de la Lande, A. | Search bioRxiv

bioRxiv2025

Computational study of heme b595 to heme d electron transfer in E. coli cytochrome bd-I oxidase

Cytochrome bd is a distinctive family of terminal oxidases present in the respiratory chains of many prokaryotes. Despite its biological importance, the redox chemistry of these proteins remains poorly understood, largely due to the presence of two b-type hemes and one d-type heme. Here, we report the first computational study of inter-heme electron transfer in the cytochrome bd family. We performed 10 s of molecular dynamics simulations of E. coli cytochrome bd-I embedded in realistic membranes, combined with quantum chemical calculations to estimate the thermodynamic parameters of electron transfer from heme b595 to heme d within the framework of Marcus theory. We further identify the respective contributions of the hemes, protein scaffold, lipid bilayer, water, and counterions to the driving force and reorganization energy. The inter-heme electronic coupling was calculated using the Projected Orbital Diabatization (POD) method in a hybrid Quantum Mechanics/Molecular Mechanics scheme and rationalized through electron transfer pathway analysis. This study provides fundamental insights into how electron transfer steps are orchestrated in the catalytic cycle of E. coli cytochrome bd-I. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/673948v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@14a29c8org.highwire.dtl.DTLVardef@1fd1c98org.highwire.dtl.DTLVardef@6053aaorg.highwire.dtl.DTLVardef@14ec40_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

NOX transmembrane electron transfer is governed by a subtly balanced, self-adjusting charge distribution

NADPH oxidases (NOX) form a family of transmembrane enzymes that catalyze the formation of reactive oxygen species. These are produced thanks to a chain of electron transfers (ET), shuttling electrons from one side of the membrane to the other, using one flavin and two heme cofactors as redox mediators. In this work we investigate the thermodynamics of the electron transfer (ET) between the two hemes contained in the transmembrane domain by means of extensive molecular dynamics simulations. We compare two proteins of the NOX5 isoform, from homo sapiens (hNOX5) and from cylindrospermum stagnale (csNOX5), a cyanobacteria. We study in detail the influence of both the density of negatively charged lipids in the membrane and of the NOX5 aminoacid sequence on the ET thermodynamic balance. The linear response formalism allows us to decompose the variation in free energy into the individual contributions of the system components (protein, membrane, solvent, etc.). We highlight the major compensatory effects of the various components in the global free energy budget in those complex systems. Although the contributions of the protein or the membrane to the ET thermodynamics can be individually strongly modified by a change in the aminoacid sequence or the membrane composition, they are largely compensated by the rest of the heme environment so that the total free energy is always found to be slightly favorable to the electron transfer. To our knowledge, this study is the first to highlight the effect of membrane charge density on inter-heme ET, providing valuable insights into the molecular mechanisms governing ET catalysis in complex membrane systems.

bioinformatics↗