Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins.

ABSTRACT: Intrinsically disordered proteins are essential for biological processes such as cell signalling, but are also associated to devastating diseases including Alzheimer's disease, Parkinson's disease or type II diabetes. Because of their lack of a stable three-dimensional structure, molecular dynamics simulations are often used to obtain atomistic details that cannot be observed experimentally. The applicability of molecular dynamics simulations depends on the accuracy of the force field chosen to represent the underlying free energy surface of the system. Here, we use replica exchange molecular dynamics simulations to test five modern force fields, OPLS, AMBER99SB, AMBER99SB*ILDN, AMBER99SBILDN-NMR and CHARMM22*, in their ability to model Aβ₄₂ , an intrinsically disordered peptide

SUBMITTER: Carballo-Pacheco M 

PROVIDER: S-EPMC5275744 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature