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Intrinsically Disordered Landscapes for Human CD4 Receptor Peptide.

Accepted version
Peer-reviewed

Type

Article

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Authors

Abstract

Because of their inherent structural plasticity, intrinsically disordered proteins (IDPs) are generally difficult to characterize, both experimentally and via simulations. In this work, an approach for studying IDPs within the potential energy landscape framework is implemented and tested. Specifically, human CD4 receptor peptide, a disordered region implicated in HIV-1 infection, is characterized via basin-hopping parallel tempering and discrete path sampling. We also investigate the effects of three state-of-the-art AMBER force fields (ff99SB-ILDN, ff14ipq, and ff14SB) on the energy landscape. The results for ff99SB-ILDN exhibit the best agreement with experiment. Metastable states identified on the free energy surface help to unify, and are consistent with, several earlier predictions, and may serve as starting points for probing the reaction interface between CD4 and HIV-1 accessory proteins.

Description

Keywords

CD4 Antigens, Humans, Intrinsically Disordered Proteins, Molecular Dynamics Simulation, Peptides, Protein Conformation

Journal Title

J Phys Chem B

Conference Name

Journal ISSN

1520-6106
1520-5207

Volume Title

122

Publisher

American Chemical Society (ACS)
Sponsorship
Engineering and Physical Sciences Research Council (EP/N035003/1)
epsrc