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Akademický článek

AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance

Autor: Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady Verkhivker

Publikováno v: Viruses, Vol 16, Iss 9, p 1458 (2024)

The most recent wave of SARS-CoV-2 Omicron variants descending from BA.2 and BA.2.86 exhibited improved viral growth and fitness due to convergent evolution of functional hotspots. These hotspots operate in tandem to optimize both receptor binding fo

Externí odkaz: https://doaj.org/article/2da3d9dd887a4b75acf443c11bfd8788

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Akademický článek

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

Autor: Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady Verkhivker

Publikováno v: Viruses, Vol 15, Iss 10, p 2073 (2023)

In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterizat

Externí odkaz: https://doaj.org/article/8da08ab04ca04659858eb93a2da3c667

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Akademický článek

Exploring Conformational Landscapes and Cryptic Binding Pockets in Distinct Functional States of the SARS-CoV-2 Omicron BA.1 and BA.2 Trimers: Mutation-Induced Modulation of Protein Dynamics and Network-Guided Prediction of Variant-Specific Allosteric Binding Sites

Autor: Gennady Verkhivker, Mohammed Alshahrani, Grace Gupta

Publikováno v: Viruses, Vol 15, Iss 10, p 2009 (2023)

A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformati

Externí odkaz: https://doaj.org/article/d79eb42259c74aec94fe47f3dcf4c2ea

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Akademický článek

Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes

Autor: Gennady Verkhivker, Mohammed Alshahrani, Grace Gupta

Publikováno v: Viruses, Vol 15, Iss 5, p 1143 (2023)

Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and alloste

Externí odkaz: https://doaj.org/article/80effa48a2624ff89aee420709f5d2d0

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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

Autor: Gennady Verkhivker, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao

Publikováno v: bioRxiv

In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-base

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e6463a5521d9e3f2e5420c20cac2a79a

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Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers : Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants

Autor: Gennady Verkhivker, Mohammed Alshahrani, Grace Gupta

Publikováno v: International Journal of Molecular Sciences; Volume 24; Issue 7; Pages: 6642

The evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity, conformational plasticity, protein stability and allosteric m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::11ee0571aeca1f316d4dc5fecc2bac4f
https://doi.org/10.1101/2023.02.28.530489

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Allosteric Control of Structural Mimicry and Mutational Escape in the SARS-CoV-2 Spike Protein Complexes with the ACE2 Decoys and Miniprotein Inhibitors: A Network-Based Approach for Mutational Profiling of Binding and Signaling

Autor: Grace Gupta, Steve Agajanian, Deniz Yasar Oztas, Gennady M. Verkhivker

Publikováno v: Journal of Chemical Information and Modeling. 61:5172-5191

We developed a computational framework for comprehensive and rapid mutational scanning of binding energetics and residue interaction networks in the SARS-CoV-2 spike protein complexes. Using this approach, we integrated atomistic simulations and conf

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4dd944cc05034ebbafb1f75baeac17fd
https://doi.org/10.1021/acs.jcim.1c00766

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