Document Detail


Computer modeling 16 S ribosomal RNA.
MedLine Citation:
PMID:  1942035     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A three-dimensional structure for 16 S RNA has been produced with a computer protocol that is not dependent on human intervention. This protocol improves upon traditional modeling techniques by using distance geometry to fold the molecule in an objective and reproducible fashion. The method is based on the secondary structure of RNA and treats the molecule as a set of double-stranded helices that are linked by flexible single-strands of variable length. Data derived from chemical cross-linking studies of 16 S RNA and tertiary phylogenetic relationships provide the constraints used to fold the molecule into a compact three-dimensional form. Possibly subjective evaluation of the input data are transformed into verifiable quantitative parameters. Relationships based on general locations within the 30 S subunit or on protein-RNA interactions have been specifically excluded. The resolution of the model exceeds that of electron micrographs and approaches that obtained in preliminary X-ray crystal structures. The model size of 245 x 190 x 140 A is compatible with that of the 30 S subunit as determined by electron microscopy. The volume of the model is 1.87 x 10(6) A which is similar to that of the small subunit in a preliminary X-ray crystal structure. The radius of gyration of the model structure of 76 A is intermediate to that seen for partially denatured and fully folded 16 S RNA. Computer graphics are used to display the results in a manner that maximizes the opportunities for human visual interpretation of the models. A format for displaying the structures has been developed that will make it possible for researchers who have not devoted themselves to ribosomal modeling to comprehend and make use of the information that the models embody. On this basis the computer-generated models are compared with models developed by other researchers and with structural data not included in the folding parameter data set.
Authors:
J M Hubbard; J E Hearst
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Journal of molecular biology     Volume:  221     ISSN:  0022-2836     ISO Abbreviation:  J. Mol. Biol.     Publication Date:  1991 Oct 
Date Detail:
Created Date:  1991-11-27     Completed Date:  1991-11-27     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  2985088R     Medline TA:  J Mol Biol     Country:  ENGLAND    
Other Details:
Languages:  eng     Pagination:  889-907     Citation Subset:  IM    
Affiliation:
Department of Chemistry, University of California, Berkeley 94720.
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MeSH Terms
Descriptor/Qualifier:
Base Sequence
Computer Simulation*
Cross-Linking Reagents
Escherichia coli / genetics
Models, Molecular
Molecular Sequence Data
Nucleic Acid Conformation
RNA, Ribosomal, 16S / chemistry*
Chemical
Reg. No./Substance:
0/Cross-Linking Reagents; 0/RNA, Ribosomal, 16S

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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