A Computational Pipeline Observes the Flexibility and Dynamics of Plant Cytochrome P450 Binding Sites.

ABSTRACT: Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on human CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. We developed a novel computational pipeline consisting of two steps. Firstly, we use molecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyze a number of binding site properties-size, flexibility, shape, hyd

SUBMITTER: Kuvek T 

PROVIDER: S-EPMC11545509 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature