Bioinspired Algorithms in Solving Three-Dimensional Protein Structure Prediction Problems

Bioinspired Algorithms in Solving Three-Dimensional Protein Structure Prediction Problems

Raghunath Satpathy (MITS Engineering College, India)
Copyright: © 2017 |Pages: 22
DOI: 10.4018/978-1-5225-2375-8.ch012
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Abstract

Proteins play a vital molecular role in all living organisms. Experimentally, it is difficult to predict the protein structure, however alternatively theoretical prediction method holds good for it. The 3D structure prediction of proteins is very much important in biology and this leads to the discovery of different useful drugs, enzymes, and currently this is considered as an important research domain. The prediction of proteins is related to identification of its tertiary structure. From the computational point of view, different models (protein representations) have been developed along with certain efficient optimization methods to predict the protein structure. The bio-inspired computation is used mostly for optimization process during solving protein structure. These algorithms now a days has received great interests and attention in the literature. This chapter aim basically for discussing the key features of recently developed five different types of bio-inspired computational algorithms, applied in protein structure prediction problems.
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1. Introduction

Proteins belong to one of the major classes of macromolecules that are ubiquitously present in the living systems. These molecules are often envisaged as the molecular machines of life because they carry out many types of functions starting from catalysis, transport, regulation movement, transport, signaling, immunity and structure determination. Due to the versatility of the proteins, it is important to study their role area in molecular and cell biology. As the number of completely sequenced genomes grows, we are faced with the important but daunting task of assigning a function to proteins encoded by newly sequenced genomes (Habeck et al., 2005). A protein, is a polymer of amino acids can adopt different conformations and the most stable state is achieved by minimization of energy is known as native state (Lee et al., 2007; Whisstock et al., 2003). Amongst the 20 different naturally occurring amino acids, any two can join in a series by forming the peptide bond (C=O ---NH linkage), that remains in a plane. Figure 1 represents the peptic bond in between two amino acids, planar feature has been shown in dotted green lines, R1 and R2 corresponds to the functional group of two amino acids.

Figure 1.

Peptide bond in between two amino acids

The primary structure consists of amino acids when present in an aqueous environment will spontaneously adopt local (secondary) and non-local (tertiary) structures while some require the presence of factors like molecular chaperones. This observation generates the hypothesis that the native state is determined by the primary sequence of amino acids. During its assembly, the amino acids present in the protein are organized in a regular local structural mostly stabilized by the hydrogen bonds. The examples of such structural entities are alpha-helices (Branson, 1951) and beta-strands (Pauling & Corey, 1951). The local arrangements of a polypeptide chain are collectively called secondary structure or two-dimensional structure. Later the assembly in the in the three-dimensional space is called tertiary structure of protein. The three-dimensional structure is usually stabilized by several non-local interactions, hydrophobic interaction, disulfide bonds and salt bridges etc. Finally, in some cases, two or more polypeptide chains, called as protein subunits can undergo assembly to form larger complexes that are regarded as the quaternary structure (Marqusee & Baldwin, 1987). It is a keen observation that during the protein folding process transition to the native state the amino acid sequences proceeds on roughly through the same intermediate states. The folding process involves several regular secondary and super secondary structural features (Oas et al., 1988), particularly α-helices and β-sheets, and afterward of tertiary ones. However, the formation of quaternary structure usually involves the assembly of already assembled subunits. The planar arrangement of the peptide bonds is most important as it helps to determine a specific overall 3D structure of a specific polypeptide protein chain (Weiss et al., 1998). The planar arrangement of atoms in the peptide bond is assumed to be rigid and the rotation of different bonds can be given as dihedral angles, ϕ (N-Cα) and ψ (Cα-C)that provide flexibility in rotation about 180 degrees around the atom connecting axis.

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