BMB 506 PROTEINS AND ENZYMES (2)

PROTEIN STRUCTURE I
Know the structure and properties of the peptide bond.
Sketch the Ramachandran plots for alanine and glycine . Know the
structure and properties of the right-handed -helix.
Structures of parallel, anti-parallel and mixed -sheets.
Understand the energetics of hydrogen bonding and ionic bonds.
Know which chemical groups in a protein can participate in hydrogen
bonding.
Understand the thermodynamics of the process by which a
polypeptide chain folds into a globular protein with a hydrophobic core
and hydrophilic exterior.

STEREOISOMERS

All amino acids except Gly have an

asymmetric C

D and L stereoisomers are mirror

images and non-superimposable.

Only L-amino acids are directly

incorporated into proteins.

Optical rotation properties of

asymmetric molecules are indicated
by lower case (d) dextrorotatory and
(l) laevorotatory.

UV ABSORPTION

Aromatic amino acids Trp Tyr

and Phe absorb UV light
associated with a to *
electronic transition

Trp has the highest extinction

coefficient of the three, with
an absorption maximum
close to 280 nm.

Depending on the Trp content

a 1 mg per ml solution of
protein has an OD280 of about
1.0.

THE PEPTIDE BOND

partial double bond
character.
Planar, normally TRANS
C -NH rotation
C -CO rotation
Fully extended chain has
= 180 and = 180 deg.
RH -helix
-57 -47
LH -helix
+57 +47
Parallel
-119 -113
Anti-parallel -139 -135

RAMACHANDRAN PLOT FOR ALANINE

A = anti-parallel -sheet
P = parallel -sheet
R = RH -helix
L = LH -helix
G = polyglycine
C = collagen

RAMACHANDRAN PLOTS FOR GLYCINE

AND PROLINE
Because glycine has a very
small side chain (H) greater
flexibility is possible in a
polypeptide chain at the
positions of glycines.
For proline the angle is
fixed at -60 o because the N
atom is part of a ring.
There are 2 favorable
angles at -55o and +145o.
Thus the polypeptide chain
has less flexibility at proline
residues.

OBSERVED RAMACHANDRAN PLOT FOR A

LARGE PROTEIN
Myeloperoxidase
Dimer 2 x 569 residues
1.8 resolution.

Most favoured (A,B,L) 88.8%

Also allowed (a,b,l,p) 11.0%
generously allowed
0.2%
Disallowed
0.0%

Ser 42 is an exception.

RIGHT HANDED -HELIX

H-bond from C=O of residue
(I) to NH of residue (I+4).
, angles correspond to
energy minimum.
Dipoles aligned.
Side chains staggered.
Internal radius of 2.3
optimal for Van der Waals
interactions.

ALPHA-HELIX DIPOLE
Allows for interaction with anions and cations at the carboxy
and amino termini

-SHEETS

3 types: parallel, anti-parallel and mixed.

All have favourable , angles and well-aligned peptide
dipoles.
Note that each chain is called a strand and multiple
stands compose a sheet.
Sheets are frequently twisted. The twist is right-handed
when the sheet is viewed along the direction of the strands.
This occurs because the , angles correspond to a broad
flat region in the energy plot.

PARALLEL -SHEET

ANTI-PARALLEL -SHEET

MIXED -SHEET
Thioredoxin from E. Coli
Example of a mixed -sheet
.
Note that neighbouring
strands in the sheet are not
necessarily consecutive in
the amino acid sequence.

OTHER FORCES INVOLVED IN

MAINTAINING PROTEIN CONFORMATON
HYDROGEN BONDS (electrostatic)
Donors ( NH, OH, NH2, NH3+) eg SER THR ASN GLN HIS
LYS ARG TRP TYR (ASP and GLU at low pH)
Acceptors ( CO, OH) eg SER THR ASN GLN ASP GLU TYR
HYDROPHOBIC INTERACTIONS
IONIC INTERACTIONS (salt bridges) ASP GLU LYS ARG HIS
COVALENT LINKS eg disulfide bond. CYS

HYDROGEN BONDS
Typically 90% of possible H-bonds involving peptide
groups and 85% involving side chains are found to occur in
proteins.
Multiple H-bonding to C=O groups is common and to NH
groups less common.
Strengths of H-bonds depend upon distances and
geometry. In C=O . H-N hydrogen bonds, O.N distances
are typically 2.8 to 3.2 A.

HYDROPHOBIC INTERACTIONS
Water-soluble proteins have a hydrophobic central core and a
hydrophilic surface.
When a hydrophobic group is exposed to water, the water
molecules surround it to form a stable cage in which the water
molecules are interconnected by H-bonds.
Consider the thermodynamics of the transfer of methane from
the hydrophobic solvent CCl4 to water. G = H - TS
H = -2.5 kcal per mole H-bond formation Favourable
S = -18 kcal per mole
Ordered water molecules Unfavourable
G = + 2.9 kcal per mole Unvavourable

HYDROPHOBIC CORE

IONIC INTERACTIONS
Also known as salt bridges between acidic amino acids:
Asp, Glu and basic amino acids Lys, Arg, His.

G = Z1 Z2 e2 / a

Z1 and Z2 are the charges on the interacting groups.

e is the charge on one electron (energy of formation of the ionic
likage inverly proportional to )
is the dielectric constan (energy of formation of the ionic
likage inverly proportional to E) E of water is high E of oil I low
a is the sum of the ionic radii
Entropic effects of release of solvating water molecules
must be taken into consideration.

DISULFIDE BRIDGES
DISULFIDE BONDS
contribute to the stabilities of
some extracellular proteins.
However, they do not direct
overall folding.
Folding is primarily directed by
the formation of a hydrophobic
core, following which disulfides
snap into position.
Disulfide bonds can be
reduced by thiol reagents such
as Dithiothreitol (DTT) or mercaptoethanol.