Abstract

The stability of protein-ligand complex is decided by the strength of the forces and interaction that holds the overall structure. The binding of ligand to its receptor involves the participation of atomic interactions of key conserved amino acid residues which are essential for functional and structural integrity of protein molecule. Understanding the binding mechanism of ligand to its receptors is important in exploring the structure activity relationships of any protein. In the present study, a dataset of nicotinamide adenine dinucleotide (NAD) binding dehydrogenase was prepared by screening 19 structural homologues using the SCOP database to study the structurally conserved atomic interactions. An interaction profile of NAD against all structural homologues was determined using protein interaction analyzer and structure parser (PIASP) program and the structurally conserved atomic interactions were identified at 50% cut off level. We identified that out of 44 ligand atoms, only single interaction (ASP: O2B-OD1) was 100% conserved throughout the family members. Thus, it is clear from this study that ligand implements varying degree of orientation for binding with receptor molecule. However, there are certain critical amino acid residues that remain conserved throughout the family and participated in all orientations. However, the interaction of aspartate protease (ASP) residue is critical to the active site of selected protein family. This residue, which is common in active site of all the chosen structures, is found to be structurally conserved throughout the family.

Key words: Structurally conserved atomic interaction, conserved residues, protein interaction analyzer and structure parser (PIASP).