Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue Journal of Chemical Theory and Computation Année : 2020

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

Résumé

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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Dates et versions

hal-03046841 , version 1 (08-12-2020)

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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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