1
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Dohnalová H, Matoušková E, Lankaš F. Temperature-dependent elasticity of DNA, RNA, and hybrid double helices. Biophys J 2024; 123:572-583. [PMID: 38340722 PMCID: PMC10938081 DOI: 10.1016/j.bpj.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Nucleic acid double helices in their DNA, RNA, and DNA-RNA hybrid form play a fundamental role in biology and are main building blocks of artificial nanostructures, but how their properties depend on temperature remains poorly understood. Here, we report thermal dependence of dynamic bending persistence length, twist rigidity, stretch modulus, and twist-stretch coupling for DNA, RNA, and hybrid duplexes between 7°C and 47°C. The results are based on all-atom molecular dynamics simulations using different force field parameterizations. We first demonstrate that unrestrained molecular dynamics can reproduce experimentally known mechanical properties of the duplexes at room temperature. Beyond experimentally known features, we also infer the twist rigidity and twist-stretch coupling of the hybrid duplex. As for the temperature dependence, we found that increasing temperature softens all the duplexes with respect to bending, twisting, and stretching. The relative decrease of the stretch moduli is 0.003-0.004/°C, similar for all the duplex variants despite their very different stretching stiffness, whereas RNA twist stiffness decreases by 0.003/°C, and smaller values are found for the other elastic moduli. The twist-stretch couplings are nearly unaffected by temperature. The stretching, bending, and twisting stiffness all include an important entropic component. Relation of our results to the two-state model of DNA flexibility is discussed. Our work provides temperature-dependent elasticity of nucleic acid duplexes at the microsecond scale relevant for initial stages of protein binding.
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Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Eva Matoušková
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Praha 6, Czech Republic.
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2
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Alenaizan A. Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions. J Phys Chem B 2022; 126:8508-8514. [PMID: 36244003 DOI: 10.1021/acs.jpcb.2c04664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.
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Affiliation(s)
- Asem Alenaizan
- Chemistry Department, King Fahd University of Petroleum and Minerals, Dhahran31261, Saudi Arabia
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3
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
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4
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Accurate modeling of DNA conformational flexibility by a multivariate Ising model. Proc Natl Acad Sci U S A 2021; 118:2021263118. [PMID: 33876759 DOI: 10.1073/pnas.2021263118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The sequence-dependent structure and deformability of DNA play a major role for binding of proteins and regulation of gene expression. So far, most efforts to model DNA flexibility are based on unimodal harmonic stiffness models at base-pair resolution. However, multimodal behavior due to distinct conformational substates also contributes significantly to the conformational flexibility of DNA. Moreover, these local substates are correlated to their nearest-neighbor substates. A description for DNA elasticity which includes both multimodality and nearest-neighbor coupling has remained a challenge, which we solve by combining our multivariate harmonic approximation with an Ising model for the substates. In a series of applications to DNA fluctuations and protein-DNA complexes, we demonstrate substantial improvements over the unimodal stiffness model. Furthermore, our multivariate Ising model reveals a mechanical destabilization for adenine (A)-tracts to undergo nucleosome formation. Our approach offers a wide range of applications to determine sequence-dependent deformation energies of DNA and to investigate indirect readout contributions to protein-DNA recognition.
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5
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Bouchal T, Durník I, Illík V, Réblová K, Kulhánek P. Importance of base-pair opening for mismatch recognition. Nucleic Acids Res 2020; 48:11322-11334. [PMID: 33080020 PMCID: PMC7672436 DOI: 10.1093/nar/gkaa896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 09/09/2020] [Accepted: 09/30/2020] [Indexed: 01/04/2023] Open
Abstract
Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structures suggests the role of DNA bending, the theoretical support is not fully convincing. Here, we present a computational study focused on a base-pair opening into the minor groove, a specific base-pair motion observed upon interaction with MutS. Propensities for the opening were evaluated in terms of two base-pair parameters: Opening and Shear. We tested all possible base pairs in anti/anti, anti/syn and syn/anti orientations and found clear discrimination between mismatches and canonical base-pairs only for the opening into the minor groove. Besides, the discrimination gap was also confirmed in hotspot and coldspot sequences, indicating that the opening could play a more significant role in the mismatch recognition than previously recognized. Our findings can be helpful for a better understanding of sequence-dependent mutability. Further, detailed structural characterization of mismatches can serve for designing anti-cancer drugs targeting mismatched base pairs.
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Affiliation(s)
- Tomáš Bouchal
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ivo Durník
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Viktor Illík
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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6
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Kriegel F, Matek C, Dršata T, Kulenkampff K, Tschirpke S, Zacharias M, Lankaš F, Lipfert J. The temperature dependence of the helical twist of DNA. Nucleic Acids Res 2018; 46:7998-8009. [PMID: 30053087 PMCID: PMC6125625 DOI: 10.1093/nar/gky599] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 06/08/2018] [Accepted: 07/20/2018] [Indexed: 01/11/2023] Open
Abstract
DNA is the carrier of all cellular genetic information and increasingly used in nanotechnology. Quantitative understanding and optimization of its functions requires precise experimental characterization and accurate modeling of DNA properties. A defining feature of DNA is its helicity. DNA unwinds with increasing temperature, even for temperatures well below the melting temperature. However, accurate quantitation of DNA unwinding under external forces and a microscopic understanding of the corresponding structural changes are currently lacking. Here we combine single-molecule magnetic tweezers measurements with atomistic molecular dynamics and coarse-grained simulations to obtain a comprehensive view of the temperature dependence of DNA twist. Experimentally, we find that DNA twist changes by ΔTw(T) = (-11.0 ± 1.2)°/(°C·kbp), independent of applied force, in the range of forces where torque-induced melting is negligible. Our atomistic simulations predict ΔTw(T) = (-11.1 ± 0.3)°/(°C·kbp), in quantitative agreement with experiments, and suggest that the untwisting of DNA with temperature is predominantly due to changes in DNA structure for defined backbone substates, while the effects of changes in substate populations are minor. Coarse-grained simulations using the oxDNA framework yield a value of ΔTw(T) = (-6.4 ± 0.2)°/(°C·kbp) in semi-quantitative agreement with experiments.
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Affiliation(s)
- Franziska Kriegel
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Christian Matek
- Technical University of Munich and Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Tomáš Dršata
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Klara Kulenkampff
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Sophie Tschirpke
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
| | - Martin Zacharias
- Physics-Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Filip Lankaš
- Department of Informatics and Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich, Amalienstr. 54, 80799 Munich, Germany
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7
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Galindo-Murillo R, Cheatham TE. Computational DNA binding studies of (–)-epigallocatechin-3-gallate. J Biomol Struct Dyn 2017; 36:3311-3323. [DOI: 10.1080/07391102.2017.1389306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, L. S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA
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8
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Internal abstraction of dynemicin A: An MD approach. J Mol Graph Model 2017; 74:251-264. [DOI: 10.1016/j.jmgm.2017.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 11/23/2022]
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9
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Zgarbová M, Jurečka P, Lankaš F, Cheatham TE, Šponer J, Otyepka M. Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. J Chem Inf Model 2017; 57:275-287. [PMID: 28059516 DOI: 10.1021/acs.jcim.6b00621] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Reliable representation of the B-DNA base-pair step twist is one of the crucial requirements for theoretical modeling of DNA supercoiling and other biologically relevant phenomena in B-DNA. It has long been suspected that the twist is inaccurately described by current empirical force fields. Unfortunately, comparison of simulation results with experiments is not straightforward because of the presence of BII backbone substates, whose populations may differ in experimental and simulation ensembles. In this work, we provide a comprehensive view of the effect of BII substates on the overall B-DNA helix twist and show how to reliably compare twist values from experiment and simulation in two scenarios. First, for longer DNA segments freely moving in solution, we show that sequence-averaged twists of different BI/BII ensembles can be compared directly because of approximate cancellation of the opposing BII effects. Second, for sequence-specific data, such as a particular base-pair step or tetranucleotide twist, can be compared only for a clearly defined BI/BII backbone conformation. For the purpose of force field testing, we designed a compact set of fourteen 22-base-pair B-DNA duplexes (Set 14) containing all 136 distinct tetranucleotide sequences and carried out a total of 84 μs of molecular dynamics simulations, primarily with the OL15 force field. Our results show that the ff99bsc0εζOL1χOL4, parmbsc1, and OL15 force fields model the B-DNA helical twist in good agreement with X-ray and minicircle ligation experiments. The comprehensive understanding obtained regarding the effect of BII substates on the base-pair step geometry should aid meaningful comparisons of various conformational ensembles in future research.
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Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17 listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17 listopadu 12, 77146 Olomouc, Czech Republic
| | - Filip Lankaš
- Laboratory of Informatics and Chemistry, University of Chemistry and Technology Prague , Technická 5, 16628 Prague, Czech Republic
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah , 30 South 2000 East, Skaggs 105, Salt Lake City, Utah 84112, United States
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17 listopadu 12, 77146 Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 61265 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17 listopadu 12, 77146 Olomouc, Czech Republic
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10
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Dršata T, Lankaš F. Multiscale modelling of DNA mechanics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:323102. [PMID: 26194779 DOI: 10.1088/0953-8984/27/32/323102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic. Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University Prague, Albertov 6, 128 43 Prague, Czech Republic
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11
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Carvalho ATP, Gouveia L, Kanna CR, Wärmländer SKTS, Platts JA, Kamerlin SCL. Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation. Epigenetics 2015; 9:1604-12. [PMID: 25625845 PMCID: PMC4622728 DOI: 10.4161/15592294.2014.988043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.
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Key Words
- AFM, Atomic Force Microscopy
- DDD, Dickerson-Drew Dodecamer
- DFT, Density Functional Theory
- DNA methylation
- DNA, Deoxyribonucleic Acid
- DNMT, DNA Methyltransferase
- LINEs, Long Interspred Transposable Elements
- MD, Molecular Dynamics
- MM, Molecular Mechanics
- MeCP, Methylated CpG-binding proteins
- PBC, Periodic Boundary Conditions
- QM, Quantum Mechanics
- RDF, Radial Distribution Functions
- RESP, Restrained Electrostatic Potentials Model
- SINEs, Short Interspred Transposable Elements
- SPME, Smooth Particle-Mesh Ewald
- TET, Translocation Proteins
- WT, Wild Type
- epigenetics
- indirect readout
- molecular dynamics
- recognition
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Affiliation(s)
- Alexandra T P Carvalho
- a Science for Life Laboratory; Department of Cell and Molecular Biology ; Uppsala University ; Uppsala , Sweden
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12
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Dršata T, Zgarbová M, Špačková N, Jurečka P, Šponer J, Lankaš F. Mechanical Model of DNA Allostery. J Phys Chem Lett 2014; 5:3831-3835. [PMID: 26278756 DOI: 10.1021/jz501826q] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The importance of allosteric effects in DNA is becoming increasingly appreciated, but the underlying mechanisms remain poorly understood. In this work, we propose a general modeling framework to study DNA allostery. We describe DNA in a coarse-grained manner by intra-base pair and base pair step coordinates, complemented by groove widths. Quadratic deformation energy is assumed, yielding linear relations between the constraints and their effect. Model parameters are inferred from standard unrestrained, explicit-solvent molecular dynamics simulations of naked DNA. We applied the approach to study minor groove binding of diamidines and pyrrole-imidazole polyamides. The predicted DNA bending is in quantitative agreement with experiment and suggests that diamidine binding to the alternating TA sequence brings the DNA closer to the A-tract conformation, with potentially important functional consequences. The approach can be readily applied to other allosteric effects in DNA and generalized to model allostery in various molecular systems.
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Affiliation(s)
- Tomáš Dršata
- †Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic
- ‡Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University Prague, Albertov 6, 128 43 Prague, Czech Republic
| | - Marie Zgarbová
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Naďa Špačková
- ∥Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- ⊥Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Petr Jurečka
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 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, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Filip Lankaš
- †Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic
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13
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Esguerra M, Nilsson L, Villa A. Triple helical DNA in a duplex context and base pair opening. Nucleic Acids Res 2014; 42:11329-38. [PMID: 25228466 PMCID: PMC4191418 DOI: 10.1093/nar/gku848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
It is fundamental to explore in atomic detail the behavior of DNA triple helices as a means to understand the role they might play in vivo and to better engineer their use in genetic technologies, such as antigene therapy. To this aim we have performed atomistic simulations of a purine-rich antiparallel triple helix stretch of 10 base triplets flanked by canonical Watson–Crick double helices. At the same time we have explored the thermodynamic behavior of a flipping Watson–Crick base pair in the context of the triple and double helix. The third strand can be accommodated in a B-like duplex conformation. Upon binding, the double helix changes shape, and becomes more rigid. The triple-helical region increases its major groove width mainly by oversliding in the negative direction. The resulting conformations are somewhere between the A and B conformations with base pairs remaining almost perpendicular to the helical axis. The neighboring duplex regions maintain a B DNA conformation. Base pair opening in the duplex regions is more probable than in the triplex and binding of the Hoogsteen strand does not influence base pair breathing in the neighboring duplex region.
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Affiliation(s)
- Mauricio Esguerra
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, SE-141 83 Huddinge, Sweden
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14
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Dršata T, Špačková N, Jurečka P, Zgarbová M, Šponer J, Lankaš F. Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning. Nucleic Acids Res 2014; 42:7383-94. [PMID: 24829460 PMCID: PMC4066768 DOI: 10.1093/nar/gku338] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/07/2014] [Accepted: 04/09/2014] [Indexed: 11/13/2022] Open
Abstract
A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexible in DNA looping. In this work, we investigate mechanical properties of symmetric AnTn and asymmetric A2n tracts for n = 3, 4, 5 using two types of coarse-grained models. The first model represents DNA as an ensemble of interacting rigid bases with non-local quadratic deformation energy, the second one treats DNA as an anisotropically bendable and twistable elastic rod. Parameters for both models are inferred from microsecond long, atomic-resolution molecular dynamics simulations. We find that asymmetric A-tracts are more rigid than the control G/C-rich sequence in localized distortions relevant for nucleosome formation, but are more flexible in global bending and twisting relevant for looping. The symmetric tracts, in contrast, are more rigid than asymmetric tracts and the control, both locally and globally. Our results can reconcile the contradictory stiffness data on A-tracts and suggest symmetric A-tracts to be more efficient in nucleosome exclusion than the asymmetric ones. This would open a new possibility of gene expression manipulation using A-tracts.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Nada Špačková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 62500 Brno, Czech Republic
| | - Filip Lankaš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
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15
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Dršata T, Kara M, Zacharias M, Lankaš F. Effect of 8-oxoguanine on DNA structure and deformability. J Phys Chem B 2013; 117:11617-22. [PMID: 24028561 DOI: 10.1021/jp407562t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
8-Oxoguanine (oxoG) is an abundant product of oxidative DNA damage. It is removed by repair glycosylases, but exactly how the enzymes recognize oxoG in the large surplus of undamaged bases is not fully understood. The lesion may induce changes in the properties of naked DNA that facilitate the recognition. In this work, we assess the effect of oxoG on DNA structure and mechanical deformability. We performed extensive unrestrained, atomic resolution molecular dynamics simulations to parametrize a nonlocal, rigid base mechanical model of DNA. Our data indicate that oxoG induces unwinding of the base pair step at the 5'-side of the lesion. This brings the damaged DNA closer to its conformation in the initial complex with bacterial glycosylase MutM. The untwisting is partially caused by different BII substate populations and is further enhanced by the base-sugar repulsion within oxoG. On the other hand, our analysis shows that damaged and undamaged DNA have very similar harmonic stiffness. These results suggest an indirect readout component of the MutM-DNA initial complex formation. They also help one to understand the effect of oxoG on the formation of nucleosomes and looped gene regulatory complexes.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstı́ 2, 166 10, Praha 6, Czech Republic
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16
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Dršata T, Lankaš F. Theoretical models of DNA flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1144] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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17
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Dršata T, Pérez A, Orozco M, Morozov AV, Sponer J, Lankaš F. Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer. J Chem Theory Comput 2012; 9:707-721. [PMID: 23976886 DOI: 10.1021/ct300671y] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Dickerson-Drew dodecamer (DD) d-[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6-2.4-µs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback-Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic ; Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
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18
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Réblová K, Šponer J, Lankaš F. Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res 2012; 40:6290-303. [PMID: 22451682 PMCID: PMC3401443 DOI: 10.1093/nar/gks258] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/07/2012] [Accepted: 03/07/2012] [Indexed: 01/06/2023] Open
Abstract
The L1 stalk is a key mobile element of the large ribosomal subunit which interacts with tRNA during translocation. Here, we investigate the structure and mechanical properties of the rRNA H76/H75/H79 three-way junction at the base of the L1 stalk from four different prokaryotic organisms. We propose a coarse-grained elastic model and parameterize it using large-scale atomistic molecular dynamics simulations. Global properties of the junction are well described by a model in which the H76 helix is represented by a straight, isotropically flexible elastic rod, while the junction core is represented by an isotropically flexible spherical hinge. Both the core and the helix contribute substantially to the overall H76 bending fluctuations. The presence of wobble pairs in H76 does not induce any increased flexibility or anisotropy to the helix. The half-closed conformation of the L1 stalk seems to be accessible by thermal fluctuations of the junction itself, without any long-range allosteric effects. Bending fluctuations of H76 with a bulge introduced in it suggest a rationale for the precise position of the bulge in eukaryotes. Our elastic model can be generalized to other RNA junctions found in biological systems or in nanotechnology.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Filip Lankaš
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
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Abstract
This article provides a retrospective on the ABC initiative in the area of all-atom molecular dynamics (MD) simulations including explicit solvent on all tetranucleotide steps of duplex B-form DNA duplex, ca. 2012. The ABC consortium has completed two phases of simulations, the most current being a set of 50-100 trajectories based on the AMBER ff99 force field together with the parmbsc0 modification. Some general perspectives on the field of MD on DNA and sequence effects on DNA structure are provided, followed by an overview our MD results, including a detailed comparison of the ff99/parmbsc0 results with crystal and NMR structures available for d(CGCGAATTCGCG). Some projects inspired by or related to the ABC initiative and database are also reviewed, including methods for the trajectory analyses, informatics of dealing with the large database of results, compressions of trajectories for efficacy of distribution, DNA solvation by water and ions, parameterization of coarse-grained models with applications and gene finding and genome annotation.
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Affiliation(s)
- David L Beveridge
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University Middletown, CT 06459, USA.
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20
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Lankaš F. Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale. INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS 2012. [DOI: 10.1039/9781849735056-00001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This chapter surveys some of the recent developments in coarse-grained modelling of nucleic acids. We first discuss models based on pseudoatoms, effective spherical particles representing groups of atoms. A major part of the chapter is devoted to models in which bases or base pairs are represented as independent, interacting rigid bodies. Two popular definitions of internal coordinates, as implemented in the programs 3DNA and Curves+, are outlined from a common perspective. Recently developed rigid base and basepair models with nonlocal quadratic interactions are presented. A statistical mechanical description of the models on their full phase space yields exact relations between model parameters and expected values of some state functions. We estimated shape and stiffness parameters for nonlocal rigid base and basepair models of a DNA oligomer containing A-tract. The parameterization is based on atomic-resolution molecular dynamics simulation data. We found that the rigid base model is consistent with a local interaction pattern, while interactions in the rigid basepair model are visibly non-local, in agreement with earlier findings. Differences in shape and stiffness parameters obtained using Curves+ and 3DNA coordinates are found to be small for structures within the B-DNA family. Anharmonic effects, coarser models, and other approaches to describe nucleic acid structure and flexibility are discussed.
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Affiliation(s)
- Filip Lankaš
- Centre for Complex Molecular Systems and Biomolecules Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6 Czech Republic
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21
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Ramakrishnan V, Jagannathan S, Shaikh AR, Rajagopalan R. Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain. J Biomol Struct Dyn 2012; 29:743-56. [DOI: 10.1080/073911012010525020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Nikolaienko TY, Bulavin LA, Hovorun DM. Structural flexibility of DNA-like conformers of canonical 2′-deoxyribonucleosides. Phys Chem Chem Phys 2012; 14:15554-61. [DOI: 10.1039/c2cp43120c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Nikolaienko TY, Bulavin LA, Hovorun DM. How Flexible are DNA Constituents? The Quantum-Mechanical Study. J Biomol Struct Dyn 2011; 29:563-75. [DOI: 10.1080/07391102.2011.10507406] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Reddy CM, Rama Krishna G, Ghosh S. Mechanical properties of molecular crystals—applications to crystal engineering. CrystEngComm 2010. [DOI: 10.1039/c003466e] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Heddi B, Oguey C, Lavelle C, Foloppe N, Hartmann B. Intrinsic flexibility of B-DNA: the experimental TRX scale. Nucleic Acids Res 2009; 38:1034-47. [PMID: 19920127 PMCID: PMC2817485 DOI: 10.1093/nar/gkp962] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
B-DNA flexibility, crucial for DNA–protein recognition, is sequence dependent. Free DNA in solution would in principle be the best reference state to uncover the relation between base sequences and their intrinsic flexibility; however, this has long been hampered by a lack of suitable experimental data. We investigated this relationship by compiling and analyzing a large dataset of NMR 31P chemical shifts in solution. These measurements reflect the BI ↔ BII equilibrium in DNA, intimately correlated to helicoidal descriptors of the curvature, winding and groove dimensions. Comparing the ten complementary DNA dinucleotide steps indicates that some steps are much more flexible than others. This malleability is primarily controlled at the dinucleotide level, modulated by the tetranucleotide environment. Our analyses provide an experimental scale called TRX that quantifies the intrinsic flexibility of the ten dinucleotide steps in terms of Twist, Roll, and X-disp (base pair displacement). Applying the TRX scale to DNA sequences optimized for nucleosome formation reveals a 10 base-pair periodic alternation of stiff and flexible regions. Thus, DNA flexibility captured by the TRX scale is relevant to nucleosome formation, suggesting that this scale may be of general interest to better understand protein-DNA recognition.
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Lankas F, Gonzalez O, Heffler LM, Stoll G, Moakher M, Maddocks JH. On the parameterization of rigid base and basepair models of DNA from molecular dynamics simulations. Phys Chem Chem Phys 2009; 11:10565-88. [PMID: 20145802 DOI: 10.1039/b919565n] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A method is described to extract a complete set of sequence-dependent material parameters for rigid base and basepair models of DNA in solution from atomistic molecular dynamics simulations. The method is properly consistent with equilibrium statistical mechanics, leads to effective shape, stiffness and mass parameters, and employs special procedures for treating spontaneous torsion angle flips and H-bond breaks, both of which can have a significant effect on the results. The method is accompanied by various analytical consistency checks that can be used to assess the equilibration of statistical averages, and different modeling assumptions pertaining to the rigidity of the bases and basepairs and the locality of the quadratic internal energy. The practicability of the approach is verified by estimating complete parameter sets for the 16-basepair palindromic oligomer G(TA)(7)C simulated in explicit water and counterions. Our results indicate that the method is capable of resolving sequence-dependent variations in each of the material parameters. Moreover, they show that the assumptions of rigidity and locality hold rather well for the base model, but not for the basepair model. For the latter, it is shown that the non-local nature of the internal energy can be understood in terms of a certain compatibility relation involving Schur complements.
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Affiliation(s)
- F Lankas
- Center for Complex Molecular Systems and Biomolecules, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic
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27
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Mallajosyula SS, Gupta A, Pati SK. Fluctuations at the Base Pair Level Effecting Charge Transfer in DNA. J Phys Chem A 2009; 113:3955-62. [DOI: 10.1021/jp8101942] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sairam S. Mallajosyula
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
| | - Ashutosh Gupta
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
| | - Swapan K. Pati
- Theoretical Sciences Unit and DST Unit on Nanoscience, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur Campus, Bangalore 560 064, India, and Department of Chemistry, Udai Pratap Autonomous College, Varanasi, Uttar Pradesh 221002, India
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28
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Sadowska-Aleksiejew A, Rak J, Voityuk AA. Effects of intra base-pairs flexibility on hole transfer coupling in DNA. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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29
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Réblová K, Lankas F, Rázga F, Krasovska MV, Koca J, Sponer J. Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 2006; 82:504-20. [PMID: 16538608 DOI: 10.1002/bip.20503] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Molecular dynamics (MD) simulations were employed to investigate the structure, dynamics, and local base-pair step deformability of the free 16S ribosomal helix 44 from Thermus thermophilus and of a canonical A-RNA double helix. While helix 44 is bent in the crystal structure of the small ribosomal subunit, the simulated helix 44 is intrinsically straight. It shows, however, substantial instantaneous bends that are isotropic. The spontaneous motions seen in simulations achieve large degrees of bending seen in the X-ray structure and would be entirely sufficient to allow the dynamics of the upper part of helix 44 evidenced by cryo-electron microscopic studies. Analysis of local base-pair step deformability reveals a patch of flexible steps in the upper part of helix 44 and in the area proximal to the bulge bases, suggesting that the upper part of helix 44 has enhanced flexibility. The simulations identify two conformational substates of the second bulge area (bottom part of the helix) with distinct base pairing. In agreement with nuclear magnetic resonance (NMR) and X-ray studies, a flipped out conformational substate of conserved 1492A is seen in the first bulge area. Molecular dynamics (MD) simulations reveal a number of reversible alpha-gamma backbone flips that correspond to transitions between two known A-RNA backbone families. The flipped substates do not cumulate along the trajectory and lead to a modest transient reduction of helical twist with no significant influence on the overall geometry of the duplexes. Despite their considerable flexibility, the simulated structures are very stable with no indication of substantial force field inaccuracies.
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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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30
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Kannan S, Kohlhoff K, Zacharias M. B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations. Biophys J 2006; 91:2956-65. [PMID: 16861282 PMCID: PMC1578486 DOI: 10.1529/biophysj.106.087163] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The twist flexibility of DNA is central to its many biological functions. Explicit solvent molecular dynamics simulations in combination with an umbrella sampling restraining potential have been employed to study induced twist deformations in DNA. Simulations allowed us to extract free energy profiles for twist deformations and were performed on six DNA dodecamer duplexes to cover all 10 possible DNA basepair steps. The shape of the free energy curves was similar for all duplexes. The calculated twist deformability was in good agreement with experiment and showed only modest variation for the complete duplexes. However, the response of the various basepair steps on twist stress was highly nonuniform. In particular, pyrimidine/purine steps were much more flexible than purine/purine steps followed by purine/pyrimidine steps. It was also possible to extract correlations of twist changes and other helical as well as global parameters of the DNA molecules. Twist deformations were found to significantly alter the local as well as global shape of the DNA modulating the accessibility for proteins and other ligands. Severe untwisting of DNA below an average of 25 degrees per basepair step resulted in the onset of a global structural transition with a significantly smaller twist at one end of the DNA compared to the other.
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31
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van Dijk M, van Dijk ADJ, Hsu V, Boelens R, Bonvin AMJJ. Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res 2006; 34:3317-25. [PMID: 16820531 PMCID: PMC1500871 DOI: 10.1093/nar/gkl412] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Intrinsic flexibility of DNA has hampered the development of efficient protein−DNA docking methods. In this study we extend HADDOCK (High Ambiguity Driven DOCKing) [C. Dominguez, R. Boelens and A. M. J. J. Bonvin (2003) J. Am. Chem. Soc.125, 1731–1737] to explicitly deal with DNA flexibility. HADDOCK uses non-structural experimental data to drive the docking during a rigid-body energy minimization, and semi-flexible and water refinement stages. The latter allow for flexibility of all DNA nucleotides and the residues of the protein at the predicted interface. We evaluated our approach on the monomeric repressor−DNA complexes formed by bacteriophage 434 Cro, the Escherichia coli Lac headpiece and bacteriophage P22 Arc. Starting from unbound proteins and canonical B-DNA we correctly predict the correct spatial disposition of the complexes and the specific conformation of the DNA in the published complexes. This information is subsequently used to generate a library of pre-bent and twisted DNA structures that served as input for a second docking round. The resulting top ranking solutions exhibit high similarity to the published complexes in terms of root mean square deviations, intermolecular contacts and DNA conformation. Our two-stage docking method is thus able to successfully predict protein−DNA complexes from unbound constituents using non-structural experimental data to drive the docking.
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32
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Abstract
The conformational deformability of nucleic acids can influence their function and recognition by proteins. A class of DNA binding proteins including the TATA box binding protein binds to the DNA minor groove, resulting in an opening of the minor groove and DNA bending toward the major groove. Explicit solvent molecular dynamics simulations in combination with the umbrella sampling approach have been performed to investigate the molecular mechanism of DNA minor groove deformations and the indirect energetic contribution to protein binding. As a reaction coordinate, the distance between backbone segments on opposite strands was used. The resulting deformed structures showed close agreement with experimental DNA structures in complex with minor groove-binding proteins. The calculated free energy of minor groove deformation was approximately 4-6 kcal mol(-1) in the case of a central TATATA sequence. A smaller equilibrium minor groove width and more restricted minor groove mobility was found for the central AAATTT and also a significantly ( approximately 2 times) larger free energy change for opening the minor groove. The helical parameter analysis of trajectories indicates that an easier partial unstacking of a central TA versus AT basepair step is a likely reason for the larger groove flexibility of the central TATATA case.
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Affiliation(s)
- Martin Zacharias
- School of Engineering and Science, International University Bremen, D-28759 Bremen, Germany.
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33
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Shih CC, Georghiou S. Large-amplitude fast motions in double-stranded DNA driven by solvent thermal fluctuations. Biopolymers 2006; 81:450-63. [PMID: 16419073 DOI: 10.1002/bip.20444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The nature of the internal dynamics of double-stranded DNA in aqueous environment remains to be established. We consider the motions to stem from thermal fluctuations/dissipations of the harmonic modes of beads (bases and sugars) in a cylindrical geometry that are tracked through the stochastic Langevin trajectories; these are characterized by parameters obtained from published data. The present approach has allowed a comparative study of the dynamics for DNA lengths in the range of 20-600 base pairs. For this range, we find that rotational motions about directions parallel to the helix axis (opening, twist) and perpendicular to it (propeller-twist, roll) contribute significantly to the dynamics. For a 20-mer at a solvent viscosity of 1 cP, the calculated fluorescence anisotropy profile exhibits a fast decay in the subnanosecond range due to large-amplitude fluctuations at the mesoscopic level. This feature reproduces the experimental behavior well, and suggests a possible way for the initiation of biological processes: they may be suddenly triggered on this scale through the occurrence of favorable thermal fluctuations. This analysis also reveals that, as is the case for a 20-mer, the dynamics of longer N-mers are dominated by internal motions, and are modulated by the viscosity of the solvent, in agreement with our previous experimental observations. Moreover, the model indicates that occurrence of partially concerted rotations of the bases due to thermal fluctuations can possibly be sustained over a DNA length of the order of 100 A at 1 ns, suggesting a possible mechanism for action-at-a-distance in transcription.
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Affiliation(s)
- Chia C Shih
- Department of Physics, University of Tennessee, Knoxville, TN 37996-1200, USA.
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34
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Barry CG, Day CS, Bierbach U. Duplex-promoted platination of adenine-N3 in the minor groove of DNA: challenging a longstanding bioinorganic paradigm. J Am Chem Soc 2005; 127:1160-9. [PMID: 15669855 DOI: 10.1021/ja0451620] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interactions of [Pt(en)Cl(ACRAMTU-S)](NO3)2 (PT-ACRAMTU, en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea) with adenine in DNA have been studied using a combination of analytical and high-resolution structural methods. For the first time, a cytotoxic platinum(II) complex has been demonstrated to form adducts in the minor groove of DNA through platination of the adenine-N3 endocyclic nitrogen. An acidic depurination assay was developed that allowed the controlled and selective (pH 2, 60 degrees C, 12 h) release of platinum-modified adenine from drug-treated nucleic acid samples. From the digested mixtures, three adducts were isolated by semipreparative reverse phase high-performance liquid chromatography and studied by electrospray ionization mass spectrometry (in-line LC-MS), variable-pH 1H NMR spectroscopy, and, where applicable, X-ray crystallography. The three species were identified as the N7 (A-I), N3 (A-II), and N1 (A-III) linkage isomers of [Pt(en)(ACRAMTU-S)(adenine)]3+ (A). Incubations carried out with the single- and double-stranded model sequences, d(TA)5 and d(TA)15, as well as native DNA indicate that the adduct profiles (A-I:A-II:A-IIIratios) are sensitive to the nature of the nucleic acid template. A-II was found to be a double-strand specific adduct. The crystal structure of this adduct has been determined, providing ultimate evidence for the N3 connectivity of platinum. A-II crystallizes in the triclinic space group P in the form of centrosymmetric dimers, {[Pt(en)(ACRAMTU-S)(adenine-N3)]2}6+. The cations are stabilized by a combination of adenine-adenine base pairing (N6...N1 2.945(5) A) and mutual acridine-adenine base stacking. Tandem mass spectra and 1H chemical shift anomalies indicate that this type of self-association is not merely a crystal packing effect but persists in solution. The monofunctional platination of adenine at its N7, N3, and N1 positions in a significant fraction of adducts breaks a longstanding paradigm in platinum-DNA chemistry, the requirement for nucleophilic attack of guanine-N7 as the principal step in cross-link formation. The biological consequences and potential therapeutic applications of the unique base and groove recognition of PT-ACRAMTU are discussed.
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Affiliation(s)
- Colin G Barry
- Department of Chemistry, Wake Forest University, PO Box 7486, Reynolda Station, Winston-Salem, North Carolina 27109, USA
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35
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Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1574-1400(05)01006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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36
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Grunenberg J. Direct Assessment of Interresidue Forces in Watson−Crick Base Pairs Using Theoretical Compliance Constants. J Am Chem Soc 2004; 126:16310-1. [PMID: 15600318 DOI: 10.1021/ja046282a] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This communication presents quantum mechanical calculations of interresidue potential constants for the Watson-Crick base pairs adenine-thymine (AT) and guanine-cytosine (GC), permitting a unique quantification of hydrogen bond strengths. Due to the calculated compliance constants, large differences between individual H bonds were found, while a repulsive character of the C-H...O bond in AT can be excluded.
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Affiliation(s)
- Jörg Grunenberg
- Institut für Organische Chemie, Hagenring 30, Technische Universität Braunschweig, D-38106 Braunschweig, Germany.
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37
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Abstract
In moving towards the simulation of larger nucleic acid assemblies over longer timescales that include more accurate representations of the environment, we are nearing the end of an era characterized by single nanosecond molecular dynamics simulation of nucleic acids. We are excited by the promise and predictability of the modeling methods, yet remain prudently cautious of sampling and force field limitations. Highlights include the accurate representation of subtle drug-DNA interactions, the detailed study of modified and unusual nucleic acid structures, insight into the influence of dynamics on the structure of DNA, and exploration of the interaction of solvent and ions with nucleic acids.
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Affiliation(s)
- Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah, 2000 East, 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112, USA.
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