Force-Field Induced Bias in the Structure of Aβ21–30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields
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- 作者：Micholas Dean Smith ; J. Srinivasa Rao ; Elizabeth Segelken ; Luis Cruz
- 刊名：Journal of Chemical Information and Modeling
- 出版年：2015
- 出版时间：December 28, 2015
- 年：2015
- 卷：55
- 期：12
- 页码：2587-2595
- 全文大小：586K
- ISSN：1549-960X
文摘
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.