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El Ahdab D, Lagardère L, Inizan TJ, Célerse F, Liu C, Adjoua O, Jolly LH, Gresh N, Hobaika Z, Ren P, Maroun RG, Piquemal JP. Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface. J Phys Chem Lett 2021; 12:6218-6226. [PMID: 34196568 PMCID: PMC8262171 DOI: 10.1021/acs.jpclett.1c01460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/10/2021] [Indexed: 05/27/2023]
Abstract
Following our previous work ( Chem. Sci. 2021, 12, 4889-4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network that is stable only at physiological pH. Structural correlations analysis between its residues and the catalytic site confirms the presence of a buried allosteric site. However, noticeable differences in allosteric connectivity are observed between PFFs and non-PFFs. Interfacial polarizable water molecules are shown to appear at the heart of this discrepancy because they are connected to the global interface H-bond network and able to adapt their dipole moment (and dynamics) to their diverse local physicochemical microenvironments. The water-interface many-body interactions appear to drive the interface volume fluctuations and to therefore mediate the allosteric interactions with the catalytic cavity.
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Affiliation(s)
- Dina El Ahdab
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Louis Lagardère
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | | | - Fréderic Célerse
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Sorbonne Université, IPCM, UMR 8232 CNRS, 75005 Paris, France
| | - Chengwen Liu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Olivier Adjoua
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Luc-Henri Jolly
- Sorbonne Université, IP2CT, FR 2622 CNRS, 75005 Paris, France
| | - Nohad Gresh
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
| | - Zeina Hobaika
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Richard G Maroun
- Université Saint-Joseph de Beyrouth, UR EGP, Centre d'Analyses et de Recherche, Faculté des Sciences, 1104 2020 Beirut, Lebanon
| | - Jean-Philip Piquemal
- Sorbonne Université, LCT, UMR 7616 CNRS, 75005 Paris, France
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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