title: Comparison of molecular dynamics simulation methods for amyloid β(1-42) monomers containing D-aspartic acid residues for predicting retention times in chromatography.
abstract: Molecular dynamics simulations of amyloid β(1-42) containing D-aspartic acid residues were performed using several continuous solvent models to investigate the usefulness of simulation methods for D-amino acid-containing proteins and peptides. Normal molecular dynamics simulations and replica exchange molecular dynamics simulations, which are one of the generalized-ensemble algorithms, were performed. Because the β-structure contents of amyloid β(1-42) peptides obtained by replica exchange molecular dynamics simulations with Onufriev-Bashford-Case generalized Born implicit solvent were qualitatively consistent with experimental data, replica exchange molecular dynamics rather than other methods appeared to be more reasonable for calculations of amyloid β(1-42) containing D-aspartic acid residues. Computational results revealed that peptides with stereoinversion of Asp23 tend to form β-sheet structures by themselves, in contrast to the wild-type peptides that form β-sheet structures only after aggregation. These results are expected to be useful for computational investigations of proteins and peptides such as prediction of retention time of peptides and proteins containing D-aspartic acid residues.
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Sendai, Miyagi 981-8558, Japan. oda@tohoku-pharm.ac.jp
authors.forename: Akifumi
authors.initials: A
authors.lastname: Oda
authors.forename: Kana
authors.initials: K
authors.lastname: Kobayashi
authors.forename: Ohgi
authors.initials: O
authors.lastname: Takahashi
mesh_terms: D000465:Algorithms; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D002851:Chromatography, High Pressure Liquid / Q000379:methods / Q000592:standards*; D056148:Chromatography, Reverse-Phase; D026603:D-Aspartic Acid / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012997:Solvents
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D012997:Solvents; C075222:amyloid beta-protein (1-42); D026603:D-Aspartic Acid