Journal article
Force-Field Induced Bias in the Structure of A beta(21-30): A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields
Journal of chemical information and modeling, v 55(12), pp 2587-2595
01 Dec 2015
PMID: 26629886
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
In this work we examine the dynamics of an intrinsically disordered protein fragment of the amyloid beta, the A beta(21-30), under seven commonly used molecular dynamics force fields (OPLS-AA, CHARMM27-CMAP, AMBER99, AMBER99SB, AMBER99SB-ILDN, AMBER03, and GROMO-S53A6), 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, 995B-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 beta structures found in experiments, our data suggest formation of helical structure might be a better choice to model the A beta(21-30) peptide.
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Details
- Title
- Force-Field Induced Bias in the Structure of A beta(21-30): A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields
- Creators
- Micholas Dean Smith - Drexel Univ, Dept Phys, Philadelphia, PA 19104 USAJ. Srinivasa Rao - Drexel UniversityElizabeth Segelken - Drexel UniversityLuis Cruz - Drexel UniversityMichael D Smith - [Retired Faculty]
- Publication Details
- Journal of chemical information and modeling, v 55(12), pp 2587-2595
- Publisher
- American Chemical Society; Washington, DC
- Number of pages
- 9
- Grant note
- TG-MCB110142 / XSEDE computational resources grant
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Physics
- Web of Science ID
- WOS:000367560200011
- Scopus ID
- 2-s2.0-84952771981
- Other Identifier
- 991019174726104721
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- Collaboration types
- Domestic collaboration
- Web of Science research areas
- Chemistry, Medicinal
- Chemistry, Multidisciplinary
- Computer Science, Information Systems
- Computer Science, Interdisciplinary Applications