Literature DB >> 9876123

Comparison of the crystal and solution structures of two RNA oligonucleotides.

J P Rife1, S C Stallings, C C Correll, A Dallas, T A Steitz, P B Moore.   

Abstract

Until recently, there were no examples of RNAs whose structures had been determined by both NMR and x-ray crystallography, and thus there was no experimental basis for assessing the accuracy of RNA solution structures. A comparison of the solution and the crystal structures of two RNAs is presented, which demonstrates that NMR can produce solution structures that resemble crystal structures and thus validates the application to RNA of a methodology developed initially for the determination of protein conformations. Models for RNA solution structures are appreciably affected by the parameters used for their refinement that describe intramolecular interactions. For the RNAs of interest here, the more realistic those parameters, the greater the similarity between solution structures and crystal structures.

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Year:  1999        PMID: 9876123      PMCID: PMC1302500          DOI: 10.1016/S0006-3495(99)77178-X

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  13 in total

1.  NMR analysis of helix I from the 5S RNA of Escherichia coli.

Authors:  S A White; M Nilges; A Huang; A T Brünger; P B Moore
Journal:  Biochemistry       Date:  1992-02-18       Impact factor: 3.162

Review 2.  Protein structure determination in solution by NMR spectroscopy.

Authors:  K Wüthrich
Journal:  J Biol Chem       Date:  1990-12-25       Impact factor: 5.157

3.  Relaxation matrix refinement of the solution structure of squash trypsin inhibitor.

Authors:  M Nilges; J Habazettl; A T Brünger; T A Holak
Journal:  J Mol Biol       Date:  1991-06-05       Impact factor: 5.469

4.  Crystallography & NMR system: A new software suite for macromolecular structure determination.

Authors:  A T Brünger; P D Adams; G M Clore; W L DeLano; P Gros; R W Grosse-Kunstleve; J S Jiang; J Kuszewski; M Nilges; N S Pannu; R J Read; L M Rice; T Simonson; G L Warren
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1998-09-01

5.  Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.

Authors:  C C Correll; B Freeborn; P B Moore; T A Steitz
Journal:  Cell       Date:  1997-11-28       Impact factor: 41.582

6.  On the conformation of the anticodon loops of initiator and elongator methionine tRNAs.

Authors:  D C Schweisguth; P B Moore
Journal:  J Mol Biol       Date:  1997-04-04       Impact factor: 5.469

7.  How accurately and precisely can RNA structure be determined by NMR?

Authors:  F H Allain; G Varani
Journal:  J Mol Biol       Date:  1997-03-28       Impact factor: 5.469

8.  Solution of the phase problem in the X-ray diffraction method for proteins with the nuclear magnetic resonance solution structure as initial model. Patterson search and refinement for the alpha-amylase inhibitor tendamistat.

Authors:  W Braun; O Epp; K Wüthrich; R Huber
Journal:  J Mol Biol       Date:  1989-04-20       Impact factor: 5.469

9.  The sarcin/ricin loop, a modular RNA.

Authors:  A A Szewczak; P B Moore
Journal:  J Mol Biol       Date:  1995-03-17       Impact factor: 5.469

10.  The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins.

Authors:  A Dallas; P B Moore
Journal:  Structure       Date:  1997-12-15       Impact factor: 5.006

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  8 in total

1.  Application of dipolar coupling data to the refinement of the solution structure of the sarcin-ricin loop RNA.

Authors:  J J Warren; P B Moore
Journal:  J Biomol NMR       Date:  2001-08       Impact factor: 2.835

2.  Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation.

Authors:  C Burkhardt; M Zacharias
Journal:  Nucleic Acids Res       Date:  2001-10-01       Impact factor: 16.971

3.  Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution.

Authors:  Carl C Correll; Kerren Swinger
Journal:  RNA       Date:  2003-03       Impact factor: 4.942

4.  The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure.

Authors:  Carl C Correll; Jutta Beneken; Matthew J Plantinga; Melissa Lubbers; Yuen-Ling Chan
Journal:  Nucleic Acids Res       Date:  2003-12-01       Impact factor: 16.971

5.  Residual dipolar coupling constants and structure determination of large DNA duplexes.

Authors:  Olivier Mauffret; Georges Tevanian; Serge Fermandjian
Journal:  J Biomol NMR       Date:  2002-12       Impact factor: 2.835

6.  Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography.

Authors:  Yasuyuki Miyazaki; Rossitza N Irobalieva; Blanton S Tolbert; Adjoa Smalls-Mantey; Kilali Iyalla; Kelsey Loeliger; Victoria D'Souza; Htet Khant; Michael F Schmid; Eric L Garcia; Alice Telesnitsky; Wah Chiu; Michael F Summers
Journal:  J Mol Biol       Date:  2010-10-08       Impact factor: 5.469

7.  Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement.

Authors:  Blanton S Tolbert; Yasuyuki Miyazaki; Shawn Barton; Benyam Kinde; Patrice Starck; Rashmi Singh; Ad Bax; David A Case; Michael F Summers
Journal:  J Biomol NMR       Date:  2010-06-15       Impact factor: 2.835

8.  Molecular dynamics simulations of sarcin-ricin rRNA motif.

Authors:  Nad'a Spacková; Jirí Sponer
Journal:  Nucleic Acids Res       Date:  2006-02-02       Impact factor: 16.971

  8 in total

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