scholarly journals Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site

2014 ◽  
Vol 10 (12) ◽  
pp. e1004010 ◽  
Author(s):  
A. Sofia F. Oliveira ◽  
João M. Damas ◽  
António M. Baptista ◽  
Cláudio M. Soares
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Molecular Dynamics Simulations ◽  
O2 Diffusion ◽  
Dynamics Simulations

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 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 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.

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