Identification and Analysis of Key Residues Involved in Folding and Binding of Protein-carbohydrate Complexes

Protein and Peptide Letters
N R Siva ShanmugamM Michael Gromiha

Abstract

Protein-carbohydrate interactions play vital roles in several biological processes in living organisms. The comparative analysis of binding site residues along with stabilizing residues in protein-carbohydrate complexes provides ample insights to understand the structure, function and recognition mechanism. The main objective of this study is to identify and analyze the residues, which are involved in both folding and binding of the protein-carbohydrate complexes. We have identified the stabilizing residues using the knowledge of hydrophobicity, longrange interactions and conservation, as well as binding site residues using a distance cutoff of 3.5Å between any heavy atoms in protein and ligand. Residues, which are common in stabilizing and binding, are termed as key residues. These key resides are analyzed with various sequence and structure based parameters such as frequency of occurrence, surrounding hydrophobicity, longrange order and conservation score. In this work, we have identified 2.45% binding site residues in a non-redundant dataset of 1130 complexes using distance-based criteria and 7.07% stabilizing residues using the concepts of hydrophobicity, long-range interactions and conservation of residues. Further, 5.9% o...Continue Reading

Citations

Dec 15, 2020·Briefings in Bioinformatics·N R Siva ShanmugamM Michael Gromiha
Sep 26, 2021·Protein Science : a Publication of the Protein Society·Joseph B ParkerMichael Blaber

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