PMID- 16800531
OWN - NLM
STAT- MEDLINE
DCOM- 20070723
LR  - 20131121
IS  - 1520-6106 (Print)
IS  - 1520-5207 (Linking)
VI  - 110
IP  - 24
DP  - 2006 Jun 22
TI  - Improved density functional theory/electrostatic calculation of the His291 
      protonation state in cytochrome C oxidase: self-consistent charges for solvation 
      energy calculation.
PG  - 12162-6
AB  - The protonation state of His291 in cytochrome c oxidase (CcO), a ligand to the 
      Cu(B) center of the enzyme, has been recently studied in this group by using 
      combined density functional theory (DFT)/electrostatic (QM/MM) calculations. On 
      the basis of these calculations, a model of the proton pumping mechanism of CcO 
      has been proposed. Due to certain technical difficulties, the procedure used in 
      the previous calculation to find partial atomic charges of the QM system for the 
      solvation energy evaluation was not entirely satisfactory; i.e., it was not 
      self-consistent. Here, we describe a procedure that resolves the problem and 
      report on the improved calculations of the protonation state of the His residue. 
      The new procedure fits the protein and reaction field potentials in the region of 
      the QM system with artificial point charges placed on a surface of a sphere 
      surrounding the QM system and a few charges inside the sphere and allows one to 
      perform DFT calculations that involve an inhomogeneous dielectric environment in 
      a self-consistent way. The procedure improves the accuracy of calculations in 
      comparison with previous work. The improved results show, however, that although 
      the absolute energies change significantly the relative energies of the 
      protonated and deprotonated states of His291 remain close to the previously 
      reported ones and therefore do not change significantly the pK(a) values reported 
      earlier. Therefore, our new improved calculations support for the proposed His291 
      model of the CcO pump.
FAU - Makhov, D V
AU  - Makhov DV
AD  - Department of Chemistry, University of California, Davis, One Shields Avenue, 
      Davis, California 95616.
FAU - Popovic, Dragan M
AU  - Popovic DM
FAU - Stuchebrukhov, Alexei A
AU  - Stuchebrukhov AA
LA  - eng
GR  - GM54052/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PL  - United States
TA  - J Phys Chem B
JT  - The journal of physical chemistry. B
JID - 101157530
RN  - 0 (Protons)
RN  - 4QD397987E (Histidine)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
SB  - IM
MH  - Electron Transport Complex IV/*chemistry
MH  - Histidine/*chemistry
MH  - Models, Molecular
MH  - Protons
MH  - Solubility
MH  - Static Electricity
EDAT- 2006/06/28 09:00
MHDA- 2007/07/24 09:00
CRDT- 2006/06/28 09:00
PHST- 2006/06/28 09:00 [pubmed]
PHST- 2007/07/24 09:00 [medline]
PHST- 2006/06/28 09:00 [entrez]
AID - 10.1021/jp0608630 [doi]
PST - ppublish
SO  - J Phys Chem B. 2006 Jun 22;110(24):12162-6. doi: 10.1021/jp0608630.