posted on 2023-12-27, 16:36authored byA. S.
F. Oliveira, J. Rubio, C. E. M. Noble, J. L. R. Anderson, J. Anders, A. J. Mulholland
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 characterized experimentally
in this work. The MD + CB approach is found to perform reliably, giving
redox potential shifts with reasonably good correlation (0.85) to
the experimental values for the mutants. The MD + CB approach also
compares well with redox potential shift predictions using a continuum
electrostatic method. The estimation method employed within the MD
+ CB approach is straightforwardly transferable to standard equilibrium
MD simulations and holds promise for redox protein engineering and
design applications.