Reconciling NMR Structures of the HIV‑1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations
Year: 2020
Type: article
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.
Institutions: Centre National de la Recherche Scientifique, Saint Joseph University, Sorbonne Université, Laboratoire de Chimie Théorique, Institut Parisien de Chimie Moléculaire, Institut Parisien de Chimie Physique et Théorique, Institut des Sciences du Calcul et des Données, The University of Texas at Austin, Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, Institut Universitaire de France
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: Welch Foundation, European Commission, Agence Nationale de la Recherche, Centre National de la Recherche Scientifique, Ministère de la Défense, Conseil National de la Recherche Scientifique, Ministry of Education and Science of Ukraine, Ministry of Defense, Grand Équipement National De Calcul Intensif, National Institutes of Health, European Research Council, National Institute of General Medical Sciences, H2020 European Research Council
OpenAlex ID: W2993746245