ci5b00308_si_001.pdf (1.1 MB)
Force-Field Induced Bias in the Structure of Aβ21–30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields
journal contribution
posted on 2015-12-28, 00:00 authored by Micholas
Dean Smith, J. Srinivasa Rao, Elizabeth Segelken, Luis CruzIn
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.