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High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations. Proc Natl Acad Sci U S A 2013; 110:16820-5. [PMID: 24043821 DOI: 10.1073/pnas.1309392110] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report the de novo folding of three hyperstable RNA tetraloops to 1-3 Å rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations.
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Šponer J, Šponer JE, Mládek A, Banáš P, Jurečka P, Otyepka M. How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists. Methods 2013; 64:3-11. [PMID: 23747334 DOI: 10.1016/j.ymeth.2013.05.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/29/2013] [Accepted: 05/30/2013] [Indexed: 12/30/2022] Open
Abstract
In this review primarily written for non-experts we explain basic methodological aspects and interpretation of modern quantum chemical (QM) computations applied to nucleic acids. We introduce current reference QM computations on small model systems consisting of dozens of atoms. Then we comment on recent advance of fast and accurate dispersion-corrected density functional theory methods, which will allow computations of small but complete nucleic acids building blocks in the near future. The qualitative difference between QM and molecular mechanics (MM, force field) computations is discussed. We also explain relation of QM and molecular simulation computations to experiments.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolská 135, 612 65 Brno, Czech Republic; CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.
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53
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Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput 2013; 9:2339-2354. [PMID: 24058302 PMCID: PMC3775469 DOI: 10.1021/ct400154j] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations.
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Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultad de Farmacia, Universidad de Barcelona, Campus Torribera, Prat de la Riba 171, Edifici Verdaguer, 080921 Santa Coloma de Gramanet, Spain
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Thomas E. Cheatham
- Departments of Medicinal Chemistry, University of Utah, 2000 East 30 South Skaggs 105, Salt Lake City, UT 84112, USA
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
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54
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Kührová P, Banáš P, Best RB, Šponer J, Otyepka M. Computer Folding of RNA Tetraloops? Are We There Yet? J Chem Theory Comput 2013; 9:2115-25. [DOI: 10.1021/ct301086z] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies
and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies
and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
| | - Robert B. Best
- Laboratory of Chemical Physics,
National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520,
United States
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- CEITEC − Central European
Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies
and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
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55
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Tubbs J, Condon DE, Kennedy S, Hauser M, Bevilacqua P, Turner DH. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry 2013; 52:996-1010. [PMID: 23286901 PMCID: PMC3571207 DOI: 10.1021/bi3010347] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/27/2012] [Indexed: 12/29/2022]
Abstract
The sequence dependence of RNA energetics is important for predicting RNA structure. Hairpins with C(n) loops are consistently less stable than hairpins with other loops, which suggests the structure of C(n) regions could be unusual in the "unfolded" state. For example, previous nuclear magnetic resonance (NMR) evidence suggested that polycytidylic acid forms a left-handed helix. In this study, UV melting experiments show that the hairpin formed by r(5'GGACCCCCGUCC) is less stable than r(5'GGACUUUUGUCC). NMR spectra for single-stranded C(4) oligonucleotide, mimicking the unfolded hairpin loop, are consistent with a right-handed A-form-like helix. Comparisons between NMR spectra and molecular dynamics (MD) simulations suggest that recent reparametrizations, parm99χ_YIL and parm99TOR, of the AMBER parm99 force field improve the agreement between structural features for C(4) determined by NMR and predicted by MD. Evidently, the force field revisions to parm99 improve the modeling of RNA energetics and therefore structure.
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Affiliation(s)
- Jason
D. Tubbs
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
| | - David E. Condon
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
| | - Scott
D. Kennedy
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
- Department
of Biochemistry and
Biophysics, University of Rochester, Rochester,
New York 14642, United States
| | - Melanie Hauser
- Department of Chemistry, Buena Vista University, Storm Lake, Iowa 50588, United
States
- Department of Chemistry
and
Center for RNA Molecular Biology, The Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Philip
C. Bevilacqua
- Department of Chemistry
and
Center for RNA Molecular Biology, The Pennsylvania State
University, University Park, Pennsylvania 16802, United
States
| | - Douglas H. Turner
- Department
of Chemistry, University of Rochester,
Rochester, New York 14627,
United States
- Center for
RNA Biology, University of Rochester, Rochester,
New York 14642,
United States
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56
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Dršata T, Pérez A, Orozco M, Morozov AV, Sponer J, Lankaš F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. J Chem Theory Comput 2012; 9:707-721. [PMID: 23976886 DOI: 10.1021/ct300671y] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Dickerson-Drew dodecamer (DD) d-[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-µs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic ; Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
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57
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Banáš P, Sklenovský P, Wedekind JE, Šponer J, Otyepka M. Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. J Phys Chem B 2012; 116:12721-34. [PMID: 22998634 PMCID: PMC3505677 DOI: 10.1021/jp309230v] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Riboswitches often occur in the 5'-untranslated regions of bacterial mRNA where they regulate gene expression. The preQ(1) riboswitch controls the biosynthesis of a hypermodified nucleoside queuosine in response to binding the queuosine metabolic intermediate. Structures of the ligand-bound and ligand-free states of the preQ(1) riboswitch from Thermoanaerobacter tengcongensis were determined recently by X-ray crystallography. We used multiple, microsecond-long molecular dynamics simulations (29 μs in total) to characterize the structural dynamics of preQ(1) riboswitches in both states. We observed different stabilities of the stem in the bound and free states, resulting in different accessibilities of the ribosome-binding site. These differences are related to different stacking interactions between nucleotides of the stem and the associated loop, which itself adopts different conformations in the bound and free states. We suggest that the loop not only serves to bind preQ(1) but also transmits information about ligand binding from the ligand-binding pocket to the stem, which has implications for mRNA accessibility to the ribosome. We explain functional results obscured by a high salt crystallization medium and help to refine regions of disordered electron density, which demonstrates the predictive power of our approach. Besides investigating the functional dynamics of the riboswitch, we have also utilized this unique small folded RNA system for analysis of performance of the RNA force field on the μs time scale. The latest AMBER parmbsc0χ(OL3) RNA force field is capable of providing stable trajectories of the folded molecule on the μs time scale. On the other hand, force fields that are not properly balanced lead to significant structural perturbations on the sub-μs time scale, which could easily lead to inappropriate interpretation of the simulation data.
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Affiliation(s)
- Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Petr Sklenovský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Joseph E. Wedekind
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Ave, Box 712, Rochester, NY 14620, USA
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
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Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys 2012; 14:15257-77. [PMID: 23072945 DOI: 10.1039/c2cp41987d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.
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59
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Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J Phys Chem B 2012; 116:9899-916. [DOI: 10.1021/jp3014817] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ivana Beššeová
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavlína Košinová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
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