Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs - PubMed (original) (raw)
Computer modeling from solution data of spinach chloroplast and of Xenopus laevis somatic and oocyte 5 S rRNAs
E Westhof et al. J Mol Biol. 1989.
Abstract
Detailed atomic models of a eubacterial 5 S rRNA (spinach chloroplast 5 S rRNA) and of a eukaryotic 5 S rRNA (somatic and oocyte 5 S rRNA from Xenopus laevis) were built using computer graphic. Both models integrate stereochemical constraints and experimental data on the accessibility of bases and phosphates towards several structure-specific probes. The base sequence was first inserted on to three-dimensional structural fragments picked up in a specially devised databank. The fragments were modified and assembled interactively on an Evans & Sutherland PS330. Modeling was finalized by stereochemical and energy refinement. In spite of some uncertainty in the relative spatial orientation of the substructures, the broad features of the models can be generalized and several conclusions can be reached: (1) both models adopt a distorted Y-shape structure, with helices B and D not far from colinearity; (2) no tertiary interactions exist between loop c and region d or loop e; (3) the internal loops, in particular region d, contain several non-canonical base-pairs of A.A, U.U and A.G types; (4) invariant residues appear to be more important for protein or RNA binding than for maintaining the tertiary structure. The models are corroborated by footprinting experiments with ribosomal proteins and by the analysis of various mutants. Such models help to clarify the structure-function relationship of 5 S rRNA and are useful for designing site-directed mutagenesis experiments.
Similar articles
- Three-dimensional model of Escherichia coli ribosomal 5 S RNA as deduced from structure probing in solution and computer modeling.
Brunel C, Romby P, Westhof E, Ehresmann C, Ehresmann B. Brunel C, et al. J Mol Biol. 1991 Sep 5;221(1):293-308. doi: 10.1016/0022-2836(91)80220-o. J Mol Biol. 1991. PMID: 1717695 - A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNAs of Xenopus laevis.
Romaniuk PJ, de Stevenson IL, Ehresmann C, Romby P, Ehresmann B. Romaniuk PJ, et al. Nucleic Acids Res. 1988 Mar 25;16(5):2295-312. doi: 10.1093/nar/16.5.2295. Nucleic Acids Res. 1988. PMID: 3357778 Free PMC article. - Effect of mutations in domain 2 on the structural organization of oocyte 5 S rRNA from Xenopus laevis.
Brunel C, Romby P, Westhof E, Romaniuk PJ, Ehresmann B, Ehresmann C. Brunel C, et al. J Mol Biol. 1990 Sep 5;215(1):103-11. doi: 10.1016/S0022-2836(05)80099-3. J Mol Biol. 1990. PMID: 2398495 - Structural studies on site-directed mutants of domain 3 of Xenopus laevis oocyte 5 S ribosomal RNA.
de Stevenson IL, Romby P, Baudin F, Brunel C, Westhof E, Ehresmann C, Ehresmann B, Romaniuk PJ. de Stevenson IL, et al. J Mol Biol. 1991 May 20;219(2):243-55. doi: 10.1016/0022-2836(91)90565-n. J Mol Biol. 1991. PMID: 2038056 - Involvement of "hinge" nucleotides of Xenopus laevis 5 S rRNA in the RNA structural organization and in the binding of transcription factor TFIIIA.
Baudin F, Romaniuk PJ, Romby P, Brunel C, Westhof E, Ehresmann B, Ehresmann C. Baudin F, et al. J Mol Biol. 1991 Mar 5;218(1):69-81. doi: 10.1016/0022-2836(91)90874-6. J Mol Biol. 1991. PMID: 2002508
Cited by
- Mitochondrial enzyme rhodanese is essential for 5 S ribosomal RNA import into human mitochondria.
Smirnov A, Comte C, Mager-Heckel AM, Addis V, Krasheninnikov IA, Martin RP, Entelis N, Tarassov I. Smirnov A, et al. J Biol Chem. 2010 Oct 1;285(40):30792-803. doi: 10.1074/jbc.M110.151183. Epub 2010 Jul 27. J Biol Chem. 2010. PMID: 20663881 Free PMC article. - Evolution of compensatory substitutions through G.U intermediate state in Drosophila rRNA.
Rousset F, Pélandakis M, Solignac M. Rousset F, et al. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10032-6. doi: 10.1073/pnas.88.22.10032. Proc Natl Acad Sci U S A. 1991. PMID: 1946420 Free PMC article. - Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli.
Westhof E, Altman S. Westhof E, et al. Proc Natl Acad Sci U S A. 1994 May 24;91(11):5133-7. doi: 10.1073/pnas.91.11.5133. Proc Natl Acad Sci U S A. 1994. PMID: 7515186 Free PMC article. - Stabilities of intrastrand pyrimidine motif DNA and RNA triple helices.
Hoyne PR, Gacy AM, McMurray CT, Maher LJ 3rd. Hoyne PR, et al. Nucleic Acids Res. 2000 Feb 1;28(3):770-5. doi: 10.1093/nar/28.3.770. Nucleic Acids Res. 2000. PMID: 10637329 Free PMC article. - Binding of TFIIIA to derivatives of 5S RNA containing sequence substitutions or deletions defines a minimal TFIIIA binding site.
Bogenhagen DF, Sands MS. Bogenhagen DF, et al. Nucleic Acids Res. 1992 Jun 11;20(11):2639-45. doi: 10.1093/nar/20.11.2639. Nucleic Acids Res. 1992. PMID: 1614850 Free PMC article.