Paper 3:

Unit 2: Proteins and Amino acids

Protein Structure Basics

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Importance of Proteins
• Muscle structure depends on protein-protein
interactions
• Transport across membranes involves protein-
solute interactions
• Nerve activity requires transmitter substance-
protein interactions
• Immune protection requires antibody-antigen
interactions

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Overview
• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary Structure

2015 RRA, BC Dept, FLS, JSS University, Mysuru

2015 RRA, BC Dept, FLS, JSS University, Mysuru
 Primary Structure
• Polypeptide chains  n(Amino Acids)

• Largest polypeptide chain approx has 5000AA but most have less than
2000AA

• Arrangement of the 20 different amino acids

in the polypeptide is the amino acid
sequence which composes the
primary structure of the protein

National Genome Research Institute

genome.gov
2015 RRA, BC Dept, FLS, JSS University, Mysuru
 20 Amino Acids

Nonpolar,
hydrophobic

Polar, uncharged

Polar, charged

http://www.people.virginia.edu/~rjh9u/aminacid.html

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Amino Acid Classification

A Venn diagram showing the relationship of the 20 naturally occurring

amino acids to a selection of physio-chemical properties thought to be
important in the determination of protein structure.

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Bond Formation

• Linking two amino acids together

• Definitions
(N-terminal, C-terminal,
polypeptide backbone,
amino acid residue,
side chains)
http://web.mit.edu/esgbio/www/lm/proteins/peptidebond.html

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Primary Structure
• What is a native protein?
• Protein conformation & problem of protein
folding
 Hydrophobic, hydrophilic
 Charge
 Chaperones

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Protein Secondary Structure
• Introduction
• Peptide bond geometry
• Ramachandran plot
• Structures

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Regular local structures formed by single
strands of peptide chain due to constraints on
backbone conformation

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Peptide Bond

2015
http://cmgm.stanford.edu/biochem/biochem201/Slides/
RRA, BC Dept, FLS, JSS University, Mysuru
 Peptide Bond
• Resonance
• C-N bond length of the peptide is 10% shorter
than that found in usual C-N amine bonds
• Peptide bond planer
• ω, angle around peptide bond,
00 for cis, 1800 for trans

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Torsion angles
• The two torsion angles of the polypeptide chain, also
called Ramachandran angles (after the Indian physicist
who first introduced the Ramachandran plot), describe
the rotations of the polypeptide backbone around the
bonds between N-Cα (called Phi, φ) and Cα-C (called
Psi, ψ).
• Most important local structural parameters that
control protein folding – (to predict its 3D folding) . \
• These angles provide the flexibility required for the
polypeptide backbone to adopt a certain fold.

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Ramachandran Plot
The Ramachandran plot provides an
easy way to view the distribution of
torsion angles of a protein structure It
also provides an overview of allowed
and disallowed regions of torsion angle
values, serving as an important
indicator of the quality of protein
three-dimensional structures

http://hykim.chungbuk.ac.kr/lectures/biochem/4-5/fig6-9(L).jpg

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Prof. G.N. Ramachandran (8 October 1922-7 April 2001)
8 October 1922
Born
Ernakulam, Kerala
7 April 2001 (aged 78)
Died
Madras, Tamil Nadu, India
Nationality Indian
Fields Biophysics
St. Joseph's College, Tiruchirappalli
Madras University
Institutions
Indian Institute of Science
Cavendish Laboratory
Madras University
Alma mater
University of Cambridge
Doctoral advisor C V Raman

Known for Ramachandran plot

***Leading scientists including Professor Linus Pauling and Professor Francis Crick regarded
Professor Ramchandran as a Nobel Prize caliber scientist of great reputation.****

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Biophys J. 1965 Nov; 5(6): 909–933. doi: 10.1016/S0006-3495(65)86759-5

2015 RRA, BC Dept, FLS, JSS University, Mysuru

2015 RRA, BC Dept, FLS, JSS University, Mysuru
 Alpha Helix

2015 RRA, BC Dept, FLS, JSS University, Mysuru

http://cmgm.stanford.edu/biochem/biochem201/Slides/
 Alpha Helix

Left-handed Right-handed

http://www.rtc.riken.go.jp
2015 RRA, BC Dept, FLS, JSS University, Mysuru
 Alpha Structure Features
• 3.6 residues per turn
• 5.4 angstroms in length per turn
• carboxyl group of residue i hydrogen bonds to
amino group of residue i+4

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Helix Structures
Φ ψ H Bond R/t A/t
Alpha -57.8 -47 i, i + 4 3.6 13

3-10 Helix -49 -26 i, i + 3 3.0 10

Pi Helix -57 -80 i , i + 5 4.4 16

2015 RRA, BC Dept, FLS, JSS University, Mysuru

http://broccoli.mfn.ki.se
 More Helix Structures

Type Φ ψ comments

• Collagen -51 153 Fibrous proteins

Three left handed helicies
(GlyXY)n, X Y = Pro / Lys

• Type II helices -79 150 left-handed helicies formed

by polyglycine

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Beta Sheet

http://www.rothamsted.bbsrc.ac.uk/notebook/courses/guide/images/sheet.gif
2015 RRA, BC Dept, FLS, JSS University, Mysuru
 Beta Sheet Features
• Sheets can be made up of any number of
strands
• Orientation and hydrogen bonding pattern of
strands gives rise to flat or twisted sheets
• Parallel sheets buried inside, while Antiparallel
sheets occurs on the surface

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 More Beta Structures
Beta Bulge chymotrypsin (1CHG.PDB)
involving residues 33 and 41-42

Anti parallel

Beta Twist pancreatic trypsin inhibitor (5PTI)

0 to 30 degrees per residue

Distortion of tetrahedral N atom

2015 RRA, BC Dept, FLS, JSS University, Mysuru http://broccoli.mfn.ki.se

 Beta turns

i + 1 Pro

i + 2 Pro or Gly

i + 3 Gly

http://rayl0.bio.uci.edu/~mjhsieh/sstour/image/betaturn.png
2015 RRA, BC Dept, FLS, JSS University, Mysuru
2015 RRA, BC Dept, FLS, JSS University, Mysuru
 Interactions
• Covalent bonds
Disulphide bond (2.2 0A) between two Cys residues
• Non-covalent bonds
Long range electrostatic interaction
Short range (4 0A) van der Waals interaction
Hydrogen bond (3 0A)

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Tertiary Protein Structure
• Defines the three dimensional conformation
of an entire peptide chain in space
• Determined by the primary structure
• Modular in nature

2015 RRA, BC Dept, FLS, JSS University, Mysuru

Aspects which determine tertiary structure

• Covalent disulfide bonds from between closely

aligned cysteine residues form the unique
Amino Acid cystine.
• Nearly all of the polar, hydrophilic R groups
are located in the surface, where they may
interact with water
• The nonpolar, hydropobic R groups are usually
located inside the molecule

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Motifs and Domains
• Motif – a small structural domain that can be
recognized in a variety of proteins
• Domain – Portion of a protein that has a
tertiary structure of its own. In larger proteins
each domain is connected to other domains
by short flexible regions of polypeptide.

2015 RRA, BC Dept, FLS, JSS University, Mysuru

2015 RRA, BC Dept, FLS, JSS University, Mysuru
2015 RRA, BC Dept, FLS, JSS University, Mysuru
2015 RRA, BC Dept, FLS, JSS University, Mysuru
 Quaternary Structure
• Not all proteins have a
quaternary structure
• A composite of multiple
poly-peptide chains is
called an oligomer or
multimeric
• Hemoglobin is an
example of a tetramer
• Globular vs. Fibrous

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Protein Folding
• Protein folding constitutes the process by
which a poly-peptide chain reduces its free
energy by taking a secondary, tertiary, and
possibly a quaternary structure

2015 RRA, BC Dept, FLS, JSS University, Mysuru

 Thermodynamics
• Proteins follow
spontaneous reactions
to reach the
conformation of lowest
free energy
• Reaction spontaneity is
modeled by the
equation ΔG= ΔH-TΔS

2015 RRA, BC Dept, FLS, JSS University, Mysuru