Working Paper
Authors
- 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
Sorbonne Université
Abstract
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.
Content

Supplementary material

NCP7 SI-rev