This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.105.064840v1 89/5/3399    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Wang, Y. Articles by Jernigan, R. L. Search for Related Content PubMed PubMed Citation Articles by Wang, Y. Articles by Jernigan, R. L.

Comparison of tRNA Motions in the Free and Ribosomal Bound Structures

Yongmei Wang ^* and Robert L. Jernigan 

^* Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152-3550; and Laurence H. Baker Center for Bioinformatics and Biological Statistics, Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011-3020

Correspondence: Address reprint requests to Robert L. Jernigan, E-mail: jernigan{at}iastate.edu.

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.

This article has been cited by other articles:

				S. Yamasaki, S. Nakamura, T. Terada, and K. Shimizu Mechanism of the Difference in the Binding Affinity of E. coli tRNAGln to Glutaminyl-tRNA Synthetase Caused by Noninterface Nucleotides in Variable Loop Biophys. J., January 1, 2007; 92(1): 192 - 200. [Abstract] [Full Text] [PDF]