Journal
NUCLEIC ACIDS RESEARCH
Volume 40, Issue 13, Pages 6290-6303Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gks258
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Funding
- Czech Science Foundation [203/09/1476, P208/11/1822, P208/12/1878, P305/12/G03, P208/12/G016]
- Grant Agency of the Academy of Sciences of the Czech Republic [KJB400040901]
- Academy of Sciences of the Czech Republic [Z40550506]
- 'CEITEC-Central European Institute of Technology' from European Regional Development Fund [CZ.1.05/1.1.00/02.0068]
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The L1 stalk is a key mobile element of the large ribosomal subunit which interacts with tRNA during translocation. Here, we investigate the structure and mechanical properties of the rRNA H76/H75/H79 three-way junction at the base of the L1 stalk from four different prokaryotic organisms. We propose a coarse-grained elastic model and parameterize it using large-scale atomistic molecular dynamics simulations. Global properties of the junction are well described by a model in which the H76 helix is represented by a straight, isotropically flexible elastic rod, while the junction core is represented by an isotropically flexible spherical hinge. Both the core and the helix contribute substantially to the overall H76 bending fluctuations. The presence of wobble pairs in H76 does not induce any increased flexibility or anisotropy to the helix. The half-closed conformation of the L1 stalk seems to be accessible by thermal fluctuations of the junction itself, without any long-range allosteric effects. Bending fluctuations of H76 with a bulge introduced in it suggest a rationale for the precise position of the bulge in eukaryotes. Our elastic model can be generalized to other RNA junctions found in biological systems or in nanotechnology.
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