PMID- 15620374
OWN - NLM
STAT- MEDLINE
DCOM- 20050329
LR  - 20161126
IS  - 0006-3002 (Print)
IS  - 0006-3002 (Linking)
VI  - 1706
IP  - 1-2
DP  - 2005 Jan 7
TI  - A molecular dynamics study of water chain formation in the proton-conducting K 
      channel of cytochrome c oxidase.
PG  - 134-46
AB  - The formation of water chains in cytochrome c oxidase (CcO) is studied by 
      molecular dynamics (MD). Focus is on water chains in the K channel that can 
      supply a proton to the binuclear center (the heme a3 Fe/CuB region), the site of 
      O2 reduction. By assessing the presence of chains of any length on a short time 
      scale (0.1 ps), a view of the kinds of chains and their persistence is obtained. 
      Chains from the entry of the channel on the inner membrane to Thr359 (Rhodobacter 
      sphaeroides numbering) are often present but are blocked at that point until a 
      rotation of the Thr359 side chain occurs, permitting formation of chains from 
      Thr359 towards the binuclear center. No continuous hydrogen-bonded water chains 
      are found connecting Thr359 and the binuclear center. Instead, waters hydrogen 
      bond from Thr359 to the hydroxyl of the heme a3 farnesyl and then continue to the 
      binuclear center via Tyr288, which has been identified as a source of a proton 
      for O2 reduction. Three hydrogen-bonded waters are found to be present in the 
      binuclear center after a sufficiently long simulation time. One is ligated to the 
      CuB and could be associated with a water (or hydroxyl) identified in the crystal 
      structure as the fourth ligand of CuB. The water hydrogen-bonded to the hydroxyl 
      of Tyr288 is extremely persistent and well positioned to participate in O2 
      reduction. The third water is located where O2 is often suggested to reside in 
      mechanistic studies of O2 reduction.
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  - Comparative Study
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 (Amino Acids)
RN  - 0 (Potassium Channels)
RN  - 0 (Proton Pumps)
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  - Amino Acids/chemistry/metabolism
MH  - Computer Simulation
MH  - Electron Transport Complex IV/chemistry/*metabolism
MH  - Heme/*analogs & derivatives/metabolism
MH  - *Models, Molecular
MH  - Potassium Channels/chemistry/*metabolism
MH  - Proton Pumps/chemistry/metabolism
MH  - Water/*metabolism
EDAT- 2004/12/29 09:00
MHDA- 2005/03/30 09:00
CRDT- 2004/12/29 09:00
PHST- 2004/05/04 00:00 [received]
PHST- 2004/10/01 00:00 [revised]
PHST- 2004/10/06 00:00 [accepted]
PHST- 2004/12/29 09:00 [pubmed]
PHST- 2005/03/30 09:00 [medline]
PHST- 2004/12/29 09:00 [entrez]
AID - S0005-2728(04)00281-6 [pii]
AID - 10.1016/j.bbabio.2004.10.004 [doi]
PST - ppublish
SO  - Biochim Biophys Acta. 2005 Jan 7;1706(1-2):134-46. doi: 
      10.1016/j.bbabio.2004.10.004.