scholarly journals A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase

2005 ◽  
Vol 1706 (1-2) ◽  
pp. 134-146 ◽  
Author(s):  
R.I. Cukier
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
K Channel ◽  
Chain Formation ◽  
Proton Conducting ◽  
Water Chain

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 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 Dewetting transitions coupled to K-channel activation in cytochrome c oxidase

2018 ◽  
Vol 9 (32) ◽  
pp. 6703-6710 ◽  
Author(s):  
Shreyas Supekar ◽  
Ville R. I. Kaila
Keyword(s):  
Free Energy ◽  
Cytochrome C ◽  
Oxygen Reduction ◽  
Cytochrome C Oxidase ◽  
Biological Membrane ◽  
Proton Gradient ◽  
K Channel ◽  
Channel Activation ◽  
Electrochemical Proton Gradient ◽  
Respiratory Chains

Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane.

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
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