The role of S477N mutation in the molecular behavior of SARS-CoV-2 spike protein: An in-silico perspective.
S477N mutation
SARS-CoV-2
molecular docking
molecular dynamics (MD) simulation
molecular interactionss
Journal
Journal of cellular biochemistry
ISSN: 1097-4644
Titre abrégé: J Cell Biochem
Pays: United States
ID NLM: 8205768
Informations de publication
Date de publication:
02 2023
02 2023
Historique:
revised:
21
12
2022
received:
03
11
2022
accepted:
27
12
2022
pubmed:
8
1
2023
medline:
25
2
2023
entrez:
7
1
2023
Statut:
ppublish
Résumé
The attachment of SARA-CoV-2 happens between ACE2 and the receptor binding domain (RBD) on the spike protein. Mutations in this domain can affect the binding affinity of the spike protein for ACE2. S477N, one of the most common mutations reported in the recent variants, is located in the RBD. Today's computational approaches in biology, especially during the SARS-CoV-2 pandemic, assist researchers in predicting a protein's behavior in contact with other proteins in more detail. In this study, we investigated the interactions of the S477N-hACE2 in silico to find the impact of this mutation on its binding affinity for ACE2 and immunity responses using dynamics simulation, protein-protein docking, and immunoinformatics methods. Our computational analysis revealed an increased binding affinity of N477 for ACE2. Four new hydrogen and hydrophobic bonds in the mutant RBD-ACE2 were formed (with S19 and Q24 of ACE2), which do not exist in the wild type. Also, the protein spike structure in this mutation was associated with an increase in stabilization and a decrease in its fluctuations at the atomic level. N477 mutation can be considered as the cause of increased escape from the immune system through MHC-II.
Substances chimiques
spike protein, SARS-CoV-2
0
Spike Glycoprotein, Coronavirus
0
Angiotensin-Converting Enzyme 2
EC 3.4.17.23
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
308-319Informations de copyright
© 2023 Wiley Periodicals LLC.
Références
Rajpal VR, Sharma S, Kumar A, et al. “Is Omicron mild”? Testing this narrative with the mutational landscape of its three lineages and response to existing vaccines and therapeutic antibodies. J Med Virol. 2022;94(8):3521-3539.
Farkas C, Mella A, Haigh JJ. Large-Scale Population Analysis of SARS-CoV-2 Whole Genome Sequences Reveals Host-mediated Viral Evolution With Emergence of Mutations in the Viral Spike Protein Associated With Elevated Mortality Rates. Cold Spring Harbor Laboratory Press; 2021.
Huang Y, Yang C, Xu X, Xu W, Liu S. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin. 2020;41(9):1141-1149.
Lan J, Ge J, Yu J, et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature. 2020;581(7807):215-220.
Garcia-Beltran WF, Lam EC, Denis K St., et al. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell. 2021;184(9):2372-2383.
Darby AC, Hiscox JA. Covid-19: variants and vaccination. BMJ. 2021;372:n771.
Barton MI, MacGowan SA, Kutuzov MA, Dushek O, Barton GJ, van der Merwe PA. Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics. eLife. 2021;10:e70658.
Liu Z, VanBlargan LA, Bloyet LM, et al. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe. 2021;29(3):477-488.
Singh A, Steinkellner G, Köchl K, Gruber K, Gruber CC. Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Sci Rep. 2021;11(1):4320.
Mahmoudi Gomari M, Rostami N, Omidi-Ardali H, Arab SS. Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. J Biomol Struct Dyn. 2022;40(12):5634-5642.
Alaofi AL, Shahid M. Mutations of SARS-CoV-2 RBD may alter its molecular structure to improve its infection efficiency. Biomolecules. 2021;11(9):1273.
Mejdani M, Haddadi K, Pham C, Mahadevan R. SARS-CoV-2 receptor-binding mutations and antibody contact sites. Antib Ther. 2021;4(3):149-158.
Eslami S, Glassy MC, Ghafouri-Fard S. A comprehensive overview of identified mutations in SARS CoV-2 spike glycoprotein among Iranian patients. Gene. 2022;813:146113.
Barnes CO, Jette CA, Abernathy ME, et al. SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature. 2020;588(7839):682-687.
Tortorici MA, Beltramello M, Lempp FA, et al. Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms. Science. 2020;370(6519):950-957.
Hodcroft EB, Zuber M, Nadeau S, et al. Emergence and Spread of a SARS-CoV-2 Variant Through Europe in the Summer of 2020. medRxiv; 2021.
Chen J, Qiu Y, Wang R, Wei G-W. Persistent Laplacian Projected Omicron BA. 4 and BA. 5 to Become New Dominating Variants. arXiv preprint; 2022. https://arxiv.org/abs/2205.00532
Guo Q, Wu C, Deng A, et al. First imported case of SARS-CoV-2 omicron subvariant BA. 4-Guangdong pProvince, China, May 4, 2022. China CDC Weekly. 2022;4:902-903.
Al-Qahtani AA. Mutations in the genome of severe acute respiratory syndrome coronavirus 2: implications for COVID-19 severity and progression. J Int Med Res. 2022;50(3):030006052210864.
Gray JJ, Moughon S, Wang C, et al. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol. 2003;331(1):281-299.
Leaver-Fay A, Tyka M, Lewis SM, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 2011;487:545-574.
Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc. 2003;125(7):1731-1737.
Kozakov D, Hall DR, Xia B, et al. The ClusPro web server for protein-protein docking. Nat Protoc. 2017;12(2):255-278.
Likova E, Petkov P, Ilieva N, Litov L. The PyMOL Molecular Graphics System, Version 2.0. Schrödinger, LLC.; 2015.
Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng Des Sel. 1995;8(2):127-134.
Laskowski RA, Thornton JM. PDBsum extras: SARS-Cov-2 and AlphaFold models. Prot Sci. 2022;31(1):283-289.
Nayeem SM, Sohail EM, Sudhir GP, Reddy MS. Computational and theoretical exploration for clinical suitability of Remdesivir drug to SARS-CoV-2. Eur J Pharmacol. 2021;890:173642.
Buß O, Rudat J, Ochsenreither K. FoldX as protein engineering tool: better than random based approaches? Comput Struct Biotechnol J. 2018;16:25-33.
Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server. Proteomics Protoc Handb. Springer; 2005:571-607.
Chovancova E, Pavelka A, Benes P, et al. CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. 2012.
Consortium U, Bateman A, Martin MJ, et al. UniProt: the universal protein knowledgebase in. 2021.
Dhanda I-A. Immune epitope database-analysis resource in 2019. Nucleic Acids Res. 47:W502-W506.
Meng X-Y, Zhang H-X, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput-Aided Drug Des. 2011;7(2):146-157.
Wu L, Zhou L, Mo M, et al. SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2. Signal Transduct Target Ther. 2022;7(1):8.
Aranda-Garcia D, Torrens-Fontanals M, Medel-Lacruz B, et al. Simulating time-resolved dynamics of biomolecular systems. 2022.
Chow E, Klepeis J, Rendleman C, Dror R, Shaw D. 9.6 new technologies for molecular dynamics simulations. In: Egelman EH, ed. Comprehensive Biophysics. Elsevier; 2012:86-104.
Singh S, Bani Baker Q, Singh DB. Chapter 18-molecular docking and molecular dynamics simulation. In: Singh DB, Pathak RK, eds. Bioinformatics. Academic Press; 2022:291-304.
Lobanov MY, Bogatyreva NS, Galzitskaya OV. Radius of gyration as an indicator of protein structure compactness. Mol Biol. 2008;42(4):623-628.
Ali S, Hassan M, Islam A, Ahmad F. A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states. Curr Protein Pept Sci. 2014;15(5):456-476.
Hubbard RE, Kamran Haider M. Hydrogen Bonds in Proteins: Role and Strength. eLS; 2010.
De Meutter J, Goormaghtigh E. Searching for a better match between protein secondary structure definitions and protein FTIR spectra. Anal Chem. 2020;93(3):1561-1568.
Rostami N, Choupani E, Hernandez Y, Arab SS, Jazayeri SM, Gomari MM. SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. JCB. 2022;123(2):417-430.
Nelson G, Buzko O, Spilman P, Niazi K, Rabizadeh S, Soon-Shiong P. Molecular Dynamic Simulation Reveals E484K Mutation Enhances Spike RBD-ACE2 Affinity and the Combination of E484K, K417N and N501Y Mutations (501Y.V2 variant) Induces Conformational Change Greater Than N501Y Mutant Alone, Potentially Resulting in an Escape Mutant. Cold Spring Harbor Laboratory; 2021.
Weichenberger CX, Sippl MJ. Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures. Structure. 2006;14(6):967-972.
Wan W-Y, Milner-White EJ. A recurring two-hydrogen-bond motif incorporating a serine or threonine residue is found both at α-helical N termini and in other situations. J Mol Biol. 1999;286(5):1651-1662.
Jawad B, Adhikari P, Podgornik R, Ching W-Y. Binding interactions between receptor-binding domain of spike protein and human angiotensin converting enzyme-2 in Omicron variant. J Phys Chem Lett. 2022;13:3915-3921.
Lan J, He X, Ren Y, et al. Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction. Cell Res. 2022;32(6):593-595.
Yuan L, Huang X-Y, Liu Z-Y, et al. A single mutation in the prM protein of Zika virus contributes to fetal microcephaly. Science. 2017;358(6365):933-936.
Siboonnan N, Wiriyarat W, Boonarkart C, et al. A serine-to-asparagine mutation at position 314 of H5N1 avian influenza virus NP is a temperature-sensitive mutation that interferes with nuclear localization of NP. Arch Virol. 2013;158(6):1151-1157.
Yamaguchi Y, Nukui Y, Kotaki A, et al. Characterization of a serine-to-asparagine substitution at position 123 in the Japanese encephalitis virus E protein. J Gen Virol. 2013;94(1):90-96.