PMID- 22178790
OWN - NLM
STAT- MEDLINE
DCOM- 20120510
LR  - 20240504
IS  - 0006-3002 (Print)
IS  - 0006-3002 (Linking)
VI  - 1817
IP  - 4
DP  - 2012 Apr
TI  - Expanding the view of proton pumping in cytochrome c oxidase through computer 
      simulation.
PG  - 518-25
LID - 10.1016/j.bbabio.2011.11.017 [doi]
AB  - In cytochrome c oxidase (CcO), a redox-driven proton pump, protons are 
      transported by the Grotthuss shuttling via hydrogen-bonded water molecules and 
      protonatable residues. Proton transport through the D-pathway is a complicated 
      process that is highly sensitive to alterations in the amino acids or the 
      solvation structure in the channel, both of which can inhibit proton pumping and 
      enzymatic activity. Simulations of proton transport in the hydrophobic cavity 
      showed a clear redox state dependence. To study the mechanism of proton pumping 
      in CcO, multi-state empirical valence bond (MS-EVB) simulations have been 
      conducted, focusing on the proton transport through the D-pathway and the 
      hydrophobic cavity next to the binuclear center. The hydration structures, 
      transport pathways, effects of residues, and free energy surfaces of proton 
      transport were revealed in these MS-EVB simulations. The mechanistic insight 
      gained from them is herein reviewed and placed in context for future studies.
CI  - Copyright A(c) 2011 Elsevier B.V. All rights reserved.
FAU - Peng, Yuxing
AU  - Peng Y
AD  - Department of Chemistry, University of Chicago, Chicago, IL, USA.
FAU - Voth, Gregory A
AU  - Voth GA
LA  - eng
GR  - R01 GM053148/GM/NIGMS NIH HHS/United States
GR  - R01 GM053148-16/GM/NIGMS NIH HHS/United States
GR  - R01-GM053148/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20111208
PL  - Netherlands
TA  - Biochim Biophys Acta
JT  - Biochimica et biophysica acta
JID - 0217513
RN  - 0 (Bacterial Proteins)
RN  - 0 (Protons)
RN  - 059QF0KO0R (Water)
RN  - 18535-39-2 (heme a)
RN  - 42VZT0U6YR (Heme)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
SB  - IM
MH  - Algorithms
MH  - Bacterial Proteins/*chemistry/metabolism
MH  - Binding Sites
MH  - Biological Transport
MH  - *Computer Simulation
MH  - Crystallography, X-Ray
MH  - Electron Transport Complex IV/*chemistry/metabolism
MH  - Heme/analogs & derivatives/chemistry/metabolism
MH  - Hydrogen Bonding
MH  - Hydrophobic and Hydrophilic Interactions
MH  - Kinetics
MH  - Models, Biological
MH  - Models, Molecular
MH  - Oxidation-Reduction
MH  - Protein Structure, Tertiary
MH  - *Protons
MH  - Review Literature as Topic
MH  - Rhodobacter sphaeroides/enzymology/metabolism
MH  - Water/chemistry/metabolism
PMC - PMC4120846
MID - NIHMS343504
EDAT- 2011/12/20 06:00
MHDA- 2012/05/11 06:00
PMCR- 2014/08/04
CRDT- 2011/12/20 06:00
PHST- 2011/10/01 00:00 [received]
PHST- 2011/11/23 00:00 [revised]
PHST- 2011/11/24 00:00 [accepted]
PHST- 2011/12/20 06:00 [entrez]
PHST- 2011/12/20 06:00 [pubmed]
PHST- 2012/05/11 06:00 [medline]
PHST- 2014/08/04 00:00 [pmc-release]
AID - S0005-2728(11)00289-1 [pii]
AID - 10.1016/j.bbabio.2011.11.017 [doi]
PST - ppublish
SO  - Biochim Biophys Acta. 2012 Apr;1817(4):518-25. doi: 10.1016/j.bbabio.2011.11.017. 
      Epub 2011 Dec 8.