51
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Mapping the Universe of RNA Tetraloop Folds. Biophys J 2017; 113:257-267. [PMID: 28673616 DOI: 10.1016/j.bpj.2017.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 11/22/2022] Open
Abstract
We report a map of RNA tetraloop conformations constructed by calculating pairwise distances among all experimentally determined four-nucleotide hairpin loops. Tetraloops with similar structures are clustered together and, as expected, the two largest clusters are the canonical GNRA and UNCG folds. We identify clusters corresponding to known tetraloop folds such as GGUG, RNYA, AGNN, and CUUG. These clusters are represented in a simple two-dimensional projection that recapitulates the relationship among the different folds. The cluster analysis also identifies 20 novel tetraloop folds that are peculiar to specific positions in ribosomal RNAs and that are stabilized by tertiary interactions. In our RNA tetraloop database we find a significant number of non-GNRA and non-UNCG sequences adopting the canonical GNRA and UNCG folds. Conversely, we find a significant number of GNRA and UNCG sequences adopting non-GNRA and non-UNCG folds. Our analysis demonstrates that there is not a simple one-to-one, but rather a many-to-many mapping between tetraloop sequence and tetraloop fold.
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52
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Pathak AK, Bandyopadhyay T. Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study. J Chem Phys 2017; 146:165104. [DOI: 10.1063/1.4982049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Arup K. Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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53
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Wales DJ, Yildirim I. Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field. J Phys Chem B 2017; 121:2989-2999. [PMID: 28319659 DOI: 10.1021/acs.jpcb.7b00819] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With current advancements in RNA based therapeutics, it is becoming crucial to utilize theoretical and computational methods to describe properly the physical properties of RNA molecules. NMR and X-ray crystallography are two powerful techniques for investigating structural properties. However, if the RNA molecules are complex or dynamic, these methods might not be adequate. For computational approaches, the quality of the force field will determine accuracy of our predictions. In this contribution, we revise the α/γ torsional parameters of RNA for amber force field using a model system representing an RNA dimer backbone. Combined with revised χ torsional parameters, previously shown to improve computational predictions, we benchmarked the revised force field on five single-stranded RNA (ssRNA) tetramers, three RNA dodecamer duplexes, and an RNA hairpin. A total of 60 μs of molecular dynamics (MD) simulations were run. We also employ the discrete path sampling (DPS) approach to compare the predictions for the revised amber force field with those for amber10. Our results indicate that the unphysical states observed with amber10 in ssRNA MD simulations are suppressed for the revised amber force field. In line with NMR experimental observations, incorporation of the revised α/γ and χ torsional parameters leads to A-form-like conformational states as the most favorable ssRNA tetramer conformations. Furthermore, the revised force field maintains the A-form geometry in regular RNA duplexes. Our revised amber force field for RNA should therefore improve structural and thermodynamic predictions for challenging RNA systems.
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Affiliation(s)
- David J Wales
- Department of Chemistry, University of Cambridge , Cambridge, Cambridgeshire CB2 1EW, United Kingdom
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University , Jupiter, Florida 33458, United States.,Scripps Research Institute , Jupiter, Florida 33458, United States
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54
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Zgarbová M, Jurečka P, Banáš P, Havrila M, Šponer J, Otyepka M. Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field. J Phys Chem B 2017; 121:2420-2433. [PMID: 28290207 DOI: 10.1021/acs.jpcb.7b00262] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The sugar-phosphate backbone of RNA can exist in diverse rotameric substates, giving RNA molecules enormous conformational variability. The most frequent noncanonical backbone conformation in RNA is α/γ = t/t, which is derived from the canonical backbone by a crankshaft motion and largely preserves the standard geometry of the RNA duplex. A similar conformation also exists in DNA, where it has been extensively studied and shown to be involved in DNA-protein interactions. However, the function of the α/γ = t/t conformation in RNA is poorly understood. Here, we present molecular dynamics simulations of several prototypical RNA structures obtained from X-ray and NMR experiments, including canonical and mismatched RNA duplexes, UUCG and GAGA tetraloops, Loop E, the sarcin-ricin loop, a parallel guanine quadruplex, and a viral pseudoknot. The stability of various noncanonical α/γ backbone conformations was analyzed with two AMBER force fields, ff99bsc0χOL3 and ff99bsc0χOL3 with the recent εζOL1 and βOL1 corrections for DNA. Although some α/γ substates were stable with seemingly well-described equilibria, many were unstable in our simulations. Notably, the most frequent noncanonical conformer α/γ = t/t was unstable in both tested force fields. Possible reasons for this instability are discussed. Our work reveals a potentially important artifact in RNA force fields and highlights a need for further force field refinement.
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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, 77146 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
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55
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Aytenfisu A, Spasic A, Grossfield A, Stern HA, Mathews DH. Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics. J Chem Theory Comput 2017; 13:900-915. [PMID: 28048939 PMCID: PMC5312698 DOI: 10.1021/acs.jctc.6b00870] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Indexed: 12/27/2022]
Abstract
The backbone dihedral parameters of the Amber RNA force field were improved by fitting using multiple linear regression to potential energies determined by quantum chemistry calculations. Five backbone and four glycosidic dihedral parameters were fit simultaneously to reproduce the potential energies determined by a high-level density functional theory calculation (B97D3 functional with the AUG-CC-PVTZ basis set). Umbrella sampling was used to determine conformational free energies along the dihedral angles, and these better agree with the population of conformations observed in the protein data bank for the new parameters than for the conventional parameters. Molecular dynamics simulations performed on a set of hairpin loops, duplexes and tetramers with the new parameter set show improved modeling for the structures of tetramers CCCC, CAAU, and GACC, and an RNA internal loop of noncanonical pairs, as compared to the conventional parameters. For the tetramers, the new parameters largely avoid the incorrect intercalated structures that dominate the conformational samples from the conventional parameters. For the internal loop, the major conformation solved by NMR is stable with the new parameters, but not with the conventional parameters. The new force field performs similarly to the conventional parameters for the UUCG and GCAA hairpin loops and the [U(UA)6A]2 duplex.
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Affiliation(s)
- Asaminew
H. Aytenfisu
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
- Center
for RNA Biology, University of Rochester
Medical Center, Rochester, New York 14642, United States
| | - Aleksandar Spasic
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
- Center
for RNA Biology, University of Rochester
Medical Center, Rochester, New York 14642, United States
| | - Alan Grossfield
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
| | - Harry A. Stern
- Center
for Integrated Research Computing, University
of Rochester, Rochester, New York 14642, United
States
| | - David H. Mathews
- Department
of Biochemistry & Biophysics, University
of Rochester Medical Center, Rochester, New York 14642, United States
- Center
for RNA Biology, University of Rochester
Medical Center, Rochester, New York 14642, United States
- Department
of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
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56
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Pinamonti G, Zhao J, Condon DE, Paul F, Noè F, Turner DH, Bussi G. Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models. J Chem Theory Comput 2017; 13:926-934. [PMID: 28001394 DOI: 10.1021/acs.jctc.6b00982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time or spatial resolution. Here we use state-of-the-art computational techniques, namely, atomistic molecular dynamics and Markov state models, to provide insight into the rapid dynamics of short RNA oligonucleotides, to elucidate the kinetics of stacking interactions. Analysis of multiple microsecond-long simulations indicates that the main relaxation modes of such molecules can consist of transitions between alternative folded states, rather than between random coils and native structures. After properly removing structures that are artificially stabilized by known inaccuracies of the current RNA AMBER force field, the kinetic properties predicted are consistent with the time scales of previously reported relaxation experiments.
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Affiliation(s)
- Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies , 265 Via Bonomea, I-34136 Trieste, Italy
| | - Jianbo Zhao
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - David E Condon
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Fabian Paul
- Department for Mathematics and Computer Science, Freie Universität , Arnimallee 6, Berlin 14195, Germany
| | - Frank Noè
- Department for Mathematics and Computer Science, Freie Universität , Arnimallee 6, Berlin 14195, Germany
| | - Douglas H Turner
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, International School for Advanced Studies , 265 Via Bonomea, I-34136 Trieste, Italy
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57
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Yang C, Lim M, Kim E, Pak Y. Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field. J Chem Theory Comput 2017; 13:395-399. [DOI: 10.1021/acs.jctc.6b00808] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Changwon Yang
- Department of Chemistry
and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
| | - Manho Lim
- Department of Chemistry
and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
| | - Eunae Kim
- College of Pharmacy, Chosun University, Gwangju 61452, South Korea
| | - Youngshang Pak
- Department of Chemistry
and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
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58
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Cesari A, Gil-Ley A, Bussi G. Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement. J Chem Theory Comput 2016; 12:6192-6200. [DOI: 10.1021/acs.jctc.6b00944] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea Cesari
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
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