Linked Life Data

20355287

Source:http://linkedlifedata.com/resource/pubmed/id/20355287

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
14
pubmed:dateCreated
2010-3-31
pubmed:abstractText
Oligoglycine peptides (from two to ten residues) complexed to the sodium ion were studied by quantum chemical and molecular mechanics calculations to understand their structural and energetic properties. Modeling such systems required the use of a polarizable force field and AMOEBA, as developed by Ren and Ponder [J. Comput. Chem., 2002, 23, 1497], was chosen. Some electrostatic and torsional parameters were re-optimized using a rigorous procedure and validated against both geometric and energetic ab initio data in the gas phase. Molecular dynamics simulations were performed on seven sodiated octa-glycine (G(8)) structures. Structural transitions were generally observed (with the notable exception of the a-helix), leading to new structures that were further proved by ab initio calculations to be of low energies. The main result is that for G(8)-Na(+), there is a compromise between sodium peptide interactions and multiple hydrogen bonding. The accuracy achieved with AMOEBA demonstrates the potential of this force field for the realistic modeling of gaseous peptides.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Apr
pubmed:issn
1463-9084
pubmed:author
pubmed:issnType
Electronic
pubmed:day
14
pubmed:volume
12
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
3450-62
pubmed:meshHeading
pubmed:year
2010
pubmed:articleTitle
Structural, energetic and dynamical properties of sodiated oligoglycines: relevance of a polarizable force field.
pubmed:affiliation
Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't