RÉBLOVÁ, Kamila, Jiří ŠPONER and Filip LANKAŠ. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Research. Oxford, UK: Oxford Press, 2012, vol. 40, No 13, p. 6290-6303. ISSN 0305-1048. doi:10.1093/nar/gks258.
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Basic information
Original name Structure and mechanical properties of the ribosomal L1 stalk three-way junction
Authors RÉBLOVÁ, Kamila (203 Czech Republic, belonging to the institution), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution) and Filip LANKAŠ (203 Czech Republic).
Edition Nucleic Acids Research, Oxford, UK, Oxford Press, 2012, 0305-1048.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10610 Biophysics
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 8.278
RIV identification code RIV/00216224:14740/12:00057882
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1093/nar/gks258
UT WoS 000306970700047
Keywords in English 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
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 6. 4. 2013 17:49.
Abstract
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.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
GBP305/12/G034, research and development projectName: Centrum biologie RNA
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