Linked Life Data

19761222

Source:http://linkedlifedata.com/resource/pubmed/id/19761222

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
41
pubmed:dateCreated
2009-10-8
pubmed:abstractText
Extradiol dioxygenases are characterized by activating dioxygen and incorporating both oxygen atoms into their substrates. Both experimental and theoretical investigations have been focused on the detection of intermediates in the reaction cycle in order to develop a general chemical mechanism of O(2) activation and insertion. However, little is known about the mechanism of how O(2) reaches the reaction sites of the related enzymes, which raises the question whether the rate of catalysis is limited by O(2) access to the active site. In this paper, two locally enhanced sampling molecular dynamics simulations were performed to determine the potential O(2) pathways inside a recently solved X-ray structure of homoprotocatechuate 2,3-dioxygenase. It is found that nominally identical subunits of the single homotetrameric structure contain distinct O(2) affinity diffusion pathways, which partly correlates with the observation of the simultaneous presence of three different reaction intermediates in four independent active sites. Residues that are critical for O(2) diffusion are also examined and discussed. In particular, we find that the breathing motion of the internal cavity defined by these residues results in O(2) migration process.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Oct
pubmed:issn
1520-5207
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
113
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
13596-603
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Locally enhanced sampling study of dioxygen diffusion pathways in homoprotocatechuate 2,3-dioxygenase.
pubmed:affiliation
Department of Engineering Mechanics, State Key Laboratory of Structural Analyses for Industrial Equipment, Dalian University of Technology, Dalian 116023, China.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't