Computer Folding of RNA Tetraloops? Are We There Yet?

J 2013

Computer Folding of RNA Tetraloops? Are We There Yet?

KUHROVA, Petra, Pavel BANÁŠ, Robert B BEST, Jiří ŠPONER, Michal OTYEPKA et. al.

Basic information

Original name

Computer Folding of RNA Tetraloops? Are We There Yet?

Authors

KUHROVA, Petra (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), Robert B BEST (840 United States of America), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution) and Michal OTYEPKA (203 Czech Republic)

Edition

Journal of Chemical Theory and Computation, WASHINGTON, AMER CHEMICAL SOC, 2013, 1549-9618

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.310

RIV identification code

RIV/00216224:14740/13:00068733

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/ct301086z

UT WoS

000317438100025

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; SARCIN RICIN LOOP; FORCE-FIELD; RIBOSOMAL-RNA; ANGSTROM RESOLUTION; CRYSTAL-STRUCTURE; ENERGY LANDSCAPE; NUCLEIC-ACIDS; DNA HAIRPIN; TERTIARY INTERACTIONS

Abstract

V originále

RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields. Although we find that the REMD simulation runs of a total of similar to 19 mu s (starting from both folded and unfolded state) in duration for each TL are still far from obtaining a representative equilibrium distribution at each temperature, we are nonetheless able to map the stable species on the folding energy landscape. The qualitative picture we obtain is consistent with experimental studies of RNA folding in that there are a number of stable on- and off-pathway intermediates en route to the native state. In particular, we have identified a misfolded-bulged state of GNRA TL, which shares many structural features with the X-ray structure of GNRA TL in the complex with restrictocin, namely the bulged out A(L4) base. Since this is the same conformation observed in the complex of the TL with restrictocin, we argue that GNRA TL is able to bind restrictocin via a "conformational selection" mechanism, with the R-L3 and A(L4) bases being exposed to the solvent prior to binding. In addition we have identified a misfolded-anti state of UUCG TL, which is structurally close to the native state except that the G(L4), nucleotide is in an anti-conformation instead of the native syn. Our data suggest that the UUCG misfolded-anti state may be a kinetic trap for the UUCG folding.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

KUHROVA, Petra, Pavel BANÁŠ, Robert B BEST, Jiří ŠPONER and Michal OTYEPKA. Computer Folding of RNA Tetraloops? Are We There Yet? Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2013, vol. 9, No 4, p. 2115-2125. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/ct301086z.

@article{1113600,
   author = {Kuhrova, Petra and Banáš, Pavel and Best, Robert B and Šponer, Jiří and Otyepka, Michal},
   article_location = {WASHINGTON},
   article_number = {4},
   doi = {http://dx.doi.org/10.1021/ct301086z},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; SARCIN RICIN LOOP; FORCE-FIELD; RIBOSOMAL-RNA; ANGSTROM RESOLUTION; CRYSTAL-STRUCTURE; ENERGY LANDSCAPE; NUCLEIC-ACIDS; DNA HAIRPIN; TERTIARY INTERACTIONS},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Computer Folding of RNA Tetraloops? Are We There Yet?},
   url = {http://pubs.acs.org/doi/pdf/10.1021/ct301086z},
   volume = {9},
   year = {2013}
}

TY  - JOUR
ID  - 1113600
AU  - Kuhrova, Petra - Banáš, Pavel - Best, Robert B - Šponer, Jiří - Otyepka, Michal
PY  - 2013
TI  - Computer Folding of RNA Tetraloops? Are We There Yet?
JF  - Journal of Chemical Theory and Computation
VL  - 9
IS  - 4
SP  - 2115-2125
EP  - 2115-2125
PB  - AMER CHEMICAL SOC
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - SARCIN RICIN LOOP
KW  - FORCE-FIELD
KW  - RIBOSOMAL-RNA
KW  - ANGSTROM RESOLUTION
KW  - CRYSTAL-STRUCTURE
KW  - ENERGY LANDSCAPE
KW  - NUCLEIC-ACIDS
KW  - DNA HAIRPIN
KW  - TERTIARY INTERACTIONS
UR  - http://pubs.acs.org/doi/pdf/10.1021/ct301086z
L2  - http://pubs.acs.org/doi/pdf/10.1021/ct301086z
N2  - RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields. Although we find that the REMD simulation runs of a total of similar to 19 mu s (starting from both folded and unfolded state) in duration for each TL are still far from obtaining a representative equilibrium distribution at each temperature, we are nonetheless able to map the stable species on the folding energy landscape. The qualitative picture we obtain is consistent with experimental studies of RNA folding in that there are a number of stable on- and off-pathway intermediates en route to the native state. In particular, we have identified a misfolded-bulged state of GNRA TL, which shares many structural features with the X-ray structure of GNRA TL in the complex with restrictocin, namely the bulged out A(L4) base. Since this is the same conformation observed in the complex of the TL with restrictocin, we argue that GNRA TL is able to bind restrictocin via a "conformational selection" mechanism, with the R-L3 and A(L4) bases being exposed to the solvent prior to binding. In addition we have identified a misfolded-anti state of UUCG TL, which is structurally close to the native state except that the G(L4), nucleotide is in an anti-conformation instead of the native syn. Our data suggest that the UUCG misfolded-anti state may be a kinetic trap for the UUCG folding.
ER  -

KUHROVA, Petra, Pavel BANÁŠ, Robert B BEST, Jiří ŠPONER and Michal OTYEPKA. Computer Folding of RNA Tetraloops? Are We There Yet? \textit{Journal of Chemical Theory and Computation}. WASHINGTON: AMER CHEMICAL SOC, 2013, vol.~9, No~4, p.~2115-2125. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct301086z.

Detailed Information on Publication Record