ci5b00308_si_001.pdf (1.1 MB)
Download file

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

Download (1.1 MB)
journal contribution
posted on 28.12.2015, 00:00 by Micholas Dean Smith, J. Srinivasa Rao, Elizabeth Segelken, Luis Cruz
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.