Linked Life Data

1946322

Source:http://linkedlifedata.com/resource/pubmed/id/1946322

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
1991-12-13
pubmed:abstractText
A novel approach for the modeling of coiled coils through molecular dynamics is described and applied to the dimerization region of the yeast transcriptional activator GCN4. Initially, a model is created consisting of C alpha atoms only, representing an idealized coiled coil with infinite pitch. Human bias in the placing of the other atoms is reduced by an automatic building procedure using simulated annealing with simple geometric restraints. The resulting all-atom model is then allowed to relax during a short molecular dynamics run using an empirical energy function and weak restraints which reflect the coiled coil assumption. These models are then further refined using unrestrained molecular dynamics in water. In this report we test the model-building procedure on the known dimerization region of catabolyte gene activator protein (CAP), part of which forms a coiled coil, and we predict the structure of the coiled coil dimerization region (the 'leucine zipper' domain) of GCN4. Several models are built, starting from different arrangements of the C alpha atoms in the initial structures. The final structures show similar crossing angles of the coiled coil, although this was not used as a restraint in the calculation. The leucines adopt a ladder-like conformation around the 2-fold axis of the coiled coil. A number of electrostatic interactions could be identified which may contribute to the stability of the helical structure of the monomers and of the dimer.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
0269-2139
pubmed:author
pubmed:issnType
Print
pubmed:volume
4
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
649-59
pubmed:dateRevised
2009-11-19
pubmed:meshHeading
pubmed:year
1991
pubmed:articleTitle
Automated modeling of coiled coils: application to the GCN4 dimerization region.
pubmed:affiliation
Howard Hughes Medical Institute, New Haven, CT 06511.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't