Linked Life Data

12421565

Source:http://linkedlifedata.com/resource/pubmed/id/12421565

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2002-11-7
pubmed:abstractText
We present a method for determining the structure of the transition state ensemble (TSE) of a protein by using phi values derived from protein engineering experiments as restraints in molecular dynamics simulations employing a realistic all-atom molecular mechanics energy function. The method uses a biasing potential to select an ensemble of structures having phi values in agreement with the experimental data set. An application to acylphosphatase (AcP), a protein for which phi values have been measured for 24 out of 98 residues, illustrates the approach. The properties of the TSE determined in this way are compared with those of a coarse-grained model obtained using a Monte Carlo (MC) sampling method based on a C(alpha) representation of the structure. The two TSEs determined at different structural resolution are consistent and complementary. While the C(alpha) model allows better sampling of the conformation space occupied by the transition state, the all-atom model offers a more detailed description of the structural and energetic properties of the conformations included in the TSE. The combination of low-resolution C(alpha) results with all-atom molecular dynamics simulations provides a powerful and general method for determining the nature of TSEs from protein engineering data.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Nov
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
15
pubmed:volume
324
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
151-63
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Determination of a transition state at atomic resolution from protein engineering data.
pubmed:affiliation
Laboratoire de Chimie Biophysique ISIS, Université Louis Pasteur, 4 rue Blaise Pascal, 67000 Strasbourg, France.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't