Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
1997-1-9
pubmed:abstractText
Multiple molecular dynamics trajectories of the solvated and neutralized 17-residue tRNA(Asp) anticodon hairpin were generated for a total of 3 ns. Explicit treatment of all long-ranged electrostatic interactions by the particle mesh Ewald algorithm, as implemented in the AMBER MD software package, effected a degree of structural stabilization not previously achieved by use of a long 16-A solvent interaction truncation scheme. The increased stability of this multiple molecular dynamics set was appropriate for an in-depth analysis of the six 500-ps-long trajectories and allowed the characterization of a number of key structural interactions. The dynamical behavior of the standard Watson-Crick base pairs, the noncanonical G30-U40 "wobble" base pair, and the psi 32-C38 pseudo-base pair is presented as well as that of two C--H... O hydrogen bonds found to contribute to the array of tertiary interactions that stabilize the seven-nucleotide native loop conformation. The least mobile residue in the loop is U33, which forms the U-turn motif and which participates in several hydrogen-bonding interactions, whereas the most mobile residue is the apical residue G34 at the wobble position, a factor undoubtedly important in its biological function. The set of multiple molecular dynamics trajectories obtained does not converge on a 500-ps time scale to a unique dynamical model but instead describes an ensemble of structural microstates accessible to the system under the present simulation protocol, which is the result of local structural heterogeneity rather than of global conformational changes.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-1384741, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-1469723, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-15299313, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-1551395, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-1610828, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-1696688, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-2047877, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-2156233, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-2163670, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-2299668, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-3513167, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-3856228, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-3897553, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-3907691, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-7521533, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-7541315, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-7608979, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-7674305, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-7707368, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-790568, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-7969422, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-8415632, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-8548450, http://linkedlifedata.com/resource/pubmed/commentcorrection/8842234-8804831
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
0006-3495
pubmed:author
pubmed:issnType
Print
pubmed:volume
71
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
940-54
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
1996
pubmed:articleTitle
H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations.
pubmed:affiliation
Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, Strasbourg, France.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't