Cross-species amino acids sequence comparison and computational docking of human IL-1Ra and rat IL-1Ra on rat receptor

Abstract

Nowadays, experimental animals are being widely used to investigate therapeutic potentials of IL-1Ra. This article states cross-species comparison of amino acid sequences of IL-1Ra and computational docking of ligands (IL-1Ra_human and IL-1Ra_rat), on rat receptor (IL-1RI_rat). The purpose of study was to understand relationship between amino acid sequences, structural and binding similarities between both ligands. We utilized molecular modeling for structure determination, sequence alignment, structure refinement and protein docking of concerned proteins. We comparatively verified amino acid sequence of both ligands using Emboss Needle method, to express pairwise sequence. Further, these sequences were used to generate 3D structural model of ligands by Phyre2, that were verified by Ramachandran plot. Docking of ligands to structure of IL-1RI_rat was attempted by using AutoDock program. The similarity and identity of sequences and structures of IL-1Ra_human and IL-1Ra_rat were 85.4% and 73.6%, respectively. Two of three receptor residues, i.e. LYS290 and ASP259, were common in docking of both ligands. This elucidates that binding sites for both ligands are apparently similar, signifying that both ligands will probably possess same therapeutic efficacy. Similarly, functional implication of significant similarity found between two species can be of great importance in future investigations, regarding use of exogenously administered IL-1Ra. © 2013 Akash MSH, et al.