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Pokorná P, Mlýnský V, Bussi G, Šponer J, Stadlbauer P. Molecular dynamics simulations reveal the parallel stranded d(GGGA) 3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble. Int J Biol Macromol 2024; 261:129712. [PMID: 38286387 DOI: 10.1016/j.ijbiomac.2024.129712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/31/2024]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of the G4 folding landscape may help to elucidate biological roles of G4s but is challenging both experimentally and computationally. Here, we achieved complete folding of a three-quartet parallel DNA G4 with (GGGA)3GGG sequence using all-atom explicit-solvent enhanced-sampling molecular dynamics (MD) simulations. The simulations suggested early formation of guanine stacks in the G-tracts, which behave as semi-rigid blocks in the folding process. The folding continues via the formation of a collapsed compact coil-like ensemble. Structuring of the G4 from the coil then proceeds via various cross-like, hairpin, slip-stranded and two-quartet ensembles and can bypass the G-triplex structure. Folding of the parallel G4 does not appear to involve any salient intermediates and is a multi-pathway process. We also carried out an extended set of simulations of parallel G-hairpins. While parallel G-hairpins are extremely unstable when isolated, they are more stable inside the coil structure. On the methodology side, we show that the AMBER DNA force field predicts the folded G4 to be less stable than the unfolded ensemble, uncovering substantial force-field issues. Overall, we provide unique atomistic insights into the folding landscape of parallel-stranded G4 but also reveal limitations of current state-of-the-art MD techniques.
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Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, Trieste 34136, Italy
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic.
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2
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Gate G, Williams A, Boldissar S, Šponer J, Szabla R, de Vries M. The tautomer-specific excited state dynamics of 2,6-diaminopurine using resonance-enhanced multiphoton ionization and quantum chemical calculations. Photochem Photobiol 2024; 100:404-418. [PMID: 38124372 DOI: 10.1111/php.13897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
2,6-Diaminopurine (2,6-dAP) is an alternative nucleobase that potentially played a role in prebiotic chemistry. We studied its excited state dynamics in the gas phase by REMPI, IR-UV hole burning, and ps pump-probe spectroscopy and performed quantum chemical calculations at the SCS-ADC(2) level of theory to interpret the experimental results. We found the 9H tautomer to have a small barrier to ultrafast relaxation via puckering of its 6-membered ring. The 7H tautomer has a larger barrier to reach a conical intersection and also has a sizable triplet yield. These results are discussed relative to other purines, for which 9H tautomerization appears to be more photostable than 7H and homosubstituted purines appear to be less photostable than heterosubstituted or singly substituted purines.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ann Williams
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Olomouc-Holice, Czech Republic
| | - Rafal Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Mattanjah de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
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3
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Kufner CL, Crucilla S, Ding D, Stadlbauer P, Šponer J, Szostak JW, Sasselov DD, Szabla R. Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern. Chem Sci 2024; 15:2158-2166. [PMID: 38332835 PMCID: PMC10848779 DOI: 10.1039/d3sc04971j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/27/2023] [Indexed: 02/10/2024] Open
Abstract
Charge separation is one of the most common consequences of the absorption of UV light by DNA. Recently, it has been shown that this process can enable efficient self-repair of cyclobutane pyrimidine dimers (CPDs) in specific short DNA oligomers such as the GAT[double bond, length as m-dash]T sequence. The mechanism was characterized as sequential electron transfer through the nucleobase stack which is controlled by the redox potentials of nucleobases and their sequence. Here, we demonstrate that the inverse sequence T[double bond, length as m-dash]TAG promotes self-repair with higher quantum yields (0.58 ± 0.23%) than GAT[double bond, length as m-dash]T (0.44 ± 0.18%) in a comparative study involving UV-irradiation experiments. After extended exposure to UV irradiation, a photostationary equilibrium between self-repair and damage formation is reached at 33 ± 13% for GAT[double bond, length as m-dash]T and at 40 ± 16% for T[double bond, length as m-dash]TAG, which corresponds to the maximum total yield of self-repair. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) simulations allowed us to assign this disparity to better stacking overlap between the G and A bases, which lowers the energies of the key A-˙G+˙ charge transfer state in the dominant conformers of the T[double bond, length as m-dash]TAG tetramer. These conformational differences also hinder alternative photorelaxation pathways of the T[double bond, length as m-dash]TAG tetranucleotide, which otherwise compete with the sequential electron transfer mechanism responsible for CPD self-repair. Overall, we demonstrate that photoinduced electron transfer is strongly dependent on conformation and the availability of alternative photodeactivation mechanisms. This knowledge can be used in the identification and prediction of canonical and modified DNA sequences exhibiting efficient electron transfer. It also further contributes to our understanding of DNA self-repair and its potential role in the photochemical selection of the most photostable sequences on the early Earth.
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Affiliation(s)
- Corinna L Kufner
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Sarah Crucilla
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
- Department of Earth and Planetary Sciences, Harvard University Cambridge Massachusetts 02138 USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital Boston Massachusetts 02114 USA
- Department of Chemistry and Chemical Biology, Harvard University Cambridge Massachusetts 02138 USA
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61200 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc Slechtitelu 241/27, 783 71, Olomouc - Holice Czech Republic
| | - Jack W Szostak
- Howard Hughes Medical Institute, The University of Chicago Chicago IL 60637 USA
- Department of Chemistry, The University of Chicago Chicago Illinois 60637 USA
| | - Dimitar D Sasselov
- Department of Astronomy, Harvard-Smithsonian Center for Astrophysics 60 Garden Street Cambridge MA 02138 USA
| | - Rafał Szabla
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology Wybrzeże Wyspiańskiego 27 Wrocław 50-370 Poland
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4
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Coulon R, Papoušková B, Mohammadi E, Otyepka M, Wunnava S, Šponer J, Šponer JE. Prebiotic Synthesis of 3',5'-Cyclic Adenosine and Guanosine Monophosphates through Carbodiimide-Assisted Cyclization. Chembiochem 2023; 24:e202300510. [PMID: 37747702 DOI: 10.1002/cbic.202300510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
3',5'-Cyclic nucleotides play a fundamental role in modern biochemical processes and have been suggested to have played a central role at the origin of terrestrial life. In this work, we suggest that a formamide-based systems chemistry might account for their availability on the early Earth. In particular, we demonstrate that in a liquid formamide environment at elevated temperatures 3',5'-cyclic nucleotides are obtained in good yield and selectivity upon intramolecular cyclization of 5'-phosphorylated nucleosides in the presence of carbodiimides.
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Affiliation(s)
- Rémi Coulon
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic
| | - Barbora Papoušková
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 77146, Olomouc, Czech Republic
| | - Elmira Mohammadi
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, V6T 1Z1, BC, Canada
| | - Michal Otyepka
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- IT4Innovations, VSB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00, Ostrava, Poruba, Czech Republic
| | - Sreekar Wunnava
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Jiří Šponer
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic
| | - Judit E Šponer
- CATRIN - Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 77900, Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200, Brno, Czech Republic
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5
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Mlýnský V, Kührová P, Stadlbauer P, Krepl M, Otyepka M, Banáš P, Šponer J. Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations. J Chem Theory Comput 2023; 19:8423-8433. [PMID: 37944118 PMCID: PMC10687871 DOI: 10.1021/acs.jctc.3c00990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Molecular dynamics (MD) simulations represent an established tool to study RNA molecules. The outcome of MD studies depends, however, on the quality of the force field (ff). Here we suggest a correction for the widely used AMBER OL3 ff by adding a simple adjustment of the nonbonded parameters. The reparameterization of the Lennard-Jones potential for the -H8···O5'- and -H6···O5'- atom pairs addresses an intranucleotide steric clash occurring in the type 0 base-phosphate interaction (0BPh). The nonbonded fix (NBfix) modification of 0BPh interactions (NBfix0BPh modification) was tuned via a reweighting approach and subsequently tested using an extensive set of standard and enhanced sampling simulations of both unstructured and folded RNA motifs. The modification corrects minor but visible intranucleotide clash for the anti nucleobase conformation. We observed that structural ensembles of small RNA benchmark motifs simulated with the NBfix0BPh modification provide better agreement with experiments. No side effects of the modification were observed in standard simulations of larger structured RNA motifs. We suggest that the combination of OL3 RNA ff and NBfix0BPh modification is a viable option to improve RNA MD simulations.
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Affiliation(s)
- Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Petra Kührová
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
- Czech
Advanced Technology and Research Institute, CATRIN, Křížkovského 511/8, Olomouc 779 00, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
- Czech
Advanced Technology and Research Institute, CATRIN, Křížkovského 511/8, Olomouc 779 00, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
- Czech
Advanced Technology and Research Institute, CATRIN, Křížkovského 511/8, Olomouc 779 00, Czech Republic
| | - Michal Otyepka
- Czech
Advanced Technology and Research Institute, CATRIN, Křížkovského 511/8, Olomouc 779 00, Czech Republic
- IT4Innovations, VSB−Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba 708 00, Czech Republic
| | - Pavel Banáš
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
- Czech
Advanced Technology and Research Institute, CATRIN, Křížkovského 511/8, Olomouc 779 00, Czech Republic
- IT4Innovations, VSB−Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba 708 00, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
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6
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Šponer JE, Šponer J, Výravský J, Matyášek R, Kovařík A, Dudziak W, Ślepokura K. Crystallization as a selection force at the polymerization of nucleotides in a prebiotic context. iScience 2023; 26:107600. [PMID: 37664611 PMCID: PMC10470394 DOI: 10.1016/j.isci.2023.107600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/14/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
Accumulation and selection of nucleotides is one of the most challenging problems surrounding the origin of the first RNA molecules on our planet. In the current work we propose that guanosine 3',5' cyclic monophosphate could selectively crystallize upon evaporation of an acidic prebiotic pool containing various other nucleotides. The conditions of the evaporative crystallization are fully compatible with the subsequent acid catalyzed polymerization of this cyclic nucleotide reported in earlier studies and may be relevant in a broad range of possible prebiotic environments. Albeit cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate under the same conditions, its crystal structure is not likely to support polymer formation.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o, Libušina třída 1, 62300 Brno, Czech Republic
- Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137 Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
| | - Wojciech Dudziak
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
| | - Katarzyna Ślepokura
- University of Wrocław, Faculty of Chemistry, 14 F. Joliot-Curie, 50-383 Wrocław, Poland
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7
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Stadlbauer P, Mlýnský V, Krepl M, Šponer J. Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. J Chem Inf Model 2023; 63:4716-4731. [PMID: 37458574 PMCID: PMC10428220 DOI: 10.1021/acs.jcim.3c00171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 08/15/2023]
Abstract
Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we performed steered molecular dynamics simulations of human telomeric GQs to study their unfolding. We examined four pulling regimes, including a very slow setup with pulling velocity and force load accessible to high-speed atomic force microscopy. We identified multiple factors affecting the unfolding mechanism, i.e.,: (i) the more the direction of force was perpendicular to the GQ channel axis (determined by GQ topology), the more the base unzipping mechanism happened, (ii) the more parallel the direction of force was, GQ opening and cross-like GQs were more likely to occur, (iii) strand slippage mechanism was possible for GQs with an all-anti pattern in a strand, and (iv) slower pulling velocity led to richer structural dynamics with sampling of more intermediates and partial refolding events. We also identified that a GQ may eventually unfold after a force drop under forces smaller than those that the GQ withstood before the drop. Finally, we found out that different unfolding intermediates could have very similar chain end-to-end distances, which reveals some limitations of structural interpretations of single-molecule spectroscopic data.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
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8
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Love O, Galindo-Murillo R, Zgarbová M, Šponer J, Jurečka P, Cheatham TE. Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition. J Chem Theory Comput 2023. [PMID: 37340948 DOI: 10.1021/acs.jctc.3c00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields. The reproducibility and accuracy of the force fields are imperative in order to produce biologically relevant data. The Amber nucleic acid force fields have been used widely since the mid-1980s, and improvement of these force fields has been a community effort with several artifacts revealed, corrected, and reevaluated by various research groups. Here, we focus on the Amber force fields for use with double-stranded DNA and present the assessment of two recently developed force field parameter sets (OL21 and Tumuc1). Extensive MD simulations were performed with six test systems and two different water models. We observe the improvement of OL21 and Tumuc1 compared to previous generations of the Amber DNA force. We did not detect any significant improvement in the performance of Tumuc1 compared to OL21 despite the reparameterization of bonded force field terms in the former; however, we did note discrepancies in Tumuc1 when modeling Z-DNA sequences.
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Affiliation(s)
- Olivia Love
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs 105, Salt Lake City, Utah 84112, United States
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, California 92010, United States
| | - Marie Zgarbová
- Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc 77146, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 65, Czech Republic
| | - Petr Jurečka
- Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, Olomouc 77146, Czech Republic
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South, Skaggs 105, Salt Lake City, Utah 84112, United States
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9
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Zhang Z, Šponer J, Bussi G, Mlýnský V, Šulc P, Simmons CR, Stephanopoulos N, Krepl M. Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. J Chem Inf Model 2023; 63:2794-2809. [PMID: 37126365 PMCID: PMC10170514 DOI: 10.1021/acs.jcim.3c00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Holliday junction (HJ) is a noncanonical four-way DNA structure with a prominent role in DNA repair, recombination, and DNA nanotechnology. By rearranging its four arms, HJ can adopt either closed or open state. With enzymes typically recognizing only a single state, acquiring detailed knowledge of the rearrangement process is an important step toward fully understanding the biological function of HJs. Here, we carried out standard all-atom molecular dynamics (MD) simulations of the spontaneous opening-closing transitions, which revealed complex conformational transitions of HJs with an involvement of previously unconsidered "half-closed" intermediates. Detailed free-energy landscapes of the transitions were obtained by sophisticated enhanced sampling simulations. Because the force field overstabilizes the closed conformation of HJs, we developed a system-specific modification which for the first time allows the observation of spontaneous opening-closing HJ transitions in unbiased MD simulations and opens the possibilities for more accurate HJ computational studies of biological processes and nanomaterials.
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Affiliation(s)
- Zhengyue Zhang
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Petr Šulc
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, 1001 S. McAllister Ave, Tempe, 85287 Arizona, United States
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 241/27, 783 71 Olomouc, Czech Republic
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10
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Kührová P, Mlýnský V, Otyepka M, Šponer J, Banáš P. Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes. J Chem Inf Model 2023; 63:2133-2146. [PMID: 36989143 PMCID: PMC10091408 DOI: 10.1021/acs.jcim.2c01438] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
RNA molecules play a key role in countless biochemical processes. RNA interactions, which are of highly diverse nature, are determined by the fact that RNA is a highly negatively charged polyelectrolyte, which leads to intimate interactions with an ion atmosphere. Although RNA molecules are formally single-stranded, canonical (Watson-Crick) duplexes are key components of folded RNAs. A double-stranded (ds) RNA is also important for the design of RNA-based nanostructures and assemblies. Despite the fact that the description of canonical dsRNA is considered the least problematic part of RNA modeling, the imperfect shape and flexibility of dsRNA can lead to imbalances in the simulations of larger RNAs and RNA-containing assemblies. We present a comprehensive set of molecular dynamics (MD) simulations of four canonical A-RNA duplexes. Our focus was directed toward the characterization of the influence of varying ion concentrations and of the size of the solvation box. We compared several water models and four RNA force fields. The simulations showed that the A-RNA shape was most sensitive to the RNA force field, with some force fields leading to a reduced inclination of the A-RNA duplexes. The ions and water models played a minor role. The effect of the box size was negligible, and even boxes with a small fraction of the bulk solvent outside the RNA hydration sphere were sufficient for the simulation of the dsRNA.
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Affiliation(s)
- Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- IT4Innovations, VSB - Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Poruba, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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11
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Mráziková K, Kruse H, Mlýnský V, Auffinger P, Šponer J. Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. J Chem Inf Model 2022; 62:6182-6200. [PMID: 36454943 DOI: 10.1021/acs.jcim.2c01064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phosphate···π, also called anion···π, contacts occur between nucleobases and anionic phosphate oxygens (OP2) in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These contacts were investigated using state-of-the-art quantum-chemical methods (QM) to characterize their physicochemical properties and to serve as a reference to evaluate AMBER force field (AFF) performance. We found that phosphate···π interaction energies calculated with the AFF for dimethyl phosphate···nucleobase model systems are less stabilizing in comparison with double-hybrid DFT and that minimum contact distances are larger for all nucleobases. These distance stretches are also observed in large-scale AFF vs QM/MM computations and classical molecular dynamics (MD) simulations on several r(gcGNRAgc) tetraloop hairpins when compared to experimental data extracted from X-ray/cryo-EM structures (res. ≤ 2.5 Å) using the WebFR3D bioinformatic tool. MD simulations further revealed shifted OP2/nucleobase positions. We propose that discrepancies between the QM and AFF result from a combination of missing polarization in the AFF combined with too large AFF Lennard-Jones (LJ) radii of nucleobase carbon atoms in addition to an exaggerated short-range repulsion of the r-12 LJ repulsive term. We compared these results with earlier data gathered on lone pair···π contacts in CpG Z-steps occurring in r(UNCG) tetraloops. In both instances, charge transfer calculations do not support any significant n → π* donation effects. We also investigated thiophosphate···π contacts that showed reduced stabilizing interaction energies when compared to phosphate···π contacts. Thus, we challenge suggestions that the experimentally observed enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops can be explained by larger London dispersion.
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Affiliation(s)
- Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg67084, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
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12
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. Small 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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13
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Krepl M, Pokorná P, Mlýnský V, Stadlbauer P, Šponer J. Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field. Nucleic Acids Res 2022; 50:12480-12496. [PMID: 36454011 PMCID: PMC9757038 DOI: 10.1093/nar/gkac1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography techniques, revealing ensemble-averaged pictures of the bound states. However, it is becoming widely accepted that better understanding of protein-RNA interactions would be obtained from ensemble descriptions. Indeed, earlier molecular dynamics simulations of bound states indicated visible dynamics at the RNA-RRM interfaces. Here, we report the first atomistic simulation study of spontaneous binding of short RNA sequences to RRM domains of HuR and SRSF1 proteins. Using a millisecond-scale aggregate ensemble of unbiased simulations, we were able to observe a few dozen binding events. HuR RRM3 utilizes a pre-binding state to navigate the RNA sequence to its partially disordered bound state and then to dynamically scan its different binding registers. SRSF1 RRM2 binding is more straightforward but still multiple-pathway. The present study necessitated development of a goal-specific force field modification, scaling down the intramolecular van der Waals interactions of the RNA which also improves description of the RNA-RRM bound state. Our study opens up a new avenue for large-scale atomistic investigations of binding landscapes of protein-RNA complexes, and future perspectives of such research are discussed.
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Affiliation(s)
| | - Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic,National Center for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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14
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Pokorná P, Krepl M, Campagne S, Šponer J. Conformational Heterogeneity of RNA Stem-Loop Hairpins Bound to FUS-RNA Recognition Motif with Disordered RGG Tail Revealed by Unbiased Molecular Dynamics Simulations. J Phys Chem B 2022; 126:9207-9221. [PMID: 36348631 DOI: 10.1021/acs.jpcb.2c06168] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
RNA-protein complexes use diverse binding strategies, ranging from structurally well-defined interfaces to completely disordered regions. Experimental characterization of flexible segments is challenging and can be aided by atomistic molecular dynamics (MD) simulations. Here, we used an extended set of microsecond-scale MD trajectories (400 μs in total) to study two FUS-RNA constructs previously characterized by nuclear magnetic resonance (NMR) spectroscopy. The FUS protein contains a well-structured RNA recognition motif domain followed by a presumably disordered RGG tail that binds RNA stem-loop hairpins. Our simulations not only provide several suggestions complementing the experiments but also reveal major methodological difficulties in studies of such complex RNA-protein interfaces. Despite efforts to stabilize the binding via system-specific force-field adjustments, we have observed progressive distortions of the RNA-protein interface inconsistent with experimental data. We propose that the dynamics is so rich that its converged description is not achievable even upon stabilizing the system. Still, after careful analysis of the trajectories, we have made several suggestions regarding the binding. We identify substates in the RNA loops, which can explain the NMR data. The RGG tail localized in the minor groove remains disordered, sampling countless transient interactions with the RNA. There are long-range couplings among the different elements contributing to the recognition, which can lead to allosteric communication throughout the system. Overall, the RNA-FUS systems form dynamical ensembles that cannot be fully represented by single static structures. Thus, albeit imperfect, MD simulations represent a viable tool to investigate dynamic RNA-protein complexes.
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Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Sébastien Campagne
- INSERM U1212, CNRS UMR 5320, ARNA Laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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15
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Fröhlking T, Mlýnský V, Janeček M, Kührová P, Krepl M, Banáš P, Šponer J, Bussi G. Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. J Chem Theory Comput 2022; 18:4490-4502. [PMID: 35699952 PMCID: PMC9281393 DOI: 10.1021/acs.jctc.2c00200] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
The
capability of
current force fields to reproduce RNA structural
dynamics is limited. Several methods have been developed to take advantage
of experimental data in order to enforce agreement with experiments.
Here, we extend an existing framework which allows arbitrarily chosen
force-field correction terms to be fitted by quantification of the
discrepancy between observables back-calculated from simulation and
corresponding experiments. We apply a robust regularization protocol
to avoid overfitting and additionally introduce and compare a number
of different regularization strategies, namely, L1, L2, Kish size,
relative Kish size, and relative entropy penalties. The training set
includes a GACC tetramer as well as more challenging systems, namely,
gcGAGAgc and gcUUCGgc RNA tetraloops. Specific intramolecular hydrogen
bonds in the AMBER RNA force field are corrected with automatically
determined parameters that we call gHBfixopt. A validation
involving a separate simulation of a system present in the training
set (gcUUCGgc) and new systems not seen during training (CAAU and
UUUU tetramers) displays improvements regarding the native population
of the tetraloop as well as good agreement with NMR experiments for
tetramers when using the new parameters. Then, we simulate folded
RNAs (a kink–turn and L1 stalk rRNA) including hydrogen bond
types not sufficiently present in the training set. This allows a
final modification of the parameter set which is named gHBfix21 and
is suggested to be applicable to a wider range of RNA systems.
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Affiliation(s)
- Thorben Fröhlking
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 65, Czech Republic
| | - Michal Janeček
- Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, Olomouc 771 46, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 65, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 65, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Slechtitelu 27, 779 00 Olomouc, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste 34136, Italy
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16
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Janicki MJ, Szabla R, Šponer J, Góra RW. Photoinduced water-chromophore electron transfer causes formation of guanosine photodamage. Phys Chem Chem Phys 2022; 24:8217-8224. [PMID: 35319053 DOI: 10.1039/d2cp00801g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-induced photolysis of aqueous guanine nucleosides produces 8-oxo-guanine and Fapy-guanine, which can induce various types of cellular malfunction. The mechanistic rationale underlying photodestructive processes of guanine nucleosides is still largely obscure. Here, we employ accurate quantum chemical calculations and demonstrate that an excited-state non-bonding interaction of guanosine and a water molecule facilitates the electron-driven proton transfer process from water to the chromophore fragment. This subsequently allows for the formation of a crucial intermediate, namely guanosine photohydrate. Further (photo)chemical reactions of this intermediate lead to the known products of guanine photodamage.
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Affiliation(s)
- Mikołaj J Janicki
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Rafał Szabla
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Robert W Góra
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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17
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Mlýnský V, Janeček M, Kührová P, Fröhlking T, Otyepka M, Bussi G, Banáš P, Šponer J. Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications. J Chem Theory Comput 2022; 18:2642-2656. [PMID: 35363478 DOI: 10.1021/acs.jctc.1c01222] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic molecular dynamics simulations represent an established technique for investigation of RNA structural dynamics. Despite continuous development, contemporary RNA simulations still suffer from suboptimal accuracy of empirical potentials (force fields, ffs) and sampling limitations. Development of efficient enhanced sampling techniques is important for two reasons. First, they allow us to overcome the sampling limitations, and second, they can be used to quantify ff imbalances provided they reach a sufficient convergence. Here, we study two RNA tetraloops (TLs), namely the GAGA and UUCG motifs. We perform extensive folding simulations and calculate folding free energies (ΔGfold°) with the aim to compare different enhanced sampling techniques and to test several modifications of the nonbonded terms extending the AMBER OL3 RNA ff. We demonstrate that replica-exchange solute tempering (REST2) simulations with 12-16 replicas do not show any sign of convergence even when extended to a timescale of 120 μs per replica. However, the combination of REST2 with well-tempered metadynamics (ST-MetaD) achieves good convergence on a timescale of 5-10 μs per replica, improving the sampling efficiency by at least 2 orders of magnitude. Effects of ff modifications on ΔGfold° energies were initially explored by the reweighting approach and then validated by new simulations. We tested several manually prepared variants of the gHBfix potential which improve stability of the native state of both TLs by ∼2 kcal/mol. This is sufficient to conveniently stabilize the folded GAGA TL while the UUCG TL still remains under-stabilized. Appropriate adjustment of van der Waals parameters for C-H···O5' base-phosphate interaction may further stabilize the native states of both TLs by ∼0.6 kcal/mol.
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Affiliation(s)
- Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Janeček
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Thorben Fröhlking
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic.,IT4Innovations, VSB─Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava-Poruba, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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18
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Matoušková E, Dršata T, Pfeifferová L, Šponer J, Réblová K, Lankaš F. RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems. Biophys J 2022; 121:705-714. [PMID: 35122735 PMCID: PMC8943727 DOI: 10.1016/j.bpj.2022.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/23/2021] [Accepted: 01/28/2022] [Indexed: 11/02/2022] Open
Abstract
Kink-turns are highly bent internal loop motifs commonly found in the ribosome and other RNA complexes. They frequently act as binding sites for proteins and mediate tertiary interactions in larger RNA structures. Kink-turns have been a topic of intense research, but their elastic properties in the folded state are still poorly understood. Here we use extensive all-atom molecular dynamics simulations to parameterize a model of kink-turn in which the two flanking helical stems are represented by effective rigid bodies. Time series of the full set of six interhelical coordinates enable us to extract minimum energy shapes and harmonic stiffness constants for kink-turns from different RNA functional classes. The analysis suggests that kink-turns exhibit isotropic bending stiffness but are highly anisotropic with respect to lateral displacement of the stems. The most flexible lateral displacement mode is perpendicular to the plane of the static bend. These results may help understand the structural adaptation and mechanical signal transmission by kink-turns in complex natural and artificial RNA structures.
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Affiliation(s)
- Eva Matoušková
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Dršata
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Lucie Pfeifferová
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Kamila Réblová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Centre of Molecular Biology and Genetics, University Hospital Brno, Czech Republic.
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology, Prague, Czech Republic.
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19
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Asha H, Stadlbauer P, Martínez-Fernández L, Banáš P, Šponer J, Improta R, Esposito L. Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine. Int J Biol Macromol 2022; 194:882-894. [PMID: 34838862 DOI: 10.1016/j.ijbiomac.2021.11.143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022]
Abstract
Guanine radical cation (G•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)3 (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G•+ (Tel21+). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21+ systems, differing in the position of G•+ in the sequence. When G•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na+ ions and increase the solvent exposed surface of G•+. Analysis of solvation patterns of G•+ provides new insights on the main reactions of G•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.
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Affiliation(s)
- Haritha Asha
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Lara Martínez-Fernández
- Departamento de Quimica, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autonoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 8, 779 00 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
| | - Luciana Esposito
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
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20
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Wunnava S, Dirscherl CF, Výravský J, Kovařík A, Matyášek R, Šponer J, Braun D, Šponer JE. Cover Feature: Acid‐Catalyzed RNA‐Oligomerization from 3’,5’‐cGMP (Chem. Eur. J. 70/2021). Chemistry 2021. [DOI: 10.1002/chem.202104216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sreekar Wunnava
- Department of Physics NanoSystems Initiative Munich and Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Christina F. Dirscherl
- Department of Physics NanoSystems Initiative Munich and Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Jakub Výravský
- Tescan Brno s.r.o. Libušina třída 1 62300 Brno Czech Republic
- Department of Geological Sciences Faculty of Science Masaryk University Kotlářská 2 61137 Brno Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics Academy of Sciences of the Czech Republic Královopolská 135 61265 Brno Czech Republic
| | - Roman Matyášek
- Institute of Biophysics Academy of Sciences of the Czech Republic Královopolská 135 61265 Brno Czech Republic
| | - Jiří Šponer
- Institute of Biophysics Academy of Sciences of the Czech Republic Královopolská 135 61265 Brno Czech Republic
| | - Dieter Braun
- Department of Physics NanoSystems Initiative Munich and Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Judit E. Šponer
- Institute of Biophysics Academy of Sciences of the Czech Republic Královopolská 135 61265 Brno Czech Republic
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21
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Smith DGA, Lolinco AT, Glick ZL, Lee J, Alenaizan A, Barnes TA, Borca CH, Di Remigio R, Dotson DL, Ehlert S, Heide AG, Herbst MF, Hermann J, Hicks CB, Horton JT, Hurtado AG, Kraus P, Kruse H, Lee SJR, Misiewicz JP, Naden LN, Ramezanghorbani F, Scheurer M, Schriber JB, Simmonett AC, Steinmetzer J, Wagner JR, Ward L, Welborn M, Altarawy D, Anwar J, Chodera JD, Dreuw A, Kulik HJ, Liu F, Martínez TJ, Matthews DA, Schaefer HF, Šponer J, Turney JM, Wang LP, De Silva N, King RA, Stanton JF, Gordon MS, Windus TL, Sherrill CD, Burns LA. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. J Chem Phys 2021; 155:204801. [PMID: 34852489 DOI: 10.1063/5.0059356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.
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Affiliation(s)
- Daniel G A Smith
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | | | - Zachary L Glick
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Jiyoung Lee
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Taylor A Barnes
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Carlos H Borca
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical and Computational Chemistry, UiT, The Arctic University of Norway, N-9037 Tromsø, Norway
| | - David L Dotson
- Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Alexander G Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Michael F Herbst
- Applied and Computational Mathematics, RWTH Aachen University, Schinkelstr. 2, 52062 Aachen, Germany
| | - Jan Hermann
- FU Berlin, Department of Mathematics and Computer Science, 14195 Berlin, Germany
| | - Colton B Hicks
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Joshua T Horton
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - Adrian G Hurtado
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794-5250, USA
| | - Peter Kraus
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth 6845, WA, Australia
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | | | - Jonathon P Misiewicz
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Levi N Naden
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | | | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Jeffrey B Schriber
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Andrew C Simmonett
- Laboratory of Computational Biology, National Institutes of Health-National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, USA
| | - Johannes Steinmetzer
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Jeffrey R Wagner
- Open Force Field Initiative, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Logan Ward
- Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Matthew Welborn
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Doaa Altarawy
- Molecular Sciences Software Institute, Blacksburg, Virginia 24060, USA
| | - Jamshed Anwar
- Department of Chemistry, Lancaster University, Lancaster LA1 4YW, United Kingdom
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Fang Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Todd J Martínez
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Devin A Matthews
- The Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California Davis, Davis, California 95616, USA
| | - Nuwan De Silva
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Rollin A King
- Department of Chemistry, Bethel University, St. Paul, Minnesota 55112, USA
| | - John F Stanton
- Quantum Theory Project, The University of Florida, 2328 New Physics Building, Gainesville, Florida 32611-8435, USA
| | - Mark S Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Theresa L Windus
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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22
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Mráziková K, Šponer J, Mlýnský V, Auffinger P, Kruse H. Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids. J Chem Inf Model 2021; 61:5644-5657. [PMID: 34738826 DOI: 10.1021/acs.jcim.1c01047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lone-pair···π (lp···π) (deoxy)ribose···nucleobase stacking is a recurring interaction in Z-DNA and RNAs that is characterized by sub-van der Waals lp···π contacts (<3.0 Å). It is a part of the structural signature of CpG Z-step motifs in Z-DNA and r(UNCG) tetraloops that are known to behave poorly in molecular dynamics (MD) simulations. Although the exact origin of the MD simulation issues remains unclear, a significant part of the problem might be due to an imbalanced description of nonbonded interactions, including the characteristic lp···π stacking. To gain insights into the links between lp···π stacking and MD, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the nonbonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, and U). Among other differences, we found that the AFF overestimates the DHDF-D3 lp···π distances by ∼0.1-0.2 Å, while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule polarizabilities and symmetry-adapted perturbation theory analysis, we inferred that the DHDF-D3 versus AFF differences partly originate in identical nucleobase carbon atom Lennard-Jones (LJ) parameters despite the presence/absence of connected electron-withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp···π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.
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Affiliation(s)
- Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Pascal Auffinger
- Architecture and Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS, 67084 Strasbourg, France
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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23
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Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 65
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27, Olomouc – Holice 783 71
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 65
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27, Olomouc – Holice 783 71
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 612 65
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau 91128
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023
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24
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Wunnava S, Dirscherl CF, Výravský J, Kovařík A, Matyášek R, Šponer J, Braun D, Šponer JE. Acid-Catalyzed RNA-Oligomerization from 3',5'-cGMP. Chemistry 2021; 27:17581-17585. [PMID: 34726799 PMCID: PMC9299008 DOI: 10.1002/chem.202103672] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 11/28/2022]
Abstract
The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3’,5’‐cyclic guanosine monophosphate (3’,5’‐cGMP) has been proposed as a candidate to create oligonucleotides of 15–20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9.
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Affiliation(s)
- Sreekar Wunnava
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Christina F Dirscherl
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Jakub Výravský
- Tescan Brno s.r.o., Libušina třída 1, 62300, Brno, Czech Republic.,Department of Geological Sciences, Faculty of Science, Masaryk University, Kotlářská 2, 61137, Brno, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Roman Matyášek
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
| | - Dieter Braun
- Department of Physics, NanoSystems Initiative Munich and Center for Nanoscience, Ludwig-Maximilians-Universität München, Amalienstrasse 54, 80799, Munich, Germany
| | - Judit E Šponer
- Institute of Biophysics Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
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25
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Zgarbová M, Šponer J, Jurečka P. Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER. J Chem Theory Comput 2021; 17:6292-6301. [PMID: 34582195 DOI: 10.1021/acs.jctc.1c00697] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although current AMBER force fields are relatively accurate for canonical B-DNA, many noncanonical structures are still described incorrectly. As noncanonical motifs are attracting increasing attention due to the role they play in living organisms, further improvement is desirable. Here, we have chosen the Z-DNA molecule, which can be considered a touchstone of the universality of empirical force fields, since the noncanonical α and γ backbone conformations native to Z-DNA are also found in protein-DNA complexes, i-motif DNA, and other noncanonical DNAs. We show that spurious α/γ conformations occurring in simulations with current AMBER force fields, OL15 and bsc1, are largely due to inaccurate α/γ parametrization. Moreover, stabilization of native Z-DNA substates involving γ = trans conformations appears to be in conflict with the correct description of the canonical B-DNA structure. Because the balance of the native and spurious conformations is influenced by nonadditive effects, this is a difficult case for an additive dihedral energy scheme such as AMBER. We propose new α/γ parameters, denoted OL21, and show that they improve the stability of native α/γ Z-DNA substates while keeping the canonical DNA description virtually unchanged, thus representing a reasonable compromise within the additive force field framework. Although further extensive testing is needed, the new modification appears to be a promising step toward a more reliable description of noncanonical DNA motifs and provides the best performance for Z-DNA molecules among current AMBER force fields.
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Affiliation(s)
- Marie Zgarbová
- Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Jurečka
- Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 77146 Olomouc, Czech Republic
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26
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Kejnovská I, Stadlbauer P, Trantírek L, Renčiuk D, Gajarský M, Krafčík D, Palacký J, Bednářová K, Šponer J, Mergny JL, Vorlíčková M. G-Quadruplex Formation by DNA Sequences Deficient in Guanines: Two Tetrad Parallel Quadruplexes Do Not Fold Intramolecularly. Chemistry 2021; 27:12115-12125. [PMID: 34145655 DOI: 10.1002/chem.202100895] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 02/05/2023]
Abstract
Guanine quadruplexes (G4s) are noncanonical forms of nucleic acids that are frequently found in genomes. The stability of G4s depends, among other factors, on the number of G-tetrads. Three- or four-tetrad G4s and antiparallel two-tetrad G4s have been characterized experimentally; however, the existence of an intramolecular (i. e., not dimeric or multimeric) two-tetrad parallel-stranded DNA G4 has never been experimentally observed. Many sequences compatible with two-tetrad G4 can be found in important genomic regions, such as promoters, for which parallel G4s predominate. Using experimental and theoretical approaches, the propensity of the model sequence AATGGGTGGGTTTGGGTGGGTAA to form an intramolecular parallel-stranded G4 upon increasing the number of GGG-to-GG substitutions has been studied. Deletion of a single G leads to the formation of intramolecular G4s with a stacked G-triad, whose topology depends on the location of the deletion. Removal of another guanine from another G-tract leads to di- or multimeric G4s. Further deletions mostly prevent the formation of any stable G4. Thus, a solitary two-tetrad parallel DNA G4 is not thermodynamically stable and requires additional interactions through capping residues. However, transiently populated metastable two-tetrad species can associate to form stable dimers, the dynamic formation of which might play additional delicate roles in gene regulation. These findings provide essential information for bioinformatics studies searching for potential G4s in genomes.
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Affiliation(s)
- Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/3, 625 00, Brno, Czech Republic
| | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Martin Gajarský
- Central European Institute of Technology, Masaryk University, Kamenice 753/3, 625 00, Brno, Czech Republic
| | - Daniel Krafčík
- Central European Institute of Technology, Masaryk University, Kamenice 753/3, 625 00, Brno, Czech Republic
| | - Jan Palacký
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Klára Bednářová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65, Brno, Czech Republic
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27
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Chen J, Cheng M, Salgado GF, Stadlbauer P, Zhang X, Amrane S, Guédin A, He F, Šponer J, Ju H, Mergny JL, Zhou J. The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology. Nucleic Acids Res 2021; 49:9548-9559. [PMID: 34379785 PMCID: PMC8450091 DOI: 10.1093/nar/gkab681] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/25/2021] [Accepted: 07/27/2021] [Indexed: 11/24/2022] Open
Abstract
Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core are often omitted. Herein, we systematically studied the effects of flanking nucleotides on structural polymorphism of 371 different oligodeoxynucleotides that adopt intramolecular G4 structures. We found out that the addition of nucleotides favors the formation of a parallel fold, defined as the ‘flanking effect’ in this work. This ‘flanking effect’ was more pronounced when nucleotides were added at the 5′-end, and depended on loop arrangement. NMR experiments and molecular dynamics simulations revealed that flanking sequences at the 5′-end abolish a strong syn-specific hydrogen bond commonly found in non-parallel conformations, thus favoring a parallel topology. These analyses pave a new way for more accurate prediction of DNA G4 folding in a physiological context.
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Affiliation(s)
- Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing210023, China
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing210023, China.,ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, IECB, Pessac33607, France
| | - Gilmar F Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, IECB, Pessac33607, France
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27,783 71, Olomouc - Holice, Czech Republic
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing210023, China
| | - Samir Amrane
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, IECB, Pessac33607, France
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, IECB, Pessac33607, France
| | - Fangni He
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing210023, China
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27,783 71, Olomouc - Holice, Czech Republic
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing210023, China
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing210023, China.,ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, IECB, Pessac33607, France.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128Palaiseau cedex, France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing210023, China
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28
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Šponer JE, Šponer J, Kovařík A, Šedo O, Zdráhal Z, Costanzo G, Di Mauro E. Questions and Answers Related to the Prebiotic Production of Oligonucleotide Sequences from 3',5' Cyclic Nucleotide Precursors. Life (Basel) 2021; 11:800. [PMID: 34440544 PMCID: PMC8400769 DOI: 10.3390/life11080800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/03/2023] Open
Abstract
Template-free nonenzymatic polymerization of 3',5' cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry.
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Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic; (J.Š.); (A.K.)
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (O.Š.); (Z.Z.)
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic; (O.Š.); (Z.Z.)
| | - Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR, Piazzale A. Moro 5, 00185 Rome, Italy; (G.C.); (E.D.M.)
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR, Piazzale A. Moro 5, 00185 Rome, Italy; (G.C.); (E.D.M.)
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29
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Janicki M, Kufner CL, Todd ZR, Kim SC, O’Flaherty DK, Szostak JW, Šponer J, Góra RW, Sasselov DD, Szabla R. Ribose Alters the Photochemical Properties of the Nucleobase in Thionated Nucleosides. J Phys Chem Lett 2021; 12:6707-6713. [PMID: 34260253 PMCID: PMC9634911 DOI: 10.1021/acs.jpclett.1c01384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Substitution of exocyclic oxygen with sulfur was shown to substantially influence the properties of RNA/DNA bases, which are crucial for prebiotic chemistry and photodynamic therapies. Upon UV irradiation, thionucleobases were shown to efficiently populate triplet excited states and can be involved in characteristic photochemistry or generation of singlet oxygen. Here, we show that the photochemistry of a thionucleobase can be considerably modified in a nucleoside, that is, by the presence of ribose. Our transient absorption spectroscopy experiments demonstrate that thiocytosine exhibits 5 times longer excited-state lifetime and different excited-state absorption features than thiocytidine. On the basis of accurate quantum chemical simulations, we assign these differences to the dominant population of a shorter-lived triplet nπ* state in the nucleoside and longer-lived triplet ππ* states in the nucleobase. This explains the distinctive photoanomerziation of thiocytidine and indicates that the nucleoside will be a less efficient phototherapeutic agent with regard to singlet oxygen generation.
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Affiliation(s)
- Mikołaj
J. Janicki
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Corinna L. Kufner
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Zoe R. Todd
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Seohyun C. Kim
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Derek K. O’Flaherty
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Molecular Biology and Center
for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jiří Šponer
- Institute
of Biophysics, Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech
Republic
- Regional
Centre of Advanced Technologies and Materials, Czech Advanced Technology
and Research Institute (CATRIN), Palacky
University Olomouc, Slechtitelu
241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Robert W. Góra
- Department
of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego
27, 50-370 Wrocław, Poland
| | - Dimitar D. Sasselov
- Department
of Astronomy, Harvard-Smithsonian Center
for Astrophysics, 60 Garden Street, Cambridge, Massachusetts 02138, United States
| | - Rafał Szabla
- EaStCHEM,
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh EH9 3FJ, U.K.
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30
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Krepl M, Damberger FF, von Schroetter C, Theler D, Pokorná P, Allain FHT, Šponer J. Recognition of N6-Methyladenosine by the YTHDC1 YTH Domain Studied by Molecular Dynamics and NMR Spectroscopy: The Role of Hydration. J Phys Chem B 2021; 125:7691-7705. [PMID: 34258996 DOI: 10.1021/acs.jpcb.1c03541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The YTH domain of YTHDC1 belongs to a class of protein "readers", recognizing the N6-methyladenosine (m6A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage. Here, we performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) to examine how dynamics and solvent interactions contribute to the m6A recognition and negative selectivity toward an unmethylated substrate. The structured water molecules surrounding the bound RNA and the methylated substrate's ability to exclude bulk water molecules contribute to the YTH domain's preference for m6A. Intrusions of bulk water deep into the binding pocket disrupt binding of unmethylated adenosine. The YTHDC1's preference for the 5'-Gm6A-3' motif is partially facilitated by a network of water-mediated interactions between the 2-amino group of the guanosine and residues in the m6A binding pocket. The 5'-Im6A-3' (where I is inosine) motif can be recognized too, but disruption of the water network lowers affinity. The D479A mutant also disrupts the water network and destabilizes m6A binding. Our interdisciplinary study of the YTHDC1 protein-RNA complex reveals an unusual physical mechanism by which solvent interactions contribute toward m6A recognition.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Fred Franz Damberger
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Dominik Theler
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Olomouc 783 71, Czech Republic
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31
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Šponer JE, Šponer J, Výravský J, Šedo O, Zdráhal Z, Costanzo G, Di Mauro E, Wunnava S, Braun D, Matyášek R, Kovařík A. Nonenzymatic, Template‐Free Polymerization of 3’,5’ Cyclic Guanosine Monophosphate on Mineral Surfaces. ChemSystemsChem 2021. [DOI: 10.1002/syst.202100017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jakub Výravský
- TESCAN Brno, s.r.o. Libušina třída 1 62300 Brno Czech Republic
- Department of Geological Sciences Faculty of Science Masaryk University Kotlářská 2 61137 Brno Czech Republic
| | - Ondrej Šedo
- Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology Masaryk University Kamenice 5 62500 Brno Czech Republic
| | - Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Sreekar Wunnava
- Physics Department Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Dieter Braun
- Physics Department Center for Nanoscience Ludwig-Maximilians-Universität München Amalienstrasse 54 80799 Munich Germany
| | - Roman Matyášek
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
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32
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Ferus M, Cassone G, Táborský V, Heays A, Petera L, Knížek A, Kalvoda T, Bouša M, Šponer J, Šponer JE, Kubelík P, Drápal J, Stehlík J, Civiš S. Thermal Decomposition of Cocaine and Methamphetamine Investigated by Infrared Spectroscopy and Quantum Chemical Simulations. ACS Omega 2021; 6:14447-14457. [PMID: 34124467 PMCID: PMC8190921 DOI: 10.1021/acsomega.1c01325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/13/2021] [Indexed: 05/16/2023]
Abstract
Examination of thermal decomposition of street samples of cocaine and methamphetamine shows that typical products detected in previous studies are accompanied by a wide palette of simple volatile compounds easily detectable by spectral techniques. These molecules increase smoke toxicity and their spectral detection can be potentially used for identification of drug samples by well-controlled laboratory thermolysis in temperature progression. In our study, street samples of cocaine and methamphetamine have been thermolyzed under vacuum over the temperature range of 350-650 °C. The volatile products (CO, HCN, CH4, C2H4, etc.) have been monitored by high-resolution Fourier-transform infrared (FTIR) spectrometry in this temperature range. The decomposition mechanism has been additionally examined theoretically by quantum-chemical calculations for the highest temperature achieved experimentally in our study and beyond. Prior to analysis, the street samples have also been characterized by FTIR, Raman spectroscopy, energy-dispersive X-ray spectroscopy, and melting point determination.
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Affiliation(s)
- Martin Ferus
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
- . Phone: +420 26605 3685
| | - Giuseppe Cassone
- Institute
for Chemical-Physical Processes, National
Research Council of Italy (IPCF-CNR), Viale F. Stagno d’Alcontres 37, 98158 Messina, Italy
- . Phone: +39 090 39 76 2220
| | - Vladimír Táborský
- Police
Presidium of the Czech Republic, Strojnická 935/27, 170 89 Prague 7, Czech Republic
- , . Phone: +420
974 834 596
| | - Alan Heays
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Lukáš Petera
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
- Faculty
of Science, Department of Inorganic Chemistry, Charles University in Prague, Hlavova 8, CZ12800 Prague 2, Czech Republic
| | - Antonín Knížek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
- Charles
University in Prague, Faculty of Science,
Department of Physical and Macromolecular Chemistry, Hlavova 8, CZ12800 Prague 2, Czech Republic
| | - Tadeáš Kalvoda
- Charles
University in Prague, Faculty of Science,
Department of Physical and Macromolecular Chemistry, Hlavova 8, CZ12800 Prague 2, Czech Republic
| | - Milan Bouša
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech
Republic
| | - Judit E. Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech
Republic
| | - Petr Kubelík
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Jan Drápal
- INTERPOL
General Secretariat, 200 Quai Charles de Gaulle 69006 Lyon, France
| | - Jan Stehlík
- Police
Presidium of the Czech Republic, Strojnická 935/27, 170 89 Prague 7, Czech Republic
| | - Svatopluk Civiš
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
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33
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Šponer JE, Šponer J. Insoluble organic matter - an "organic" cradle of life: Comment on the paper "Insoluble organic matter in chondrites: Archetypal melanin-like PAH-based multifunctionality at the origin of life?" by Marco d'Ischia et al. Phys Life Rev 2021; 38:135-136. [PMID: 34049815 DOI: 10.1016/j.plrev.2021.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic.
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, CZ-61265 Brno, Czech Republic
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34
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Szabla R, Zdrowowicz M, Spisz P, Green NJ, Stadlbauer P, Kruse H, Šponer J, Rak J. 2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions. Nat Commun 2021; 12:3018. [PMID: 34021158 PMCID: PMC8139960 DOI: 10.1038/s41467-021-23300-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/20/2021] [Indexed: 01/04/2023] Open
Abstract
High-yielding and selective prebiotic syntheses of RNA and DNA nucleotides involve UV irradiation to promote the key reaction steps and eradicate biologically irrelevant isomers. While these syntheses were likely enabled by UV-rich prebiotic environment, UV-induced formation of photodamages in polymeric nucleic acids, such as cyclobutane pyrimidine dimers (CPDs), remains the key unresolved issue for the origins of RNA and DNA on Earth. Here, we demonstrate that substitution of adenine with 2,6-diaminopurine enables repair of CPDs with yields reaching 92%. This substantial self-repairing activity originates from excellent electron donating properties of 2,6-diaminopurine in nucleic acid strands. We also show that the deoxyribonucleosides of 2,6-diaminopurine and adenine can be formed under the same prebiotic conditions. Considering that 2,6-diaminopurine was previously shown to increase the rate of nonenzymatic RNA replication, this nucleobase could have played critical roles in the formation of functional and photostable RNA/DNA oligomers in UV-rich prebiotic environments. UV-induced photodamage that likely occurred during the prebiotic synthesis of DNA and RNA is still an untackled issue for their origin on early Earth. Here, the authors show that substitution of 2,6-diaminopurine for adenine enables repair of cyclobutane pyrimidine dimers with high yields, and demonstrate that both 2,6-diaminopurine and adenine nucleosides can be formed under the same prebiotic conditions.
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Affiliation(s)
- Rafał Szabla
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK. .,Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
| | | | - Paulina Spisz
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | | | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Janusz Rak
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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35
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Janeček M, Kührová P, Mlýnský V, Otyepka M, Šponer J, Banáš P. W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model. J Chem Theory Comput 2021; 17:3495-3509. [PMID: 33999623 DOI: 10.1021/acs.jctc.0c00976] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Representation of electrostatic interactions by a Coulombic pairwise potential between atom-centered partial charges is a fundamental and crucial part of empirical force fields used in classical molecular dynamics simulations. The broad success of the AMBER force-field family originates mainly from the restrained electrostatic potential (RESP) charge model, which derives partial charges to reproduce the electrostatic field around the molecules. However, the description of the electrostatic potential around molecules by standard RESP may be biased for some types of molecules. In this study, we modified the RESP charge derivation model to improve its description of the electrostatic potential around molecules and thus electrostatic interactions in the force field. In particular, we reoptimized the atomic radii for definition of the grid points around the molecule, redesigned the restraining scheme, and included extra point (EP) charges. The RESP fitting was significantly improved for aromatic heterocyclic molecules. Thus, the suggested W-RESP(-EP) charge derivation model shows some potential for improving the performance of the nucleic acid force fields, for which the poor description of nonbonded interactions, such as the underestimated stability of base pairing, is well-established. We also report some preliminary simulation tests (around 1 ms of simulation data) on A-RNA duplexes, tetranucleotides, and tetraloops. The simulations reveal no adverse effects, while the description of base-pairing interactions might be improved. The new charges can thus be used in future attempts to improve the nucleic acid simulation force fields, in combination with reparametrization of the other terms.
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Affiliation(s)
- Michal Janeček
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
| | - Vojtěch Mlýnský
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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36
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Petroff CA, Cassone G, Šponer J, Hutchison GR. Intrinsically Polar Piezoelectric Self-Assembled Oligopeptide Monolayers. Adv Mater 2021; 33:e2007486. [PMID: 33759260 DOI: 10.1002/adma.202007486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Flexible, biocompatible piezoelectric materials are of considerable research interest for a variety of applications, but many suffer from low response or high cost to manufacture. Herein, novel piezoelectric force and touch sensors based on self-assembled monolayers of oligopeptides are presented, which produce large piezoelectric voltage response and are easily manufactured without the need for electrical poling. While the devices generate modest piezoelectric charge constants (d33 ) of up to 9.8 pC N-1 , they exhibit immense piezoelectric voltage constants (g33 ) up to 2 V m N-1 . Furthermore, a flexible device prototype is demonstrated that produces open-circuit voltages of nearly 6 V under gentle bending motion. Improvements in peptide selection and device construction promise to further improve the already outstanding voltage response and open the door to numerous practical applications.
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Affiliation(s)
- Christopher A Petroff
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council, Viale F. Stagno d'Alcontres 37, Messina, 98158, Italy
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno, 61265, Czech Republic
| | - Geoffrey R Hutchison
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA, 15261, USA
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37
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Živković ML, Gajarský M, Beková K, Stadlbauer P, Vicherek L, Petrová M, Fiala R, Rosenberg I, Šponer J, Plavec J, Trantírek L. Insight into formation propensity of pseudocircular DNA G-hairpins. Nucleic Acids Res 2021; 49:2317-2332. [PMID: 33524154 PMCID: PMC7913771 DOI: 10.1093/nar/gkab029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
We recently showed that Saccharomyces cerevisiae telomeric DNA can fold into an unprecedented pseudocircular G-hairpin (PGH) structure. However, the formation of PGHs in the context of extended sequences, which is a prerequisite for their function in vivo and their applications in biotechnology, has not been elucidated. Here, we show that despite its ‘circular’ nature, PGHs tolerate single-stranded (ss) protrusions. High-resolution NMR structure of a novel member of PGH family reveals the atomistic details on a junction between ssDNA and PGH unit. Identification of new sequences capable of folding into one of the two forms of PGH helped in defining minimal sequence requirements for their formation. Our time-resolved NMR data indicate a possibility that PGHs fold via a complex kinetic partitioning mechanism and suggests the existence of K+ ion-dependent PGH folding intermediates. The data not only provide an explanation of cation-type-dependent formation of PGHs, but also explain the unusually large hysteresis between PGH melting and annealing noted in our previous study. Our findings have important implications for DNA biology and nanotechnology. Overrepresentation of sequences able to form PGHs in the evolutionary-conserved regions of the human genome implies their functionally important biological role(s).
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Affiliation(s)
- Martina Lenarčič Živković
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,Slovenian NMR Centre, National Institute of Chemistry, Ljubljana SI-1000, Slovenia
| | - Martin Gajarský
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Kateřina Beková
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Lukáš Vicherek
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Šponer
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Brno 61265, Czech Republic
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana SI-1000, Slovenia.,EN-FIST Centre of Excellence, Ljubljana SI-1001, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
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38
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Stadlbauer P, Islam B, Otyepka M, Chen J, Monchaud D, Zhou J, Mergny JL, Šponer J. Insights into G-Quadruplex-Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding. J Chem Theory Comput 2021; 17:1883-1899. [PMID: 33533244 DOI: 10.1021/acs.jctc.0c01176] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enhance its peroxidase activity, creating a G4-DNAzyme. The biocatalytic properties of G4-DNAzymes have been thoroughly studied and used for biosensing purposes. Despite hundreds of applications and massive experimental efforts, the atomistic details of the reaction mechanism remain unclear. To help select between the different hypotheses currently under investigation, we use extended explicit-solvent molecular dynamics (MD) simulations to scrutinize the G4/hemin interaction. We find that besides the dominant conformation in which hemin is stacked atop the external G-quartets, hemin can also transiently bind to the loops and be brought to the external G-quartets through diverse delivery mechanisms. The simulations do not support the catalytic mechanism relying on a wobbling guanine. Similarly, the catalytic role of the iron-bound water molecule is not in line with our results; however, given the simulation limitations, this observation should be considered with some caution. The simulations rather suggest tentative mechanisms in which the external G-quartet itself could be responsible for the unique H2O2-promoted biocatalytic properties of the G4/hemin complexes. Once stacked atop a terminal G-quartet, hemin rotates about its vertical axis while readily sampling shifted geometries where the iron transiently contacts oxygen atoms of the adjacent G-quartet. This dynamics is not apparent from the ensemble-averaged structure. We also visualize transient interactions between the stacked hemin and the G4 loops. Finally, we investigated interactions between hemin and on-pathway folding intermediates of the parallel-stranded G4 fold. The simulations suggest that hemin drives the folding of parallel-stranded G4s from slip-stranded intermediates, acting as a G4 chaperone. Limitations of the MD technique are briefly discussed.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Barira Islam
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 8, 779 00 Olomouc, Czech Republic
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - David Monchaud
- Institut de Chimie Moléculaire (ICMUB), CNRS UMR6302, UBFC, Dijon 21078, France
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.,Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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39
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Zhang Z, Vögele J, Mráziková K, Kruse H, Cang X, Wöhnert J, Krepl M, Šponer J. Phosphorothioate Substitutions in RNA Structure Studied by Molecular Dynamics Simulations, QM/MM Calculations, and NMR Experiments. J Phys Chem B 2021; 125:825-840. [PMID: 33467852 DOI: 10.1021/acs.jpcb.0c10192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Phosphorothioates (PTs) are important chemical modifications of the RNA backbone where a single nonbridging oxygen of the phosphate is replaced with a sulfur atom. PT can stabilize RNAs by protecting them from hydrolysis and is commonly used as a tool to explore their function. It is, however, unclear what basic physical effects PT has on RNA stability and electronic structure. Here, we present molecular dynamics (MD) simulations, quantum mechanical (QM) calculations, and NMR spectroscopy measurements, exploring the effects of PT modifications in the structural context of the neomycin-sensing riboswitch (NSR). The NSR is the smallest biologically functional riboswitch with a well-defined structure stabilized by a U-turn motif. Three of the signature interactions of the U-turn: an H-bond, an anion-π interaction, and a potassium binding site; are formed by RNA phosphates, making the NSR an ideal model for studying how PT affects RNA structure and dynamics. By comparing with high-level QM calculations, we reveal the distinct physical properties of the individual interactions facilitated by the PT. The sulfur substitution, besides weakening the direct H-bond interaction, reduces the directionality of H-bonding while increasing its dispersion and induction components. It also reduces the induction and increases the dispersion component of the anion-π stacking. The sulfur force-field parameters commonly employed in the literature do not reflect these distinctions, leading to the unsatisfactory description of PT in simulations of the NSR. We show that it is not possible to accurately describe the PT interactions using one universal set of van der Waals sulfur parameters and provide suggestions for improving the force-field performance.
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Affiliation(s)
- Zhengyue Zhang
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Faculty of Science, Masaryk University, Kotlarska 2, 602 00 Brno, Czech Republic
| | - Jennifer Vögele
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Klaudia Mráziková
- Faculty of Science, Masaryk University, Kotlarska 2, 602 00 Brno, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Xiaohui Cang
- Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 65 Brno, Czech Republic
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Costanzo G, Šponer JE, Šponer J, Cirigliano A, Benedetti P, Giliberti V, Polito R, Di Mauro E. Front Cover: Sustainability and Chaos in the Abiotic Polymerization of 3′,5′ Cyclic Guanosine Monophosphate: The Role of Aggregation (ChemSystemsChem 1/2021). ChemSystemsChem 2021. [DOI: 10.1002/syst.202000057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Angela Cirigliano
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Piero Benedetti
- Department of Biology University of Padua (Italy) On leave at: Centro Linceo “Beniamino Segre” Accademia Nazionale dei Lincei via della Lungara 10 00165 Rome Italy
| | - Valeria Giliberti
- Center for Life NanoSciences Istituto Italiano di Tecnologia (IIT) Viale Regina Elena 291 00166 Rome Italy
| | - Raffaella Polito
- Department of Physics Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
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41
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Costanzo G, Šponer JE, Šponer J, Cirigliano A, Benedetti P, Giliberti V, Polito R, Di Mauro E. Sustainability and Chaos in the Abiotic Polymerization of 3’,5’ Cyclic Guanosine Monophosphate: The Role of Aggregation. ChemSystemsChem 2020. [DOI: 10.1002/syst.202000056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Giovanna Costanzo
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Angela Cirigliano
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
| | - Piero Benedetti
- Department of Biology University of Padua (Italy) On leave at: Centro Linceo “Beniamino Segre” Accademia Nazionale dei Lincei via della Lungara 10 00165 Rome Italy
| | - Valeria Giliberti
- Center for Life NanoSciences Istituto Italiano di Tecnologia (IIT) Viale Regina Elena 291 00166 Rome Italy
| | - Raffaella Polito
- Department of Physics Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| | - Ernesto Di Mauro
- Institute of Molecular Biology and Pathology, CNR Piazzale A. Moro 5 00185 Rome Italy
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Ferus M, Rimmer P, Cassone G, Knížek A, Civiš S, Šponer JE, Ivanek O, Šponer J, Saeidfirozeh H, Kubelík P, Dudžák R, Petera L, Juha L, Pastorek A, Křivková A, Krůs M. One-Pot Hydrogen Cyanide-Based Prebiotic Synthesis of Canonical Nucleobases and Glycine Initiated by High-Velocity Impacts on Early Earth. Astrobiology 2020; 20:1476-1488. [PMID: 32955922 DOI: 10.1089/ast.2020.2231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chemical environments of young planets are assumed to be significantly influenced by impacts of bodies lingering after the dissolution of the protoplanetary disk. We explore the chemical consequences of impacts of these bodies under reducing planetary atmospheres dominated by carbon monoxide, methane, and molecular nitrogen. Impacts were simulated by using a terawatt high-power laser system. Our experimental results show that one-pot impact-plasma-initiated synthesis of all the RNA canonical nucleobases and the simplest amino acid glycine is possible in this type of atmosphere in the presence of montmorillonite. This one-pot synthesis begins with de novo formation of hydrogen cyanide (HCN) and proceeds through intermediates such as cyanoacetylene and urea.
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Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Paul Rimmer
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom
- Cavendish Astrophysics, University of Cambridge, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Giuseppe Cassone
- Institute for Physical-Chemical Processes, National Research Council, Messina, Italy
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Ondřej Ivanek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Homa Saeidfirozeh
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Roman Dudžák
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Libor Juha
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Adam Pastorek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Anna Křivková
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Miroslav Krůs
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
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Mráziková K, Mlýnský V, Kührová P, Pokorná P, Kruse H, Krepl M, Otyepka M, Banáš P, Šponer J. UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations. J Chem Theory Comput 2020; 16:7601-7617. [PMID: 33215915 DOI: 10.1021/acs.jctc.0c00801] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Explicit solvent atomistic molecular dynamics (MD) simulations represent an established technique to study structural dynamics of RNA molecules and an important complement for diverse experimental methods. However, performance of molecular mechanical (MM) force fields (ff's) remains far from satisfactory even after decades of development, as apparent from a problematic structural description of some important RNA motifs. Actually, some of the smallest RNA molecules belong to the most challenging systems for MD simulations and, among them, the UUCG tetraloop is saliently difficult. We report a detailed analysis of UUCG MD simulations, depicting the sequence of events leading to the loss of the UUCG native state during MD simulations. The total amount of MD simulation data analyzed in this work is close to 1.3 ms. We identify molecular interactions, backbone conformations, and substates that are involved in the process. Then, we unravel specific ff deficiencies using diverse quantum mechanical/molecular mechanical (QM/MM) and QM calculations. Comparison between the MM and QM methods shows discrepancies in the description of the 5'-flanking phosphate moiety and both signature sugar-base interactions. Our work indicates that poor behavior of the UUCG tetraloop in simulations is a complex issue that cannot be attributed to one dominant and straightforwardly correctable factor. Instead, there is a concerted effect of multiple ff inaccuracies that are coupled and amplifying each other. We attempted to improve the simulation behavior by some carefully tailored interventions, but the results were still far from satisfactory, underlying the difficulties in development of accurate nucleic acid ff's.
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Affiliation(s)
- Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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Pokorná P, Krepl M, Šponer J. Residues flanking the ARK me3T/S motif allow binding of diverse targets to the HP1 chromodomain: Insights from molecular dynamics simulations. Biochim Biophys Acta Gen Subj 2020; 1865:129771. [PMID: 33153976 DOI: 10.1016/j.bbagen.2020.129771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND The chromodomain (CD) of HP1 proteins is an established H3K9me3 reader that also binds H1, EHMT2 and H3K23 lysine-methylated targets. Structural experiments have provided atomistic pictures of its recognition of the conserved ARKme3S/T motif, but structural dynamics' contribution to the recognition may have been masked by ensemble averaging. METHODS We acquired ~350 μs of explicit solvent molecular dynamics (MD) simulations of the CD domain interacting with several peptides using the latest AMBER force fields. RESULTS The simulations reproduced the experimentally observed static binding patterns well but also revealed visible structural dynamics at the interfaces. While the buried K0me3 and A-2 target residues are tightly bound, several flanking sidechains sample diverse sites on the CD surface. Different amino acid positions of the targets can substitute for each other by forming mutually replaceable interactions with CD, thereby explaining the lack of strict requirement for cationic H3 target residues at the -3 position. The Q-4 residue of H3 targets further stabilizes the binding. The recognition pattern of the H3K23 ATKme3A motif, for which no structure is available, is predicted. CONCLUSIONS The CD reads a longer target segment than previously thought, ranging from positions -7 to +3. The CD anionic clamp can be neutralized not only by the -3 and -1 residues, but also by -7, -6, -5 and +3 residues. GENERAL SIGNIFICANCE Structural dynamics, not immediately apparent from the structural data, contribute to molecular recognition between the HP1 CD domain and its targets. Mutual replaceability of target residues increases target sequence flexibility.
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Affiliation(s)
- Pavlína Pokorná
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
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45
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Bizzarri BM, Manini P, Lino V, d'Ischia M, Kapralov M, Krasavin E, Mráziková K, Šponer J, Šponer JE, Di Mauro E, Saladino R. High‐Energy Proton‐Beam‐Induced Polymerization/Oxygenation of Hydroxynaphthalenes on Meteorites and Nitrogen Transfer from Urea: Modeling Insoluble Organic Matter? Chemistry 2020; 26:14919-14928. [DOI: 10.1002/chem.202002318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/06/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Bruno Mattia Bizzarri
- Ecological and Biological Sciences Department (DEB) University of Tuscia Via S. Camillo de Lellis snc 01100 Viterbo Italy
| | - Paola Manini
- Department of Chemical Sciences University of Naples Federico II Campus Monte S. Angelo Via Cinthia 21 80126 Naples Italy
| | - Valeria Lino
- Department of Chemical Sciences University of Naples Federico II Campus Monte S. Angelo Via Cinthia 21 80126 Naples Italy
| | - Marco d'Ischia
- Department of Chemical Sciences University of Naples Federico II Campus Monte S. Angelo Via Cinthia 21 80126 Naples Italy
| | - Michail Kapralov
- Joint Institute for Nuclear Research JINR's Laboratory of Radiation Biology Dubna Russia
| | - Eugene Krasavin
- Joint Institute for Nuclear Research JINR's Laboratory of Radiation Biology Dubna Russia
| | - Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic
| | - Ernesto Di Mauro
- Ecological and Biological Sciences Department (DEB) University of Tuscia Via S. Camillo de Lellis snc 01100 Viterbo Italy
| | - Raffaele Saladino
- Ecological and Biological Sciences Department (DEB) University of Tuscia Via S. Camillo de Lellis snc 01100 Viterbo Italy
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46
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Školáková P, Badri Z, Foldynová-Trantírková S, Ryneš J, Šponer J, Fojtová M, Fajkus J, Marek R, Vorlíčková M, Mergny JL, Trantírek L. Composite 5-methylations of cytosines modulate i-motif stability in a sequence-specific manner: Implications for DNA nanotechnology and epigenetic regulation of plant telomeric DNA. Biochim Biophys Acta Gen Subj 2020; 1864:129651. [DOI: 10.1016/j.bbagen.2020.129651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/14/2022]
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47
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Mohammadi E, Petera L, Saeidfirozeh H, Knížek A, Kubelík P, Dudžák R, Krůs M, Juha L, Civiš S, Coulon R, Malina O, Ugolotti J, Ranc V, Otyepka M, Šponer J, Ferus M, Šponer JE. Formic Acid, a Ubiquitous but Overlooked Component of the Early Earth Atmosphere. Chemistry 2020; 26:12075-12080. [PMID: 32293757 DOI: 10.1002/chem.202000323] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/11/2020] [Indexed: 01/19/2023]
Abstract
Terrestrial volcanism has been one of the dominant geological forces shaping our planet since its earliest existence. Its associated phenomena, like atmospheric lightning and hydrothermal activity, provide a rich energy reservoir for chemical syntheses. Based on our laboratory simulations, we propose that on the early Earth volcanic activity inevitably led to a remarkable production of formic acid through various independent reaction channels. Large-scale availability of atmospheric formic acid supports the idea of the high-temperature accumulation of formamide in this primordial environment.
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Affiliation(s)
- Elmira Mohammadi
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic.,Faculty of Science, Charles University, Albertov 2030, 12843, Prague, Czech Republic
| | - Homa Saeidfirozeh
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic.,Faculty of Science, Charles University, Albertov 2030, 12843, Prague, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic.,Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, 18221, Prague 8, Czech Republic
| | - Roman Dudžák
- Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, 18221, Prague 8, Czech Republic.,Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 1782/3, 18200, Prague 8, Czech Republic
| | - Miroslav Krůs
- Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 1782/3, 18200, Prague 8, Czech Republic
| | - Libor Juha
- Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, 18221, Prague 8, Czech Republic.,Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 1782/3, 18200, Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic
| | - Rémi Coulon
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Ondřej Malina
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Juri Ugolotti
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Václav Ranc
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic
| | - Judit E Šponer
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
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Abstract
Excellent convergence properties for the (aug-)cc-pVnZ-F12 basis set family, purpose-made for explicitly correlated calculations, are demonstrated with conventional wave function methods and Kohn-Sham density functional theory for various ground and excited-state calculations. Among the ground-state properties studied are dipole moments, covalent bond lengths, and interaction and reaction energies. For excited states, we looked at vertical excitation energies, UV absorption, and excited-state absorption spectra. Convergence is compared against the basis sets cc-pVnZ, def2-nVD, aug-pcseg-n, and nZaPa-NR. It is established that the cc-pVnZ-F12 family consistently yields results of n + 1 quality and better. Especially, the cc-pVDZ-F12 basis set is found to be a basis set of good cost vs performance trade-off.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
| | - Rafał Szabla
- EaStCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
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49
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Mlýnský V, Kührová P, Kühr T, Otyepka M, Bussi G, Banáš P, Šponer J. Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. J Chem Theory Comput 2020; 16:3936-3946. [PMID: 32384244 DOI: 10.1021/acs.jctc.0c00228] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Determination of RNA structural-dynamic properties is challenging for experimental methods. Thus, atomistic molecular dynamics (MD) simulations represent a helpful technique complementary to experiments. However, contemporary MD methods still suffer from limitations of force fields (ffs), including imbalances in the nonbonded ff terms. We have recently demonstrated that some improvement of state-of-the-art AMBER RNA ff can be achieved by adding a new term for H-bonding called gHBfix, which increases tuning flexibility and reduces risk of side-effects. Still, the first gHBfix version did not fully correct simulations of short RNA tetranucleotides (TNs). TNs are key benchmark systems due to availability of unique NMR data, although giving too much weight on improving TN simulations can easily lead to overfitting to A-form RNA. Here we combine the gHBfix version with another term called tHBfix, which separately treats H-bond interactions formed by terminal nucleotides. This allows to refine simulations of RNA TNs without affecting simulations of other RNAs. The approach is in line with adopted strategy of current RNA ffs, where the terminal nucleotides possess different parameters for terminal atoms than the internal nucleotides. Combination of gHBfix with tHBfix significantly improves the behavior of RNA TNs during well-converged enhanced-sampling simulations using replica exchange with solute tempering. TNs mostly populate canonical A-form like states while spurious intercalated structures are largely suppressed. Still, simulations of r(AAAA) and r(UUUU) TNs show some residual discrepancies with primary NMR data which suggests that future tuning of some other ff terms might be useful. Nevertheless, the tHBfix has a clear potential to improve modeling of key biochemical processes, where interactions of RNA single stranded ends are involved.
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Affiliation(s)
- Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Tomáš Kühr
- Department of Computer Science, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, SISSA, via Bonomea 265, 34136 Trieste, Italy
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
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50
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Islam B, Stadlbauer P, Vorlíčková M, Mergny JL, Otyepka M, Šponer J. Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations. J Chem Theory Comput 2020; 16:3447-3463. [PMID: 32163706 DOI: 10.1021/acs.jctc.9b01068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-quadruplexes (GQs) are four-stranded noncanonical DNA and RNA architectures that can be formed by guanine-rich sequences. The stability of GQs increases with the number of G-quartets, and three G-quartets generally form stable GQs. However, the stability of two-quartet GQs is an open issue. To understand the intrinsic stability of two-quartet GQ stems, we have carried out a series of unbiased molecular dynamics (MD) simulations (505 μs in total) of two- and four-quartet DNA and RNA GQs, with attention paid mainly to parallel-stranded arrangements. We used AMBER DNA parmOL15 and RNA parmOL3 force fields and tested different ion and water models. Two-quartet parallel-stranded DNA GQs unfolded in all the simulations, while the equivalent RNA GQ was stable in most of the simulations. GQs composed of two stacked units of two-quartet GQs were stable for both DNA and RNA. The simulations suggest that a minimum of three quartets are needed to form an intrinsically stable all-anti parallel-stranded DNA GQ. Parallel two-quartet DNA GQ may exist if substantially stabilized by another molecule or structural element, including multimerization. On the other hand, we predict that isolated RNA two-quartet parallel GQs may form, albeit being weakly stable. We also show that ionic parameters and water models should be chosen with caution because some parameter combinations can cause spurious instability of GQ stems. Some in-so-far unnoticed limitations of force-field description of multiple ions inside the GQs are discussed, which compromise the capability of simulations to fully capture the effect of increase in the number of quartets on the GQ stability.
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Affiliation(s)
- Barira Islam
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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