Linked Life Data

11455608

Source:http://linkedlifedata.com/resource/pubmed/id/11455608

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2001-7-16
pubmed:abstractText
An intermediate-resolution model of small, homogeneous peptides is introduced, and discontinuous molecular dynamics simulation is applied to study secondary structure formation. Physically, each model residue consists of a detailed three-bead backbone and a simplified single-bead side-chain. Excluded volume and hydrogen bond interactions are constructed with discontinuous (i.e., hard-sphere and square-well) potentials. Simulation results show that the backbone motion of the model is limited to realistic regions of Phi-Psi conformational space. Model polyalanine chains undergo a locally cooperative transition to form alpha-helices that are stabilized by backbone hydrogen bonding, while model polyglycine chains tend to adopt nonhelical structures. When side-chain size is increased beyond a critical diameter, steric interactions prevent formation of long alpha-helices. These trends in helicity as a function of residue type have been well documented by experimental, theoretical, and simulation studies and demonstrate the ability of the intermediate-resolution model developed in this work to accurately mimic realistic peptide behavior. The efficient algorithm used permits observation of the complete helix-coil transition within 15 min on a single-processor workstation, suggesting that simulations of very long times are possible with this model.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
0887-3585
pubmed:author
pubmed:issnType
Print
pubmed:day
15
pubmed:volume
44
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
344-60
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2001
pubmed:articleTitle
alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model.
pubmed:affiliation
Department of Chemical Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, U.S. Gov't, Non-P.H.S.