BEŠŠEOVÁ, Ivana, Pavel BANÁŠ, Petra KUEHROVA, Pavlina KOSINOVA, Michal OTYEPKA and Jiří ŠPONER. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. Journal of Physical Chemistry B. WASHINGTON: American Chemical Society, 2012, vol. 116, No 33, p. 9899-9916. ISSN 1520-6106. doi:10.1021/jp3014817.
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Basic information
Original name Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration
Authors BEŠŠEOVÁ, Ivana (703 Slovakia), Pavel BANÁŠ (203 Czech Republic), Petra KUEHROVA (203 Czech Republic), Pavlina KOSINOVA (203 Czech Republic), Michal OTYEPKA (203 Czech Republic) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution).
Edition Journal of Physical Chemistry B, WASHINGTON, American Chemical Society, 2012, 1520-6106.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10610 Biophysics
Country of publisher United States of America
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 3.607
RIV identification code RIV/00216224:14740/12:00057883
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1021/jp3014817
UT WoS 000307749100003
Keywords in English MOLECULAR-DYNAMICS SIMULATIONS; UNIQUE TETRANUCLEOTIDE SEQUENCES; PARTICLE MESH EWALD; METAL-ION BINDING; NUCLEIC-ACIDS; B-DNA; CRYSTAL-STRUCTURES; BASE SEQUENCE; LIQUID WATER; LOOP-E
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 6. 4. 2013 06:44.
Abstract
We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 mu s of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al. AMBER RNA force field bsc0 chi(OL3), while several other RNA force fields have been tested. The calculations show that the A-RNA helix compactness, described mainly by geometrical parameters inclination, base pair roll, and helical rise, is sequence-dependent. In the calculated set of structures, the inclination varies from 10 degrees to 24 degrees. On the basis of simulations with modified bases (inosine and 2,6-diaminopurine), we suggest that the sequence-dependence of purely canonical A-RNA double helix is caused by the steric shape of the base pairs, i.e., the van der Waals interactions. The electrostatic part of stacking does not appear to affect the A-RNA shape. Especially visible is the role of the minor groove amino group of purines. This resembles the so-called Dickerson-Calladine mechanical rules suggested three decades ago for the DNA double helices. We did not identify any long-living backbone substate in A-RNA double helices that would resemble, for example, the B-DNA BI/BII dynamics. The variability of the A-RNA compactness is due to mutual movements of the consecutive base pairs coupled with modest change of the glycosidic chi torsion. The simulations further show that the A-RNA compactness is modestly affected by the water model used, while the effect of ionic conditions, investigated in the range from net-neutral condition to similar to 0.8 M monovalent ion excess salt, is smaller.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
GD203/09/H046, research and development projectName: Biochemie na rozcestí mezi in silico a in vitro
Investor: Czech Science Foundation
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