1
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Jin L, Tan YL, Wu Y, Wang X, Shi YZ, Tan ZJ. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA (NEW YORK, N.Y.) 2019; 25:1532-1548. [PMID: 31391217 PMCID: PMC6795135 DOI: 10.1261/rna.071662.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 05/08/2023]
Abstract
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we used our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict three-dimensional (3D) structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations. Moreover, the comparisons with extensive experimental data show that the model can make reliable predictions on the stability for various RNA kissing complexes over wide ranges of monovalent/divalent ion concentrations. Notably, for RNA kissing complexes, our further analyses show the important contribution of coaxial stacking to the 3D structures and stronger stability than the corresponding kissing-interface duplexes at high salts. Furthermore, our comprehensive analyses for RNA kissing complexes reveal that the thermally folding pathway for a complex sequence is mainly determined by the relative stability of two possible folded states of kissing complex and extended duplex, which can be significantly modulated by its sequence.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yao Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xunxun Wang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan 430073, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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2
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Lammert H, Wang A, Mohanty U, Onuchic JN. RNA as a Complex Polymer with Coupled Dynamics of Ions and Water in the Outer Solvation Sphere. J Phys Chem B 2018; 122:11218-11227. [PMID: 30102033 DOI: 10.1021/acs.jpcb.8b06874] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We unravel the internal and collective modes of a widely studied 58-nucleotide rRNA fragment in solvent using atomically detailed molecular dynamics simulations. The variation of lifetimes for water hydrogen bonds with nucleotide groups indicates heterogeneity of water dynamics on the RNA surface. The time scales of interactions of the discrete water molecules with RNA nucleotides extend from several hundred picoseconds to a few nanoseconds. We determine all of the association sites and the spatial distribution of residence times for Mg2+, K+, and water molecules in those sites. We provide insights into the population of Mg2+ and K+ ions and water molecules in the outer sphere and how their fluctuations are intricately linked with the kinetics of the 58-mer. We find that many of the long-lived Mg2+ sites identified from the simulations agree with the locations of ions in the X-ray structure. We determine the excess ion atmosphere around the rRNA and compare it with experimental data. We investigate the collective behavior of RNA, ions, and water, by performing a joint principle component analysis for the Cartesian coordinates of the RNA phosphorus atoms and for the occupation counts of the association sites. Our results indicate that the 58-mer system is a complex polymer, composed of RNA that is encased by a fluctuating network of associated counterions, co-ions, and water.
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Affiliation(s)
| | - Ailun Wang
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Udayan Mohanty
- Department of Chemistry , Boston College , Chestnut Hill , Massachusetts 02467 , United States
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3
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 326] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - 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, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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4
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Abi-Ghanem J, Rabin C, Porrini M, Dausse E, Toulmé JJ, Gabelica V. Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes. Chemphyschem 2017; 18:2782-2790. [PMID: 28762245 DOI: 10.1002/cphc.201700337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/29/2017] [Indexed: 01/03/2023]
Abstract
In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications.
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Affiliation(s)
- Josephine Abi-Ghanem
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Clémence Rabin
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Massimiliano Porrini
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Eric Dausse
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Jean-Jacques Toulmé
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Valérie Gabelica
- Univ. Bordeaux, INSERM, CNRS, Laboratoire Acides Nucléiques, Régulations Naturelle et Artificielle, ARNA, U1212, UMR5320, IECB, 2 rue Robert Escarpit, 33607, Pessac, France
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5
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Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. J Phys Chem B 2015; 119:15176-90. [DOI: 10.1021/acs.jpcb.5b08876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marek Havrila
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- 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
| | - Petr Jurečka
- 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
| | - Pavel Banáš
- 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
| | - Miroslav Krepl
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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6
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Islam B, Stadlbauer P, Krepl M, Koca J, Neidle S, Haider S, Sponer J. Extended molecular dynamics of a c-kit promoter quadruplex. Nucleic Acids Res 2015; 43:8673-93. [PMID: 26245347 PMCID: PMC4605300 DOI: 10.1093/nar/gkv785] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/21/2015] [Indexed: 01/29/2023] Open
Abstract
The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex.
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Affiliation(s)
- Barira Islam
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jaroslav Koca
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic National Center for Biomolecular Research, Faculty of Science, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiri Sponer
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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7
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Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J Phys Chem Lett 2014; 5:1771-82. [PMID: 26270382 DOI: 10.1021/jz500557y] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.
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Affiliation(s)
- Jiří Šponer
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- ‡CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- §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
| | - Petr Jurečka
- §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
| | - Marie Zgarbová
- §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
| | - 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
| | - Marek Havrila
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- ‡CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
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8
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Krepl M, Réblová K, Koča J, Sponer J. Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops. J Phys Chem B 2013; 117:5540-55. [PMID: 23534440 DOI: 10.1021/jp401482m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop, and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 μs of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has an unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. Our analysis suggests that the anti orientation might be a mis-refinement, although even the anti interaction would be compatible with the sequence pattern and observed tertiary interaction. Alternatively, the anti conformation may be a real substate whose population could be pH-dependent, since the guanine syn orientation requires protonation of cytosine in the tertiary contact. In absence of structural data, we use molecular modeling to explore the GCCA tetraloop that is dominant in bacteria and suggest that the GCCA tetraloop is structurally similar to the YNMG tetraloop. Kink-turn Kt-77 is unusual due to its 11-nucleotide bulge. The simulations indicate that the long bulge is a stalk-specific eight-nucleotide insertion into consensual kink-turn only subtly modifying its structural dynamics. We discuss a possible evolutionary role of helix H78 and a mechanism of L1 stalk interaction with tRNA. We also assess the simulation methodology. The simulations provide a good description of the studied systems with the latest bsc0χOL3 force field showing improved performance. Still, even bsc0χOL3 is unable to fully stabilize an essential sugar-edge H-bond between the bulge and non-canonical stem of the kink-turn. Inclusion of Mg(2+) ions may deteriorate the simulations. On the other hand, monovalent ions can in simulations readily occupy experimental Mg(2+) binding sites.
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Affiliation(s)
- Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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9
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Sehdev P, Crews G, Soto AM. Effect of Helix Stability on the Formation of Loop–Loop Complexes. Biochemistry 2012; 51:9612-23. [DOI: 10.1021/bi300481v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Preeti Sehdev
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
| | - Gordon Crews
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
| | - Ana Maria Soto
- Department
of Chemistry, ‡Molecular Biology, Biochemistry and Bioinformatics Program, Towson University, Towson, Maryland
21252, United States
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10
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Robbins TJ, Wang Y. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations. J Biomol Struct Dyn 2012; 31:1311-23. [PMID: 23153112 DOI: 10.1080/07391102.2012.732344] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Monovalent (Na(+)) and divalent (Mg(2+)) ion distributions around the Dickerson-Drew dodecamer were studied by atomistic molecular dynamics (MD) simulations with AMBER molecular modeling software. Different initial placements of ions were tried and the resulting effects on the ion distributions around DNA were investigated. For monovalent ions, results were found to be nearly independent of initial cation coordinates. However, Mg(2+) ions demonstrated a strong initial coordinate dependent behavior. While some divalent ions initially placed near the DNA formed essentially permanent direct coordination complexes with electronegative DNA atoms, Mg(2+) ions initially placed further away from the duplex formed a full, nonexchanging, octahedral first solvation shell. These fully solvated cations were still capable of binding with DNA with events lasting up to 20 ns, and in comparison were bound much longer than Na(+) ions. Force field parameters were also investigated with modest and little differences arising from ion (ions94 and ions08) and nucleic acid description (ff99, ff99bsc0, and ff10), respectively. Based on known Mg(2+) ion solvation structure, we conclude that in most cases Mg(2+) ions retain their first solvation shell, making only solvent-mediated contacts with DNA duplex. The proper way to simulate Mg(2+) ions around DNA duplex, therefore, should begin with ions placed in the bulk water.
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Affiliation(s)
- Timothy J Robbins
- a Department of Chemistry , University of Memphis , Memphis , TN , 38152 , USA
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11
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Railsback JG, Singh A, Pearce RC, McKnight TE, Collazo R, Sitar Z, Yingling YG, Melechko AV. Weakly charged cationic nanoparticles induce DNA bending and strand separation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:4261-4265. [PMID: 22711427 DOI: 10.1002/adma.201104891] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/17/2012] [Indexed: 06/01/2023]
Abstract
Weakly charged cationic nanoparticles cause structural changes including local denaturing and compaction to DNA under mild conditions. The charged ligands bind to the phosphate backbone of DNA and the uncharged ligands penetrate the helix and disrupt base pairing. Mobility shifts in electrophoresis, molecular dynamics, and UV-vis spectrophotometry give clues to the details of the interactions.
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Affiliation(s)
- Justin G Railsback
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695, USA
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12
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Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J Phys Chem B 2012; 116:9899-916. [DOI: 10.1021/jp3014817] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ivana Beššeová
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavlína Košinová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
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13
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Allnér O, Nilsson L, Villa A. Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations. J Chem Theory Comput 2012; 8:1493-502. [PMID: 26596759 DOI: 10.1021/ct3000734] [Citation(s) in RCA: 273] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Magnesium ions have an important role in the structure and folding mechanism of ribonucleic acid systems. To properly simulate these biophysical processes, the applied molecular models should reproduce, among other things, the kinetic properties of the ions in water solution. Here, we have studied the kinetics of the binding of magnesium ions with water molecules and nucleic acid systems using molecular dynamics simulation in detail. We have validated the parameters used in biomolecular force fields, such as AMBER and CHARMM, for Mg(2+) ions and also for the biologically relevant ions Na(+), K(+), and Ca(2+) together with three different water models (TIP3P, SPC/E, and TIP5P). The results show that Mg(2+) ions have a slower exchange rate than Na(+), K(+), and Ca(2+) in agreement with the experimental trend, but the simulated value underestimates the experimentally observed Mg(2+)-water exchange rate by several orders of magnitude, irrespective of the force field and water model. A new set of parameters for Mg(2+) was developed to reproduce the experimental kinetic data. This set also leads to better reproduction of structural data than existing models. We have applied the new parameter set to Mg(2+) binding with a monophosphate model system and with the purine riboswitch, add A-riboswitch. In line with the Mg(2+)-water results, the newly developed parameters show a better description of the structure and kinetics of the Mg(2+)-phosphate binding than all other models. The characterization of the ion binding to the riboswitch system shows that the new parameter set does not affect the global structure of the ribonucleic acid system or the number of ions involved in direct or indirect binding. A slight decrease in the number of water-bridged contacts between A-riboswitch and the Mg(2+) ion is observed. The results support the ability of the newly developed parameters to improve the kinetic description of the Mg(2+) and phosphate ions and their applicability in nucleic acid simulation.
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Affiliation(s)
- Olof Allnér
- Karolinska Institutet, Department of Biosciences and Nutrition, Center for Biosciences, SE-141 83 HUDDINGE, Sweden
| | - Lennart Nilsson
- Karolinska Institutet, Department of Biosciences and Nutrition, Center for Biosciences, SE-141 83 HUDDINGE, Sweden
| | - Alessandra Villa
- Karolinska Institutet, Department of Biosciences and Nutrition, Center for Biosciences, SE-141 83 HUDDINGE, Sweden
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Réblová K, Šponer JE, Špačková N, Beššeová I, Šponer J. A-minor tertiary interactions in RNA kink-turns. Molecular dynamics and quantum chemical analysis. J Phys Chem B 2011; 115:13897-910. [PMID: 21999672 DOI: 10.1021/jp2065584] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The RNA kink-turn is an important recurrent RNA motif, an internal loop with characteristic consensus sequence forming highly conserved three-dimensional structure. Functional arrangement of RNA kink-turns shows a sharp bend in the phosphodiester backbone. Among other signature interactions, kink-turns form A-minor interaction between their two stems. Most kink-turns possess extended A-minor I (A-I) interaction where adenine of the second A•G base pair of the NC-stem interacts with the first canonical pair of the C-stem (i.e., the receptor pair) via trans-sugar-edge/sugar-edge (tSS) and cis-sugar-edge/sugar-edge (cSS) interactions. The remaining kink-turns have less compact A-minor 0 (A-0) interaction with just one tSS contact. We show that kink-turns with A-I in ribosomal X-ray structures keep G═C receptor base pair during evolution while the inverted pair (C═G) is not realized. In contrast, kink-turns with A-0 in the observed structures alternate G═C and C═G base pairs in sequences. We carried out an extended set (~5 μs) of explicit-solvent molecular dynamics simulations of kink-turns to rationalize this structural/evolutionary pattern. The simulations were done using a net-neutral Na(+) cation atmosphere (with ~0.25 M cation concentration) supplemented by simulations with either excess salt KCl atmosphere or inclusion of Mg(2+). The results do not seem to depend on the treatment of ions. The simulations started with X-ray structures of several kink-turns while we tested the response of the simulated system to base substitutions, modest structural perturbations and constraints. The trends seen in the simulations reveal that the A-I/G═C arrangement is preferred over all three other structures. The A-I/C═G triple appears structurally entirely unstable, consistent with the covariation patterns seen during the evolution. The A-0 arrangements tend to shift toward the A-I pattern in simulations, which suggests that formation of the A-0 interaction is likely supported by the surrounding protein and RNA molecules. A-0 may also be stabilized by additional kink-turn nucleotides not belonging to the kink-turn consensus, as shown for the kink-turn from ribosomal Helix 15. Quantum-chemical calculations on all four A-minor triples suggest that there is a different balance of electrostatic and dispersion stabilization in the A-I/G═C and A-I/C═G triples, which may explain different behavior of these otherwise isosteric triples in the context of kink-turns.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.
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