scholarly journals Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations

2016 ◽  
Vol 1857 (9) ◽  
pp. 1594-1606 ◽  
Author(s):  
Longhua Yang ◽  
Åge A. Skjevik ◽  
Wen-Ge Han Du ◽  
Louis Noodleman ◽  
Ross C. Walker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Molecular Dynamics Simulations ◽  
Cytochrome C Oxidase ◽  
Proton Pumping ◽  
Dynamics Simulations ◽  
Water Exit

scholarly journals Data for molecular dynamics simulations of B-type cytochrome c oxidase with the Amber force field

Data in Brief ◽  
2016 ◽  
Vol 8 ◽  
pp. 1209-1214 ◽  
Author(s):  
Longhua Yang ◽  
Åge A. Skjevik ◽  
Wen-Ge Han Du ◽  
Louis Noodleman ◽  
Ross C. Walker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Cytochrome C Oxidase ◽  
Amber Force Field ◽  
Dynamics Simulations

scholarly journals Protonation Dynamics in the K-Channel of Cytochrome c Oxidase Estimated from Molecular Dynamics Simulations

Processes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 265
Author(s):  
Vincent Stegmaier ◽  
Rene F. Gorriz ◽  
Petra Imhof
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Cytochrome C Oxidase ◽  
Proton Transport ◽  
K Channel ◽  
Proton Transfer Reactions ◽  
Dynamics Simulations ◽  
Hydrogen Bonded

Proton transfer reactions are one of the most fundamental processes in biochemistry. We present a simplistic approach for estimating proton transfer probabilities in a membrane protein, cytochrome c oxidase. We combine short molecular dynamics simulations at discrete protonation states with a Monte Carlo approach to exchange between those states. Requesting for a proton transfer the existence of a hydrogen-bonded connection between the two source and target residues of the exchange, restricts the acceptance of transfers to only those in which a proton-relay is possible. Together with an analysis of the hydrogen-bonded connectivity in one of the proton-conducting channels of cytochrome c oxidase, this approach gives insight into the protonation dynamics of the hydrogen-bonded networks. The connectivity and directionality of the networks are coupled to the conformation of an important protein residue in the channel, K362, rendering proton transfer in the entire channel feasible in only one of the two major conformations. Proton transport in the channel can thus be regulated by K362 not only through its possible role as a proton carrier itself, but also by allowing or preventing proton transport via water residues.

scholarly journals Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations

2017 ◽  
Vol 114 (48) ◽  
pp. E10339-E10348 ◽  
Author(s):  
Vivek Sharma ◽  
Pablo G. Jambrina ◽  
Markus Kaukonen ◽  
Edina Rosta ◽  
Peter R. Rich
Keyword(s):  
Molecular Dynamics ◽  
Proton Transfer ◽  
Molecular Dynamics Simulations ◽  
Proton Pumping ◽  
General Role ◽  
Adequate Hydration ◽  
Lipid Solvent ◽  
Respiratory Chains ◽  
Dynamics Simulations ◽  
H Channels

Proton pumping A-type cytochrome c oxidase (CcO) terminates the respiratory chains of mitochondria and many bacteria. Three possible proton transfer pathways (D, K, and H channels) have been identified based on structural, functional, and mutational data. Whereas the D channel provides the route for all pumped protons in bacterial A-type CcOs, studies of bovine mitochondrial CcO have led to suggestions that its H channel instead provides this route. Here, we have studied H-channel function by performing atomistic molecular dynamics simulations on the entire, as well as core, structure of bovine CcO in a lipid-solvent environment. The majority of residues in the H channel do not undergo large conformational fluctuations. Its upper and middle regions have adequate hydration and H-bonding residues to form potential proton-conducting channels, and Asp51 exhibits conformational fluctuations that have been observed crystallographically. In contrast, throughout the simulations, we do not observe transient water networks that could support proton transfer from the N phase toward heme a via neutral His413, regardless of a labile H bond between Ser382 and the hydroxyethylfarnesyl group of heme a. In fact, the region around His413 only became sufficiently hydrated when His413 was fixed in its protonated imidazolium state, but its calculated pKa is too low for this to provide the means to create a proton transfer pathway. Our simulations show that the electric dipole moment of residues around heme a changes with the redox state, hence suggesting that the H channel could play a more general role as a dielectric well.

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