PMID- 24262070
OWN - NLM
STAT- MEDLINE
DCOM- 20140723
LR  - 20211021
IS  - 1520-510X (Electronic)
IS  - 0020-1669 (Print)
IS  - 0020-1669 (Linking)
VI  - 52
IP  - 24
DP  - 2013 Dec 16
TI  - Density functional study for the bridged dinuclear center based on a 
      high-resolution X-ray crystal structure of ba3 cytochrome c oxidase from Thermus 
      thermophilus.
PG  - 14072-88
LID - 10.1021/ic401858s [doi]
AB  - Strong electron density for a peroxide type dioxygen species bridging the Fea3 
      and CuB dinuclear center (DNC) was observed in the high-resolution (1.8 A) X-ray 
      crystal structures (PDB entries 3S8G and 3S8F) of ba3 cytochrome c oxidase (CcO) 
      from Thermus thermophilus. The crystals represent the as-isolated X-ray 
      photoreduced CcO structures. The bridging peroxide was proposed to arise from the 
      recombination of two radiation-produced HO(*) radicals formed either very near to 
      or even in the space between the two metals of the DNC. It is unclear whether 
      this peroxide species is in the O2(2-), O2(*)(-), HO2(-), or the H2O2 form and 
      what is the detailed electronic structure and binding geometry including the DNC. 
      In order to answer what form of this dioxygen species was observed in the DNC of 
      the 1.8 A X-ray CcO crystal structure (3S8G), we have applied broken-symmetry 
      density functional theory (BS-DFT) geometric and energetic calculations (using 
      OLYP potential) on large DNC cluster models with different Fea3-CuB oxidation and 
      spin states and with O2(2-), O2(*)(-), HO2(-), or H2O2 in the bridging position. 
      By comparing the DFT optimized geometries with the X-ray crystal structure 
      (3S8G), we propose that the bridging peroxide is HO2(-). The X-ray crystal 
      structure is likely to represent the superposition of the 
      Fea3(2+)-(HO2(-))-CuB(+) DNC's in different states (Fe(2+) in low spin (LS), 
      intermediate spin (IS), or high spin (HS)) with the majority species having the 
      proton of the HO2(-) residing on the oxygen atom (O1) which is closer to the 
      Fea3(2+) site in the Fea3(2+)-(HO-O)(-)-CuB(+) conformation. Our calculations 
      show that the side chain of Tyr237 is likely trapped in the deprotonated 
      Tyr237(-) anion form in the 3S8G X-ray crystal structure.
FAU - Du, Wen-Ge Han
AU  - Du WG
AD  - Department of Integrative Structural and Computational Biology, TPC15, The 
      Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 
      92037, United States.
FAU - Noodleman, Louis
AU  - Noodleman L
LA  - eng
GR  - R01 GM100934/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20131121
PL  - United States
TA  - Inorg Chem
JT  - Inorganic chemistry
JID - 0366543
RN  - 059QF0KO0R (Water)
RN  - 789U1901C5 (Copper)
RN  - E1UOL152H7 (Iron)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
RN  - S88TT14065 (Oxygen)
SB  - IM
MH  - *Computer Simulation
MH  - Copper/chemistry
MH  - Crystallography, X-Ray
MH  - Electron Transport Complex IV/*chemistry
MH  - Hydrogen Bonding
MH  - Iron/chemistry
MH  - *Models, Molecular
MH  - Oxygen/chemistry
MH  - *Quantum Theory
MH  - Thermus thermophilus/*enzymology
MH  - Water/chemistry
PMC - PMC3925067
MID - NIHMS543660
EDAT- 2013/11/23 06:00
MHDA- 2014/07/24 06:00
PMCR- 2014/12/16
CRDT- 2013/11/23 06:00
PHST- 2013/11/23 06:00 [entrez]
PHST- 2013/11/23 06:00 [pubmed]
PHST- 2014/07/24 06:00 [medline]
PHST- 2014/12/16 00:00 [pmc-release]
AID - 10.1021/ic401858s [doi]
PST - ppublish
SO  - Inorg Chem. 2013 Dec 16;52(24):14072-88. doi: 10.1021/ic401858s. Epub 2013 Nov 
      21.