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  4. Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface
 
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research article

Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface

El Ahdab, Dina
•
Lagardere, Louis
•
Inizan, Theo Jaffrelot
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July 8, 2021
The Journal of Physical Chemistry Letters

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 mu s) 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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Type
research article
DOI
10.1021/acs.jpclett.1c01460
Web of Science ID

WOS:000672734200027

Author(s)
El Ahdab, Dina
•
Lagardere, Louis
•
Inizan, Theo Jaffrelot
•
Celerse, Frederic  
•
Liu, Chengwen
•
Adjoua, Olivier
•
Jolly, Luc-Henri
•
Gresh, Nohad
•
Hobaika, Zeina
•
Ren, Pengyu
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Date Issued

2021-07-08

Publisher

AMER CHEMICAL SOC

Published in
The Journal of Physical Chemistry Letters
Volume

12

Issue

26

Start page

6218

End page

6226

Subjects

Chemistry, Physical

•

Nanoscience & Nanotechnology

•

Materials Science, Multidisciplinary

•

Physics, Atomic, Molecular & Chemical

•

Chemistry

•

Science & Technology - Other Topics

•

Materials Science

•

Physics

•

molecular-dynamics

•

recognition. impact

•

inhibitors

•

force

•

simulations

•

proteinase

•

networks

•

systems

•

sites

Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCMD  
Available on Infoscience
July 31, 2021
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/180329
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