Linked Life Data

17596847

Source:http://linkedlifedata.com/resource/pubmed/id/17596847

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2007-8-28
pubmed:abstractText
We develop a mixed elastic network model (MENM) to study large-scale conformational transitions of proteins between two (or more) known structures. Elastic network potentials for the beginning and end states of a transition are combined, in effect, by adding their respective partition functions. The resulting effective MENM energy function smoothly interpolates between the original surfaces, and retains the beginning and end structures as local minima. Saddle points, transition paths, potentials of mean force, and partition functions can be found efficiently by largely analytic methods. To characterize the protein motions during a conformational transition, we follow "transition paths" on the MENM surface that connect the beginning and end structures and are invariant to parameterizations of the model and the mathematical form of the mixing scheme. As illustrations of the general formalism, we study large-scale conformation changes of the motor proteins KIF1A kinesin and myosin II. We generate possible transition paths for these two proteins that reveal details of their conformational motions. The MENM formalism is computationally efficient and generally applicable even for large protein systems that undergo highly collective structural changes.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Oct
pubmed:issn
1097-0134
pubmed:author
pubmed:copyrightInfo
2007 Wiley-Liss, Inc.
pubmed:issnType
Electronic
pubmed:day
1
pubmed:volume
69
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
43-57
pubmed:meshHeading
pubmed:year
2007
pubmed:articleTitle
Protein conformational transitions explored by mixed elastic network models.
pubmed:affiliation
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Extramural, Research Support, N.I.H., Intramural