Homology Modeling

David Shiuan

Department of Life Scienceand Institute of Biotechnology

National Dong Hwa University

Why Modeling ?

X-ray diffraction electron diffraction map electron density map

Missing chains and residues in PDB structures

No structure available

Erwin Schrodinger

John Pople1964 NobleComputation Chemistry

Walter Kohn1960 NobleDensity-Function theory

Polypeptide Chain

Structural Models are a unique source of information

The first solved protein crystal structure was of Sperm Whale myoglobin determined by Max Perutz and Sir John Cowdery Kendrew in 1958. They were aw

arded the Nobel Prize in Chemistry in 1962

Modeling – Prediction of 3D Structures

Homology Modeling Structures of similar molecules available

Threading Prediction-based threading detecting the fold type an

d aligning a protein of unknown structure and a protein of known structure for low levels of sequence identity ( < 25%)

Ab initio predicts the structure of proteins from the sequence a

nd using molecular energy calculations (Schrodinger equation), do not use experimental parameters.

Threading, A new approach to protein fold recognition. Nature 358

(1992 ) 86-89

An alternative strategy of recognizing known motifs or folds in sequences looks promising

Threading is an approach to fold recognition which used a detailed 3-D representation of protein structure. The idea was to physically "thread" a sequence of amino acid side chains onto a backbone structure (a fold) and to evaluate this proposed 3-D structure using a set of pair potentials and (importantly) a separate solvation potential.

View saccharide with JMol-Applet Chemis3D-Applet

Bystroff C & Shao Y. (2002). Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA.

Bioinformatics 18 Suppl 1, S54-61.

Ab initioStructure Prediction

Comparative Protein Modelling

Proteins with high sequence similarity is reflected by distinct structure similarity

Comparative protein modelling (Homology Modeling) is presently the most reliable method.

Comparative model building consist of the extrapolation of the structure for a new (target) sequence from the known 3D-structure of related family members (templates).

Building The Model 1. Framework construction

By averaging the position of each atom in the target sequence, based on the location of the corresponding

atoms in the template

Building The Model 2. Building non-conserved

loops

Although most of the known 3D-structures available share no overall similarity with the template, there may be similarities in the loop regions, and these can be inserted as loop structure in the new protein model

Building The Model 3. Completing the backbone

Since the loop building only adds C atoms, the backbone carbonyl and nitrogens must be completed in these regions.

This step can be performed by using a library of pentapeptide backbone fragments derived from the PDB entri

es

Building The Model

4. Adding side chains

For many of the protein side chains there is no structural information available in the templates. These cannot therefore be built during the framework generation and must be added later

Building The Model

5. Model refinement

Idealisation of bond geometry and removal of unfavourable non-bonded contacts can be performed by energy minimisation with force fields such as CHARMM, AMBER or GROMOS.

How to Superimpose Two

Proteins

Open the PDB file 11MUP Open the PDB file 21OBP Color by secondary structure

Use the "Iterative Magic Fit"

or the“Improve Fit" item of the "Tools" menu

How SWISS-MODEL works

Probabilities of SWISS-MODEL accuracy for target-template identity

classes

224 aa

224 aa

We have identified three new families of insulin homologs in C. elegans.

Comparative protein modelling remarkably confirms these predictions

Example/Swiss Model:

Insulin-like growth factors in C. elegans.