Linked Life Data

16245262

Source:http://linkedlifedata.com/resource/pubmed/id/16245262

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2006-1-23
pubmed:abstractText
We present a minimalist approach for the modeling of the three-dimensional structure of multistranded alpha-helical coiled coils. The approach is based on empirical principles introduced by F. H. C. Crick (F. H. C. Crick, Acta Crystallogr, 1953, Vol. 6, pp. 689-697). Crick hypothesized that keeping the distance between the residues at the interacting interface of alpha-helices constant would lead to supercoiling or the formation of a coiled coil through the knobs-into-holes mode of packing. We have implemented the latter hypothesis in a simulating annealing protocol in the simple form of interhelical distance restraints (two per heptad) between Calpha at the interfacial positions and. To demonstrate the authenticity of Crick's hypothesis and the precision and accuracy of our approach, we have modeled the crystal structures of six synthetic coiled coils in dimeric, trimeric, and tetrameric states. The mean root mean square deviations (RMSDs) between the backbone atoms of the ensemble of structures calculated and those of the corresponding geometric averages is always below 0.76 A, indicating that our protocol has an excellent degree of convergence and precision. The RMSDs between the backbone atoms of each of the six geometric average structures and the backbone of the corresponding crystal structures all range between 0.43 and 0.95 A, indicative of excellent accuracy and proving the authenticity of Crick's hypothesis. Moreover, without specifying any dihedral angles, we found that in 81% of the occurrences, the most populated conformer of the side chains at positions and in the ensembles calculated were identical to those observed in the crystal structures. This shows that our simple approach, which is the simplest reported so far, can generate accurate results for the backbone and side chains. Finally, as a test case for a wider application of our approach in the field of structural proteomics, we describe the successful modeling of the overall structure of SNARE and the organization of its interfacial ionic layer known to play an important functional role.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
0006-3525
pubmed:author
pubmed:copyrightInfo
Copyright (c) 2005 Wiley Periodicals, Inc.
pubmed:issnType
Print
pubmed:day
15
pubmed:volume
81
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
202-14
pubmed:dateRevised
2006-11-15
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Simple and versatile restraints for the accurate modeling of alpha-helical coiled-coil structures of multiple strandedness, orientation and composition.
pubmed:affiliation
Département de Pharmacologie, Faculté de Médecine, Université de Sherbrooke 3001, 12e Avenue Nord, Sherbrooke, Qc J1H 5N4, Canada.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't