Linked Life Data

9669560

Source:http://linkedlifedata.com/resource/pubmed/id/9669560

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
1998-9-28
pubmed:abstractText
Parallel version of AMBER 4.1 was ported and optimised on the Indian parallel supercomputer PARAM OpenFrame built around Sun Ultra Sparc processors. This version of AMBER program was then used to carry out molecular dynamics (MD) simulations on 5'-TGACCAGCTGGTC-3', a substrate for PvuII enzyme. MD simulations in water are carried out under following conditions: (i) unconstrained at 300 K (230 ps); (ii) unconstrained at 283 K (500 ps); (iii) Watson-Crick basepair constrained at 283 K (1 ns); and (iv) Watson-Crick basepair constrained with ions at 283 K (1.2 ns). In all these simulation studies, the molecule was observed to be bending and maximum distortions in the double helix around was seen around the G7:C7' basepair, which is the phosphodiester bond that is cleaved by PvuII. Analysis of MD simulation with ions carried out for 1.2 ns also pointed out that the conformation of double helix alternates between a conformation close to B-form and close to A-form. It is argued that a bent non-standard conformation is recognised by the PvuII enzyme. The maximum bend occurs at the G7:C7' region, weakening the phosphodiester bond and allows His48 to get placed in such a fashion to permit the scission through a general base mechanism. The bending and distortion observed is a property of the sequence which acts as a substrate for PvuII enzyme. This is confirmed by carrying out MD studies on the Dickerson's sequence d(CGCGAATTCGCG)2 as a reference molecule, which practically does not bend or get deformed.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
0739-1102
pubmed:author
pubmed:issnType
Print
pubmed:volume
15
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1155-65
pubmed:dateRevised
2008-8-19
pubmed:meshHeading
pubmed:year
1998
pubmed:articleTitle
Molecular dynamics simulation of a 13-mer duplex DNA: a PvuII substrate.
pubmed:affiliation
Bioinformatics Centre, University of Pune, Ganeshkind, India. kolaskar@bioinfo.ernet.in
pubmed:publicationType
Journal Article