Investigation of Optimum Conformations and Structure Analysis of RL and LR Nests using Ramachandran Plot

Investigation of Optimum Conformations and Structure Analysis of RL and LR Nests using Ramachandran Plot

Sumukh Deshpande (University of Hail, Saudi Arabia), Saikat Kumar Basu (University of Lethbridge, Canada) and Pooja Purohit (Almas International, Saudi Arabia)
DOI: 10.4018/978-1-4666-8693-9.ch007
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Abstract

We have surveyed polypeptides with the optimal conformations of nests which are the common anion-binding motifs comprising 8% of the amino acids which are characterized by a structural depression or a hole. Using automated bioinformatics algorithm, novel ring structure of the nest has been found. Using automated algorithm, models of polypeptides were made in-silico (computationally) and oxygen atoms are inserted along the extension of the NH groups. These sophisticated algorithms allow insertion of atoms along the NH group at the correct distance which causes extension of the group thus forming hydrogen bond. Optimal conformations of these structures are found from these customized models. This study chapter provides a demonstration of an important discovery of optimum conformations of RL and LR nests by the use of sophisticated bioinformatics automation pipeline and a unique application of automation and control in bioinformatics.
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Introduction

Robotics and Automation has revolutionized current technologies. Automation is widely used in the area of scientific research. One of the major applications of automation lies in the area of bioinformatics (Ochoa et al., 2011). One of the bioinformatics techniques involves the usage of automated algorithms and control in the development and discovery for optimum structures of protein structure motif called as nests. These structural motifs form polypeptide main chain structure consisting mainly of α-helix and β-sheet which forms secondary, tertiary and quaternary structures in proteins. But apart from these two major conformations, other conformations also exist. Some of them are 310Helix, α-sheets, nests, niches, asx turns, β bulges, β turns (type I and I’, type II and II’), ST staples, ST turns, Schellman loops (Watson & Milner-White, 2002a; Duddy, 2004). Nests are formed when the main chain NH groups of three successive residues bind a common anion-binding motif. In nests, when main chain NH groups bind an anionic atom it forms a depression and or a hole in which the anion fits thus forming a nest structure (Torrance, 2009; Watson & Milner-White, 2002a; Watson & Milner-White, 2002b; Milner-White, 2004; Milner-White & Russell, 2005; Milner-White, 2006). Nests are more common structures among all the other conformations and 8% of the amino acids take part in forming nests. Like nests, a structure known as niche also exist. A niche is formed main chain CO (Carbonyl) groups of three successive residues bind a cationic atom or group often HOH or NH2 (Torrance, 2009). Nests are defined by two alternative enantiomeric main chain polypeptide conformations with four characteristic main chain dihedral angles of two successive amino acid residues: φii and φi+1i+1. Negative φ values are considered to be right-handed (R) and positive φ values left-handed (L). The two types of conformations RL and LR are found in native proteins (Watson, 2002; Watson & Milner-White, 2002; Milner-White, 2004). Nests are also found in compound or overlapping formation where a combination of right handed and left handed residues make compound nests such as RLRL nests, LRLR, RLLR. Some of the examples of compound nests include P-loops of nucleotide tri-phosphate binding proteins with five consecutive NH groups facing into a concavity forming an LRLR structure (Watson, 2002; Watson & Milner-White, 2002; Milner-White, 2004; Milner-White & Russell, 2008).

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