PMID- 31566371
OWN - NLM
STAT- MEDLINE
DCOM- 20191120
LR  - 20231019
IS  - 1520-510X (Electronic)
IS  - 0020-1669 (Print)
IS  - 0020-1669 (Linking)
VI  - 58
IP  - 20
DP  - 2019 Oct 21
TI  - DFT Fe(a3)-O/O-O Vibrational Frequency Calculations over Catalytic Reaction Cycle 
      States in the Dinuclear Center of Cytochrome c Oxidase.
PG  - 13933-13944
LID - 10.1021/acs.inorgchem.9b01840 [doi]
AB  - Density functional vibrational frequency calculations have been performed on 
      eight geometry optimized cytochrome c oxidase (CcO) dinuclear center (DNC) 
      reaction cycle intermediates and on the oxymyoglobin (oxyMb) active site. The 
      calculated Fe-O and O-O stretching modes and their frequency shifts along the 
      reaction cycle have been compared with the available resonance Raman (rR) 
      measurements. The calculations support the proposal that in state 
      A[Fe(a3)(3+)-O(2)(-*)...Cu(B)(+)] of CcO, O(2) binds with Fe(a3)(2+) in a similar 
      bent end-on geometry to that in oxyMb. The calculations show that the observed 20 
      cm(-1) shift of the Fe(a3)-O stretching mode from the P(R) to F state is caused 
      by the protonation of the OH(-) ligand on Cu(B)(2+) 
      (P(R)[Fe(a3)(4+) horizontal lineO(2-)...HO(-)-Cu(B)(2+)] --> 
      F[Fe(a3)(4+) horizontal lineO(2-)...H(2)O-Cu(B)(2+)]), and that the H(2)O ligand is still on the 
      Cu(B)(2+) site in the rR identified F[Fe(a3)(4+) horizontal lineO(2-)...H(2)O-Cu(B)(2+)] state. 
      Further, the observed rR band at 356 cm(-1) between states P(R) and F is likely 
      an O-Fe(a3)-porphyrin bending mode. The observed 450 cm(-1) low Fe(a3)-O 
      frequency mode for the O(H) active oxidized state has been reproduced by our 
      calculations on a nearly symmetrically bridged Fe(a3)(3+)-OH-Cu(B)(2+) structure 
      with a relatively long Fe(a3)-O distance near 2 A. Based on Badger's rule, the 
      calculated Fe(a3)-O distances correlate well with the calculated nu(Fe-O)(-2/3) 
      (nu(Fe-O) is the Fe(a3)-O stretching frequency) with correlation coefficient R = 
      0.973.
FAU - Du, Wen-Ge Han
AU  - Du WH
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 - 20190930
PL  - United States
TA  - Inorg Chem
JT  - Inorganic chemistry
JID - 0366543
RN  - 0 (Ligands)
RN  - E1UOL152H7 (Iron)
RN  - EC 1.9.3.1 (Electron Transport Complex IV)
RN  - S88TT14065 (Oxygen)
SB  - IM
MH  - Biocatalysis
MH  - Catalytic Domain
MH  - Crystallography, X-Ray
MH  - *Density Functional Theory
MH  - Electron Transport Complex IV/chemistry/*metabolism
MH  - Iron/*chemistry/metabolism
MH  - Ligands
MH  - Models, Molecular
MH  - Oxygen/*chemistry/metabolism
MH  - Vibration
PMC - PMC6839913
MID - NIHMS1057466
EDAT- 2019/10/01 06:00
MHDA- 2019/11/21 06:00
PMCR- 2020/10/21
CRDT- 2019/10/01 06:00
PHST- 2019/10/01 06:00 [pubmed]
PHST- 2019/11/21 06:00 [medline]
PHST- 2019/10/01 06:00 [entrez]
PHST- 2020/10/21 00:00 [pmc-release]
AID - 10.1021/acs.inorgchem.9b01840 [doi]
PST - ppublish
SO  - Inorg Chem. 2019 Oct 21;58(20):13933-13944. doi: 10.1021/acs.inorgchem.9b01840. 
      Epub 2019 Sep 30.