Vet World Vol.12 December-2019 Article-21
Research Article
Veterinary World, 12(12): 20236-2045
https://doi.org/10.14202/vetworld.2019.20236-2045
Comparative modeling and mutual docking of structurally uncharacterized heat shock protein 70 and heat shock factor-1 proteins in water buffalo
2. Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India.
3. Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, Rajasthan, India.
4. Department of Agriculture, Maharishi Markandeshwar University, Ambala, Haryana, India.
5. Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India.
6. Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India.
Background and Aim: In this study, a wide range of in silico investigation of Bubalus bubalis (BB) heat shock protein 70 (HSP70) and heat shock factor-1 (HSF1) has been performed, ranging from sequence evaluation among species to homology modeling along with their docking studies to decipher the interacting residues of both molecules.
Materials and Methods: Protein sequences of BB HSP70 and HSF1 were retrieved from NCBI database in FASTA format. Primary and secondary structure prediction were computed using Expasy ProtParam server and Phyre2 server, respectively. TMHMM server was used to identify the transmembrane regions in HSP70. Multiple sequence alignment and comparative analysis of the protein was carried out using MAFFT and visualization was created using ESPript 3.0. Phylogenetic analysis was accomplished by COBALT. Interactions of HSP70 with other proteins were studied using STRING database. Modeller 9.18, RaptorX, Swiss-Modeller, Phyre2, and I-TASSER were utilized to design the three-dimensional structure of these proteins followed by refinement; energy minimization was accomplished using ModRefiner and SPDBV program. Stereochemical quality along with the accuracy of the predicted models and their visualization was observed by PROCHECK program of PDBsum and UCSF Chimera, respectively. ClusPro 2.0 server was accessed for the docking of the receptor protein with the ligand.
Results: The lower value of Grand Average of Hydropathy indicates the more hydrophilic nature of HSP70 protein. Value of the instability index (II) classified the protein as stable. No transmembrane region was reported for HSP70 by TMHMM server. Phylogenetic analysis based on multiple sequence alignments (MSAs) by COBALT indicated more evolutionarily closeness of Bos indicus (BI) with Bos taurus as compared to BI and BB. STRING database clearly indicates the HSF1 as one of the interacting molecules among 10 interacting partners with HSP 70. The best hit of 3D model of HSP70 protein and HSF1 was retrieved from I-TASSER and Phyre2, respectively. Interacting residues and type of bonding between both the molecules which were docked by ClusPro 2.0 were decoded by PIC server. Hydrophobic interactions, protein-protein main-chain-side-chain hydrogen bonds, and protein-protein side-chain-side-chain hydrogen bonds were delineated in this study.
Conclusion: This is the first-ever study on in silico interaction of HSP70 and HSF1 proteins in BB. Several bioinformatics web tools were utilized to study secondary structure along with comparative modeling, physicochemical properties, and protein-protein interaction. The various interacting amino acid residues of both proteins have been indicated in this study. Keywords: Bubalus bubalis, docking, heat shock proteins, heat shock factor-1, heat shock protein 70, homology modeling.
Keywords: Bubalus bubalis, docking, heat shock proteins, heat shock factor-1, heat shock protein 70, homology modeling.
How to cite this article: Singh R, Gurao A, Rajesh C, Mishra SK, Rani S, Behl A, Kumar V, Kataria RS (2019) Comparative modeling and mutual docking of structurally uncharacterized heat shock protein 70 and heat shock factor-1 proteins in water buffalo, Veterinary World, 12(12): 2036-2045.
Received: 13-08-2019 Accepted: 13-11-2019 Published online: 23-12-2019
Corresponding author: R. S. Kataria E-mail: katariaranji@yahoo.co.in
DOI: 10.14202/vetworld.2019.20236-2045
Copyright: Singh, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.