Linked Life Data

16139299

Source:http://linkedlifedata.com/resource/pubmed/id/16139299

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
4
pubmed:dateCreated
2005-9-13
pubmed:abstractText
The plastic network model (PNM) is used to generate a conformational change pathway for Escherichia coli adenylate kinase based on two crystal structures, namely that of an open and a closed conformer. In this model, the energy basins corresponding to known conformers are connected at their lowest common energies. The results are used to evaluate and analyze the minimal energy pathways between these basins. The open to closed transition analysis provides an identification of hinges that is in agreement with the existing definitions based on the available X-ray structures. The elastic energy distribution and the C(alpha) pseudo-dihedral variation provide similar information on these hinges. The ensemble of the 45 published structures for this protein and closely related proteins is shown to always be within 3.0 A of the pathway, which corresponds to a conformational change between two end structures that differ by a C(alpha)-atom root-mean-squared deviation of 7.1A.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
30
pubmed:volume
352
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
807-22
pubmed:dateRevised
2007-11-15
pubmed:meshHeading
pubmed:year
2005
pubmed:articleTitle
Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase.
pubmed:affiliation
Department of Chemistry and Chemical Biology, Harvard University, Cambridge MA 02138, USA. maragakis@cmt.harvard.edu
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural