RÉBLOVÁ, Kamila, Judit ŠPONEROVÁ, Naděžda ŠPAČKOVÁ, Ivana BEŠŠEOVÁ and Jiří ŠPONER. A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. JOURNAL OF PHYSICAL CHEMISTRY B. Washington: American Chemical Society, 2011, vol. 115, No 47, p. 13897-13910. ISSN 1520-6106. Available from: https://dx.doi.org/10.1021/jp2065584. |
Other formats:
BibTeX
LaTeX
RIS
@article{975008, author = {Réblová, Kamila and Šponerová, Judit and Špačková, Naděžda and Beššeová, Ivana and Šponer, Jiří}, article_location = {Washington}, article_number = {47}, doi = {http://dx.doi.org/10.1021/jp2065584}, keywords = {EDGE BASE-PAIRS; BOX C/D RNA; NUCLEIC-ACIDS; INTERACTION POTENTIALS; ISOSTERICITY MATRICES; STRUCTURAL DYNAMICS; CRYSTAL-STRUCTURE; FORCE-FIELD; BASIS-SETS; SIMULATIONS}, language = {eng}, issn = {1520-6106}, journal = {JOURNAL OF PHYSICAL CHEMISTRY B}, title = {A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis}, volume = {115}, year = {2011} }
TY - JOUR ID - 975008 AU - Réblová, Kamila - Šponerová, Judit - Špačková, Naděžda - Beššeová, Ivana - Šponer, Jiří PY - 2011 TI - A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis JF - JOURNAL OF PHYSICAL CHEMISTRY B VL - 115 IS - 47 SP - 13897-13910 EP - 13897-13910 PB - American Chemical Society SN - 15206106 KW - EDGE BASE-PAIRS KW - BOX C/D RNA KW - NUCLEIC-ACIDS KW - INTERACTION POTENTIALS KW - ISOSTERICITY MATRICES KW - STRUCTURAL DYNAMICS KW - CRYSTAL-STRUCTURE KW - FORCE-FIELD KW - BASIS-SETS KW - SIMULATIONS N2 - The RNA kink-turn is an important recurrent RNA motif; an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A center dot G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G=C receptor base pair during evolution while the inverted pair (C=G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G=C and C=G base pairs in sequences. We carried out an extended set (similar to 5 mu s) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with similar to 0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G=C and A-I/C=G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns. ER -
RÉBLOVÁ, Kamila, Judit ŠPONEROVÁ, Naděžda ŠPAČKOVÁ, Ivana BEŠŠEOVÁ and Jiří ŠPONER. A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis. \textit{JOURNAL OF PHYSICAL CHEMISTRY B}. Washington: American Chemical Society, 2011, vol.~115, No~47, p.~13897-13910. ISSN~1520-6106. Available from: https://dx.doi.org/10.1021/jp2065584.
|