PMID- 12615353
OWN - NLM
STAT- MEDLINE
DCOM- 20030627
LR  - 20190610
IS  - 0006-3002 (Print)
IS  - 0006-3002 (Linking)
VI  - 1557
IP  - 1-3
DP  - 2003 Mar 6
TI  - Computer simulation of water in cytochrome c oxidase.
PG  - 99-107
AB  - Statistical mechanics and molecular dynamics simulations have been carried out to 
      study the distribution and dynamics of internal water molecules in bovine heart 
      cytochrome c oxidase (CcO). CcO is found to be capable of holding plenty of 
      water, which in subunit I alone amounts to about 165 molecules. The dynamic 
      characterization of these water molecules is carried out. The nascent water 
      molecules produced in the redox reaction at the heme a(3)-CuB binuclear site form 
      an intriguing chain structure. The chain begins at the position of Glu242 at the 
      end of the D channel, and has a fork structure, one branch of which leads to the 
      binuclear center, and the other to the propionate d of heme a(3). The branch that 
      leads to the binuclear center has dynamic access both to the site where the 
      formation of water occurs, and to delta-nitrogen of His291. From the binuclear 
      center, the chain continues to run into the K channel. The stability of this 
      hydrogen bond network is examined dynamically. The catalytic site is located at 
      the hydrophobic region, and the nascent water molecules are produced at the top 
      of the energy hill. The energy gradient is utilized as the mechanism of water 
      removal from the protein. The water exit channels are explored using 
      high-temperature dynamics simulations. Two putative channels for water exit from 
      the catalytic site have been identified. One is leading directly toward Mg(2+) 
      site. However, this channel is only open when His291 is dissociated from CuB. If 
      His291 is bound to CuB, the only channel for water exit is the one that 
      originates at E242 and leads toward the middle of the membrane. This is the same 
      channel that is presumably used for oxygen supply.
FAU - Zheng, Xuehe
AU  - Zheng X
AD  - Department of Chemistry, University of California, One Shields Avenue, Davis, CA 
      95616, USA.
FAU - Medvedev, Dmitry M
AU  - Medvedev DM
FAU - Swanson, Jessica
AU  - Swanson J
FAU - Stuchebrukhov, Alexei A
AU  - Stuchebrukhov AA
LA  - eng
GR  - GM54052/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  - EC 1.9.3.1 (Electron Transport Complex IV)
SB  - IM
MH  - Animals
MH  - Binding Sites
MH  - Catalytic Domain
MH  - Cattle
MH  - Computer Simulation
MH  - Electron Transport Complex IV/*chemistry
MH  - Models, Chemical
MH  - Models, Molecular
MH  - Molecular Conformation
MH  - Protons
MH  - Water/*chemistry
EDAT- 2003/03/05 04:00
MHDA- 2003/06/28 05:00
CRDT- 2003/03/05 04:00
PHST- 2003/03/05 04:00 [pubmed]
PHST- 2003/06/28 05:00 [medline]
PHST- 2003/03/05 04:00 [entrez]
AID - S0005272803000021 [pii]
AID - 10.1016/s0005-2728(03)00002-1 [doi]
PST - ppublish
SO  - Biochim Biophys Acta. 2003 Mar 6;1557(1-3):99-107. doi: 
      10.1016/s0005-2728(03)00002-1.