Theoretical study of the cytochrome bc1 complex reaction mechanism
type: CreativeWork
description: The bc1 complex is an enzyme which plays a critical role in energy production through photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q- cycle, which is well established and operates via quinol substrates that bind the protein at their active sites. Despite decades of research, the quinol-protein interaction that initiates the Q-cycle has not yet been completely described. Furthermore, the initial charge transfer reactions that take place following quinol binding, lack a physical description. The present dissertation presents a comprehensive study of the primary reaction mechanism of the bc1 complex from the photosynthetic purple bacterium Rhodobacter capsulatus. By using theoretical methods, such as classical molecular dynamics simulations and quantum density functional theory calculations, we investigated the molecular structure and function of the bc1 complex to provide a quantitative description of the primary events that occur during and after quinol binding. First, we studied the binding motifs of a quinol molecule at its active site of the bc1 complex. Our investigations suggested a novel configuration of amino acid residues responsible for quinol binding and provided new insights into the role of the different amino acid residues that hold the quinol molecule at the Qo-site of the bc1 complex. The calculations were performed for two Qo-site models, differing in the protonation state of a histidine residue that is proven to be fundamental in the binding and further reaction. The findings were consistent with some features of earlier molecular dynamics simulations, but these identified also rearrangements of binding site residues not discussed previously. Secondly, by exploring all possible single and paired-charge reaction pathways, we studied the electron and proton transfer reactions that trigger the Q-cycle. In particular, the coupled nature of the first electron and proton transfer reactions was revealed, accompan…
abstract: The bc1 complex is an enzyme which plays a critical role in energy production through photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q- cycle, which is well established and operates via quinol substrates that bind the protein at their active sites. Despite decades of research, the quinol-protein interaction that initiates the Q-cycle has not yet been completely described. Furthermore, the initial charge transfer reactions that take place following quinol binding, lack a physical description. The present dissertation presents a comprehensive study of the primary reaction mechanism of the bc1 complex from the photosynthetic purple bacterium Rhodobacter capsulatus. By using theoretical methods, such as classical molecular dynamics simulations and quantum density functional theory calculations, we investigated the molecular structure and function of the bc1 complex to provide a quantitative description of the primary events that occur during and after quinol binding. First, we studied the binding motifs of a quinol molecule at its active site of the bc1 complex. Our investigations suggested a novel configuration of amino acid residues responsible for quinol binding and provided new insights into the role of the different amino acid residues that hold the quinol molecule at the Qo-site of the bc1 complex. The calculations were performed for two Qo-site models, differing in the protonation state of a histidine residue that is proven to be fundamental in the binding and further reaction. The findings were consistent with some features of earlier molecular dynamics simulations, but these identified also rearrangements of binding site residues not discussed previously. Secondly, by exploring all possible single and paired-charge reaction pathways, we studied the electron and proton transfer reactions that trigger the Q-cycle. In particular, the coupled nature of the first electron and proton transfer reactions was revealed, accompan…
author: Barragan Diaz, Angela M.
language: en
keywords: Cytochrome bc1 Complex, Molecular Dynamics Simulations, Proton-coupled electron transfer, PCET, Quinol binding, Quinol oxidation, Quantum Chemistry
date published: 2020-08-26T23:54:32Z
date modified: 2026-07-22T22:24:47Z
provider: University of Illinois - Urbana-Champaign
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University of Illinois at Urbana-Champaign

PropertyValue
property ID: Handle
value: http://hdl.handle.net/2142/108108