In-silico Characterization of HspBP1 Gene for Identification of SNPs Associated with Silent Estrus Behavior in Buffalo

Silent estrus behavior in buffalo is a great challenge to the sustainability of the dairy sector in Pakistan. To deal with reproductive failure, selection of animals with good estrus signs is crucial at the time of breeding. The current study analyzed the heat shock binding protein 1 (HspBP1) to identify the single nucleotide polymorphisms (SNPs) that may interfere with the normal expression of heat signs. The coding sequence (CDS) of the gene and 25 SNPs were retrieved from the ENSEMBL database. Mutated CDS were constructed manually, incorporating the SNPs in the wild-type gene, and analyzed via CELLO, Expasy ProtParam, PHYRE2.2, SWISS-MODEL, HDOCK tools, and GROMACS. Analysis revealed that SNPs HspBP1E56*, HspBP1V88G, HspBP1C94*, HspBP1C129X, and HspBP1V202X altered the location of mutated proteins to extracellular and nucleus. Variant HspBP1E317* changed protein location to mitochondria. These SNPs imparted greater alkalinity, less thermostability, and in-vitro stability to the proteins in addition to truncated structures. The docking scores of the complexes of HspBP1V88G, HspBP1C94*, HspBP1E56*, HspBP1A50D, and HspBP1L13Q with HSP70 were more negative than that of the wild-type HspBP1-HSP70 complex, suggesting that the predicted binding affinity is lower than that of the wild-type. It indicated that the selected variants could interfere or modify the interaction between HspBP1 and HSP70. Molecular dynamics (MD) simulations analysis, based on PCA, Rg, RMSD, and FEL data, demonstrated the dynamically disruptive impact of three SNPs, HspBP1V88G, HspBP1C94*, and HspBP1C129X, and the moderate impact of the HspBP1V202X variant. Variants identified in the current study, after validation through genotype-phenotype association studies, might contribute to reproductive enhancement in buffalo and livestock surveillance in the country.