Unravelling Constant pH Molecular Dynamics in Oligopeptides with Explicit Solvation Model.

ABSTRACT: An accurate description of the protonation state of amino acids is essential to correctly simulate the conformational space and the mechanisms of action of proteins or other biochemical systems. The pH and the electrochemical environments are decisive factors to define the effective pKa of amino acids and, therefore, the protonation state. However, they are poorly considered in Molecular Dynamics (MD) simulations. To deal with this problem, constant pH Molecular Dynamics (cpHMD) methods have been developed in recent decades, demonstrating a great ability to consider the effective pKa of amino acids within complex structures. Nonetheless, there are very few studies that assess the effect of these approaches in the conformational sampling. In a previous work of our research group, we detecte

SUBMITTER: Privat C 

PROVIDER: S-EPMC8512540 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature