Comprehensive Analysis of Coupled Proline Cis-Trans States in Bradykinin Using ωBP-REMD Simulations.

ABSTRACT: It is well-known that proline (Pro) cis-trans isomerization plays a decisive role in the folding and stabilization of proteins. The conformational coupling between isomerization states of different Pro residues in proteins during conformational adaptation processes is not well understood. In the present work, we investigate the coupled cis-trans isomerization of three Pro residues using bradykinin (BK), a partially unstructured nonapeptide hormone, as a model system. We use a recently developed enhanced-sampling molecular dynamics method (ω-bias potential replica exchange molecular dynamics; ωBP-REMD) that allows us to exhaustively sample all combinations of Pro isomer states and obtain converged probability densities of all eight state combinations within 885 ns ωBP-REMD simulations. In a

SUBMITTER: Kienlein M 

PROVIDER: S-EPMC10976632 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature