Dynamic water networks in cytochrome cbb3 oxidase

Area of Science:

• Biochemistry
• Molecular Biology
• Bioenergetics

Background:

• Heme-copper oxidases (HCOs) are crucial terminal electron acceptors in aerobic respiration.
• They catalyze oxygen reduction to water and pump protons across membranes.
• Proton transfer channels are essential for these processes, but their mechanisms remain unclear, especially in C-type HCOs.

Purpose of the Study:

• To identify proton transfer pathways in the C-type heme-copper oxidase, cytochrome cbb(3).
• To elucidate the role of conserved residues and water molecules in proton translocation.
• To understand the mechanism of redox-coupled proton pumping in this enzyme family.

Main Methods:

• Molecular dynamics (MD) simulations to observe water dynamics.
• Continuum electrostatic approaches to analyze charge distributions.
• Quantum chemical cluster calculations to study protonation states and redox potentials.

Main Results:

• MD simulations revealed stable water chains connecting conserved Glu323 to both sides of the membrane.
• Electrostatic and quantum chemical calculations indicated increased proton affinity of Glu323 upon heme b(3) reduction.
• Protonation of Glu323 was proposed as a mechanism for tuning heme b(3) redox potential.

Conclusions:

• Stable water chains form potential proton uptake and transfer pathways in cytochrome cbb(3).
• The conserved Glu323 residue plays a key role in proton transfer and redox potential modulation.
• These findings provide insights into the mechanism of proton pumping in C-type heme-copper oxidases.