More on Proteins- Amino Acids, Protein Secondary

Structure

Manu Madhavan

Lecture 12

Manu Madhavan ISC 211 Lecture 12 1 / 27

Outline

Protein
Chemical Properties
Secondary Structure Prediction
Refer: chapter 7 of Krane & Raymer [Kra02]

Manu Madhavan ISC 211 Lecture 12 2 / 27

Protein Structure

Manu Madhavan ISC 211 Lecture 12 3 / 27

Proteins

Molecular machinery that regulates almost all biological functions

Collagen - support and strengthen connective tissue
Myosin - support skeletal muscles
Melanin- color to hair
Various enzymes
Proteins in interactions with DNA (Gene), RNA (and other proteins)
enable the production of new proteins and regulates their level of
activities

Manu Madhavan ISC 211 Lecture 12 4 / 27

Proteins

Proteins are linear chains of Amino Acids

Amino acid chains quickly folded in to compact globular structure
Understanding the forces that drive protein folding is most challengin
question
We need to:
predict secondary (and tertiary) structure
predict protein folding

Watch: Protein Folding

Manu Madhavan ISC 211 Lecture 12 5 / 27

Amino Acids
Building blocks of proteins
Proteins are constructed from linear chain of 20 amino acids
Each amino acid has a backbone of Amide (-NH) group, Alpha
Carboxy group and carbocylic acid (-COOH) group
To alpha group side chain is attached- side cahin is unique for each
amino acid

Manu Madhavan ISC 211 Lecture 12 6 / 27

Amino Acids

Amino acides can be of 3 types:

Hydorphobic
Polar amino acids
Charged Amino acids
The order of AA in a protein primary sequence determines its
secondary structure

Manu Madhavan ISC 211 Lecture 12 7 / 27

Amino Acids

Chain of amino acids is referred to as peptide chain (larger chains are

called polypeptide)
Two amino acids are joined together by dipeptide bond
Each amino acids in the chain are called residues

Manu Madhavan ISC 211 Lecture 12 8 / 27

Amino Acids

The end at which an unbounded amino group presents is called

Amino terminus (N-Terminus)
The end at which an unbounded carboxy group presents is called
Carbocy terminus (C-Terminus)
The direction of polypeptide chain is from N-terminus to C-Terminus
This sequence is generally called Primary Structure of protein

Manu Madhavan ISC 211 Lecture 12 9 / 27

Secondary Structure- Rotations

The non-side-chain atmos of AA in a polypeptide chain form the

protein backbone, which is more or less fixed
The two bond between the alpha carbon and other backbone atoms
are the only two rotatable bonds in the protein backbone.
ϕ- The angle of rotation about the bond between the amide nitrogen
and the alpha alpha carbon
ψ- the angle between alpha carbon and the carbony group (carboxyl
group after dipeptide bond)
Entire protein structure can be specified by the ϕ and ψ angles
Steric collision- overlap between space occupied between atoms

Manu Madhavan ISC 211 Lecture 12 10 / 27

Rotations

Manu Madhavan ISC 211 Lecture 12 11 / 27

Secondary Structure

Regular, recurrent arrangement in space of adjacent amino acid

residues in a polypeptide chain
Maintained by hydrogen bonds between amide hydrogen and carbonyl
oxygen of peptide backbone
Commonly occurring secondary structures:
Alpha helices
Beta strands
Turns (bends)
Coil (irregular)

Manu Madhavan ISC 211 Lecture 12 12 / 27

Alpha Helix

A rod-like structure whose inner

section is formed by a tightly
coiled main chain, with its side
chains extending outward in a
helical array
ϕ and ψ angles are roughly
−60o
Spring like helical structure with
3.6 amino acids per complete
360o
Tightly packed

Manu Madhavan ISC 211 Lecture 12 13 / 27

Beta Strands

A β-strand is a stretch of
polypeptide chain typically 3 to
10 amino acids long with
backbone in an extended
conformation
ϕ = −135o and ψ = 1350
β-sheets contain β-strands
connected laterally to form a
plane like structure
Loosly packed

Manu Madhavan ISC 211 Lecture 12 14 / 27

Beta Turn

Turns generally occur when the

protein chain needs to change
direction in order to connect two
other elements of secondary
structure.

Manu Madhavan ISC 211 Lecture 12 15 / 27

Structure Determination

X-ray crystallography is a common method for determining protein

structure
Watch this video
Databases for protein structure details: PDB, SCOP (Structural
classification of Proteins)

Manu Madhavan ISC 211 Lecture 12 16 / 27

 Protein Secondary Structure Prediction

Manu Madhavan

Lecture 12-b

Manu Madhavan ISC 211 Lecture 12-b 17 / 27

Overview

Secondary Structure is based on the rotation of main chain- ϕ and ψ

All rotations are not allowed (due to chemical/physical properties of
other molecules)
Allowed/not allowed rotations can be analysed based on
Ramachandran plots
Dictionary of Secondary Structure of Proteins (DSSP): DSSP

Manu Madhavan ISC 211 Lecture 12-b 18 / 27

Secondary Structure Prediction Methods

Statisitcal Method (Chau -Fasman algorithm)

Information Theory based method (GOR method)
Hydrophobicity based method
MSA based method
ML based mehtod
Ensemble based methods

Manu Madhavan ISC 211 Lecture 12-b 19 / 27

Statistical Method

Compute the preference of each amino acid being part of a secondary

structure
Each residue has a propensity value-preference of residue being part
of secondary structure
The region of secondary structure is predicted based on the propensity
value

Manu Madhavan ISC 211 Lecture 12-b 20 / 27

Propensity

Percentage of residue i in α−helix

Propensityα (i) = Percentage ofall residues in α−helix

Percentage of residue i in α − helix = NN(i) α (i)

Percentage ofall residues in α − helix = NNα

Example:
Suppose out of 10 aline, 7 are in α-helix,
Percentage of residue i in α − helix = 70%
Suppose out of 100 residue, 80 are α-helix, then
Percentage ofall residues in α − helix = 80%
70
Propensitya lpha(Aline) = 80

Manu Madhavan ISC 211 Lecture 12-b 21 / 27

Chou–Fasman method

Algorithm for assigning secondary structure

The method is based on analyses of the relative frequencies of each
amino acid in alpha helices, beta sheets, and turns based on known
protein structures solved with X-ray crystallography.
Each amino acid is assigned several conformational parameters, P(a),
P(b), and P(turn)- representing the propensity of each amino acid to
participate in alpha helices, beta sheets, and beta turns, respectively,
were determined based on observed frequencies in a set of sample
Each amino acid is assigned four turn parameters, f(i), f(i+1), f(i+2),
and f(i+3), corresponding to the frequency with which the amino acid
was observed in the first, second, third, or fourth position of a hairpin
turn.

Manu Madhavan ISC 211 Lecture 12-b 22 / 27

Chou-Fasman Parameters

Manu Madhavan ISC 211 Lecture 12-b 23 / 27

Chou-Fasman Method

Manu Madhavan ISC 211 Lecture 12-b 24 / 27

Chou-Fasman Method

Manu Madhavan ISC 211 Lecture 12-b 25 / 27

Chou-Fasman Example

Manu Madhavan ISC 211 Lecture 12-b 26 / 27

References I

Dan E Krane, Fundamental concepts of bioinformatics, Pearson Education India,

2002.

Manu Madhavan ISC 211 Lecture 12-b 27 / 27