title: Force-Field Induced Bias in the Structure of Aβ21-30: A Comparison of OPLS, AMBER, CHARMM, and GROMOS Force Fields.
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.
authors.affiliation: Department of Physics, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States.
authors.forename: Micholas Dean
authors.initials: MD
authors.lastname: Smith
authors.affiliation: Department of Physics, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States.|Department of Physics, New Jersey Institute of Technology , University Heights, Newark, New Jersey 07102-1982, United States.
authors.forename: J Srinivasa
authors.initials: JS
authors.lastname: Rao
authors.affiliation: Department of Physics, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Segelken
authors.affiliation: Department of Physics, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States.
authors.forename: Luis
authors.initials: L
authors.lastname: Cruz
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry
chemical_list: D016229:Amyloid beta-Peptides; D012997:Solvents; D014867:Water