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Comparison of tRNA Motions in the Free and Ribosomal Bound Structures

Authors :
Wang, Yongmei
Jernigan, Robert L.
Source :
Biophysical Journal; November 2005, Vol. 89 Issue: 5 p3399-3409, 11p
Publication Year :
2005

Abstract

A general method is presented that allows the separation of the rigid body motions from the nonrigid body motions of structural subunits when bound in a complex. The application presented considers the motions of the tRNAs: free, bound to the ribosome and to a synthase. We observe that both the rigid body and nonrigid body motions of the structural subunits are highly controlled by the large ribosomal assembly and are important for the functional motions of the assembly. For the intact ribosome, its major parts, the 30S and the 50S subunits, are found to have counterrotational motions in the first few slowest modes, which are consistent with the experimentally observed ratchet motion. The tRNAs are found to have on average ∼72–75% rigid body motions and principally translational motions within the first 100 slow modes of the complex. Although the three tRNAs exhibit different apparent total motions, after the rigid body motions are removed, the remaining internal motions of all three tRNAs are essentially the same. The direction of the translational motions of the tRNAs are in the same direction as the requisite translocation step, especially in the first slowest mode. Surprisingly the small intrinsically flexible mRNA has all of its internal motions completely inhibited and shows mainly a rigid-body translation in the slow modes of the ribosome complex. On the other hand, the required nonrigid body motions of the tRNA during translocation reveal that the anticodon-stem-loop, as well as the acceptor arm, of the tRNA enjoy a large mobility but act as rigid structural units. In summary, the ribosome exerts its control by enforcing rigidity in the functional parts of the tRNAs as well as in the mRNA.

Details

Language :
English
ISSN :
00063495 and 15420086
Volume :
89
Issue :
5
Database :
Supplemental Index
Journal :
Biophysical Journal
Publication Type :
Periodical
Accession number :
ejs17938240
Full Text :
https://doi.org/10.1529/biophysj.105.064840