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

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

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NMR processing:

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NMR assignment:

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Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

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GeNMR

I-TASSER

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Amber

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Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

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Promega- Proline

Secondary structure from chemical shifts:

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TALOS

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Methyl S2

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Proshift

PPM

CheShift-2- Cα

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Shifty

Camcoil

Poulsen_rc_CS

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Protein disorder:

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Protein solubility:

Isotope labeling:

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03-18-2020, 10:42 AM

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

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

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

J Chem Theory Comput. 2020 Mar 16;:

Authors: El Khoury L, Célerse F, Lagardère L, Jolly LH, Derat E, Hobaika Z, Maroun RG, Ren P, Bouaziz S, Gresh N, Piquemal JP

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.

PMID: 32178519 [PubMed - as supplied by publisher]

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