Basic Applied Bioinformatics

CHAPTER 29Prediction of Tertiary Structure of Protein: Sequence Homology

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

29.1 INTRODUCTION

Prediction of the tertiary structure of a peptide sequence is done by either comparative modeling (when the experimentally determined structure of a homologous protein is available) or ab initio approaches (when the structure of the homologous protein is not available).

COMPARATIVE PROTEIN MODELING

This approach uses previously reported structures as templates, as it assumes that two homologous proteins (descended from a common ancestral amino acid sequence) will share similar structures, and that the protein folds have become comparatively more conserved during the process of evolution than the respective amino acid sequence.

De novo or ab initio method

The principle behind this method is to predict the protein structure, based on physical principles and energy minimization of the best predicted protein structure. The salient features of all of the ab initio methods are:

1. Representing the target protein with regard to protein conformation space. This assumes that the conformations which minimize the energy function could be the native structures of the target protein.
2. Determining the compatibility of energy functions with the protein representation is crucial.
3. Suitable algorithms to search the conformational space to minimize the energy function are used.

29.2 OBJECTIVE

To predict the tertiary structure ...