Building a three-dimensional model of rat albumin molecule by homology modeling

Abstract

Albumin is known as being able to cleave ester bonds in organophosphates (OP) and serve as a major means of OP detoxification due to its large amount in the blood serum. Most of in vivo toxicological studies are conducted on rodents, mice and rats. To adequately extrapolate results of ligand/albumin interaction studies to a human organism, it is necessary to carry out a comparative analysis of the rat (RSA) and human (HSA) albumin structure by in silico methods. X-ray diffraction analysis of RSA has not been done as yet, and the RSA structure is still undetermined. The aim of this study was to build a three-dimensional (3D) model of RSA by homology modeling. As templates, 14 RSA homologs were selected from the Protein Data Bank. A 3D model of the RSA molecule was built using the RSA primary sequence and 3D models of the selected templates. The 3D model geometry was improved by the energy minimization method. The quality of the model was evaluated by 9 parameters. According to this evaluation, in 97% of protein structures from the comparative dataset these parameters were worse than in the obtained model. It was concluded that this model is suitable for further research, specifically, for in silico studies of the RSA/OP interaction and comparative evolutionary analysis of RSA and HSA.