Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins.

ABSTRACT: Computer simulations are used for identifying the secondary structure properties of ordered and disordered proteins. However, our recent studies showed that the chosen computer simulation protocol, simulation technique, and force field parameter set for a disordered protein impact its predicted secondary structure properties. Here, we compare the outcome from computer simulations utilizing molecular dynamics simulations without parallel tempering techniques using various force field parameter sets and temperature-replica exchange molecular dynamics simulations both for a model ordered and two model disordered proteins. Specifically, the model ordered protein is the third IgG-binding domain of Protein G (GB3) and the two model disordered proteins are amyloid-β(1-40) and α-synuclein in water

SUBMITTER: Coskuner-Weber O 

PROVIDER: S-EPMC8724382 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature