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J R Soc Interface. 2019 Jul 26;16(156):20190075. doi: 10.1098/rsif.2019.0075. Epub 2019 Jul 10.

Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.

Author information

1
Laboratoire de Biochimie Théorique, CNRS UPR9080, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie, 75005 Paris , France.

Abstract

Dynamics are a key feature of protein function, and this is especially true of gating residues, which occupy cavity or tunnel lining positions in the protein structure, and will reversibly switch between open and closed conformations in order to control the diffusion of small molecules within a protein's internal matrix. Earlier work on globins and hydrogenases have shown that these gating residues can be detected using a multiscale scheme combining all-atom classic molecular dynamics simulations and coarse-grain calculations of the resulting conformational ensemble mechanical properties. Here, we show that the structural variations observed in the conformational ensembles produced by NMR spectroscopy experiments are sufficient to induce noticeable mechanical changes in a protein, which in turn can be used to identify residues important for function and forming a mechanical nucleus in the protein core. This new approach, which combines experimental data and rapid coarse-grain calculations and no longer needs to resort to time-consuming all-atom simulations, was successfully applied to five different protein families.

KEYWORDS:

NMR conformational ensembles; coarse-grain simulations; elastic network model; protein gating residues; proteins mechanics

PMID:
31288649
PMCID:
PMC6685036
[Available on 2020-07-01]
DOI:
10.1098/rsif.2019.0075

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