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Titolo:
Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex
Autore:
Schneider, C; Brandl, M; Suhnel, J;
Indirizzi:
Inst Mol Biotechnol, D-07708 Jena, Germany Inst Mol Biotechnol Jena Germany D-07708 otechnol, D-07708 Jena, Germany
Titolo Testata:
JOURNAL OF MOLECULAR BIOLOGY
fascicolo: 4, volume: 305, anno: 2001,
pagine: 659 - 667
SICI:
0022-2836(20010126)305:4<659:MDSRCS>2.0.ZU;2-H
Fonte:
ISI
Lingua:
ENG
Soggetto:
5S RIBOSOMAL-RNA; DOUBLE HELIX; CRYSTAL-STRUCTURE; NUCLEIC-ACIDS; B-DNA; SYNTHETASE; TRANSITION; TETRALOOP; PROTEINS; NMR;
Keywords:
molecular dynamics; RNA; water-mediated base-pair; conformational switch;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
29
Recensione:
Indirizzi per estratti:
Indirizzo: Suhnel, J Inst Mol Biotechnol, Postfach 100813, D-07708 Jena, Germany InstMol Biotechnol Postfach 100813 Jena Germany D-07708 ermany
Citazione:
C. Schneider et al., "Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex", J MOL BIOL, 305(4), 2001, pp. 659-667

Abstract

A 4 ns molecular dynamics simulation of an RNA duplex (r-GGACUUCGGUCC)(2) in solution with Na+ and Cl- as counterions was performed. The X-ray structure of this duplex includes two water-mediated uracil-cytosine pairs. In contrast to the other base-pairs in the duplex the water-mediated pairs switch between different conformations. One conformation corresponds to the geometry of the water-mediated UC pairs in the duplex X-ray structure with water acting both as hydrogen-bond donor and acceptor. Another conformation is close to that of a water-mediated UC base-pair found in the X-ray structureof the 23 S rRNA sarcin/ricin domain. Ln this case the oxygen of the watermolecule is linked to two-base donor sites. For a very short time also a direct UC base-pair and a further conformation that is similar to the one found in the RNA duplex structure but exhibits an increased H3(U)...N3(C) distance is observed. Water molecules with unusually long residence times are involved in the water-mediated conformations. These results indicate that the dynamic behaviour of the water-mediated UC base-pairs differs from that of the duplex Watson-Crick and non-canonical guanine-uracil pairs with two or three direct hydrogen bonds. The conformational variability and increased flexibility has to be taken into account when considering these base-pairs as RNA building blocks and as recognition motifs. (C) 2001 Academic Press.

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Documento generato il 01/12/20 alle ore 01:08:45