PMID- 15178480
OWN - NLM
STAT- MEDLINE
DCOM- 20040721
LR  - 20161126
IS  - 0006-3002 (Print)
IS  - 0006-3002 (Linking)
VI  - 1656
IP  - 2-3
DP  - 2004 Jun 7
TI  - Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase.
PG  - 189-202
AB  - Proton transfer/translocation is studied in cytochrome c oxidase (CcO) by a 
      combination of quantum mechanics (QM) for the transferring protons and classical 
      molecular dynamics (MD) for the protein and solvent. The possibility of a 
      glutamate, Glu286 in the Rhodobacter sphaeroides numbering scheme, acting as a 
      rely point for proton translocation is investigated. The MD finds a 
      hydrogen-bonded cycle of two waters and the carboxylate oxygens of Glu286. The 
      possibility of protonating Glu286 to form neutral GluH is studied and we find 
      that, as experimentally inferred, this glutamate can spend most of its time as 
      GluH. Since translocation relies on the presence of water chains within CcO 
      channels, MD is used to assess their formation. Glu286 and Mg(2+) can be 
      connected by continuous hydrogen-bonded chains that are robust, though transient, 
      and the protein appears spongy above (toward the outer membrane) the Mg(2+). In 
      contrast, the D-channel spanning Asp132, close to the inner membrane surface, to 
      Glu286, forms water chains that are much sparser and do not continuously connect 
      these residues. Rather, there are chains spanning Glu286 to the vicinity of 
      Asn140, and other more robust and ramified water structures that connect Asp132 
      with waters close to Asn140.
FAU - Cukier, R I
AU  - Cukier RI
AD  - Department of Chemistry, Michigan State University, East Lansing, MI 48824-1322, 
      USA. cukier@cem.msu.edu
LA  - eng
GR  - GM 47274/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, U.S. Gov't, P.H.S.
PL  - Netherlands
TA  - Biochim Biophys Acta
JT  - Biochimica et biophysica acta
JID - 0217513
RN  - 0 (Protons)
RN  - 059QF0KO0R (Water)
RN  - 3KX376GY7L (Glutamic Acid)
RN  - 7006-34-0 (Asparagine)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
RN  - I38ZP9992A (Magnesium)
RN  - S88TT14065 (Oxygen)
SB  - IM
MH  - Asparagine/chemistry
MH  - Computer Simulation
MH  - Electron Transport Complex IV/*chemistry/*metabolism
MH  - Glutamic Acid/chemistry
MH  - Hydrogen Bonding
MH  - Magnesium/metabolism
MH  - Models, Molecular
MH  - Oxygen/chemistry
MH  - Protein Conformation
MH  - *Protons
MH  - *Quantum Theory
MH  - Rhodobacter sphaeroides/enzymology
MH  - *Thermodynamics
MH  - Water/chemistry
EDAT- 2004/06/05 05:00
MHDA- 2004/07/22 05:00
CRDT- 2004/06/05 05:00
PHST- 2003/10/27 00:00 [received]
PHST- 2004/03/08 00:00 [revised]
PHST- 2004/03/11 00:00 [accepted]
PHST- 2004/06/05 05:00 [pubmed]
PHST- 2004/07/22 05:00 [medline]
PHST- 2004/06/05 05:00 [entrez]
AID - S0005272804000532 [pii]
AID - 10.1016/j.bbabio.2004.03.006 [doi]
PST - ppublish
SO  - Biochim Biophys Acta. 2004 Jun 7;1656(2-3):189-202. doi: 
      10.1016/j.bbabio.2004.03.006.