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Literature DB >> 8415714

Reproducing the three-dimensional structure of a tRNA molecule from structural constraints.

Abstract

The three-dimensional structure of yeast tRNA(Phe) was reproduced at atomic resolution with the automated RNA modeling program MC-SYM, which is based on a constraint-satisfaction algorithm. Structural constraints used in the modeling were derived from the secondary structure, four tertiary base pairs, and other information available prior to the determination of the x-ray crystal structure of the tRNA. The program generated 26 solutions (models), all of which had the familiar "L" form of tRNA and root-mean-square deviations from the crystal structure in the range of 3.1-3.8 A. The interaction between uridine-8 and adenosine-14 was crucial in the modeling procedure, since only this among the tertiary pairs is necessary and sufficient to reproduce the L form of tRNA. Other tertiary interactions were critical in reducing the number of solutions proposed by the program.

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Year: 1993 PMID： 8415714 PMCID： PMC47577 DOI： 10.1073/pnas.90.20.9408

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

13 in total

1. A note on crystal packing and global helix structure in short A-DNA duplexes.

Authors: U Heinemann
Journal: J Biomol Struct Dyn Date: 1991-02

2. Predicting the three-dimensional folding of transfer RNA with a computer modeling protocol.

Authors: J M Hubbard; J E Hearst
Journal: Biochemistry Date: 1991-06-04 Impact factor: 3.162

3. The combination of symbolic and numerical computation for three-dimensional modeling of RNA.

Authors: F Major; M Turcotte; D Gautheret; G Lapalme; E Fillion; R Cedergren
Journal: Science Date: 1991-09-13 Impact factor: 47.728

4. Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets.

Authors: D Gautheret; F Major; R Cedergren
Journal: J Mol Biol Date: 1993-02-20 Impact factor: 5.469

5. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.

Authors: E Westhof; P Dumas; D Moras
Journal: Acta Crystallogr A Date: 1988-03-01 Impact factor: 2.290

6. Detailed molecular model for transfer ribonucleic acid.

Authors: M Levitt
Journal: Nature Date: 1969-11-22 Impact factor: 49.962

7. Molecular model for transfer RNA.

Authors: J Ninio; A Favre; M Yaniv
Journal: Nature Date: 1969-09-27 Impact factor: 49.962

8. Crystal structure of yeast tRNAAsp.

Authors: D Moras; M B Comarmond; J Fischer; R Weiss; J C Thierry; J P Ebel; R Giegé
Journal: Nature Date: 1980-12-25 Impact factor: 49.962

9. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles.

Authors: G J Quigley; N C Seeman; A H Wang; F L Suddath; A Rich
Journal: Nucleic Acids Res Date: 1975-12 Impact factor: 16.971

10. Temperature jump relaxation studies on the interactions between transfer RNAs with complementary anticodons. The effect of modified bases adjacent to the anticodon triplet.

Authors: C Houssier; H Grosjean
Journal: J Biomol Struct Dyn Date: 1985-10

23 in total

1. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.

Authors: Christian Marck; Henri Grosjean
Journal: RNA Date: 2002-10 Impact factor: 4.942

2. Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances.

Authors: Christophe Pakleza; Jean A H Cognet
Journal: Nucleic Acids Res Date: 2003-02-01 Impact factor: 16.971

Reproducing the three-dimensional structure of a tRNA molecule from structural constraints.

1. A note on crystal packing and global helix structure in short A-DNA duplexes.

2. Predicting the three-dimensional folding of transfer RNA with a computer modeling protocol.

3. The combination of symbolic and numerical computation for three-dimensional modeling of RNA.

4. Modeling the three-dimensional structure of RNA using discrete nucleotide conformational sets.

5. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals.

6. Detailed molecular model for transfer ribonucleic acid.

7. Molecular model for transfer RNA.

8. Crystal structure of yeast tRNAAsp.

9. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles.

10. Temperature jump relaxation studies on the interactions between transfer RNAs with complementary anticodons. The effect of modified bases adjacent to the anticodon triplet.

1. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.

2. Biopolymer Chain Elasticity: A novel concept and a least deformation energy principle predicts backbone and overall folding of DNA TTT hairpins in agreement with NMR distances.

3. Turning limited experimental information into 3D models of RNA.

4. Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons.

5. Constancy of organellar genome copy numbers during leaf development and senescence in higher plants.

6. MS3D structural elucidation of the HIV-1 packaging signal.

7. Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

8. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.

9. Predicting RNA structure by multiple template homology modeling.

10. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.