2016
DOI: 10.1021/jacs.6b04849
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Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation

Abstract: A key part of the respiratory and photosynthetic pathways is the bc1 protein complex embedded in the inner membrane of mitochondria and the plasma membrane of photosynthetic bacteria. The protein complex pumps protons across the membrane to maintain an electrostatic potential, which is in turn used to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecula… Show more

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Cited by 34 publications
(116 citation statements)
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“…This approach contrasts with usual methods for studying association between biomolecules which enhance sampling of a ligand that binds to a single region of the protein ( 61 ). However, similar approaches to the one employed here were recently used to study the interactions between the amino acid side chains and DNA ( 62 ) and to investigate binding of molecular oxygen to a respiratory protein ( 63 ).…”
Section: Resultsmentioning
confidence: 99%
“…This approach contrasts with usual methods for studying association between biomolecules which enhance sampling of a ligand that binds to a single region of the protein ( 61 ). However, similar approaches to the one employed here were recently used to study the interactions between the amino acid side chains and DNA ( 62 ) and to investigate binding of molecular oxygen to a respiratory protein ( 63 ).…”
Section: Resultsmentioning
confidence: 99%
“…Irradiation driven chemistry (IDC) is based on the quantum transformations that are induced in molecular systems by their irradiation by external fields of different modality (X-rays, lasers, electrons/positrons, ions, etc) and the dynamics of molecular system which can be also influenced by external factors like temperature, pressure, external fields, etc. Highly perturbed dynamical molecular systems can only be described from first principles within the time dependent density functional theory (TDTDFT), or any of its equivalents, if the size of the molecular system is sufficiently small, typically hundreds of atoms [10][11][12][13][14].…”
Section: Introductionmentioning
confidence: 99%
“…The former employed high oxygen concentrations to achieve good statistics, while the latter included only a single water by random replacement of water molecules. 6 The parameters used for the simulations are summarized in Table 1, and the simulation box is illustrated in Fig. 2.…”
Section: Molecular Dynamics Simulation Protocolmentioning
confidence: 99%
“…Molecular oxygen was modeled following an earlier study. 6 The system was equilibrated, first under constant pressure (NPT ensemble) to allow the simulation box to shrink and acquire a physiological density, while further equilibration continued through employing constant volume simulation (NVT ensemble). Constraints on the system were gradually released: first, only the solvent was equilibrated, then the side chains and cofactors of the ETF were released, and finally, the protein backbone was released as well to equilibrate the whole system.…”
Section: Molecular Dynamics Simulation Protocolmentioning
confidence: 99%