Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields

Document Type

Article

Publication Date

12-28-2015

Abstract

In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid β, the Aβ21-30, under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMOS53A6), and three water models (TIP3P, TIP4P, and SPC/E). We find that the tested force fields and water models have little effect on the measures of radii of gyration and solvent accessible surface area (SASA); however, secondary structure measures and intrapeptide hydrogen-bonding are significantly modified, with AMBER (99, 99SB, 99SB-ILDN, and 03) and CHARMM22/27 force-fields readily increasing helical content and the variety of intrapeptide hydrogen bonds. On the basis of a comparison between the population of helical and β structures found in experiments, our data suggest that force fields that suppress the formation of helical structure might be a better choice to model the Aβ21-30 peptide.

Identifier

84952771981 (Scopus)

Publication Title

Journal of Chemical Information and Modeling

External Full Text Location

https://doi.org/10.1021/acs.jcim.5b00308

e-ISSN

1549960X

ISSN

15499596

PubMed ID

26629886

First Page

2587

Last Page

2595

Issue

12

Volume

55

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