These are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information. For more information, please see our FAQs.
2 files

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

revised on 27.02.2020, 18:01 and posted on 28.02.2020, 07:03 by Léa El Khoury, Frédéric Célerse, Louis Lagardere, Luc-Henri Jolly, Étienne Derat, Zeina Hobaika, Richard G. Maroun, Pengyu Ren, Serge Bouaziz, Nohad Gresh, Jean-Philip Piquemal
Using polarizable (AMOEBA) and non-polarizable (CHARMM) force fields, we compare the relative free-energy stability of two extreme conformations of the HIV-1 NCp7 nucleocapsid 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.


Extreme-scale Mathematically-based Computational Chemistry

European Research Council

Find out more...

Specificity and Selectivity in Protein-Ion Binding

National Institute of General Medical Sciences

Find out more...


Email Address of Submitting Author


Sorbonne Université



ORCID For Submitting Author


Declaration of Conflict of Interest

no conflict of interest