Document Detail


Ribosomal dynamics inferred from variations in experimental measurements.
MedLine Citation:
PMID:  14561879     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The crystal structures of the ribosome reveal remarkable complexity and provide a starting set of snapshots with which to understand the dynamics of translation. To augment the static crystallographic models with dynamic information present in crosslink, footprint, and cleavage data, we examined 2691 proximity measurements and focused on the subset that was apparently incompatible with >40 published crystal structures. The measurements from this subset generally involve regions of the structure that are functionally conserved and structurally flexible. Local movements in the crystallographic states of the ribosome that would satisfy biochemical proximity measurements show coherent patterns suggesting alternative conformations of the ribosome. Three different types of data obtained for the two subunits display similar "mismatching" patterns, suggesting that the signals are robust and real. In particular, there is an indication of coherent motion in the decoding region within the 30S subunit and central protuberance and surrounding areas of the 50S subunit. Directions of rearrangements fluctuate around the proposed path of tRNA translocation and the plane parallel to the interface of the two subunits. Our results demonstrate that systematic combination and analysis of noisy, apparently incompatible data sources can provide biologically useful signals about structural dynamics.
Authors:
Irene S Gabashvili; Michelle Whirl-Carrillo; Michael Bada; D Rey Banatao; Russ B Altman
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  RNA (New York, N.Y.)     Volume:  9     ISSN:  1355-8382     ISO Abbreviation:  RNA     Publication Date:  2003 Nov 
Date Detail:
Created Date:  2003-10-16     Completed Date:  2003-12-24     Revised Date:  2013-06-09    
Medline Journal Info:
Nlm Unique ID:  9509184     Medline TA:  RNA     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1301-7     Citation Subset:  IM    
Affiliation:
Department of Genetics and Section on Medical Informatics, Stanford University, Stanford, California 94305-5479, USA.
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MeSH Terms
Descriptor/Qualifier:
Crystallography, X-Ray
Models, Molecular
Nucleic Acid Conformation
RNA, Ribosomal / chemistry*
Ribosomes / chemistry*
Grant Support
ID/Acronym/Agency:
GM-08294/GM/NIGMS NIH HHS; HG11223/HG/NHGRI NIH HHS; LM-05652/LM/NLM NIH HHS; LM-06422/LM/NLM NIH HHS
Chemical
Reg. No./Substance:
0/RNA, Ribosomal
Comments/Corrections

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


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