig. 5b. It can be seen that little or no color is developed in the negative control well (absence
of DD-CPase), whereas samples containing the DD-CPase enzyme showed a color
development due to the release of D-alanine which is also seen in the positive control well
containing D-alanine. A gradual increase in the color intensity is observed with an increase in
the concentration of peptide substrate
Membrane preparation and PBP assay:
Membranes of B. subtilis were prepared by sonic disruption of the cells and differential
centrifugation as described previously. Labelling of the membranes with [3H]
benzylpenicillin was performed in accordance with the optimum binding conditions
established for B. subtilis. After labelling, the membrane proteins were separated by sodium
dodecyl sulphate-polyacrylamide slab gel electrophoresis and the radioactive PBPs were
detected by fluorography. E. coli membranes were also prepared by sonication and
differential centrifugation, but the assay for their PBPs was performed by a different protocol.
Proteins from the inner membrane were selectively dissolved with the deter- gent Sarkosyl
(ICN Pharmaceuticals, Inc., Plainview, N.Y.) and separated from the insoluble material by
centrifugation prior to gel electrophoresis. Quantitation of the PBPs on fluorographs was
done as described previously, with a scanning densitometer (Biomed Instruments, Inc.,
Fullerton, Calif.).(23)
Isolation and Purification of Mycobacterium
Bacterial strain: M. smegmatis SN2 was obtained from the Indian Institute of Science,
Bangalore, India. Growth conditions. M. smegmatis was grown in nutrient broth containing
10 g of peptone, 10 g of beef extract, and 5 g of NaCl per liter on a rotary shaker at 200 rpm
and 37°C. Preparation of bacterial membrane fractions. Strains grown to the logarithmic
phase were harvested by centrifugation at 7,000 x g for 10 min at 4'C and washed twice in 50
mM Tris-HCl (pH 7.5) containing 10 mM MgCl2. The pellet was suspended in the same
buffer containing DNase (2, ug/ml) and disrupted in a sonicator (Labsonic 2000; B. Braun,
Melsungen, Germany) for 15 min in bursts of 3 min each. Unbroken cells were removed by
centrifugation at 7,000 x g for 10 min, walls were removed by centrifugation at 20,000 x g for
20 min, and membrane fractions were collected by centrifugation at 100,000 x g for 90 min at
4°C, washed twice, and suspended in 10 mM Tris-HCl (pH 7.5). PBP assays. To inhibit the
P-lactamase activity, mem- branes were first incubated with 2 x 10-5 M beta-iodopen-
icillanic acid for 20 min at 30'C. Samples (100 jig) of membrane proteins were incubated at
30°C for 10 min with different concentrations of [35S] benzylpenicillin (0.5 mCi/ mmol) (Du
Pont Co., Wilmington, Del.). The reaction was stopped by addition of an excess of
nonradioactive penicillin and sodium lauroyl sarcosinate (final concentration, 1%). After the
samples were allowed to stand at room temperature for 20 min, sodium dodecyl sulfate (SDS)
gel denaturing buffer was added and boiled immediately for 3 min. Samples were applied on
10% SDS gels. For the purified PBP, 0.5, ug of protein was used in each assay. In
competition experiments, purified PBP was first incubated with different concentrations of
the competing antibiotic for 10 min at 30'C and then with saturating concentrations of
radioactive penicillin for 10 min at 30°C; termination of the reaction was done in the usual
manner. Solubilization of membranes with Triton X-100. Mem- branes (849 mg) were
solubilized in 10 mM Tris-HCl (pH 8.0) containing 1 M LiCl, 0.1 mM DTE (dithioerythrol),
and 1% Triton X-100 (buffer A) on ice for 60 min. The supernatant was collected after
centrifugation at 100,000 x g for 90 min. Purification of the 49,500-Mr PBP from the Triton
X-100 extract by affinity chromatography on ampicillin-linked CH Sepharose 4B. The
affinity chromatography reagent was prepared as described by Coyette et al. (1). The Triton
X-100 extract (60 mg of protein) was mixed with 4 g of ampicillin- linked CH Sepharose 4B
in 5.5 ml (final volume). The suspension was stirred gently for 30 min at 4°C and then for 30
min at 30°C. The unbound proteins were removed by filtration through a sintered glass filter.
The bound membrane proteins were eluted by gentle agitation for 30 min at 30°C with 15 ml
of 1 M hydroxylamine (pH 8) in buffer A, and the supernatant was collected after
centrifugation. The procedure was repeated five times. The extracts containing penicillin-
binding activity were pooled, dialyzed against 10 mM Tris-HCl (pH 8.0) containing 0.1%
Triton X-100 and 0.1 mM DTE (buffer B), and loaded on a 2-ml DE-52 column equilibrated
in buffer B. The bound protein was eluted with buffer B containing 0.1 M NaCl. Fractions
containing penicillin-binding activity were pooled (200, g of protein) and analyzed by SDS
gel electrophoresis and fluorography. Monitoring the purification. Protein samples (50 pl)
were incubated with 5 RI of [14C] penicillin (50 mCi/mmol; final concentration, 34, ug/ml)
for 10 min at 30°C and then precipitated with 0.5 ml of 5% trichloroacetic acid and 5, ul of
10% Triton X-100 by the method of Waxman and Strominger (18). Samples were kept on ice
for 5 min, and the precipitate was collected on Whatman GF/C filter circles with a Millipore
filtration apparatus. The filters were washed four times with 2 ml of 5% trichloroacetic acid
and then washed four times with 2 ml of47% ethanol containing 0.01 N HCI. Filters were
dried and counted. Determination of enzymatic activities. The DD-carboxypeptidase activity
was estimated by measuring the hydrolysis of the tripeptide Ac2-L-Lys-D-Ala-D-Ala (a
generous gift from J.-M. Ghuysen), and the transpeptidase activity was measured by using
Gly-Gly as the acceptor (12). Briefly, AC2-L- Lys-D-Ala-D-Ala was incubated with the
purified PBP at 37°C for 30 min in the absence or presence of the acceptor Gly-Gly. The D-
Ala released was estimated by addition of a mixture of o-dianisidine, flavin adenine
dinucleotide, peroxidase, and D-amino acid oxidase and incubation for 10 min at 37°C, and
then a mixture of methanol-sulfuric acid-water (5:6:5) was added. Spectrophotometric
readings were re- corded at 535 nm. Standard curves were prepared by using D-Ala
alone.(24)
BIOINFORMATICS FOR PBPs
After isolation and purification of protein i.e. PBPs, further studies and sequencing can be
done using bioinformatic tools.
ENTREZ
Entrez is a biological serach engine which is used to determine protein sequence. The
Entrez Global Query Cross-Database Search System is a federated search engine, or web
portal that allows users to search many discrete health sciences databases at the National
Center for Biotechnology Information (NCBI) website. The NCBI is a part of the National
Library of Medicine (NLM), which is itself a department of the National Institutes of Health
(NIH), which in turn is a part of the United States Department of Health and Human Services.
The name ―Entrez‖ (a greeting meaning ―Come in‖ in French) was chosen to reflect the spirit
of welcoming the public to search the content available from the NLM.
Entrez Global Query is an integrated search and retrieval system that provides access to all
databases simultaneously with a single query string and user interface. Entrez can efficiently
retrieve related sequences, structures, and references. The Entrez system can provide views of
gene and protein sequences and chromosome maps.
DATABASE
Databases are the effective electronic cabinet are convinient efficient method of storing
information
PROTEIN DATABANK (PDB)
Protein databases are used to identify the sequence of the protein
: There 2 types of protein databases
They are Primarily protein databases (PIR,MIPS,Swiss-PROT,TrEMBL, NRL-3D),and
Secondary databases( PROSITE , profile,pfam,PRINTS, BLOCKS, IDENTITY)
SECONDARY STRUCTURE
The Secondary structure can be predicted using methods such as
Chou- Fassmans Method,
GOR method,etc
TERTIARY STRUCTURE
While tertiary structure can be predicted by two methods Exprimental methods such as
X ray Crystallography, NMR Spectroscopy
But as the experimental methods are time consuming so recently computational methods are
used.
HOMOLOGY MODELING
Homology modeling, also known as comparative modeling of protein is the technique which
allows to construct an unknown atomic-resolution model of the ―target‖ protein from:
1. Its amino acid sequence and
2. An experimental 3D structure of a related homologous protein
Afterwords sequences can be compared and identified by pairwise and multiple sequence
alignments with the help of software such as Clustal X
Conserved region can be identified by software such as Bioedit
3D structure can be built using SPDBV
Also docking can give an idea about interactive of drug molecular and protein which is
useful for drug desiging.
Clostridium perfringens
Scientific classification
Kingdom: Bacteria
Phylum: Firmicutes
Class: Clostridia
Order: Clostridiales
Family: Clostridiaceae
Genus: Clostridium
Species: C. perfringens

Clostridium perfringens is also known as C. welchii, or Bacillus welchii is a Gram-positive,

rod-shaped, anaerobic, spore-forming pathogenic bacterium of the genus Clostridium. C.
perfringens is generally present in nature as well as found as a normal component of decaying
vegetation, marine sediment, the intestinal tract of humans and other vertebrates, insects, and
soil. It has the shortest generation time in thioglycolate medium that is 6.3 minutes.
C. perfringens is the most common causes of food poisoning in the United States,after
Staphylococcus aureus. However, sometimes it is harmless,even if ingested.
Infections due to C. perfringens show symptoms like tissue necrosis, bacteremia,
emphysematous cholecystitis, and gas gangrene, which is also known as clostridial
myonecrosis. The name perfringens is comes from the Latin word (meaning "through") and
frango ("burst"), because rupture of tissue during during gas gangrene. In gas gangrene alfa
toxins are responsible for making gaps in plasma membrane of cell and affect cellular
function . C. perfringens can participate in polymicrobial anaerobic infections. When
infection is due to normal flora,it cause minor disease.
Food poisoning in humans is caused by type A strains which is able to produce the CPE (for
Clostridium perfringens enterotoxin),which is a polypeptide of 35.5 kDa that accumulates in
the beginning of the sporulation and later excreted to the media when it get lysates at the end
of the sporulation. It is coded by the cpe gene, it is present only in 5%of strain A and it
observed in the chromosome or in an external plasmid
Foodborne illness, due to C.perefringens is generally because of improper handeling of
food,with poorly prepared meat and poultry, or when food is properly prepared, but left as it
is to stand too long, . The C. perfringens enterotoxin (CPE) mediating diseases are heat-labile
( they inactivated at 74 °C (165 °F)). They are generally present in contaminated food if not
heated properly, and feces. Incubation time for it is between 6 and 24 (commonly 10–12)
hours after ingestion of contaminated food.
C.perfringens is common agent for gas gangrene. Some symptoms for gas gangrene include
blisters, tachycardia, swelling, and jaundice. Etc.
A strain of C. perfringens might present in multiple sclerosis (MS) nascent lesions. Tests in
mice shows that a toxin made by a rare strain of C. perfringens caused MS-like damage in the
brain . MS patients were found to be 10 times more immune-reactive to the epsilon toxin than
healthy people. (25)
PBPs of C. perfringens
Total Six penicillin binding protein were studied until now having ,molecular weight from
approximately 42,000 to 100,000 were detected in the cytoplasmic membrane. The relative
affinities of the PBPs for 16 beta-lactam antibiotics were determined. Most of the drugs
saturated PBP 3 and 4 at concentrations equal to their minimal inhibitory concentrations,they
suggest that these PBPs are the killing targets for beta-lactams. Mecillinam showed unique
properties because it had a higher affinity for PBP 5 than for other PBPs also it was the only
agent tested which caused inhibition of growth without saturating PBP4,other beta lactam
antibiotic test shows filament formation,regardless of showing pattern of binding.
Bacteria contain multiple penicillin-binding proteins (PBPs) in their cytoplasmic
membranes. These proteins have enzymatic activity, which is important for peptidoglycan
synthesis, and perform specific functions related to elongation, septation, and maintenance of
shape of cell . PBPs are also the "targets" of beta-lactam antibiotics. To understand the
mechanism of action of beta-lactam antibiotics and some basic principles of bacterial growth
and division interaction of drug and receptor are very useful. PBPs have been studied in
different bacteria, but not in obligate anaerobes. In this study, they report the presence of six
PBPs in Clostridium perfringens.they also determine the relative affinities of each PBP for all
beta-lactam antibiotics, they also give conclusions about which PBPs are considered as
primary targets for beta-lactam antibiotics. This species of anaerobe is a well-established and
cause serious infection for which beta- lactam antibiotics are usually drugs of choice PBPs.
Multiple PBPs were present in each of the strains of C. perfringens. PBP 5 and 6 were the
major bands. The Sarcosyl-insoluble fraction was also subjected to sodium dodecyl sulfate-
polyacrylamide gel electrophoresis and autoradiography; when PBPis not detected in material
that means they get soluble in sarcosyl. PBPs of strain 607 were also assayed by using
saturating concentrations of [I4C] benzylpenicillin, and the pattern was identical to that
obtained by using [125I]furazlocillin. To identify the possibility that the binding patterns of
whole cells might differ from those of membrane preparations, therefore washed cells of
strain 607 were incubated with [125I]furazlocillin at 30˚C for 10 min. Then PBPs isolated
and subjected to electrophoresis and autoradiography again ,resulting that PBPs were
identical to those obtained with isolated membrane preparations. To determine whether there
might be inter- strain differences in the binding patterns, we compared the PBPs of strains
2696, 2499, and 2533 with those of strain 607 but results were similar, with a few small
exceptions. Strain 2696 exhibited two additional faint bands, one above and one below PBP
5. In strain 2499, PBP 3 was weaker and PBP 4 was stronger than the corresponding bands in
strain 607. ThePBPs of strain 2533 observed to be same as those of strain 607.
Release of bound beta-lactam from PBPs. We studied the liability of the bonds between
antibiotic and PBPs. Membranes of strain 607 bound with [125I]furazlocilhin were incubated
with excess nonradioactive penicillin G at 30°C for 2 hrs and then electrophoresis and
autoradiography performed . All six PBPs appeared to be identical to those of membranes
bound with [ 125I]furazlocillin but not incubated with excess penicillin. This indicates that
the half-life of the PBP-[ 125I]furazlocillin complex is considerably more than 2 hrs.for all
six PBPs of C. perfringens.For Binding patterns of beta-lactam antibiotics; Mecillinam had a
unique binding pattern. Several observations can be made regarding the binding properties of
the remaining 15 agents.
(i) All 15 beta-lactams completely saturated PBP 4 at their MICs. Most agents showed
partial binding to PBP 4 at lower concentrations.
(ii) All agents except furazlocillin and carbenicillin saturated PBP 3 at their MICs. These
two agents saturated PBP 3 at four times the MICs.
(iii) None of the antibiotics saturated PBP 1 or 2 at or below their MICs. However,
cephalothin, cephaloridine, and cefoxitin showed partial binding of PBP 2 at their
MICs. These were the only agents tested which contain a thiophene ring on the side
chain of the beta-lactam ring.
(iv) The concentrations at which different beta-lactams bind PBP 5 and 6 were quite
variable. In contrast to all other beta-lactams assayed, mecillinam failed to saturate
PBP 4 even at Morphological effects of beta-lactam antibiotics.
Phase-contrast microscopy of strain 607 shows that exponential-phase cultures in BHIS
consisted of approximately equal proportions of short filaments and bacilli. The other strains
showed different proportions of these two morphological forms. However, in stationary-
phase cultures, all cells were bacilli. The addition of penicillin G, mecillinam, cephalothin,
cefoperazone, furazlocillin, and ampicillin to logarithmic-phase cultures of strain 607 all
induced long filament formation; the average length of these filaments was approximately 10
to 15 times the length of a bacillus, and some were much longer.
C. perfringens contained multiple PBPin cytoplasmic membrneshich are like those found in
aerobic bacteria and having typical pattern that observed in other bacilli which shows major
bands of lower molecular weightof PBPs of C. perfringens. PBP 3 and 4 were saturated by
beta-lactams at their MICs suggesting that these proteins are the killing targets for beta-
lactams. This constancy of the killing target resembles the situation in Bacillus subtilis, in
which PBP 2 seems to be the lethal receptor. By contrast, the killing of E. coli cells results
from binding of different PBPs by different agents. The variability of the concentrations at
which different beta-lactams bind PBP 5 and 6 of C. perfringens suggests that the lower-
molecular- weight PBPs are not important targets for the lethal action of these agents. For
example, cefoperazone completely saturated PBP 3 and 4 and caused cell death at
concentrations which resulted in no detectable binding to PBP 5 and 6. In this regard, the
latter proteins are similar to the low-molecular-weight PBPs of E. coli, which have been
identified as carboxypeptidases, enzymes which probably play a role in regulating the degree
of cross-linkage of peptidoglycan. However, PBP 5 and 6 of C. perfringens formed stable
complexes with beta-lactams, having half-lives of more than 2 h; by comparison, PBP 5 and
6 of E. coli have half-lives of 20 min or less.
Mecillinam has activity against many gram- negative bacteria but is less active against
gram- positive organisms. Indeed, its MIC for C. perfringens was much higher than that of
the other antibiotics used in this study. In E. coli, mecillinam binds specifically to PBP 2 and
causes the conversion of rods into ovoid cells. In addition, its mode of action is different
from that of other beta-lactams; it does not inhibit any of the three known classes of
penicillin-sensitive enzymes of E. coli (transpeptidases, endopeptidases, and
carboxypeptidases). The binding properties of mecillinam to the PBPs of C. perfringens were
unique. Mecillinam had a higher affinity for PBP 5 than for other PBPs, and it was the only
beta-lactam tested which caused inhibition of growth without saturating PBP 4. This
property may enable the use of mecillinam as a probe for studying the role of PBP 5 of C.
perfringens in cell growth and division in future investigations.
The morphological effects on C. perfringens of six beta-lactams (penicillin G, mecillinam,
cephalothin, cefoperazone, furazlocillin, and ampicillin) were observed. All six agents
induced marked filament formation, suggesting interference with septum formation. This
effect of mecillinam is surprising becausethis agent causes formation of ovoid cells while
mecillinam has recently been reported to cause filamentation in Fusobacterium nucleatum,
which is an anaerobic, gram-negative bacillus.
It is clear that PBP 3 or 4 or both are important for septum formation because all agents
showed some degree of binding to these PBPs at concentrations which induced filaments.
Furthermore, binding experiments suggested that PBP 3 and 4 are the lethal targets for beta-
lactam antibiotics. Since one mechanism by which beta-lactams exert their lethal effect is by
inhibiting a transpeptidase involved in the terminal stages of peptidoglycan synthesis, an
intriguing hypothesis is that PBP 3 or 4 or both are vital transpeptidases involved in septum
formation. However, further study is needed to identify the specific functions and enzyme
activities of these proteins.
In summary, the cytoplasmic membrane of C. perfringens contains multiple PBPs. The
concentrations at which beta-lactams saturate PBP 3 and 4 correlate well with the MICs of
the agents, suggesting that these proteins are the lethal targets. Further investigation of the
PBPs of C. perfringens will be interesting to identify specific functions of individual PBPs
and to assess the role of PBPs in the recent observation of decreasing susceptibility of this
species to penicillin.
Current Research
1) A current research conducted by International Association for Food Protection examined
the inhibitory effects green tea extracts had on the germination of C. perfringens spores in
abusive-chilled retail cooked meat . The experiment was carried out by treating samples of
thawed pork, beef and chicken with different concentration levels of green tea extracts along
with ―heat activated (75 degrees C for 20 min) three-strain spore cocktail‖ . Then these
samples were incubated in a 71 C water bath for an hour . Then the temperature of the
samples was allowed to drop from 54.4 to 7.2 C . The first round of experiment was tested
without adding any green tea extracts, and germination of C. perfringens population thrived.
The second round of experiment was carried out with the addition of GTL, which was a
green tea extract with low level of catechin, but inhibition of C. perfringens growth was not
observed . However, when GTE, which was a green tea extract containing high level of
catechin, was added to the meat samples, germination of C. perfringens population was
inhibited [9]. The results of this research were significant, because the uptake of catechin
could decrease the chance of C. perfringens spores from germinating during abusive cooling.
Thus the risk of human or animals being affected by ingested C. perfringens spores is
reduced.
2) A recent study conducted by Departments of Medicine, Microbiology and Immunology at
Vanderbilt University School of Medicine focused on the inhibiting activities of two
monoclonal neutralizing antibodies against the epsilon-toxin produced by C. perfringens,
which could cause human to suffer from edema of heart, kidney and brain [10]. According to
the study, when cultured MDCK cells were stained with membrane-impermeant dye 7-
aminoactinomycin D, it showed that both antibodies were effective in inhibiting the epsilon-
toxin from forming spores in the MDCK cell membranes [10]. Both antibodies were capable
of recognizing epitopes in the region containing amino acids 134 to 145, which was a region
that ―overlaps an amphipathic loop corresponding to the putative membrane insertion
domain of the toxin‖ [10]. This is an important finding, because once the epitopes
recognized by these antibodies are identified, it will allow scientists to develop therapeutic
means to act against the detrimental effects of the toxin.
3) Although C. perfringens is a pathogen responsible for many cases of avian enteritis, there
was insufficient knowledge on which toxins are the primary causative agent of these avian
diseases. A current study done by California Animal Health and Food Safety Laboratory
System at University of California Davis compared the toxinotypes of C. perfringens isolates
obtained from infected birds, including quail, chickens, turkey and psittacines, against the
toxinotypes of 19 isolates obtained from birds that were not infected by C. perfringens. The
results showed that the toxinotype of all C. perfringens isolates obtained from both the
diseased and the healthy birds belonged to type A, which is a type of C. perfringens that are
capable of producing alpha-toxins. Many of the isolates contained the gene that encodes the
beta2 toxin, but about half of the isolates failed to make the beta 2 toxin. The significance of
this result is that avian enteritis is not associated with the specific C. perfringens toxinotypes.
Application to Biotechnology
C. perfringens is a mesophile who has a fastest growth rate at the temperature of 37˚ C.
When the spores of C. perfringens are exposed to a hyperthermal condition with a
temperature of 105˚C for five minutes, their sensitivity to polymyxin and neomycin is
increased significantly. Polymyxin is an antibiotic that damages the structure, the
permeability and the rigidity of the bacterial plasma membrane, making the cell membrane
too fragile to maintain the osmotic equilibrium. Neomycin is a metabolic inhibitor that stops
protein synthesis. Therefore, polymyxin and neomycin can be used together to kill C.
perfringens cells after exposing them to super high temperature for a short amount of time.
This discovery is beneficial to human and animals, because the combination of polymyxin
and neomycin can be used to control C. perfringens, which presents a threat as a toxic
causative agent of many food-borne diseases. The results also implied that refrigerated food
should be heated properly before eating them, because it can reduce the risk of getting C.
perfringens-related illnesses.
Another beneficial biotechnological application discovered by researchers focused on the
relationship between C. perfringens‘ penicillin-binding proteins and the beta-lactam
antibiotics. A physical map of C. perfringens was assembled using pulsed-field gel
electrophoresis (PFGE), which made the genetic study of C. perfringens and its virulence
factors more feasible. Using the physical map, researchers have identified 6 penicillin-
binding proteins (PBPs) in the C. perfringens‘ membranes. Like many aerobic bacteria, C.
perfringens have many PBPs in their cytoplasmic membrane. Some of these proteins play
important roles in murein synthesis, cell elongation, and maintenance of cell rigidity. When
beta- lactam antibiotics are induced to the cells, ―PBP 3 and 4 were saturated by beta-lactam
at their MICs…and caused cell death at concentrations which resulted in no detectable
binding to PBP 5 and 6‖. PBP 3 and 4 are higher-molecular-weight PBPs comparing to the
molecular weight of the other PBP 5 and 6. Due to their important roles in the growth of the
bacterial cells, many beta-lactam antibiotics were designed to recognize PBPs as their
targets.(25)
Materials and Methods:
Primary sequence analysis-
Sequence-
Uniprot (Universal Protein Resource ) is a comprehensive resource for protein sequence and
annotation data .The databases are the UniProt Knowledgebase (UniProtKB) , UniProt
Refrence Clusters (UniRef), UniProt Archive (uniParc). The FASTA format of amino acid
sequence of C. perfrigens penicillin binding protein with identity number QX8J01 was
retrieved from UniProt protein sequence database as a target sequence whose three
dimensional structure to be predicted.(2)

Similaritiy search-
Basic Alignment Search Tool (BLAST) is a program used to perform or to identify the
similar sequences from the database. It is classified as; Nucleotide BLAST – Search a
nucleotide database using nucleotide query,Protein BLAST – search protein database using
protein query,blastX – search protein database using translated nucleotide query,tblastn-
search translated nucleotide database using a protein query,tblastx- search translated
nucleotide using translated nucleotide query. The protein BLAST of extracted sequence
QX8J01 was performed to find out similar sequences and the sequence with good similarity
percentage and query sequence (3DWK) is selected to perform further work.(3)
Secondary structure prediction:
Chau Fasman method-
The Chou Fasman method is an empirical technique for the prediction of tertiary structure in
proteins. The method based on analysis of relative frequencies of each amino acid in alpha
helices, beta sheets and turns based on known protein structure solved with X-ray
crystallography. From these frequencies a set of probability parameters were derived for
appearance Chou of each amino acid in each secondary type and these parameters are used to
predict the probability that a given sequences of amino acid would form a helix, beta sheets
or turns in protein. Secondary structure analysis of selected sequence was carried out by
using Chou Fasman server. This method used to analyze the number alpha helix, beta sheets,
turns present in that protein.(8)

3D STRUCTURE PREDICTION:
Homology modeling-
Homology modeling is used to predict three-dimensional structure of protein. Here two
sequences are compared. Query sequence : The protein sequence with unknown 3D structure
i.e. Target sequence and Template: The protein sequence which is previously searched and
whose 3D structure is known. The three dimensional model of C.perfringence PBP was
predicted by using SWISS Model server which is a fully automated protein structure
homology modeling server.(9)

VISUALIZATION OF 3D STRUCTURE
CHIMERA
UCSF Chimera is an extensible program for interactive visualization and analysis of
molecular structures and related data, including density maps, supramolecular assemblies,
sequence alignments, docking results, trajectories, and conformational ensembles. High-
quality images and movies can be created. Chimera includes complete documentation and
can be downloaded free of charge for noncommercial use.Chimera is developed by the
Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of
California, San Francisco.We done general structure analysis i.e.hydrogen addition and
partial charge assignment,high-quality hydrogen bond, contact, and clash detection automatic
identification of atom.(6)

RasMol
RasMol is the visualizing software having molecular graphics to visualize 3D structure
protein, enzyme, and nucleic acid. This is used to determine 3D structure of any given
protein. Using RasMol one can identify number of helices, number of Beta sheets and loops
present in protein, overall arrangement and orientation, number of specific amino acid
specially presence of disulfide Bond in the given protein. We used command line for
understanding 3D structure of protein. RasMol allows the execution aap interactive command
type at the "RasMol>" prompt in the command line. Command must give on separate line. It
is useful to find bond angle, bond distance, we can change background colour and protein
colour etc. It is easy to study specific part of protein by giving restrict type of Command.
Used command are RasMol>background white, RasMol>show all sequence,
RasMol>wireframe on.(5)

Model Validation:
The predicted three-dimensional model of penicillin binding protein was analyzed and

optimized by using Ramachandran Plot Server and ProSA online program for its reliability.

ProSA -The protein structure analysis (ProSA) used for the refinement and validation of

experimental protein structures and in structure prediction and modelling. For structure

analysis of PBP from Clostridium perfringens , predicted structure was submitted to

server.(4)

Ramchandran plot: A Ramachandran plot is used for two reason. One is to show in theory

which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue

in a protein .Second is based on Ramchandran Principle of steric collisions hinders the

conformations.The Ramachandran Principle says that alpha helices, beta strands, and turns

are the most likely conformations for a polypeptide chain to adopt, because most other

conformations are impossible due to steric collisions between atoms. Disallowed regions

generally involve steric hindrance between the side chain C-beta methylene group and main

chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four

quadrants of the Ramachandran plot; allowed region, is observed as solid black lines, or outer

limit region, is represented with a dotted black line.(7)

Molecular docking:
Prediction of interaction at molecular level is aim of molecular docking. Docking has
application ranging from protein engineering to drug designing. SWISS Dock is server used
for docking of small molecules on target protein. Interaction between predicted model and
penicillin was performed using SWISS Dock online server. Swiss Dock, a web service is to
predict the molecular interactions that may occur between a target protein and a small
molecule. SwissDock is developed by A. Grosdidier, Vincent Zoete and Olivier Michielin,
from the Molecular Modeling Group of the Swiss Institute of Bioinformatics in Lausanne,
Switzerland. Calculations are performed on the Vital-IT cluster (status). SwissDock is based
on the docking software EADock DSS, has simple and integrated interface whose algorithm
consists of the following steps:

1. Many binding modes are generated either in a box (local docking) or near all target
cavities (blind docking).
2. Simultaneously, their charmm energies are estimated on a grid.
3. The binding modes with the most favorable energies are evaluated with facts, and
clustered
4. The most favorable clusters can be visualized online and downloaded on your
computer

SwissDock allows the user to upload structure files for a protein and a ligand, and
returns the results by e-mail. To facilitate the upload of the protein and ligand files, we
can prepare these input files using the program UCSF Chimera.(10)
RESULTS AND DISCUSSION:

Primary sequence analysis-

The sequence of penicillin binding protein of C. perfringrnce (Accession Number: Q8XJ01)
with unknown structure having 679 amino acids was taken from UniPort protein sequence
database.

>sp|Q8XJ01|PBPA_CLOPE Penicillin-binding protein 1A OS=Clostridium

perfringens (strain 13 / Type A) OX=195102 GN=pbpA PE=3 SV=1
MTERKREHKDRKQNKNSPKNQSKVTKFLKWFFIGILLLGITAVTVVGIYVLSIIRSSPEL
DVQAIQSLNQPSILYDDQGNFMDNVITREQRYVVKSEEIPDNLKKAFVAIEDERFYEHKG
IDIKRIFGVIASNIKGKLSGSNTVQGASTITQQLIKNAVLTNEVSYERKIKEMYLALELE
KHLSKDEILTTYLNTIPMGGYQYGVSAAAQRFFSKNVSDLNLVECAYLGGLTQAPTSYDG
LSEANKENPSRYLNRTKSVLFKMHELGYISSEQYNDAINEIDTNGIKFTPNNKLSKTNFE
WFTRPAITQVKQDLMDKYKYTQEEVDKLIANGGLKIYTSMDRNLQNNVQKVLDDPNNYKA
ITNNPNEKNEDGVYKLQASATIIDYKTGHVKALVGGRGEQPAMSHNRAYYDLKSIGSATK
PLTVYGPAIDLGLGGAGSVVNDSPLSNKELSSTGYKDQPKNEYNSYRGPLTFREAIKISS
NLAAIKVANEVGVSNSIAYGEKLGLVYGPHSRGISTTALGQFQNDPNNPDGGNTYTLASA
FGVFGNNGVKTNAKLYTKVLDSHGNVILDTSTPEETKIFSPQASYIVYDMLKDQVESGSA
KSAKFGNIPVAGKTGTTTGDKDYLFAGLTPYYSAAIWIGYDKPREMRTSSGTVTSPIFGK
IMGLAHKDLQYKEVDNLVE

FASTA Format Sequence

Blast compares the given sequence with other sequence, which are present in the data, and
after comparison, it shows results by means of the query sequence, similarity percentage and
gives E value. Template penicillin binding protein from S.aureus PDB ID 3DWKA was
identified by using BLASTp showed 84% max identity with the target. It has E value -68.

Secondary structure prediction:

The Chou Fasman method for secondary structure prediction identified alpha helices,beta
sheets, turns and coils.The PBP of Clostridium perfringens with accession number Q8XJO1
contains 678 amino acids of which,Alpha helices are 411.(percent-60.0 ,Beta sheets are
428.(percent-63.0) and Turns are 99.(percent-14.6)
 CHOU FASMAN ANALYSIS

Homology modeling of penicillin binding protein of C. perfringence

Homology modeling (comparative modeling) is one of the computational structure prediction
methods that are used to determine 3D structure of a protein from its amino acid sequence
based on its template. The basis for homology modeling is two major observations. First
protein 3D structure is particularly determined by its amino acid sequence. Second the
structure of proteins is more conserved and the change happens at a much slower rate in
relative to the sequence during evolution. As a result, similar sequences fold into identical
structures and even sequences with low relation take similar structures. Swiss Model is an
automated server used to predict the three dimensional structure of the protein simply by
providing accession number of that protein or amino acid sequence. Predicted 3D structure
visualized by UCSF chimera.

HOMOLOGY MODELING CHIMERA visualization

Model Validation:
Accuracy of the constructed model can determine its further application in various areas.
Thus, verification and validation of models are necessary. ProSA and Ramchandran plot
server were popular tools used for the determination of the stereochemistry of the model in
homology modeling. The Z-score value for penicillin binding protein was found to be -7.87
showing acceptable range as per experimental values determined through ProSA server

PROSA validation of model

Structure showing high energy as red color and low energy as blue
Ramchandran plot:
The Ramachandran plot is also powerful determinant of the quality of protein structure.
Residues with a problem of stereochemistry will fall out of the acceptable regions of the
Ramachandran plot. The Ramachandran plot for the penicillin binding protein determines the
phi–psi bond angle evaluation. The Ramachandran plot showed about % residues in the
favoured region, % residues in the allowed region, % residues in the generously allowed
regions and % residues in the disallowed region. Thus, overall % residues were found to be
in the allowed region. A good quality model would be expected to have over 90% in the most
favoured regions. Thus, the predicted 3-dimensional model of PBP is of good quality.

RAMCHANDRAN PLOT

Molecular docking :
Molecular docking is a key tool in structural molecular biology and computer-assisted drug
design. The goal of ligand–protein docking is to predict the predominant binding mode(s) of
a ligand with a protein of known three-dimensional structure. Successful docking methods
search high-dimensional spaces effectively and use a scoring function that correctly ranks
candidate dockings. Docking can be used to perform virtual screening on large libraries of
compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the
target, which is invaluable in lead optimization. Study of interaction between predicted 3D
model of penicillin binding protein and penicillin was done using SWISS Dock server and
results was analyzed by aid of ProteinPlus server. Estimated binding energy of docked
complex is -7.26 kcal/mol. Gly531, Tyr535 and Thr 536 forms hydrogen bond with
penicillin.
SWISS DOCKING showing interaction between PBP and Penicillin
 SUMMARY AND CONCLUSION

The three dimensional structure of penicillin binding protein from C.perfringence build by
using Swiss model server, three dimensional structure of PBP stabilized mainly by secondary
elements such as helix, sheets, β and γ turns. Further predicted three dimensional structure
of penicillin binding protein analysed by online server such as Ramchandran Plot Server and
ProSA shows good quality of structure with Z score -7.87. These build models are then
visualized by the visualization tools like Chimera. The predicted model comprises helices,
beta sheets and loops. Predicted three dimensional homology model of penicillin binding
protein from C.perfringence has clinical significance, as penicillin-binding protein is
responsible for beta lactam resistance. Interaction study between penicillin binding protein
and penicillin shows that penicillin forms stable hydrogen bond with gly 531, tyr 535 and thr
536.Thus, this structural study could be helpful for structure base drug discovery against beta
lactam resistant microorganisms.
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