Linked Life Data

17149487

Source:http://linkedlifedata.com/resource/pubmed/id/17149487

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
48
pubmed:dateCreated
2006-12-6
pubmed:abstractText
The effect of hydrogen bonding to the primary quinone (Q(A) and Q(*)(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q(*)(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Dec
pubmed:issn
1463-9076
pubmed:author
pubmed:issnType
Print
pubmed:day
28
pubmed:volume
8
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
5659-70
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Protein-cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study.
pubmed:affiliation
Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't