Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Structural Dynamics of Elbow Segment of E. coli Ribosomal A-site Finger. Comparison of Simulations with Cryo-EM Data and with Equivalent Segments in Other Species.

Helix 38 (H38) of the large ribosomal subunit is a long, bent structure connecting with the small subunit through intersubunit bridge B1a. Its elbow segment, known as a kink-turn (Kt-38) in the Haloarcula marismortui ribosome, is the likely source of its dynamical properties, important for translational fidelity. The archaeal and bacterial crystal structures reveal similar topologies of the elbow segment across species, even though the sequences, 2D structures and local interactions in the region are very diverse. We have carried out explicit solvent molecular dynamics simulations of the H38 elbows of four different species. The directional flexibility of the E.coli H38 elbow inferred from the simulations is consistent with the conformational changes observed by cryo-EM of the ribosome in several functional states. We suggest that the simulations properly capture intrinsic thermal fluctuations of this rRNA segment which are of functional importance. Further, the H38 elbows of all four studied species possess similar stochastic fluctuations and directional intrinsic flexibilities. The elbows in three bacterial ribosomes can be considered as structural analogs of Kt-38 present in archaea. Thus, the elbow of H38 illustrates how large RNAs can utilize diverse sequences to achieve equivalent or similar topologies and dynamics properties.

Kamila Reblova1
Filip Razga1,2
Wen Li3
Haixiao Gao3
Joachim Frank4
Jiri Sponer1

1Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135
61265 Brno, Czech Republic
2National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
3Wadsworth Center
Albany, NY 12201, USA
4Department of Biochemistry and Molecular Biophysics, and Department of Biological Sciences, Columbia University
New York, NY 10032, USA