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Exploring Global Motions and Correlations in the Ribosome

Joanna Trylska ^* , Valentina Tozzini ^*  and J. Andrew McCammon ^* 

^* Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California; Interdisciplinary Centre for Mathematical and Computational Modelling Warsaw University, Warsaw, Poland; NEST-Scuola Normale Superiore, Pisa, Italy; and Howard Hughes Medical Institute and Department of Pharmacology, University of California at San Diego, La Jolla, California

Correspondence: Address reprint requests to Joanna Trylska, ICM Warsaw University, Zwirki i Wigury 93, 02-089 Warsaw, Poland. Tel.: 48-22-5540-843; Fax: 48-22-5540-801; E-mail: joanna{at}icm.edu.pl.

We studied slower global coupled motions of the ribosome with half a microsecond of coarse-grained molecular dynamics. A low-resolution anharmonic network model that allows for the evolution of tertiary structure and long-scale sampling was developed and parameterized. Most importantly, we find that functionally important movements of L7/L12 and L1 lateral stalks are anticorrelated. Other principal directions of motions include widening of the tRNA cleft and the rotation of the small subunit which occurs as one block and is in phase with the movement of L1 stalk. The effect of the dynamical correlation pattern on the elongation process is discussed. Small fluctuations of the 3' tRNA termini and anticodon nucleotides show tight alignment of substrates for the reaction. Our model provides an efficient and reliable way to study the dynamics of large biomolecular systems composed of both proteins and nucleic acids.

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