PMID- 29308889
OWN - NLM
STAT- MEDLINE
DCOM- 20180320
LR  - 20190205
IS  - 1520-510X (Electronic)
IS  - 0020-1669 (Print)
IS  - 0020-1669 (Linking)
VI  - 57
IP  - 3
DP  - 2018 Feb 5
TI  - A Water Dimer Shift Activates a Proton Pumping Pathway in the P(R) --> F Transition 
      of ba(3) Cytochrome c Oxidase.
PG  - 1048-1059
LID - 10.1021/acs.inorgchem.7b02461 [doi]
AB  - Broken-symmetry density functional calculations have been performed on the 
      [Fe(a3)(4+),Cu(B)(2+)] state of the dinuclear center (DNC) for the P(R) --> F part 
      of the catalytic cycle of ba(3) cytochrome c oxidase (CcO) from Thermus 
      thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that 
      the movement of the H(2)O molecules in the DNC affects the pK(a) values of the 
      residue side chains of Tyr237 and His376(+), which are crucial for proton 
      transfer/pumping in ba(3) CcO from Tt. The calculated lowest energy structure of 
      the DNC in the [Fe(a3)(4+),Cu(B)(2+)] state (state F) is of the form 
      Fe(a3)(4+) horizontal lineO(2-)...Cu(B)(2+), in which the H(2)O ligand that resulted from 
      protonation of the OH(-) ligand in the P(R) state is dissociated from the 
      Cu(B)(2+) site. The calculated Fe(a3)(4+) horizontal lineO(2-) distance in F (1.68 A) is 0.03 A 
      longer than that in P(R) (1.65 A), which can explain the different 
      Fe(a3)(4+) horizontal lineO(2-) stretching modes in P (804 cm(-1)) and F (785 cm(-1)) identified 
      by resonance Raman experiments. In this F state, the Cu(B)(2+)...O(2-) 
      (ferryl-oxygen) distance is only around 2.4 A. Hence, the subsequent O(H) state 
      [Fe(a3)(3+)-OH(-)-Cu(B)(2+)] with a mu-hydroxo bridge can be easily formed, as 
      shown by our calculations.
FAU - Han Du, Wen-Ge
AU  - Han Du WG
AUID- ORCID: 0000-0001-5876-1943
AD  - Department of Integrative Structural and Computational Biology, The Scripps 
      Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, 
      United States.
FAU - Gotz, Andreas W
AU  - Gotz AW
AUID- ORCID: 0000-0002-8048-6906
AD  - San Diego Supercomputer Center, University of California San Diego , 9500 Gilman 
      Drive MC0505, La Jolla, California 92093, United States.
FAU - Noodleman, Louis
AU  - Noodleman L
AUID- ORCID: 0000-0001-8176-4448
AD  - Department of Integrative Structural and Computational Biology, The Scripps 
      Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, 
      United States.
LA  - eng
GR  - R01 GM100934/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20180108
PL  - United States
TA  - Inorg Chem
JT  - Inorganic chemistry
JID - 0366543
RN  - 0 (Organometallic Compounds)
RN  - 0 (Proton Pumps)
RN  - 059QF0KO0R (Water)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
SB  - IM
MH  - Biocatalysis
MH  - Dimerization
MH  - Electron Transport Complex IV/chemistry/*metabolism
MH  - Models, Molecular
MH  - Molecular Conformation
MH  - Organometallic Compounds/chemistry/*metabolism
MH  - Proton Pumps/*metabolism
MH  - Thermus thermophilus/enzymology
MH  - Water/chemistry/*metabolism
PMC - PMC5825212
MID - NIHMS942401
EDAT- 2018/01/09 06:00
MHDA- 2018/03/21 06:00
PMCR- 2019/02/05
CRDT- 2018/01/09 06:00
PHST- 2018/01/09 06:00 [pubmed]
PHST- 2018/03/21 06:00 [medline]
PHST- 2018/01/09 06:00 [entrez]
PHST- 2019/02/05 00:00 [pmc-release]
AID - 10.1021/acs.inorgchem.7b02461 [doi]
PST - ppublish
SO  - Inorg Chem. 2018 Feb 5;57(3):1048-1059. doi: 10.1021/acs.inorgchem.7b02461. Epub 
      2018 Jan 8.