Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations.

ABSTRACT: The tunable design of protein redox potentials promises to open a range of applications in biotechnology and catalysis. Here, we introduce a method to calculate redox potential changes by combining fluctuation relations with molecular dynamics simulations. It involves the simulation of reduced and oxidized states, followed by the instantaneous conversion between them. Energy differences introduced by the perturbations are obtained using the Kubo-Onsager approach. Using a detailed fluctuation relation coupled with Bayesian inference, these are postprocessed into estimates for the redox potentials in an efficient manner. This new method, denoted MD + CB, is tested on a de novo four-helix bundle heme protein (the m4D2 "maquette") and five designed mutants, including some mutants charac

SUBMITTER: Oliveira ASF 

PROVIDER: S-EPMC10782445 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature