ArticleBiophysical journal2012
From static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Role of conformational change and K-path ligands in controlling cytochromeBiochemical Society transactions · 2017Review
- Revisiting Kadenbach: Electron flux rate through cytochrome c-oxidase determines the ATP-inhibitory effect and subsequent production of ROS.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Translocator Protein 18 kDa (TSPO): An Old Protein with New Functions?Biochemistry · 2016Article
- Biomimetic Membranes for Multi-Redox Center Proteins.International journal of molecular sciences · 2016Review
- Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site.PLoS computational biology · 2014Article
- Structural and functional assessment of perilipin 2 lipid binding domain(s).Biochemistry · 2014Article
- Conserved glycine 232 in the ligand channel of ba3 cytochrome oxidase from Thermus thermophilus.Biochemistry · 2014Article
- Phase-sensitive detection in modulation excitation spectroscopy applied to potential induced electron transfer in cytochrome c oxidase.Applied spectroscopy · 2014Article
- Time-resolved surface-enhanced IR-absorption spectroscopy of direct electron transfer to cytochrome c oxidase from R. sphaeroides.Biophysical journal · 2013Article
- Computational prediction and in vitro analysis of potential physiological ligands of the bile acid binding site in cytochrome c oxidase.Biochemistry · 2013Article
- A conserved amphipathic ligand binding region influences k-path-dependent activity of cytochrome C oxidase.Biochemistry · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Crystallographic structure and deuterium accessibility comparisons of CcO in different redox states have suggested conformational changes of mechanistic significance. To predict the intrinsic flexibility and low energy motions in CcO, this work has analyzed available high-resolution crystallographic structures with ProFlex and elNémo computational methods. The results identify flexible regions and potential conformational changes in CcO that correlate well with published structural and biochemical data and provide mechanistic insights. CcO is predicted to undergo rotational motions on the interior and exterior of the membrane, driven by transmembrane helical tilting and bending, coupled with rocking of the β-sheet domain. Consequently, the proton K-pathway becomes sufficiently flexible for internal water molecules to alternately occupy upper and lower parts of the pathway, associated with conserved Thr-359 and Lys-362 residues. The D-pathway helices are found to be relatively rigid, with a highly flexible entrance region involving the subunit I C-terminus, potentially regulating the uptake of protons. Constriction and dilation of hydrophobic channels in RsCcO suggest regulation of the oxygen supply to the binuclear center. This analysis points to coupled conformational changes in CcO and their potential to influence both proton and oxygen access.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.