Prediction of Structural and Functional Aspects of Protein: In-Silico Approach

Introduction

A protein is a sequence produced by combination of 20 amino acids. Amino acids are characterized by polar (hydrophilic) and non polar (hydrophobic) based on its residue. These amino acids are associated to each other with peptide bond to form a protein sequence (Laskowskiet al., 2003). The fabrication of a protein sequence is much effortless than the determination of a protein structure. However, the structure of a protein gives much more impending in the function of the protein than its sequence. Consequently, a number of methods for the computational prediction of protein structure from its sequence have been developed. Protein structure prediction is the prediction of the three-dimensional structure of a protein from its amino acid sequence that is, the prediction of its secondary, tertiary, and quaternary structure from its primary structure. The native structure is the 3D structure of the protein sequence. It necessitates knowing the native protein structure so that we can find out the function of that protein structure. There are numerous algorithms used to predict the native confirmation of a protein. Protein sequences are folded on lattice with non overlapping amino acid chain. These self circumventing conformations produced native structures which have smallest energy configuration. The protein sequence-structure gap is broadening speedily. The number of identified protein sequences (Bairoch and Apweiler, 2000) is blasting as a outcome of genome and other sequencing projects. The rising number of protein sequences is much bigger than the escalating number of known protein structures (Berman et al., 2000). Hence, computational predictive tools for protein structures are badly needed to narrow the widening gap. Prediction of 3D protein structure from the amino acid sequence is one of the most exigent tribulations in theoretical structural biology (Montelione et al., 1999; Skolnick et al., 2000).Three-dimensional protein structures still cannot be correctly predicted straight from sequences. A transitional but helpful step is to predict the protein secondary structure, which is a way to simplify the prediction problem by projecting the very complicated 3D structure onto one dimension, i.e. onto a string of secondary structural coursework for each residue.

Fortitude of the exclusive tertiary (three-dimensional) structure of a protein from its amino acid sequence alone is one of the most significant and exigent problems in modern biology. The information on the tertiary structure of a protein is pretty decisive in accepting the function and biological responsibility of the protein. At present, genome-sequencing projects are producing an extraordinary amount of linear amino-acid sequences. An exponential growth of protein sequence database in current years by far outpaces the experimental determination of protein tertiary structures. Structure prediction is vitally dissimilar from the inverse problem of protein design. Protein structure prediction is one of the most key targets accomplished by bioinformatics and theoretical chemistry; it is extremely important in medicine and biotechnology for designing of the drug and novel enzymes.

This chapter begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights.