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Coarse-Grained Prediction of Peptide Binding to G-Protein Coupled Receptors.

Abstract：

:In this study, we used the Martini Coarse-Grained model with no applied restraints to predict the binding mode of some peptides to G-Protein Coupled Receptors (GPCRs). Both the Neurotensin-1 and the chemokine CXCR4 receptors were used as test cases. Their ligands, NTS8-13 and CVX15 peptides, respectively, were initially positioned in the surrounding water box. Using a protocol based on Replica Exchange Molecular Dynamics (REMD), both opening of the receptors and entry of the peptides into their dedicated pockets were observed on the μs time-scale. After clustering, the most statistically representative orientations were closely related to the X-ray structures of reference, sharing both RMSD lower than 3 Å and most of the native contacts. These results demonstrate that such a model, that does not require access to tremendous computational facilities, can be helpful in predicting peptide binding to GPCRs as well as some of the receptor's conformational changes required for this key step. We also discuss how such an approach can now help to predict, de novo, the interactions of GPCRs with other intra- or extracellular peptide/protein partners.

journal_name

J Chem Inf Model

journal_title

Journal of chemical information and modeling

authors

Delort B,Renault P,Charlier L,Raussin F,Martinez J,Floquet N

doi

10.1021/acs.jcim.6b00503

subject

Has Abstract

pub_date

2017-03-27 00:00:00

pages

562-571

issue

3

eissn

1549-9596

issn

1549-960X

journal_volume

57

pub_type

杂志文章

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