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A reduction-oxidation reaction is commonly called a redox reaction. In a redox reaction, electrons are transferred from one species to another rather than being shared between or among atoms. The reducing agent or reductant is the species that loses electrons and gets oxidized in the process. The species that gains electrons and gets reduced in the process is the oxidizing agent or oxidant. Redox reactions are represented as two separate equations called half-reactions, where one equation...
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Ladder diagrams are useful tools for understanding redox equilibrium reactions, especially the effects of concentration changes on the electrochemical potential of the reaction. The vertical axis in the redox ladder diagrams represents the electrochemical potential, E. The area of predominance is demarcated using the Nernst equation.
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A current produced due to the redox reactions of the analyte at the working and auxiliary electrodes is called a faradaic current. The reaction can be divided into two types. The current generated due to the reduction of the analyte is called cathodic current, and it carries a positive charge. In contrast, the current produced by analyte oxidation is known as an anodic current, and it has a negative charge. The applied potential at the working electrode determines the faradaic current flow, and...
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Redox titration is a chemical analysis technique used to determine the concentration of an unknown substance by measuring the electron transfer in a redox (reduction-oxidation) reaction. The process involves gradually adding a titrant with a known concentration of an oxidizing or reducing agent, to the analyte, the solution with an unknown concentration, until reaching the endpoint, which indicates the completion of the reaction between the two substances. Ensuring the analyte is in a single...
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Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations.

A S F Oliveira1,2,3, J Rubio4,5, C E M Noble2,3

  • 1Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.

Journal of Chemical Theory and Computation
|December 27, 2023
PubMed
Summary

We developed a new computational method (MD + CB) to accurately predict changes in protein redox potentials. This approach combines molecular dynamics simulations with fluctuation relations, showing reliable performance for protein engineering and design.

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Area of Science:

  • Biochemistry and Biophysics
  • Computational Chemistry
  • Protein Engineering

Background:

  • Tunable protein redox potentials are crucial for biotechnology and catalysis.
  • Accurate prediction of redox potential shifts is essential for protein design.

Purpose of the Study:

  • To introduce and validate a novel computational method (MD + CB) for calculating redox potential changes in proteins.
  • To assess the accuracy and applicability of the MD + CB method for designed protein mutants.

Main Methods:

  • Combining fluctuation relations with molecular dynamics (MD) simulations.
  • Simulating reduced and oxidized protein states and their interconversion.
  • Utilizing Kubo-Onsager approach and Bayesian inference for efficient redox potential estimation.

Main Results:

  • The MD + CB method demonstrated reliable performance in predicting redox potential shifts.
  • A good correlation (0.85) was observed between MD + CB predictions and experimental values for designed mutants.
  • MD + CB results compared favorably with continuum electrostatic methods.

Conclusions:

  • The MD + CB approach offers an efficient and accurate way to estimate redox potentials in proteins.
  • This method is transferable to standard MD simulations, promising advancements in redox protein engineering and design.