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Chen YT, Yang H, Chu JW. Mechanical codes of chemical-scale specificity in DNA motifs. Chem Sci 2023; 14:10155-10166. [PMID: 37772098 PMCID: PMC10529945 DOI: 10.1039/d3sc01671d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023] Open
Abstract
In gene transcription, certain sequences of double-stranded (ds)DNA play a vital role in nucleosome positioning and expression initiation. That dsDNA is deformed to various extents in these processes leads us to ask: Could the genomic DNA also have sequence specificity in its chemical-scale mechanical properties? We approach this question using statistical machine learning to determine the rigidity between DNA chemical moieties. What emerges for the polyA, polyG, TpA, and CpG sequences studied here is a unique trigram that contains the quantitative mechanical strengths between bases and along the backbone. In a way, such a sequence-dependent trigram could be viewed as a DNA mechanical code. Interestingly, we discover a compensatory competition between the axial base-stacking interaction and the transverse base-pairing interaction, and such a reciprocal relationship constitutes the most discriminating feature of the mechanical code. Our results also provide chemical-scale understanding for experimental observables. For example, the long polyA persistence length is shown to have strong base stacking while its complement (polyAc) exhibits high backbone rigidity. The mechanical code concept enables a direct reading of the physical interactions encoded in the sequence which, with further development, is expected to shed new light on DNA allostery and DNA-binding drugs.
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
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2
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Alves CC, Donadi EA, Giuliatti S. Structural Characterization of the Interaction of Hypoxia Inducible Factor-1 with Its Hypoxia Responsive Element at the -964G > A Variation Site of the HLA-G Promoter Region. Int J Mol Sci 2021; 22:ijms222313046. [PMID: 34884849 PMCID: PMC8657931 DOI: 10.3390/ijms222313046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Human Antigen Leukocyte-G (HLA-G) gene encodes an immune checkpoint molecule that has restricted tissue expression in physiological conditions; however, the gene may be induced in hypoxic conditions by the interaction with the hypoxia inducible factor-1 (HIF1). Hypoxia regulatory elements (HRE) located at the HLA-G promoter region and at exon 2 are the major HIF1 target sites. Since the G allele of the −964G > A transversion induces higher HLA-G expression when compared to the A allele in hypoxic conditions, here we analyzed HIF1-HRE complex interaction at the pair-atom level considering both −964G > A polymorphism alleles. Mouse HIF2 dimer crystal (Protein Data Bank ID: 4ZPK) was used as template to perform homology modelling of human HIF1 quaternary structure using MODELLER v9.14. Two 3D DNA structures were built from 5′GCRTG’3 HRE sequence containing the −964G/A alleles using x3DNA. Protein-DNA docking was performed using the HADDOCK v2.4 server, and non-covalent bonds were computed by DNAproDB server. Molecular dynamic simulation was carried out per 200 ns, using Gromacs v.2019. HIF1 binding in the HRE containing −964G allele results in more hydrogen bonds and van der Waals contact formation than HRE with −964A allele. Protein-DNA complex trajectory analysis revealed that HIF1-HRE-964G complex is more stable. In conclusion, HIF1 binds in a more stable and specific manner at the HRE with G allele.
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Affiliation(s)
- Cinthia C. Alves
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Eduardo A. Donadi
- Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Silvana Giuliatti
- Department of Genetic, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
- Correspondence:
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3
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Strelnikov IA, Kovaleva NA, Zubova EA. Variability of the DNA Backbone Geometry in DNA-Protein Complexes: Experimental Data Analysis. J Chem Inf Model 2021; 61:4783-4794. [PMID: 34529915 DOI: 10.1021/acs.jcim.1c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have analyzed and compared the available experimental data (PDB) on the backbone geometry of the DNA in solution (NMR), in crystals (X-rays), and in complexes with proteins (X-rays and cryo-electron microscopy). The deoxyribose (pseudorotational angle τ0) and ε/ζ (BI-BII transition in phosphates) flexibilities are practically the same in the four samples. The α/γ mobility is minimal in crystalline DNA: on the histograms, there is one canonical and one noncanonical t/t peak. The α/γ mobility increases in DNA solutions (three more noncanonical peaks) and is maximal in DNA-protein complexes (another additional peak). On a large amount of data, we have confirmed that the three main degrees of freedom of the sugar-phosphate backbone are "orthogonal": changes in any of the angles τ0, (ζ-ε), and (γ-α) occur, as a rule, at a constant (usually canonical) value of any other. In the DNA-protein complexes, none of the geometrical parameters commonly used to distinguish the A and B forms of DNA, except for Zp and its simpler analog Zp', show an unambiguous correlation with τ0. Proteins, binding to DNA, in 59% of cases change the local shape of the helix up to the characteristic of the A-form without switching the deoxyribose conformation from south to north. However, we have found simple local characteristics of one nucleotide that correlate with the angles τ0 and (ζ-ε). These are the angles C3'C1'N* and C4'C3'P(2), respectively. They are orthogonal in DNA-protein complexes exactly as the pair τ0 and (ζ-ε). Most characteristics of DNA in complexes with proteins are the same in X-ray and in cryo-EM data, except for the histogram for the angle τ0. We offer a possible explanation for this difference. We also discuss the artifacts on the ε/ζ histogram for DNA in solutions caused by the currently used NMR refinement protocols.
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Affiliation(s)
- Ivan A Strelnikov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
| | - Natalya A Kovaleva
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
| | - Elena A Zubova
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119991, Russia
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4
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Ben Imeddourene A, Zargarian L, Buckle M, Hartmann B, Mauffret O. Slow motions in A·T rich DNA sequence. Sci Rep 2020; 10:19005. [PMID: 33149183 PMCID: PMC7642443 DOI: 10.1038/s41598-020-75645-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/12/2020] [Indexed: 01/09/2023] Open
Abstract
In free B-DNA, slow (microsecond-to-millisecond) motions that involve equilibrium between Watson-Crick (WC) and Hoogsteen (HG) base-pairing expand the DNA dynamic repertoire that could mediate DNA-protein assemblies. R1ρ relaxation dispersion NMR methods are powerful tools to capture such slow conformational exchanges in solution using 13C/15 N labelled DNA. Here, these approaches were applied to a dodecamer containing a TTAAA element that was assumed to facilitate nucleosome formation. NMR data and inferred exchange parameters assign HG base pairs as the minor, transient conformers specifically observed in three successive A·T base pairs forming the TAA·TTA segment. The abundance of these HG A·T base pairs can be up to 1.2% which is high compared to what has previously been observed. Data analyses support a scenario in which the three adenines undergo non-simultaneous motions despite their spatial proximity, thus optimising the probability of having one HG base pair in the TAA·TTA segment. Finally, revisiting previous NMR data on H2 resonance linewidths on the basis of our results promotes the idea of there being a special propensity of A·T base pairs in TAA·TTA tracts to adopt HG pairing. In summary, this study provides an example of a DNA functional element submitted to slow conformational exchange. More generally, it strengthens the importance of the role of the DNA sequence in modulating its dynamics, over a nano- to milli-second time scale.
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Affiliation(s)
- A Ben Imeddourene
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - L Zargarian
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - M Buckle
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - B Hartmann
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France
| | - O Mauffret
- LBPA, ENS de Paris-Saclay, UMR 8113 CNRS, Institut D'Alembert, Université Paris-Saclay, 4, avenue des Sciences, 91190, Gif-sur-Yvette, France.
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5
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Retureau R, Foloppe N, Elbahnsi A, Oguey C, Hartmann B. A dynamic view of DNA structure within the nucleosome: Biological implications. J Struct Biol 2020; 211:107511. [PMID: 32311461 DOI: 10.1016/j.jsb.2020.107511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Most of eukaryotic cellular DNA is packed in nucleosome core particles (NCPs), in which the DNA (DNANCP) is wrapped around histones. The influence of this organization on the intrinsic local dynamics of DNA is largely unknown, in particular because capturing such information from experiments remains notoriously challenging. Given the importance of dynamical properties in DNA functions, we addressed this issue using CHARMM36 MD simulations of a nucleosome containing the NCP positioning 601 sequence and four related free dodecamers. Comparison between DNANCP and free DNA reveals a limited impact of the dense DNA-histone interface on correlated motions of dinucleotide constituents and on fluctuations of inter base pair parameters. A characteristic feature intimately associated with the DNANCP super-helical path is a set of structural periodicities that includes a marked alternation of regions enriched in backbone BI and BII conformers. This observation led to uncover a convincing correspondence between the sequence effect on BI/BII propensities in both DNANCP and free DNA, strengthening the idea that the histone preference for particular DNA sequences relies on those intrinsic structural properties. These results offer for the first time a detailed view of the DNA dynamical behavior within NCP. They show in particular that the DNANCP dynamics is substantial enough to preserve the ability to structurally adjust to external proteins, for instance remodelers. Also, fresh structural arguments highlight the relevance of relationships between DNA sequence and structural properties for NCP formation. Overall, our work offers a more rational framework to approach the functional, biological roles of NCP.
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Affiliation(s)
- Romain Retureau
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | | | - Ahmad Elbahnsi
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France; LPTM, UMR8089, CNRS, CY Cergy Paris Université, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Christophe Oguey
- LPTM, UMR8089, CNRS, CY Cergy Paris Université, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Brigitte Hartmann
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, Laboratoire de biologie et pharmacologie appliquée, 61 avenue du Président Wilson, 94235 Cachan cedex, France.
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6
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Dans PD, Balaceanu A, Pasi M, Patelli AS, Petkevičiūtė D, Walther J, Hospital A, Bayarri G, Lavery R, Maddocks JH, Orozco M. The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules. Nucleic Acids Res 2019; 47:11090-11102. [PMID: 31624840 PMCID: PMC6868377 DOI: 10.1093/nar/gkz905] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/25/2019] [Accepted: 10/06/2019] [Indexed: 12/12/2022] Open
Abstract
We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distribution of its stochastic dynamics. Our analysis includes a study of first and second moments of the equilibrium distribution, which can be accurately captured by a harmonic model, but with nonlocal sequence-dependence. We characterize the sequence-dependent choreography of backbone and base movements modulating the non-Gaussian or anharmonic effects manifested in the higher moments of the dynamics of the duplex when sampling the equilibrium distribution. Contrary to prior assumptions, such anharmonic deformations are not rare in DNA and can play a significant role in determining DNA conformation within complexes. Polymorphisms in helical geometries are particularly prevalent for certain tetranucleotide sequence contexts and are always coupled to a complex network of coordinated changes in the backbone. The analysis of our simulations, which contain instances of all tetranucleotide sequences, allow us to extend Calladine-Dickerson rules used for decades to interpret the average geometry of DNA, leading to a set of rules with quantitative predictive power that encompass nonlocal sequence-dependence and anharmonic fluctuations.
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Affiliation(s)
- Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
- Department of Biological Sciences, University of the Republic (UdelaR), CENUR Gral. Rivera 1350, 50000 Salto, Uruguay
| | - Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Marco Pasi
- LBPA, École normale supérieure Paris-Saclay, 61 Av. du Pdt Wilson, Cachan 94235, France
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - Alessandro S Patelli
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Daiva Petkevičiūtė
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
- Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, Studentų g. 50, 51368 Kaunas, Lithuania
| | - Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Richard Lavery
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - John H Maddocks
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
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7
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Nguyen TTV, Xie X, Xu J, Wu Y, Hong M, Liu X. Plasmonic bimetallic nanodisk arrays for DNA conformation sensing. NANOSCALE 2019; 11:19291-19296. [PMID: 31560008 DOI: 10.1039/c9nr06101k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The integration of large-scale 2D bimetallic Ag/Au nanodisk arrays with gold nanoparticles is developed for sensing DNA conformation with the assistance of 3D finite-difference time-domain simulation. The optimized system comprising Ag/Au nanodisk arrays and gold nanoparticles offers a more than 6-fold enhancement in surface plasmon resonance shift, enabling the feasibility for sensitive DNA detection with a detection limit down to 100 femtomolar. Importantly, owing to the distance-dependent nature of the surface plasmon signal, sensitive differentiation of DNA conformations can be achieved with a conventional optical measurement. This platform could provide new exciting capabilities for a reliable, reproducible, and label-free assay analysis for investigating the conformations of DNA and other biological molecules.
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Affiliation(s)
- Thanh Thi Van Nguyen
- Advanced Materials for Micro- and Nano-Systems Programme, Singapore-MIT Alliance, 117576, Singapore
| | - Xiaoji Xie
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Jiahui Xu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Yiming Wu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore.
| | - Minghui Hong
- Department of Electrical and Computer Engineering, National University of Singapore, 117576, Singapore
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore. and The N.1 Institute for Health, National University of Singapore, 28 Medical Dr. #05-COR, 117456, Singapore and Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University, Fuzhou, 350207, P. R. China
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8
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Zhitnikova M, Shestopalova A. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations. J Biomol Struct Dyn 2017; 35:3384-3397. [DOI: 10.1080/07391102.2016.1255259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- M.Y. Zhitnikova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
| | - A.V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
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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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Balaceanu A, Pasi M, Dans PD, Hospital A, Lavery R, Orozco M. The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA. J Phys Chem Lett 2017; 8:21-28. [PMID: 27935717 DOI: 10.1021/acs.jpclett.6b02451] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
An accurate understanding of DNA backbone transitions is likely to be the key for elucidating the puzzle of the intricate sequence-dependent mechanical properties that govern most of the biologically relevant functions of the double helix. One factor believed to be important in indirect recognition within protein-DNA complexes is the combined effect of two DNA backbone torsions (ε and ζ) which give rise to the well-known BI/BII conformational equilibrium. In this work we explain the sequence-dependent BII propensity observed in RpY steps (R = purine; Y = pyrimidine) at the tetranucleotide level with the help of a previously undetected C-H···O contact between atoms belonging to adjacent bases. Our results are supported by extensive multimicrosecond molecular dynamics simulations from the Ascona B-DNA Consortium, high-level quantum mechanical calculations, and data mining of the experimental structures deposited in the Protein Data Bank.
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Affiliation(s)
- Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Marco Pasi
- MMSB, Univ. Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, Lyon 69367, France
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham , University Park NG7 2RD, U.K
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain
| | - Richard Lavery
- MMSB, Univ. Lyon I/CNRS UMR 5086, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, Lyon 69367, France
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10-12, Barcelona 08028, Spain
- Joint BSC-IRB Program in Computational Biology, Institute for Research in Biomedicine , Baldiri Reixac 10-12, Barcelona 08028, Spain
- Department of Biochemistry and Biomedicine, Faculty of Biology, University of Barcelona . Diagonal 643, Barcelona 08028, Spain
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11
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High-resolution biophysical analysis of the dynamics of nucleosome formation. Sci Rep 2016; 6:27337. [PMID: 27263658 PMCID: PMC4897087 DOI: 10.1038/srep27337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 12/14/2022] Open
Abstract
We describe a biophysical approach that enables changes in the structure of DNA to be followed during nucleosome formation in in vitro reconstitution with either the canonical "Widom" sequence or a judiciously mutated sequence. The rapid non-perturbing photochemical analysis presented here provides 'snapshots' of the DNA configuration at any given moment in time during nucleosome formation under a very broad range of reaction conditions. Changes in DNA photochemical reactivity upon protein binding are interpreted as being mainly induced by alterations in individual base pair roll angles. The results strengthen the importance of the role of an initial (H3/H4)2 histone tetramer-DNA interaction and highlight the modulation of this early event by the DNA sequence. (H3/H4)2 binding precedes and dictates subsequent H2A/H2B-DNA interactions, which are less affected by the DNA sequence, leading to the final octameric nucleosome. Overall, our results provide a novel, exciting way to investigate those biophysical properties of DNA that constitute a crucial component in nucleosome formation and stabilization.
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12
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Che X, Zhang J, Zhu Y, Yang L, Quan H, Gao YQ. Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions. J Phys Chem B 2016; 120:2670-80. [PMID: 26878265 DOI: 10.1021/acs.jpcb.5b11531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cyclic dinucleotides are able to trigger the innate immune system by activating STING. It was found that the binding affinity of asymmetric 2'3'-cGAMP to symmetric dimer of STING is 3 orders of magnitude higher than that of the symmetric 3'3'-cyclic dinucleotides. Such a phenomenon has not been understood yet. Here we show that the subtle changes in phosphodiester linkage of CDNs lead to their distinct structural properties which correspond to the varied binding affinities. 2'-5' and/or 3'-5' linked CDNs adopt specific while different types of ribose puckers and backbone conformations. That ribose conformations and base types have different propensities for anti or syn glycosidic conformations further affects the overall flexibility of CDNs. The counterbalance between backbone ring tension and electrostatic repulsion, both affected by the ring size, also contributes to the different flexibility of CDNs. Our calculations reveal that the free energy cost for 2'3'-cGAMP to adopt the STING-bound structure is smaller than that for 3'3'-cGAMP and cyclic-di-GMP. These findings may serve as a reference for design of CDN-analogues as vaccine adjuvants. Moreover, the cyclization pattern of CDNs closely related to their physiological roles suggests the importance of understanding structural properties in the study of protein-ligand interactions.
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Affiliation(s)
- Xing Che
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Jun Zhang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Yanyu Zhu
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Lijiang Yang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Hui Quan
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
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13
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Imeddourene AB, Xu X, Zargarian L, Oguey C, Foloppe N, Mauffret O, Hartmann B. The intrinsic mechanics of B-DNA in solution characterized by NMR. Nucleic Acids Res 2016; 44:3432-47. [PMID: 26883628 PMCID: PMC4838374 DOI: 10.1093/nar/gkw084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/01/2016] [Indexed: 12/19/2022] Open
Abstract
Experimental characterization of the structural couplings in free B-DNA in solution has been elusive, because of subtle effects that are challenging to tackle. Here, the exploitation of the NMR measurements collected on four dodecamers containing a substantial set of dinucleotide sequences provides new, consistent correlations revealing the DNA intrinsic mechanics. The difference between two successive residual dipolar couplings (ΔRDCs) involving C6/8-H6/8, C3′-H3′ and C4′-H4′ vectors are correlated to the 31P chemical shifts (δP), which reflect the populations of the BI and BII backbone states. The δPs are also correlated to the internucleotide distances (Dinter) involving H6/8, H2′ and H2″ protons. Calculations of NMR quantities on high resolution X-ray structures and controlled models of DNA enable to interpret these couplings: the studied ΔRDCs depend mostly on roll, while Dinter are mainly sensitive to twist or slide. Overall, these relations demonstrate how δP measurements inform on key inter base parameters, in addition to probe the BI↔BII backbone equilibrium, and shed new light into coordinated motions of phosphate groups and bases in free B-DNA in solution. Inspection of the 5′ and 3′ ends of the dodecamers also supplies new information on the fraying events, otherwise neglected.
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Affiliation(s)
- Akli Ben Imeddourene
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France Université Pierre et Marie Curie, 4 Place Jussieu, 75005 Paris, France
| | - Xiaoqian Xu
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France Department of Life Sciences, East China Normal University, 200062 Shanghai, People's Republic of China
| | - Loussiné Zargarian
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Christophe Oguey
- Laboratoire de Physique Théorique et Modélisation, UMR 8089, CNRS, Université de Cergy-Pontoise, Cergy-Pontoise, France
| | | | - Olivier Mauffret
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Brigitte Hartmann
- Laboratoire de Biologie et Pharmacologie Appliquée, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
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14
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Ben Imeddourene A, Elbahnsi A, Guéroult M, Oguey C, Foloppe N, Hartmann B. Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics. PLoS Comput Biol 2015; 11:e1004631. [PMID: 26657165 PMCID: PMC4689557 DOI: 10.1371/journal.pcbi.1004631] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/28/2015] [Indexed: 01/30/2023] Open
Abstract
The accurate prediction of the structure and dynamics of DNA remains a major challenge in computational biology due to the dearth of precise experimental information on DNA free in solution and limitations in the DNA force-fields underpinning the simulations. A new generation of force-fields has been developed to better represent the sequence-dependent B-DNA intrinsic mechanics, in particular with respect to the BI ↔ BII backbone equilibrium, which is essential to understand the B-DNA properties. Here, the performance of MD simulations with the newly updated force-fields Parmbsc0εζOLI and CHARMM36 was tested against a large ensemble of recent NMR data collected on four DNA dodecamers involved in nucleosome positioning. We find impressive progress towards a coherent, realistic representation of B-DNA in solution, despite residual shortcomings. This improved representation allows new and deeper interpretation of the experimental observables, including regarding the behavior of facing phosphate groups in complementary dinucleotides, and their modulation by the sequence. It also provides the opportunity to extensively revisit and refine the coupling between backbone states and inter base pair parameters, which emerges as a common theme across all the complementary dinucleotides. In sum, the global agreement between simulations and experiment reveals new aspects of intrinsic DNA mechanics, a key component of DNA-protein recognition.
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Affiliation(s)
- Akli Ben Imeddourene
- LBPA, CNRS, ENS Cachan, Université Paris-Saclay, Cachan, France
- Université Pierre et Marie Curie, Paris, France
| | - Ahmad Elbahnsi
- LBPA, CNRS, ENS Cachan, Université Paris-Saclay, Cachan, France
- LPTM, UMR 8089, Université de Cergy-Pontoise, Cergy-Pontoise, France
| | - Marc Guéroult
- UMR S665, INSERM, Université Paris Diderot, INTS, Paris, France
| | - Christophe Oguey
- LPTM, UMR 8089, Université de Cergy-Pontoise, Cergy-Pontoise, France
| | | | - Brigitte Hartmann
- LBPA, CNRS, ENS Cachan, Université Paris-Saclay, Cachan, France
- * E-mail: (NF); (BH)
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15
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Zgarbová M, Šponer J, Otyepka M, Cheatham TE, Galindo-Murillo R, Jurečka P. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA. J Chem Theory Comput 2015; 11:5723-36. [PMID: 26588601 DOI: 10.1021/acs.jctc.5b00716] [Citation(s) in RCA: 332] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.
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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
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah , 30 South 2000 East, Skaggs 105, Salt Lake City, Utah 84112, United States
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, University of Utah , 30 South 2000 East, Skaggs 105, Salt Lake City, Utah 84112, United States
| | - 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
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16
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Robertson JC, Cheatham TE. DNA Backbone BI/BII Distribution and Dynamics in E2 Protein-Bound Environment Determined by Molecular Dynamics Simulations. J Phys Chem B 2015; 119:14111-9. [PMID: 26482568 DOI: 10.1021/acs.jpcb.5b08486] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BI and BII conformational substates in the DNA backbone typify canonical B-form DNA. The BI and BII substates are important for structural variation of DNA and have been implicated in protein-nucleic acid recognition mechanisms. Recent refinements have been made to nucleic acid force fields employed in molecular dynamics simulations that demonstrate a better ability to model the BI and BII states, leading to overall improved modeling of DNA structure and dynamics. These force field improvements have yet to be significantly demonstrated in the context of a protein-DNA system extended to long time scales. Our plan was to run molecular dynamics simulations of a well-studied protein-DNA system (E2-DNA) into the microsecond time scale and determine the ability of the force field to populate BII states in the DNA backbone consistent with dinucleotide steps crystallized in the BII conformation. The results showed that the dinucleotide steps in the E2-DNA complex with the highest BII populations from simulation trajectories corresponded to the dinucleotide steps crystallized in the BII state and that decoy BI and BII states converge to the same results within approximately one microsecond.
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Affiliation(s)
- James C Robertson
- Department of Medicinal Chemistry, College of Pharmacy, 2000 East 30 South Skaggs 307, The University of Utah , Salt Lake City, Utah 84112-5820, United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, 2000 East 30 South Skaggs 307, The University of Utah , Salt Lake City, Utah 84112-5820, United States
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17
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Savelyev A, MacKerell AD. Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding. J Chem Theory Comput 2015; 11:4473-85. [PMID: 26575937 DOI: 10.1021/acs.jctc.5b00508] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, we reported the differential impact of the monovalent cations Li(+), Na(+), K(+), and Rb(+) on DNA conformational properties. These were identified from variations in the calculated solution-state X-ray DNA spectra as a function of the ion type in solvation buffer in MD simulations using our recently developed polarizable force field based on the classical Drude oscillator. Changes in the DNA structure were found to mainly involve variations in the minor groove width. Because minor groove dimensions vary significantly in protein-DNA complexes and have been shown to play a critical role in both specific and nonspecific DNA readout, understanding the origins of the observed differential DNA modulation by the first-group monovalent ions is of great biological importance. In the present study, we show that the primary microscopic mechanism for the phenomenon is the formation of water-mediated hydrogen bonds between solvated cations located inside the minor groove and simultaneously to two DNA strands, a process whose intensity and impact on DNA structure depends on both the type of ion and the DNA sequence. Additionally, it is shown that the formation of such ion-DNA hydrogen bond complexes appreciably modulates the conformation of the backbone by increasing the population of the BII substate. Notably, the differential impact of the ions on DNA conformational behavior is only predicted by the Drude polarizable model for DNA with virtually no effect observed from MD simulations utilizing the additive CHARMM36 model. Analysis of dipole moments of the water shows the Drude SWM4 model to possess high sensitivity to changes in the local environment, which indicates the important role of electronic polarization in the salt-dependent conformational properties. This also suggests that inclusion of polarization effects is required to model even relatively simple biological systems, such as DNA, in various ionic solutions.
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Affiliation(s)
- Alexey Savelyev
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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18
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Xu X, Ben Imeddourene A, Zargarian L, Foloppe N, Mauffret O, Hartmann B. NMR studies of DNA support the role of pre-existing minor groove variations in nucleosome indirect readout. Biochemistry 2014; 53:5601-12. [PMID: 25102280 DOI: 10.1021/bi500504y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We investigated how the intrinsic sequence-dependent properties probed via the phosphate linkages (BI ↔ BII equilibrium) influence the preferred shape of free DNA, and how this affects the nucleosome formation. First, this exploits NMR solution studies of four B-DNA dodecamers that together cover 39 base pairs of the 5' half of the sequence 601, of special interest for nucleosome formation. The results validate our previous prediction of a systematic, general sequence effect on the intrinsic backbone BII propensities. NMR provides new evidence that the backbone behavior is intimately coupled to the minor groove width. Second, application of the backbone behavior predictions to the full sequence 601 and other relevant sequences demonstrates that alternation of intrinsic low and high BII propensities, coupled to intrinsic narrow and wide minor grooves, largely coincides with the sinusoidal variations of the DNA minor groove width observed in crystallographic structures of the nucleosome. This correspondence is much poorer with low affinity sequences. Overall, the results indicate that nucleosome formation involves an indirect readout process implicating pre-existing DNA minor groove conformations. It also illustrates how the prediction of the intrinsic structural DNA behavior offers a powerful framework to gain explanatory insight on how proteins read DNA.
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Affiliation(s)
- Xiaoqian Xu
- LBPA, UMR 8113, ENS de Cachan CNRS , 61 avenue du Président Wilson, 94235 Cachan cedex, France
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19
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Savelyev A, MacKerell AD. All-atom polarizable force field for DNA based on the classical Drude oscillator model. J Comput Chem 2014; 35:1219-39. [PMID: 24752978 PMCID: PMC4075971 DOI: 10.1002/jcc.23611] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/19/2014] [Accepted: 03/23/2014] [Indexed: 12/16/2022]
Abstract
Presented is a first generation atomistic force field (FF) for DNA in which electronic polarization is modeled based on the classical Drude oscillator formalism. The DNA model is based on parameters for small molecules representative of nucleic acids, including alkanes, ethers, dimethylphosphate, and the nucleic acid bases and empirical adjustment of key dihedral parameters associated with the phosphodiester backbone, glycosidic linkages, and sugar moiety of DNA. Our optimization strategy is based on achieving a compromise between satisfying the properties of the underlying model compounds in the gas phase targeting quantum mechanical (QM) data and reproducing a number of experimental properties of DNA duplexes in the condensed phase. The resulting Drude FF yields stable DNA duplexes on the 100-ns time scale and satisfactorily reproduce (1) the equilibrium between A and B forms of DNA and (2) transitions between the BI and BII substates of B form DNA. Consistency with the gas phase QM data for the model compounds is significantly better for the Drude model as compared to the CHARMM36 additive FF, which is suggested to be due to the improved response of the model to changes in the environment associated with the explicit inclusion of polarizability. Analysis of dipole moments associated with the nucleic acid bases shows the Drude model to have significantly larger values than those present in CHARMM36, with the dipoles of individual bases undergoing significant variations during the MD simulations. Additionally, the dipole moment of water was observed to be perturbed in the grooves of DNA.
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Affiliation(s)
- Alexey Savelyev
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
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20
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Savelyev A, MacKerell AD. Balancing the interactions of ions, water, and DNA in the Drude polarizable force field. J Phys Chem B 2014; 118:6742-57. [PMID: 24874104 PMCID: PMC4064693 DOI: 10.1021/jp503469s] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Recently we presented a first-generation
all-atom Drude polarizable
force field for DNA based on the classical Drude oscillator model,
focusing on optimization of key dihedral angles followed by extensive
validation of the force field parameters. Presently, we describe the
procedure for balancing the electrostatic interactions between ions,
water, and DNA as required for development of the Drude force field
for DNA. The proper balance of these interactions is shown to impact
DNA stability and subtler conformational properties, including the
conformational equilibrium between the BI and BII states, and the
A and B forms of DNA. The parametrization efforts were simultaneously
guided by gas-phase quantum mechanics (QM) data on small model compounds
and condensed-phase experimental data on the hydration and osmotic
properties of biologically relevant ions and their solutions, as well
as theoretical predictions for ionic distribution around DNA oligomer.
In addition, fine-tuning of the internal base parameters was performed
to obtain the final DNA model. Notably, the Drude model is shown to
more accurately reproduce counterion condensation theory predictions
of DNA charge neutralization by the condensed ions as compared to
the CHARMM36 additive DNA force field, indicating an improved physical
description of the forces dictating the ionic solvation of DNA due
to the explicit treatment of electronic polarizability. In combination
with the polarizable DNA force field, the availability of Drude polarizable
parameters for proteins, lipids, and carbohydrates will allow for
simulation studies of heterogeneous biological systems.
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Affiliation(s)
- Alexey Savelyev
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
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21
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Xiao S, Zhu H, Wang L, Liang H. DNA conformational flexibility study using phosphate backbone neutralization model. SOFT MATTER 2014; 10:1045-1055. [PMID: 24983118 DOI: 10.1039/c3sm52345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Due to the critical role of DNA in the processes of the cell cycle, the structural and physicochemical properties of DNA have long been of concern. In the present work, the effect of interplay between the DNA duplex and metal ions in solution on the DNA structure and conformational flexibility is studied by comparing the structure and dynamic conformational behavior of a duplex in a normal form and its “null isomer” using molecular dynamics methods. It was found that the phosphate neutralization changes the cation atmosphere around the DNA duplex greatly, increases the major groove width, decreases the minor groove width, and reduces the global bending direction preference. We also noted that the probability of BI phosphate linkages increases significantly because of the charge reduction in the backbone phosphate groups. More importantly, we found that the electrostatic effect on the DNA conformational flexibility is dependent on the sequence; that is, the phosphate backbone neutralization induces the global dynamic bending to be less flexible for GC-rich sequences but more flexible for AT-rich sequences.
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22
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Zhitnikova MY, Boryskina OP, Shestopalova AV. Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. J Biomol Struct Dyn 2013; 32:1670-85. [PMID: 23998351 DOI: 10.1080/07391102.2013.830579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Variations of the shape and polarity of the DNA grooves caused by changes of the DNA conformation play an important role in the DNA readout. Despite the fact that non-canonical trans and gauche- conformations of the DNA backbone angle γ (O5'-C5'-C4'-C3') are frequently found in the DNA crystal structures, their possible role in the DNA recognition has not been studied systematically. In order to fill in this gap, we analyze the available high-resolution crystal structures of the naked and complexed DNA. The analysis shows that the non-canonical γ angle conformations are present both in the naked and bound DNA, more often in the bound vs. naked DNA, and in the nucleotides with the A-like vs. the B-like sugar pucker. The alternative angle γ torsions are more frequently observed in the purines with the A-like sugar pucker and in the pyrimidines with the B-like sugar conformation. The minor groove of the nucleotides with non-canonical γ angle conformation is more polar, while the major groove is more hydrophobic than in the nucleotides with the classical γ torsions due to variations in exposure of the polar and hydrophobic groups of the DNA backbone. The propensity of the nucleotides with different γ angle conformations to participate in the protein-nucleic acid contacts in the minor and major grooves is connected with their sugar pucker and sequence-specific. Our findings imply that the angle γ transitions contribute to the process of the protein-DNA recognition due to modification of the polar/hydrophobic profile of the DNA grooves.
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Affiliation(s)
- Mariia Yu Zhitnikova
- a O. Ya. Usikov Institute for Radiophysics and Electronics of the National Academy of Sciences of Ukraine , Acad. Proskura Street, 12, Kharkiv , 61085 , Ukraine
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23
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Čech P, Kukal J, Černý J, Schneider B, Svozil D. Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics 2013; 14:205. [PMID: 23800225 PMCID: PMC3694522 DOI: 10.1186/1471-2105-14-205] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/28/2013] [Indexed: 12/03/2022] Open
Abstract
Background A growing number of crystal and NMR structures reveals a considerable structural polymorphism of DNA architecture going well beyond the usual image of a double helical molecule. DNA is highly variable with dinucleotide steps exhibiting a substantial flexibility in a sequence-dependent manner. An analysis of the conformational space of the DNA backbone and the enhancement of our understanding of the conformational dependencies in DNA are therefore important for full comprehension of DNA structural polymorphism. Results A detailed classification of local DNA conformations based on the technique of Fourier averaging was published in our previous work. However, this procedure requires a considerable amount of manual work. To overcome this limitation we developed an automatic classification method consisting of the combination of supervised and unsupervised approaches. A proposed workflow is composed of k-NN method followed by a non-hierarchical single-pass clustering algorithm. We applied this workflow to analyze 816 X-ray and 664 NMR DNA structures released till February 2013. We identified and annotated six new conformers, and we assigned four of these conformers to two structurally important DNA families: guanine quadruplexes and Holliday (four-way) junctions. We also compared populations of the assigned conformers in the dataset of X-ray and NMR structures. Conclusions In the present work we developed a machine learning workflow for the automatic classification of dinucleotide conformations. Dinucleotides with unassigned conformations can be either classified into one of already known 24 classes or they can be flagged as unclassifiable. The proposed machine learning workflow permits identification of new classes among so far unclassifiable data, and we identified and annotated six new conformations in the X-ray structures released since our previous analysis. The results illustrate the utility of machine learning approaches in the classification of local DNA conformations.
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Affiliation(s)
- Petr Čech
- Laboratory of Informatics and Chemistry, ICT Prague, Technická 5, Prague 6, 166 28, Czech Republic
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24
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Zgarbová M, Luque FJ, Šponer J, Cheatham TE, Otyepka M, Jurečka P. Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters. J Chem Theory Comput 2013; 9:2339-2354. [PMID: 24058302 PMCID: PMC3775469 DOI: 10.1021/ct400154j] [Citation(s) in RCA: 221] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations.
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Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina (IBUB), Facultad de Farmacia, Universidad de Barcelona, Campus Torribera, Prat de la Riba 171, Edifici Verdaguer, 080921 Santa Coloma de Gramanet, Spain
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Thomas E. Cheatham
- Departments of Medicinal Chemistry, University of Utah, 2000 East 30 South Skaggs 105, Salt Lake City, UT 84112, USA
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 771 46, Olomouc, Czech Republic
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25
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Sharma M, Predeus AV, Mukherjee S, Feig M. DNA bending propensity in the presence of base mismatches: implications for DNA repair. J Phys Chem B 2013; 117:6194-205. [PMID: 23621762 DOI: 10.1021/jp403127a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA bending is believed to facilitate the initial recognition of the mismatched base for repair. The repair efficiencies are dependent on both the mismatch type and neighboring nucleotide sequence. We have studied bending of several DNA duplexes containing canonical matches: A:T and G:C; various mismatches: A:A, A:C, G:A, G:G, G:T, C:C, C:T, and T:T; and a bis-abasic site: X:X. Free-energy profiles were generated for DNA bending using umbrella sampling. The highest energetic cost associated with DNA bending is observed for canonical matches while bending free energies are lower in the presence of mismatches, with the lowest value for the abasic site. In all of the sequences, DNA duplexes bend toward the major groove with widening of the minor groove. For homoduplexes, DNA bending is observed to occur via smooth deformations, whereas for heteroduplexes, kinks are observed at the mismatch site during strong bending. In general, pyrimidine:pyrimidine mismatches are the most destabilizing, while purine:purine mismatches lead to intermediate destabilization, and purine:pyrimidine mismatches are the least destabilizing. The ease of bending is partially correlated with the binding affinity of MutS to the mismatch pairs and subsequent repair efficiencies, indicating that intrinsic DNA bending propensities are a key factor of mismatch recognition.
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Affiliation(s)
- Monika Sharma
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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Foloppe N, Guéroult M, Hartmann B. Simulating DNA by molecular dynamics: aims, methods, and validation. Methods Mol Biol 2013; 924:445-468. [PMID: 23034759 DOI: 10.1007/978-1-62703-017-5_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The structure and dynamics of the B-DNA double helix involves subtle sequence-dependent effects which are decisive for its function, but difficult to characterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics simulations with the major force fields in use today. We explain why a critical analysis of the MD trajectories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood.
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27
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Dixit SB, Mezei M, Beveridge DL. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations. J Biosci 2012; 37:399-421. [PMID: 22750979 DOI: 10.1007/s12038-012-9223-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the observed water and ion atmosphere around the DNA sequences is the MD simulation is in good agreement with experimental observations.
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Affiliation(s)
- Surjit B Dixit
- Chemistry Department and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06457, USA
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Guéroult M, Boittin O, Mauffret O, Etchebest C, Hartmann B. Mg2+ in the major groove modulates B-DNA structure and dynamics. PLoS One 2012; 7:e41704. [PMID: 22844516 PMCID: PMC3402463 DOI: 10.1371/journal.pone.0041704] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 12/12/2022] Open
Abstract
This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg(2+) close to an ApG step. These simulations showed that the hydrated Mg(2+) forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg(2+). The binding of Mg(2+) modulates the behavior of the 5'-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5'-phosphate group and Mg(2+) strengthen both the DNA-cation binding and the BII character of the 5'-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes.
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Affiliation(s)
- Marc Guéroult
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris, France
| | - Olivier Boittin
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Oliver Mauffret
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
| | - Catherine Etchebest
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Brigitte Hartmann
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
- * E-mail:
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29
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Temiz NA, Donohue DE, Bacolla A, Luke BT, Collins JR. The role of methylation in the intrinsic dynamics of B- and Z-DNA. PLoS One 2012; 7:e35558. [PMID: 22530050 PMCID: PMC3328458 DOI: 10.1371/journal.pone.0035558] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/20/2012] [Indexed: 11/27/2022] Open
Abstract
Methylation of cytosine at the 5-carbon position (5 mC) is observed in both prokaryotes and eukaryotes. In humans, DNA methylation at CpG sites plays an important role in gene regulation and has been implicated in development, gene silencing, and cancer. In addition, the CpG dinucleotide is a known hot spot for pathologic mutations genome-wide. CpG tracts may adopt left-handed Z-DNA conformations, which have also been implicated in gene regulation and genomic instability. Methylation facilitates this B-Z transition but the underlying mechanism remains unclear. Herein, four structural models of the dinucleotide d(GC)(5) repeat sequence in B-, methylated B-, Z-, and methylated Z-DNA forms were constructed and an aggregate 100 nanoseconds of molecular dynamics simulations in explicit solvent under physiological conditions was performed for each model. Both unmethylated and methylated B-DNA were found to be more flexible than Z-DNA. However, methylation significantly destabilized the BII, relative to the BI, state through the Gp5mC steps. In addition, methylation decreased the free energy difference between B- and Z-DNA. Comparisons of α/γ backbone torsional angles showed that torsional states changed marginally upon methylation for B-DNA, and Z-DNA. Methylation-induced conformational changes and lower energy differences may contribute to the transition to Z-DNA by methylated, over unmethylated, B-DNA and may be a contributing factor to biological function.
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Affiliation(s)
- Nuri A Temiz
- In Silico Research Centers of Excellence, Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America.
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Hart K, Foloppe N, Baker CM, Denning EJ, Nilsson L, MacKerell AD. Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. J Chem Theory Comput 2012; 8:348-362. [PMID: 22368531 PMCID: PMC3285246 DOI: 10.1021/ct200723y] [Citation(s) in RCA: 390] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The B-form of DNA can populate two different backbone conformations: BI and BII, defined by the difference between the torsion angles ε and ζ (BI = ε-ζ < 0 and BII = ε-ζ > 0). BI is the most populated state, but the population of the BII state, which is sequence dependent, is significant and accumulating evidence shows that BII affects the overall structure of DNA, and thus influences protein-DNA recognition. This work presents a reparametrization of the CHARMM27 additive nucleic acid force field to increase the sampling of the BII form in MD simulations of DNA. In addition, minor modifications of sugar puckering were introduced to facilitate sampling of the A form of DNA under the appropriate environmental conditions. Parameter optimization was guided by quantum mechanical data on model compounds, followed by calculations on several DNA duplexes in the condensed phase. The selected optimized parameters were then validated against a number of DNA duplexes, with the most extensive tests performed on the EcoRI dodecamer, including comparative calculations using the Amber Parm99bsc0 force field. The new CHARMM model better reproduces experimentally observed sampling of the BII conformation, including sampling as a function of sequence. In addition, the model reproduces the A form of the 1ZF1 duplex in 75 % ethanol, and yields a stable Z-DNA conformation of duplex (GTACGTAC) in its crystal environment. The resulting model, in combination with a recent reoptimization of the CHARMM27 force field for RNA, will be referred to as CHARMM36.
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Affiliation(s)
- Katarina Hart
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 HUDDINGE, Sweden
| | | | - Christopher M. Baker
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
| | - Elizabeth J. Denning
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 HUDDINGE, Sweden
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA
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31
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Abstract
DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models.
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Affiliation(s)
- Thomas Gaillard
- BioMaPS Institute for Quantitative Biology, Rutgers – The State University of New Jersey, Piscataway, New Jersey 08854-8087
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
| | - David A. Case
- BioMaPS Institute for Quantitative Biology, Rutgers – The State University of New Jersey, Piscataway, New Jersey 08854-8087
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32
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Oguey C, Foloppe N, Hartmann B. Understanding the sequence-dependence of DNA groove dimensions: implications for DNA interactions. PLoS One 2010; 5:e15931. [PMID: 21209967 PMCID: PMC3012109 DOI: 10.1371/journal.pone.0015931] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 11/30/2010] [Indexed: 01/05/2023] Open
Abstract
Background The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. Methodology/Principal Findings The present study is based on the analysis of datasets of free and protein-bound DNA crystal structures, and from a compilation of NMR 31P chemical shifts measured on free DNA in solution on a broad range of representative sequences. The 31P chemical shifts can be interpreted in terms of the BI↔BII backbone conformations and dynamics. The grooves width and depth of free and protein-bound DNA are found to be clearly related to the BI/BII backbone conformational states. The DNA propensity to undergo BI↔BII backbone transitions is highly sequence-dependent and can be quantified at the dinucleotide level. This dual relationship, between DNA sequence and backbone behavior on one hand, and backbone behavior and groove dimensions on the other hand, allows to decipher the link between DNA sequence and groove dimensions. It also firmly establishes that proteins take advantage of the intrinsic DNA groove properties. Conclusions/Significance The study provides a general framework explaining how the DNA sequence shapes the groove dimensions in free and protein-bound DNA, with far-reaching implications for DNA-protein indirect readout in both specific and non specific interactions.
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Affiliation(s)
- Christophe Oguey
- Laboratoire de Physique Théorique et Modélisation, UMR-8089, Centre National de la Recherche Scientifique et Université de Cergy-Pontoise, Cergy-Pontoise, France
| | - Nicolas Foloppe
- UMR-S665, Institut National de la Santé et de la Recherche Médicale et Université Paris Diderot, Institut National de la Transfusion Sanguine, Paris, France
- * E-mail: (BH); (NF)
| | - Brigitte Hartmann
- UMR-S665, Institut National de la Santé et de la Recherche Médicale et Université Paris Diderot, Institut National de la Transfusion Sanguine, Paris, France
- * E-mail: (BH); (NF)
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33
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Boryskina OP, Tkachenko MY, Shestopalova AV. Variability of DNA structure and protein-nucleic acid reconginition. ACTA ACUST UNITED AC 2010. [DOI: 10.7124/bc.00016a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- O. P. Boryskina
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - M. Yu. Tkachenko
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
| | - A. V. Shestopalova
- A. Usikov Institute of Radio Physics and Electronics, National Academy of Sciences of Ukraine
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34
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Abi-Ghanem J, Heddi B, Foloppe N, Hartmann B. DNA structures from phosphate chemical shifts. Nucleic Acids Res 2010; 38:e18. [PMID: 19942687 PMCID: PMC2817473 DOI: 10.1093/nar/gkp1061] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 10/14/2009] [Accepted: 11/01/2009] [Indexed: 01/04/2023] Open
Abstract
For B-DNA, the strong linear correlation observed by nuclear magnetic resonance (NMR) between the (31)P chemical shifts (deltaP) and three recurrent internucleotide distances demonstrates the tight coupling between phosphate motions and helicoidal parameters. It allows to translate deltaP into distance restraints directly exploitable in structural refinement. It even provides a new method for refining DNA oligomers with restraints exclusively inferred from deltaP. Combined with molecular dynamics in explicit solvent, these restraints lead to a structural and dynamical view of the DNA as detailed as that obtained with conventional and more extensive restraints. Tests with the Jun-Fos oligomer show that this deltaP-based strategy can provide a simple and straightforward method to capture DNA properties in solution, from routine NMR experiments on unlabeled samples.
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Affiliation(s)
- Joséphine Abi-Ghanem
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Brahim Heddi
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Nicolas Foloppe
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
| | - Brigitte Hartmann
- INTS, INSERM S-665, 6 rue Alexandre Cabanel, Paris 75015, IBPC, CNRS UPR 9080, 13 rue Pierre et Marie Curie, Paris 75005, France and 51 Natal Road, Cambridge CB1 3NY, UK
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35
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Sequence-Dependent DNA Flexibility Mediates DNase I Cleavage. J Mol Biol 2010; 395:123-33. [DOI: 10.1016/j.jmb.2009.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 10/09/2009] [Accepted: 10/12/2009] [Indexed: 11/17/2022]
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36
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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: 64] [Impact Index Per Article: 4.3] [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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37
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Téletchéa S, Skauge T, Sletten E, Kozelka J. Cisplatin Adducts on a GGG Sequence within a DNA Duplex Studied by NMR Spectroscopy and Molecular Dynamics Simulations. Chemistry 2009; 15:12320-37. [DOI: 10.1002/chem.200901158] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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38
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Santini GPH, Cognet JAH, Xu D, Singarapu KK, Hervé du Penhoat C. Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGAAAGC). J Phys Chem B 2009; 113:6881-93. [PMID: 19374420 DOI: 10.1021/jp8100656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Determination of DNA solution structure is a difficult task even with the high-sensitivity method used here based on simulated annealing with 35 restraints/residue (Cryoprobe 750 MHz NMR). The conformations of both the phosphodiester linkages and the dinucleotide segment encompassing the sharp turn in single-stranded DNA are often underdetermined. To obtain higher quality structures of a DNA GNRA loop, 5'-d(GCGAAAGC)-3', we have used a mesoscopic molecular modeling approach, called Biopolymer Chain Elasticity (BCE), to provide reference conformations. By construction, these models are the least deformed hairpin loop conformation derived from canonical B-DNA at the nucleotide level. We have further explored this molecular conformation at the torsion angle level with AMBER molecular mechanics using different possible (epsilon,zeta) constraints to interpret the 31P NMR data. This combined approach yields a more accurate molecular conformation, compatible with all the NMR data, than each method taken separately, NMR/DYANA or BCE/AMBER. In agreement with the principle of minimal deformation of the backbone, the hairpin motif is stabilized by maximal base-stacking interactions on both the 5'- and 3'-sides and by a sheared G.A mismatch base pair between the first and last loop nucleotides. The sharp turn is located between the third and fourth loop nucleotides, and only two torsion angles beta6 and gamma6 deviate strongly with respect to canonical B-DNA structure. Two other torsion angle pairs epsilon3,zeta3 and epsilon5,zeta5 exhibit the newly recognized stable conformation BIIzeta+ (-70 degrees, 140 degrees). This combined approach has proven to be useful for the interpretation of an unusual 31P chemical shift in the 5'-d(GCGAAAGC)-3' hairpin.
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Affiliation(s)
- Guillaume P H Santini
- Laboratoire de Biophysique Moleculaire, Cellulaire et Tissulaire, UMR 7033 CNRS, Universite Pierre et Marie Curie Paris 6, Genopole Campus 1, 5 rue Henri Desbrueres, Evry 91030, France
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39
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Kahn TR, Fong KK, Jordan B, Lek JC, Levitan R, Mitchell PS, Wood C, Hatcher ME. An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites. Biochemistry 2009; 48:1315-21. [PMID: 19166330 DOI: 10.1021/bi8015235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy and a library of FTIR marker bands have been used to examine the structure and relative flexibilities conferred by different flanking sequences on the EcoRI binding site. This approach allowed us to examine unique peaks and subtle changes in the spectra of d(AAAGAATTCTTT)(2), d(TTCGAATTCGAA)(2), and d(CGCGAATTCGCG)(2) and thereby identify local changes in base pairing, base stacking, backbone conformation, glycosidic bond rotation, and sugar puckering in the studied sequences. The changes in flanking sequences induce differences in the sugar puckers, glycosidic bond rotation, and backbone conformations. Varying levels of local flexibility are observed within the sequences in agreement with previous biological activity assays. The results also provide supporting evidence for the presence of a splay in the G(4)-C(9) base pair of the EcoRI binding site and a potential pocket of flexibility at the G(4) cleavage site that have been proposed in the literature. In sum, we have demonstrated that FTIR is a powerful methodology for studying the effect of flanking sequences on DNA structure and flexibility, for it can provide information about the local structure of the nucleic acid and the overall relative flexibilities conferred by different flanking sequences.
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Affiliation(s)
- Talia R Kahn
- Joint Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, USA
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40
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Gonçalves C, Ardourel MY, Decoville M, Breuzard G, Midoux P, Hartmann B, Pichon C. An optimized extended DNA kappa B site that enhances plasmid DNA nuclear import and gene expression. J Gene Med 2009; 11:401-11. [DOI: 10.1002/jgm.1312] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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41
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Curuksu J, Zacharias M, Lavery R, Zakrzewska K. Local and global effects of strong DNA bending induced during molecular dynamics simulations. Nucleic Acids Res 2009; 37:3766-73. [PMID: 19380377 PMCID: PMC2699519 DOI: 10.1093/nar/gkp234] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
DNA bending plays an important role in many biological processes, but its molecular and energetic details as a function of base sequence remain to be fully understood. Using a recently developed restraint, we have studied the controlled bending of four different B-DNA oligomers using molecular dynamics simulations. Umbrella sampling with the AMBER program and the recent parmbsc0 force field yield free energy curves for bending. Bending 15-base pair oligomers by 90 degrees requires roughly 5 kcal mol(-1), while reaching 150 degrees requires of the order of 12 kcal mol(-1). Moderate bending occurs mainly through coupled base pair step rolls. Strong bending generally leads to local kinks. The kinks we observe all involve two consecutive base pair steps, with disruption of the central base pair (termed Type II kinks in earlier work). A detailed analysis of each oligomer shows that the free energy of bending only varies quadratically with the bending angle for moderate bending. Beyond this point, in agreement with recent experiments, the variation becomes linear. An harmonic analysis of each base step yields force constants that not only vary with sequence, but also with the degree of bending. Both these observations suggest that DNA is mechanically more complex than simple elastic rod models would imply.
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Affiliation(s)
- Jeremy Curuksu
- Computational Biology, School of Engineering and Science, Jacobs University, Campus Ring 1, D-28759 Bremen, Germany
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42
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MacKerell AD. Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA. J Phys Chem B 2009; 113:3235-44. [PMID: 19708270 PMCID: PMC2784611 DOI: 10.1021/jp8102782] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Canonical forms of duplex DNA are known to sample well-defined regions of the alpha, beta, gamma, epsilon, and zeta dihedral angles that define the conformation of the phosphodiester linkage in the backbone of oligonucleotides. While extensive studies of base composition and base sequence dependent effects on the sampling of the A, B1, and BII canonical forms of duplex DNA have been presented, our understanding of the intrinsic contribution of the five dihedral degrees of freedom associated with the phosphodiester linkage to the conformational properties of duplex DNA is still limited. To better understand this contribution, ab initio quantum mechanical (QM) calculations were performed on a model compound representative of the phosphodiester backbone to systematically sample the energetics about the alpha, beta, gamma, epsilon, and zeta dihedral angles relevant to the conformational properties of duplex DNA. Low-energy regions of dihedral potential energy surfaces are shown to correlate with the regions of dihedral space sampled in experimental crystal structures of the canonical forms of DNA, validating the utility of the model compound and emphasizing the contribution of the intrinsic mechanical properties of the phosphodiester backbone to the conformational properties of duplex DNA. Those contributions include the relative stability of the A, BI, and BII conformations of duplex DNA, where the gas-phase energetics favor the BI form over the A and BII forms. In addition, subtle features of the potential energy surfaces mimic changes in the probability distributions of alpha, beta, gamma, epsilon, and zeta dihedral angles in A, BI, and BII forms of DNA as well as with conformations sampled in single-stranded DNA. These results show that the intrinsic mechanical properties of the phosphodiester backbone make a significant contribution to conformational properties of duplex DNA observed in the condensed phase and allow for the prediction that single-stranded DNA primarily samples folded conformations thereby possibly lowering the entropic barrier to the formation of duplex DNA.
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Affiliation(s)
- Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA.
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Hart K, Nilsson L. Investigation of transcription factor Ndt80 affinity differences for wild type and mutant DNA: a molecular dynamics study. Proteins 2009; 73:325-37. [PMID: 18433057 DOI: 10.1002/prot.22062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics simulations and free energy calculations have been performed on the transcription factor Ndt80 either in complex with the native DNA sequence or with a mutant DNA with a switched central base pair, C5-G5' to G5-C5'. This mutant has been shown to have a 100-fold decrease in binding affinity of Ndt80, and in this study we explain this both structurally and energetically. The major interactions between the protein and the DNA were maintained in the simulations, apart from around the mutation site. The crystal structure of the Ndt80-DNA complex revealed that R177 makes a base specific bidentate interaction with G5' which is part of a conserved 5'-YpG-3' step. In the simulation with the mutant DNA, the side chain of R177 changes conformation and makes three new stable hydrogen bonds to the DNA backbone. This in turn induces a conformational change in the DNA backbone of the T6'-G5' step from the unusual BII state to the canonical BI state. The affinity difference for the protein-DNA complex with the native DNA compared with the mutant DNA is only about 3 kcal/mol. The free energy calculations of the base pair switch indicated a larger difference than what was found experimentally, about 7.7 kcal/mol, but this is explained in structural terms using the 10 ns simulations of the solvated complexes and the rearrangement of the R177 side chain.
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Affiliation(s)
- Katarina Hart
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden
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Heddi B, Foloppe N, Oguey C, Hartmann B. Importance of Accurate DNA Structures in Solution: The Jun–Fos Model. J Mol Biol 2008; 382:956-70. [DOI: 10.1016/j.jmb.2008.07.047] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 07/11/2008] [Accepted: 07/19/2008] [Indexed: 01/10/2023]
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Svozil D, Sponer JE, Marchan I, Pérez A, Cheatham TE, Forti F, Luque FJ, Orozco M, Sponer J. Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. J Phys Chem B 2008; 112:8188-97. [PMID: 18558755 DOI: 10.1021/jp801245h] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The anionic sugar-phosphate backbone of nucleic acids substantially contributes to their structural flexibility. To model nucleic acid structure and dynamics correctly, the potentially sampled substates of the sugar-phosphate backbone must be properly described. However, because of the complexity of the electronic distribution in the nucleic acid backbone, its representation by classical force fields is very challenging. In this work, the three-dimensional potential energy surfaces with two independent variables corresponding to rotations around the alpha and gamma backbone torsions are studied by means of high-level ab initio methods (B3LYP/6-31+G*, MP2/6-31+G*, and MP2 complete basis set limit levels). The ability of the AMBER ff99 [Wang, J. M.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049-1074] and parmbsc0 [Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughten, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829] force fields to describe the various alpha/gamma conformations of the DNA backbone accurately is assessed by comparing the results with those of ab initio quantum chemical calculations. Two model systems differing in structural complexity were used to describe the alpha/gamma energetics. The simpler one, SPM, consisting of a sugar and methyl group linked through a phosphodiester bond was used to determine higher-order correlation effects covered by the CCSD(T) method. The second, more complex model system, SPSOM, includes two deoxyribose residues (without the bases) connected via a phosphodiester bond. It has been shown by means of a natural bond orbital analysis that the SPSOM model provides a more realistic representation of the hyperconjugation network along the C5'-O5'-P-O3'-C3' linkage. However, we have also shown that quantum mechanical investigations of this model system are nontrivial because of the complexity of the SPSOM conformational space. A comparison of the ab initio data with the ff99 potential energy surface clearly reveals an incorrect ff99 force-field description in the regions where the gamma torsion is in the trans conformation. An explanation is proposed for why the alpha/gamma flips are eliminated so successfully when the parmbsc0 force-field modification is used.
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Affiliation(s)
- Daniel Svozil
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo namesti 2, 166 10, Prague 6, Czech Republic.
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Kurz M. Compatible solute influence on nucleic acids: many questions but few answers. SALINE SYSTEMS 2008; 4:6. [PMID: 18522725 PMCID: PMC2430576 DOI: 10.1186/1746-1448-4-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 06/03/2008] [Indexed: 12/21/2022]
Abstract
Compatible solutes are small organic osmolytes including but not limited to sugars, polyols, amino acids, and their derivatives. They are compatible with cell metabolism even at molar concentrations. A variety of organisms synthesize or take up compatible solutes for adaptation to extreme environments. In addition to their protective action on whole cells, compatible solutes display significant effects on biomolecules in vitro. These include stabilization of native protein and nucleic acid structures. They are used as additives in polymerase chain reactions to increase product yield and specificity, but also in other nucleic acid and protein applications. Interactions of compatible solutes with nucleic acids and protein-nucleic acid complexes are much less understood than the corresponding interactions of compatible solutes with proteins. Although we may begin to understand solute/nucleic acid interactions there are only few answers to the many questions we have. I summarize here the current state of knowledge and discuss possible molecular mechanisms and thermodynamics.
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Affiliation(s)
- Matthias Kurz
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich Wilhelms-Universität Bonn, Bonn, Germany.
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Heddi B, Foloppe N, Bouchemal N, Hantz E, Hartmann B. Quantification of DNA BI/BII backbone states in solution. Implications for DNA overall structure and recognition. J Am Chem Soc 2007; 128:9170-7. [PMID: 16834390 DOI: 10.1021/ja061686j] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The backbone states of B-DNA influence its helical parameters, groove dimensions, and overall curvature. Therefore, detection and fine characterization of these conformational states are desirable. Using routine NMR experiments on a nonlabeled B-DNA oligomer and analyzing high-resolution X-ray structures, we investigated the relationship between interproton distances and backbone conformational states. The three H2'i-H6/8i+1, H2' 'i-H6/8i+1, and H6/8i-H6/8i+1 sequential distances were found cross-correlated and linearly coupled to epsilon-zeta values in X-ray structures and 31P chemical shifts (deltaP) in NMR that reflect the interconversion between the backbone BI (epsilon-zeta < 0 degrees ) and BII (epsilon-zeta > 0 degrees) states. These relationships provide a detailed check of the NMR data consistency and the possibility to extend the set of restraints for structural refinement through various extrapolations. Furthermore, they allow translation of deltaP in terms of BI/BII ratios. Also, comparison of many published deltaP in solution to crystal data shows that the impact of sequence on the BI/BII propensities is similar in both environments and is therefore an intrinsic and general property of B-DNA. This quantification of the populations of BI and BII is of general interest because these sequence-dependent backbone states act on DNA overall structure, a key feature for DNA-protein-specific recognition.
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Affiliation(s)
- Brahim Heddi
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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Teletchéa S, Komeda S, Teuben JM, Elizondo-Riojas MA, Reedijk J, Kozelka J. A pyrazolato-bridged dinuclear platinum(II) complex induces only minor distortions upon DNA-binding. Chemistry 2007; 12:3741-53. [PMID: 16514681 DOI: 10.1002/chem.200500923] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The cytotoxic, pyrazolato-bridged dinuclear platinum(II) complex [(cis-{Pt(NH3)2})2(mu-OH)(mu-pz)]2+ (pz=pyrazolate) has been found to cross-link two adjacent guanines of a double-stranded DNA decamer without destabilizing the duplex and without changing the directionality of the helix axis. A 1H NMR study of the oligonucleotide d(CTCTG*G*TCTC)-d(GAGACCAGAG), cross-linked at the two G* guanines by [(cis-{Pt(NH3)2})2(mu-pz)]3+, and molecular dynamics simulations of the explicitly solvated duplex were performed to characterize the structural details of the adduct. The dinuclear platinum cross-link unwinds the helix by approximately 15 degrees , that is, to a similar extent as the widely used antitumor drug cisplatin, but, in contrast to the latter, induces no significant bend in the helix axis. The Watson-Crick base-pairing remains intact, and the melting temperature of the duplex is unaffected by the cross-link. The helical twist is considerably reduced between the two platinated bases, as becomes manifest in an unusually short sequential H1'-H1' distance. This unwinding also affects the sugar ring of the guanosine in the 3'-position to the cross-link, which presents an N<-->S equilibrium. This is the first cytotoxic platinum complex that has been successfully designed by envisioning the structural consequences of its binding to DNA.
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Affiliation(s)
- Stéphane Teletchéa
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, UMR 8601 CNRS, 45, rue des Saints-Pères, 75270 Paris Cedex 06, France
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René B, Masliah G, Antri SE, Fermandjian S, Mauffret O. Conformations and Dynamics of the Phosphodiester Backbone of a DNA Fragment That Bears a Strong Topoisomerase II Cleavage Site. J Phys Chem B 2007; 111:4235-43. [PMID: 17391020 DOI: 10.1021/jp0683115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics of the DNA phosphodiester backbone conformations have been studied for a strong topoisomerase II cleavage site (site 22) using molecular dynamics simulations in explicit water and in the presence of sodium ions. We investigated the backbone motions and more particularly the BI/BII transitions involving the epsilon and zeta angles. The consensus cleavage site is adjacent to the phosphate which shows the most important phosphodiester backbone flexibility in the sequence. We infer that these latter properties could be responsible for the preferential cleavage at this site possibly through the perturbation of the cleavage/ligation activities of the topoisomerase II. More generally, the steps pur-pur and pyr-pur are those presenting the highest BII contents. Relations are observed between the backbone phosphodiester BI/BII transitions and the flexibility of the deoxyribose sugar and the helical parameters such as roll. The roll is sequence dependent when the related phosphate is in the BI form, whereas this appears not to be true when it is in the BII form. The BI/BII transitions are associated with water migration, and new relations are observed with counterions. Indeed, it is observed that a strong coupling exists between the BII form and the presence of sodium ions near the adjacent sugar deoxyribose. The presence of sodium ions in the O4' surroundings or their binding could assist the BI to BII transition by furnishing energy. The implications of these new findings and, namely, their importance in the context of the sequence-dependent behavior of BI/BII transitions will be investigated in future studies.
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Affiliation(s)
- Brigitte René
- UMR 8113 CNRS, Laboratoire de Biotechnologies et Pharmacologie Génétique Appliquée (Ecole Normale Supérieure de Cachan), Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif Cedex, France
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Heddi B, Foloppe N, Hantz E, Hartmann B. The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J Mol Biol 2007; 368:1403-11. [PMID: 17395202 DOI: 10.1016/j.jmb.2007.03.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 03/01/2007] [Accepted: 03/06/2007] [Indexed: 11/17/2022]
Abstract
The influence of monovalent cations on DNA conformation and readout is an open question. This NMR study of DNA with either Na(+) or K(+) at physiological concentrations shows that the nature of the cation affects the (31)P chemical shifts (deltaP) and the sequential distances H2'(i)-H6/8(i+1), H2"(i)-H6/8(i+1), and H6/8(i)-H6/8(i+1). The deltaP and distance variations ascertain that the nature of the cation affects the DNA overall structure, i.e. both the conformational equilibria between the backbone BI (epsilon-zeta <0 degrees ) and BII (epsilon-zeta >0 degrees ) states and the helical parameters, via their strong mechanical coupling. These results reveal that Na(+) and K(+) interactions with DNA are different and sequence-dependent. These ions modulate the overall intrinsic properties of DNA, and possibly its packaging and readout.
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Affiliation(s)
- Brahim Heddi
- Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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