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2021 6
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Page 1
Computational analysis of protein stability and allosteric interaction networks in distinct conformational forms of the SARS-CoV-2 spike D614G mutant: reconciling functional mechanisms through allosteric model of spike regulation.
Verkhivker GM, Agajanian S, Oztas D, Gupta G. Verkhivker GM, et al. Among authors: gupta g. J Biomol Struct Dyn. 2022;40(20):9724-9741. doi: 10.1080/07391102.2021.1933594. Epub 2021 Jun 1. J Biomol Struct Dyn. 2022. PMID: 34060425
Comparative Analysis of Conformational Dynamics and Systematic Characterization of Cryptic Pockets in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 Spike Complexes with the ACE2 Host Receptor: Confluence of Binding and Structural Plasticity in Mediating Networks of Conserved Allosteric Sites.
Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Alshahrani M, et al. Among authors: gupta g. Viruses. 2023 Oct 10;15(10):2073. doi: 10.3390/v15102073. Viruses. 2023. PMID: 37896850 Free PMC article.
Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms.
Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Xiao S, et al. Among authors: gupta g. J Chem Inf Model. 2023 Aug 28;63(16):5272-5296. doi: 10.1021/acs.jcim.3c00778. Epub 2023 Aug 7. J Chem Inf Model. 2023. PMID: 37549201
AlphaFold2-Enabled Atomistic Modeling of Epistatic Binding Mechanisms for the SARS-CoV-2 Spike Omicron XBB.1.5, EG.5 and FLip Variants: Convergent Evolution Hotspots Cooperate to Control Stability and Conformational Adaptability in Balancing ACE2 Binding and Antibody Resistance.
Raisinghani N, Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Raisinghani N, et al. Among authors: gupta g. bioRxiv [Preprint]. 2023 Dec 12:2023.12.11.571185. doi: 10.1101/2023.12.11.571185. bioRxiv. 2023. PMID: 38168257 Free PMC article. Preprint.
Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes.
Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Alshahrani M, et al. Among authors: gupta g. bioRxiv [Preprint]. 2023 Sep 12:2023.09.11.557205. doi: 10.1101/2023.09.11.557205. bioRxiv. 2023. PMID: 37745525 Free PMC article. Preprint.
Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships.
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Verkhivker G, et al. Among authors: gupta g. bioRxiv [Preprint]. 2023 May 4:2023.05.03.539337. doi: 10.1101/2023.05.03.539337. bioRxiv. 2023. PMID: 37205479 Free PMC article. Updated. Preprint.
22 results