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Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations

Abstract : Using polarizable (AMOEBA) and nonpolarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 nucleocapsid protein NCp7 that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75−1.9 kcal/ mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.
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https://hal.archives-ouvertes.fr/hal-03046841
Contributor : Serge Bouaziz Connect in order to contact the contributor
Submitted on : Tuesday, December 8, 2020 - 4:10:05 PM
Last modification on : Thursday, November 10, 2022 - 4:35:04 AM
Long-term archiving on: : Tuesday, March 9, 2021 - 7:43:43 PM

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Léa El-Khoury, Frederic Célerse, Louis Lagardère, Luc-Henri Jolly, Etienne Derat, et al.. Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations. Journal of Chemical Theory and Computation, 2020, 16 (4), pp.2013 - 2020. ⟨10.1021/acs.jctc.9b01204⟩. ⟨hal-03046841⟩

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