Publication details

Structure and mechanical properties of the ribosomal L1 stalk three-way junction

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Authors

RÉBLOVÁ Kamila ŠPONER Jiří LANKAŠ Filip

Year of publication 2012
Type Article in Periodical
Magazine / Source Nucleic Acids Research
MU Faculty or unit

Central European Institute of Technology

Citation
web http://nar.oxfordjournals.org/content/40/13/6290
Doi http://dx.doi.org/10.1093/nar/gks258
Field Biophysics
Keywords MOLECULAR-DYNAMICS SIMULATIONS; TRANSFER-RNA TRANSLOCATION; A-SITE FINGER; EUKARYOTIC 80S RIBOSOME; BASE-PAIR LEVEL; 70S RIBOSOME; CRYSTAL-STRUCTURE; TERTIARY INTERACTIONS; MESSENGER-RNA; CRYOELECTRON MICROSCOPY
Attached files
Description 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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