| RÉBLOVÁ, Kamila, Jiří ŠPONER a Filip LANKAŠ. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Research. Oxford, UK: Oxford Press, 2012, roč. 40, č. 13, s. 6290-6303. ISSN 0305-1048. doi:10.1093/nar/gks258. |
Další formáty:
BibTeX
LaTeX
RIS
@article{1076052,
author = {Réblová, Kamila and Šponer, Jiří and Lankaš, Filip},
article_location = {Oxford, UK},
article_number = {13},
doi = {http://dx.doi.org/10.1093/nar/gks258},
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},
language = {eng},
issn = {0305-1048},
journal = {Nucleic Acids Research},
title = {Structure and mechanical properties of the ribosomal L1 stalk three-way junction},
url = {http://nar.oxfordjournals.org/content/40/13/6290},
volume = {40},
year = {2012}
}
TY - JOUR
ID - 1076052
AU - Réblová, Kamila - Šponer, Jiří - Lankaš, Filip
PY - 2012
TI - Structure and mechanical properties of the ribosomal L1 stalk three-way junction
JF - Nucleic Acids Research
VL - 40
IS - 13
SP - 6290-6303
EP - 6290-6303
PB - Oxford Press
SN - 03051048
KW - MOLECULAR-DYNAMICS SIMULATIONS
KW - TRANSFER-RNA TRANSLOCATION
KW - A-SITE FINGER
KW - EUKARYOTIC 80S RIBOSOME
KW - BASE-PAIR LEVEL
KW - 70S RIBOSOME
KW - CRYSTAL-STRUCTURE
KW - TERTIARY INTERACTIONS
KW - MESSENGER-RNA
KW - CRYOELECTRON MICROSCOPY
UR - http://nar.oxfordjournals.org/content/40/13/6290
L2 - http://nar.oxfordjournals.org/content/40/13/6290
N2 - 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.
ER -
RÉBLOVÁ, Kamila, Jiří ŠPONER a Filip LANKAŠ. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. \textit{Nucleic Acids Research}. Oxford, UK: Oxford Press, 2012, roč.~40, č.~13, s.~6290-6303. ISSN~0305-1048. doi:10.1093/nar/gks258.
|
