Prediction of nonsynonymous SNPs consequences in heat shock protein 70 (Hsp70) gene of bubalus bubalis on structure and function of its protein

Recent advances in DNA sequencing and computational algorithms revealed the SNPs of highest value. Laboratory study of gene and its alleles is difficult and time consuming. In this study, we used several computational algorithms to demonstrate the effects of gene structure and function of heat shock protein 70 (HSP70) in buffalo. HSP70 is a chaperone molecule that expressed in response to stress. On the other hand, buffalo is one of the resistant animals to heat stress. In this study from Affymetrix 90K SNP chip in 112 Khuzestan buffalo and published sequence information is used for Hindi buffalo. In Khuzestan buffalo dataset, snp was not found, but one snp was recognized in Hindi buffalo. Snp analysis (Methionine/Threonine) was done using SIFT,PROVEAN.SIFT with calculate factor 1 and PROVEAN algorithm with calculate factor 0.33 which showed this mutation or SNP effect is non-destructive and with the normal protein operation. I-mutant algorithm was used to check mutant hsp70 protein stability, and predict SNP impacts on the stability of the protein using regression based on the changes in free energy (DDG=0.47) showed that "met5thr" snp at 25 ºC ,PH=7 decrease the protein stability. Validation of the model by Ramachandran and ProSA Zscore maps indicates a slight deviation in the mutated protein compared to the normal model. Molecular docking and how to hsp70 connect to its ligand adenosine diphosphate (ADP) indicates in both the natural and mutated models that mutation leads to decrease in protein stability and change its structure, which also changes the structure of ligand binding site. But generally in this study the mutation does not show significant and destructive effect on protein structure.