Cysteine oxidation in proteins: structure, biophysics, and simulation

D Garrido Ruiz, A Sandoval-Perez, AV Rangarajan… - Biochemistry, 2022 - ACS Publications
Cysteine side chains can exist in distinct oxidation states depending on the pH and redox
potential of the environment, and cysteine oxidation plays important yet complex regulatory …

Constant ph molecular dynamics simulations: Current status and recent applications

VM de Oliveira, R Liu, J Shen - Current opinion in structural biology, 2022 - Elsevier
Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …

Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity

Y Gu, MJ Guberman-Pfeffer, V Srikanth, C Shen… - Nature …, 2023 - nature.com
OmcZ nanowires produced by Geobacter species have high electron conductivity (> 30 S
cm− 1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire …

Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire

MJ Guberman-Pfeffer - The Journal of Physical Chemistry B, 2022 - ACS Publications
A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS)
from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors …

Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations

ASF Oliveira, J Rubio, CEM Noble… - Journal of Chemical …, 2023 - ACS Publications
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 …

Measuring and predicting warhead and residue reactivity

E Awoonor-Williams, J Kennedy, CN Rowley - Annual Reports in Medicinal …, 2021 - Elsevier
The development of a covalent inhibitor requires the incorporation of an appropriate
warhead into the chemical structure of the inhibitor and the selection of an appropriate …

Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers

RJ Wei, U Khaniya, J Mao, J Liu, VS Batista… - Photosynthesis …, 2023 - Springer
Protons participate in many reactions. In proteins, protons need paths to move in and out of
buried active sites. The vectorial movement of protons coupled to electron transfer reactions …

From Hot Water to Dry Dirt: Microbes Use Cytochrome 'Nanowires' of Similar Conductivity but Different Structure

MJ Guberman-Pfeffer - bioRxiv, 2023 - biorxiv.org
Micron-scale electron transfer through polymeric cytochrome 'nanowires' powers prokaryotic
life from hydrothermal vents to terrestrial soils in ways not fully understood. How much …

Computing proton-coupled redox potentials of fluorotyrosines in a protein environment

CR Reinhardt, R Sequeira, C Tommos… - The Journal of …, 2020 - ACS Publications
The oxidation of tyrosine to form the neutral tyrosine radical via proton-coupled electron
transfer is essential for a wide range of biological processes. The precise measurement of …

Heme Hopping Falls Short: What Explains Anti-Arrhenius Conductivity in a Multi-heme Cytochrome Nanowire?

MJ Guberman-Pfeffer - bioRxiv, 2022 - biorxiv.org
A helical homopolymer of the outer-membrane cytochrome type S (OmcS) was proposed to
electrically connect a common soil bacterium, Geobacter sulfurreducens, with minerals and …