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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Edlich-Muth C, Artero JB, Callow P, Przewloka MR, Watson AA, Zhang W, Glover DM, Debski J, Dadlez M, Round AR, Forsyth VT, Laue ED. The pentameric nucleoplasmin fold is present in Drosophila FKBP39 and a large number of chromatin-related proteins. J Mol Biol 2015; 427:1949-63. [PMID: 25813344 PMCID: PMC4414354 DOI: 10.1016/j.jmb.2015.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/17/2015] [Accepted: 03/17/2015] [Indexed: 11/28/2022]
Abstract
Nucleoplasmin is a histone chaperone that consists of a pentameric N-terminal domain and an unstructured C-terminal tail. The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family. Here, we report the first structure of a nucleoplasmin-like domain (NPL) from the unrelated Drosophila protein, FKBP39, and we present evidence that this protein associates with chromatin. Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2. Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.
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Affiliation(s)
- Christian Edlich-Muth
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Jean-Baptiste Artero
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Phil Callow
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Marcin R Przewloka
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH Cambridge, United Kingdom
| | - Aleksandra A Watson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - Wei Zhang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom
| | - David M Glover
- Department of Genetics, University of Cambridge, Downing Street, CB2 3EH Cambridge, United Kingdom
| | - Janusz Debski
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego Street, 02-106 Warsaw, Poland
| | - Michal Dadlez
- Mass Spectrometry Laboratory, Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego Street, 02-106 Warsaw, Poland
| | - Adam R Round
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-European Molecular Biology Laboratory-CNRS, 71 Avenue des Martyrs, 38042 Grenoble, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, Grenoble, Cedex 9, France; Faculty of Natural Sciences, Keele University, ST5 5BG Staffordshire, United Kingdom
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, United Kingdom.
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Hall JP, Sanchez-Weatherby J, Alberti C, Quimper CH, O'Sullivan K, Brazier JA, Winter G, Sorensen T, Kelly JM, Cardin DJ, Cardin CJ. Controlled dehydration of a ruthenium complex-DNA crystal induces reversible DNA kinking. J Am Chem Soc 2014; 136:17505-12. [PMID: 25393319 DOI: 10.1021/ja508745x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hydration-dependent DNA deformation has been known since Rosalind Franklin recognized that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fiber diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)](2+) (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven data sets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation.
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Affiliation(s)
- James P Hall
- Chemistry Department, University of Reading , Whiteknights, Reading, Berkshire RG6 6AD, United Kingdom
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Haupt M, Blakeley MP, Fisher SJ, Mason SA, Cooper JB, Mitchell EP, Forsyth VT. Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein. IUCRJ 2014; 1:429-38. [PMID: 25485123 PMCID: PMC4224461 DOI: 10.1107/s2052252514021113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/22/2014] [Indexed: 05/12/2023]
Abstract
Human transthyretin has an intrinsic tendency to form amyloid fibrils and is heavily implicated in senile systemic amyloidosis. Here, detailed neutron structural studies of perdeuterated transthyretin are described. The analyses, which fully exploit the enhanced visibility of isotopically replaced hydrogen atoms, yield new information on the stability of the protein and the possible mechanisms of amyloid formation. Residue Ser117 may play a pivotal role in that a single water molecule is closely associated with the γ-hydrogen atoms in one of the binding pockets, and could be important in determining which of the two sites is available to the substrate. The hydrogen-bond network at the monomer-monomer interface is more extensive than that at the dimer-dimer interface. Additionally, the edge strands of the primary dimer are seen to be favourable for continuation of the β-sheet and the formation of an extended cross-β structure through sequential dimer couplings. It is argued that the precursor to fibril formation is the dimeric form of the protein.
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Affiliation(s)
- Melina Haupt
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Matthew P. Blakeley
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Stuart J. Fisher
- Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, Salzburg, 5020, Austria
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Sax A. Mason
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
| | - Jon B. Cooper
- Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, United Kingdom
| | - Edward P. Mitchell
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Business Development Office, European Synchrotron Radiation Facility, Grenoble, 38042, France
| | - V. Trevor Forsyth
- Facility of Natural Sciences, Institute of Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue-Langevin, 71, avenue des Martyrs, Grenoble, CS 20156, France
- Partnership for Structural Biology, 71, avenue des Martyrs, Grenoble, CS 20156, France
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5
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Sawada D, Nishiyama Y, Langan P, Forsyth VT, Kimura S, Wada M. Water in crystalline fibers of dihydrate β-chitin results in unexpected absence of intramolecular hydrogen bonding. PLoS One 2012; 7:e39376. [PMID: 22724007 PMCID: PMC3378566 DOI: 10.1371/journal.pone.0039376] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
The complete crystal structure (including hydrogen) of dihydrate β-chitin, a homopolymer of N-acetylglucosamine hydrate, was determined using high-resolution X-ray and neutron fiber diffraction data collected from bathophilous tubeworm Lamellibrachia satsuma. Two water molecules per N-acetylglucosamine residue are clearly localized in the structure and these participate in most of the hydrogen bonds. The conformation of the labile acetamide groups and hydroxymethyl groups are similar to those found in anhydrous β-chitin, but more relaxed. Unexpectedly, the intrachain O3-H…O5 hydrogen bond typically observed for crystalline β,1–4 glycans is absent, providing important insights into its relative importance and its relationship to solvation.
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Affiliation(s)
- Daisuke Sawada
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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Yang M, Szyc Ł, Elsaesser T. Vibrational dynamics of the water shell of DNA studied by femtosecond two-dimensional infrared spectroscopy. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2011.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yang M, Szyc Ł, Elsaesser T. Decelerated water dynamics and vibrational couplings of hydrated DNA mapped by two-dimensional infrared spectroscopy. J Phys Chem B 2011; 115:13093-100. [PMID: 21972952 DOI: 10.1021/jp208166w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Double-stranded DNA oligomers containing 23 alternating adenine-thymine base pairs are studied at different hydration levels by femtosecond two-dimensional (2D) infrared spectrosopy. Coupled NH stretching modes of the A-T pairs and OH stretching excitations of the water shell are discerned in the 2D spectra. Limited changes of NH stretching frequencies and line shapes with increasing hydration suggest spectral dynamics governed by DNA rather than water fluctuations. In contrast, OH stretching excitations of the water shell around fully hydrated DNA undergo spectral diffusion on a ~500 fs time scale. The center line slopes of the 2D spectra of hydrated DNA demonstrate a slower decay of the frequency-time correlation function (TCF) than that in neat water, as is evident from a comparison with 2D spectra of neat H(2)O and theoretical TCFs. We attribute this behavior to reduced structural fluctuations of the water shell and a reduced rate of resonant OH stretching energy transfer.
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Affiliation(s)
- Ming Yang
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Berlin, Germany
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8
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Tiggelaar SM, Mossou E, Callow P, Callow S, Teixeira SCM, Mitchell EP, Mitraki A, Forsyth VT. Neutron fibre diffraction studies of amyloid using H2O/D2O isotopic replacement. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:332-5. [PMID: 21393837 PMCID: PMC3053157 DOI: 10.1107/s1744309111002351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 01/16/2011] [Indexed: 01/09/2023]
Abstract
The first neutron fibre diffraction studies of an amyloid system are presented. The techniques used to prepare the large samples needed are described, as well as the procedures used to isotopically replace H2O in the sample by D2O. The results demonstrate the feasibility of this type of approach for the pursuit of novel structural analyses that will strongly complement X-ray fibre diffraction studies and probe aspects of amyloid structure that to date have remained obscure. The approach is demonstrated using an amyloid form of the peptide NSGAITIG, but is equally applicable for the study of other systems such as Alzheimer's Aβ peptide.
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Affiliation(s)
- Sarah M. Tiggelaar
- Partnership for Structural Biology, Institut Laue–Langevin, France
- Vanderbilt University, Tennessee, USA
| | - Estelle Mossou
- Partnership for Structural Biology, Institut Laue–Langevin, France
- EPSAM/ISTM, Keele University, England
| | - Phil Callow
- Partnership for Structural Biology, Institut Laue–Langevin, France
- EPSAM/ISTM, Keele University, England
| | - Shirley Callow
- Vanderbilt University, Tennessee, USA
- EPSAM/ISTM, Keele University, England
| | - Susana C. M. Teixeira
- Partnership for Structural Biology, Institut Laue–Langevin, France
- EPSAM/ISTM, Keele University, England
| | - Edward P. Mitchell
- EPSAM/ISTM, Keele University, England
- European Synchrotron Radiation Facility, France
| | | | - V. Trevor Forsyth
- Partnership for Structural Biology, Institut Laue–Langevin, France
- EPSAM/ISTM, Keele University, England
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10
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Leal RMF, Teixeira SCM, Blakeley MP, Mitchell EP, Forsyth VT. A preliminary neutron crystallographic study of an A-DNA crystal. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:232-5. [PMID: 19255472 PMCID: PMC2650452 DOI: 10.1107/s1744309109002668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 01/21/2009] [Indexed: 11/10/2022]
Abstract
The LADI-III diffractometer at the Institut Laue-Langevin has been used to carry out a preliminary neutron crystallographic study of the self-complementary DNA oligonucleotide d(AGGGGCCCCT)(2) in the A conformation. The results demonstrate the viability of a full neutron crystallographic analysis with the aim of providing enhanced information on the ion-water networks that are known to be important in stabilizing A-DNA. This is the first account of a single-crystal neutron diffraction study of A-DNA. The study was carried out with the smallest crystal used to date for a neutron crystallographic study of a biological macromolecule.
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Affiliation(s)
- Ricardo M. F. Leal
- ESRF, 6 Rue Jules Horowitz, Grenoble, France
- Institut Laue–Langevin, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Susana C. M. Teixeira
- Institut Laue–Langevin, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | | | - Edward P. Mitchell
- ESRF, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - V. Trevor Forsyth
- Institut Laue–Langevin, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
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11
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Chocholousová J, Feig M. Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment. J Phys Chem B 2007; 110:17240-51. [PMID: 16928023 DOI: 10.1021/jp0627675] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Differences in conformational sampling of DNA with two sets of atomic radii that are used to define the dielectric interface between the solute and the continuum dielectric model of the solvent are investigated. Results suggest that depending on the choice of atomic radii agreement is either closer to experimental data or to explicit solvent simulations. Furthermore, partial conformational transitions toward A-DNA conformations when salt is added within the implicit solvent framework are observed.
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Affiliation(s)
- Jana Chocholousová
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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12
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Gardner KH, English AD, Forsyth VT. New Insights into the Structure of Poly(p-phenylene terephthalamide) from Neutron Fiber Diffraction Studies. Macromolecules 2004. [DOI: 10.1021/ma048445l] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. H. Gardner
- DuPont Central Research and Development, Experimental Station, Wilmington, Delaware 19880; Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716; Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble Cedex 9, France; and Lennard Jones Laboratory, School of Chemistry and Physics, Keele University, Staffordshire ST5 5BG, UK
| | - A. D. English
- DuPont Central Research and Development, Experimental Station, Wilmington, Delaware 19880; Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716; Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble Cedex 9, France; and Lennard Jones Laboratory, School of Chemistry and Physics, Keele University, Staffordshire ST5 5BG, UK
| | - V. T. Forsyth
- DuPont Central Research and Development, Experimental Station, Wilmington, Delaware 19880; Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716; Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble Cedex 9, France; and Lennard Jones Laboratory, School of Chemistry and Physics, Keele University, Staffordshire ST5 5BG, UK
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Fuller W, Forsyth T, Mahendrasingam A. Water-DNA interactions as studied by X-ray and neutron fibre diffraction. Philos Trans R Soc Lond B Biol Sci 2004; 359:1237-47; discussion 1247-8. [PMID: 15306379 PMCID: PMC1693411 DOI: 10.1098/rstb.2004.1501] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
X-ray fibre-diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration-driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real-time X-ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre-diffraction studies of DNA is complemented by information from X-ray single-crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.
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Affiliation(s)
- Watson Fuller
- School of Chemistry and Physics, Keele University, Keele ST5 5BG, UK.
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Feig M, Pettitt BM. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. J Mol Biol 1999; 286:1075-95. [PMID: 10047483 DOI: 10.1006/jmbi.1998.2486] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hydration around the DNA fragment d(C5T5).(A5G5) is presented from two molecular dynamics simulations of 10 and 12 ns total simulation time. The DNA has been simulated as a flexible molecule with both the CHARMM and AMBER force fields in explicit solvent including counterions and 0.8 M additional NaCl salt. From the previous analysis of the DNA structure B-DNA conformations were found with the AMBER force-field and A-DNA conformations with CHARMM parameters. High-resolution hydration patterns are compared between the two conformations and between C.G and T.A base-pairs from the homopolymeric parts of the simulated sequence. Crystallographic results from a statistical analysis of hydration sites around DNA crystal structures compare very well with the simulation results. Differences between the crystal sites and our data are explained by variations in conformation, sequence, and limitations in the resolution of water sites by crystal diffraction. Hydration layers are defined from radial distribution functions and compared with experimental results. Excellent agreement is found when the measured experimental quantities are compared with the equivalent distribution of water molecules in the first hydration shell. The number of water molecules bound to DNA was found smaller around T.A base-pairs and around A-DNA as compared to B-DNA. This is partially offset by a larger number of water molecules in hydrophobic contact with DNA around T.A base-pairs and around A-DNA. The numbers of water molecules in minor and major grooves have been correlated with helical roll, twist, and inclination angles. The data more fully explain the observed B-->A transition at low humidity.
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Affiliation(s)
- M Feig
- Department of Chemistry and Institute for Molecular Design, University of Houston, 4800 Calhoun, Houston, TX, 77204-5641, USA
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Shotton MW, Pope LH, Forsyth T, Langan P, Denny RC, Giesen U, Dauvergne MT, Fuller W. A high-angle neutron fibre diffraction study of the hydration of deuterated A-DNA. Biophys Chem 1997; 69:85-96. [PMID: 9440211 DOI: 10.1016/s0301-4622(97)00090-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A high-angle neutron fibre diffraction study of the hydration of A-DNA has been performed using the single-crystal diffractometer D19 at the Institut Laue-Langevin (Grenoble, France). The sample was prepared using deuterated DNA extracted from E. Coli cells cultured on deuterated nutrients. In common with our previous neutron fibre diffraction studies of DNA, this work exploits the ability to isotopically replace H2O around the DNA by D2O. However this study benefitted additionally from the fact that the hydrogen atoms which are covalently bonded to carbon atoms in the DNA sugars and bases were replaced by deuterium so that incoherent scattering and absorption effects were minimised. Successive cycles of Fourier synthesis and Fourier difference synthesis allowed water peaks to be identified and their positional and occupancy parameters to be refined against the observed diffraction data. The results confirm the main hydration features noted in our earlier studies with a clear network of water running along the inside edge of the major groove linking successive OI phosphate oxygen atoms. The central core of water running along the axis of the double helix is very much clearer in this work. Additionally this study shows chains of ordered water lying in the centre of the major groove.
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Affiliation(s)
- M W Shotton
- Physics Department, Keele University, Staffordshire, UK
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Forsyth VT, Langan P, Whalley MA, Mahendrasingam A, Wilson CC, Giesen U, Dauvergne MT, Mason SA, Fuller W. Time-of-flight Laue fiber diffraction studies of perdeuterated DNA. BASIC LIFE SCIENCES 1996; 64:359-67. [PMID: 9031520 DOI: 10.1007/978-1-4615-5847-7_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The diffractometer SXD at the Rutherford Appleton Laboratory ISIS pulsed neutron source has been used to record high resolution time-of-flight Laue fiber diffraction data from DNA. These experiments, which are the first of their kind, were undertaken using fibers of DNA in the A conformation and prepared using deuterated DNA in order to minimise incoherent background scattering. These studies complement previous experiments on instrument D19 at the Institut Laue Langevin using monochromatic neutrons. Sample preparation involved drawing large numbers of these deuterated DNA fibers and mounting them in a parallel array. The strategy of data collection is discussed in terms of camera design, sample environment and data collection. The methods used to correct the recorded time-of-flight data and map it into the final reciprocal space fiber diffraction dataset are also discussed. Difference Fourier maps showing the distribution of water around A-DNA calculated on the basis of these data are compared with results obtained using data recorded from hydrogenated A-DNA on D19. Since the methods used for sample preparation, data collection and data processing are fundamentally different for the monochromatic and Laue techniques, the results of these experiments also afford a valuable opportunity to independently test the data reduction and analysis techniques used in the two methods.
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Affiliation(s)
- V T Forsyth
- Department of Physics, Keele University, Staffordshire, United Kingdom
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Fuller W, Forsyth VT, Mahendrasingam A, Langan P, Pigram WJ, Mason SA, Wilson CC. DNA hydration studied by neutron fiber diffraction. BASIC LIFE SCIENCES 1996; 64:345-58. [PMID: 9031519 DOI: 10.1007/978-1-4615-5847-7_30] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institut Laue-Langevin. Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformational transitions in the DNA double-helix.
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Affiliation(s)
- W Fuller
- Department of Physics, Keele University, Staffordshire, United Kingdom
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Hummer G, Soumpasis DM. Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for B-DNA. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 50:5085-5095. [PMID: 9962594 DOI: 10.1103/physreve.50.5085] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Langan P, Forsyth VT, Mahendrasingam A, Pigram WJ, Mason SA, Fuller W. A high angle neutron fibre diffraction study of the hydration of the A conformation of the DNA double helix. J Biomol Struct Dyn 1992; 10:489-503. [PMID: 1492921 DOI: 10.1080/07391102.1992.10508664] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A high angle neutron fibre diffraction study of the distribution of water around the A-form of DNA has been performed using the diffractometer D19 at the Institut Laue-Langevin, Grenoble. These experiments have exploited the ability to replace H2O surrounding the DNA by D2O so that isotopic difference Fourier maps can be computed in which peaks are identified with the distribution of water in the unit cell. All peaks of significant height have been accounted for by four families of water molecules whose positions and occupancies have been determined using least squares refinement. The coordinates of the water peaks making up each family do not deviate significantly from a regular helical arrangement with the same parameters as the DNA. Two of these families are of particular interest. The first consists of water molecules in the major groove linking successive charged phosphate oxygens along the polynucleotide chains. The second is associated with bases in the major groove and forms a central core of density along the helix axis. These two families provide a layer of hydration lining the interior wall of the major groove leaving a central channel to accommodate cations. The relationship between these observations and conformational stability is discussed.
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Affiliation(s)
- P Langan
- Department of Physics, Keele University, Staffordshire
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Forsyth VT, Langan P, Mahendrasingam A, Fuller W, Mason SA. High-angle neutron fiber diffraction studies of DNA. ACTA ACUST UNITED AC 1992. [DOI: 10.1080/10448639208218778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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