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Biedermannová L, Černý J, Malý M, Nekardová M, Schneider B. Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks. Acta Crystallogr D Struct Biol 2022; 78:1032-1045. [PMID: 35916227 PMCID: PMC9344474 DOI: 10.1107/s2059798322006234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
Database-derived water probability densities around structurally and sequentially distinct DNA dinucleotide fragments reproduce the known hydration motifs, which thus can be used as building blocks to predict DNA hydration. Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the ‘spine of hydration’ in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.
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2
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Liu T, Yu T, Zhang S, Wang Y, Zhang W. Thermodynamic and kinetic properties of a single base pair in A-DNA and B-DNA. Phys Rev E 2021; 103:042409. [PMID: 34005973 DOI: 10.1103/physreve.103.042409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/27/2021] [Indexed: 11/07/2022]
Abstract
Double stranded DNA can adopt different forms, the so-called A-, B-, and Z-DNA, which play different biological roles. In this work, the thermodynamic and the kinetic parameters for the base-pair closing and opening in A-DNA and B-DNA were calculated by all-atom molecular dynamics simulations at different temperatures. The thermodynamic parameters of the base pair in B-DNA were in good agreement with the experimental results. The free energy barrier of breaking a single base stack results from the enthalpy increase ΔH caused by the disruption of hydrogen bonding and base-stacking interactions, as well as water and base interactions. The free energy barrier of base pair closing comes from the unfavorable entropy loss ΔS caused by the restriction of torsional angles and hydration. It was found that the enthalpy change ΔH and the entropy change ΔS for the base pair in A-DNA are much larger than those in B-DNA, and the transition rates between the opening and the closing state for the base pair in A-DNA are much slower than those in B-DNA. The large difference of the enthalpy and entropy change for forming the base pair in A-DNA and B-DNA results from different hydration in A-DNA and B-DNA. The hydration pattern observed around DNA is an accompanying process for forming the base pair, rather than a follow-up of the conformation.
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Affiliation(s)
- Taigang Liu
- Department of Physics Wuhan University, Wuhan 430072, China.,School of Medical Engineering, Xinxiang Medical University, Xinxiang 453003, China
| | - Ting Yu
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Shuhao Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
| | - Yujie Wang
- Department of Physics Wuhan University, Wuhan 430072, China.,Department of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466000, China
| | - Wenbing Zhang
- Department of Physics Wuhan University, Wuhan 430072, China
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Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 128:63-73. [DOI: 10.1016/j.pbiomolbio.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 04/16/2017] [Accepted: 05/23/2017] [Indexed: 01/19/2023]
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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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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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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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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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9
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Kang NS, No KT, Jhon MS. A Study of the Hydrogen-bonded Network Around the Left-handed and Right-handed DNA in an Ionic Solution. MOLECULAR SIMULATION 2010. [DOI: 10.1080/0892702031000065764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Nam Sook Kang
- a Department of Chemistry and CAMD Research Center , Soong Sil University , Seoul , 156-743 , South Korea
| | - Kyung Tai No
- a Department of Chemistry and CAMD Research Center , Soong Sil University , Seoul , 156-743 , South Korea
| | - Mu Shik Jhon
- b Department of Chemistry , Korea Advanced Institute of Science and Technology , 373-1 Kusung-dong Yusung-gu, Taejon , 305-701 , South Korea
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11
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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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13
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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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14
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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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15
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Sletmoen M, Maurstad G, Sikorski P, Paulsen BS, Stokke BT. Characterisation of bacterial polysaccharides: steps towards single-molecular studies. Carbohydr Res 2004; 338:2459-75. [PMID: 14670709 DOI: 10.1016/j.carres.2003.07.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Techniques used in studies of polysaccharides, including chemical composition, linkage pattern, and higher order structures are in constant development. They provide information necessary for understanding of the polysaccharide properties and functions. Here, recent advancements in studies of the polysaccharides at the single-molecule level are highlighted. Over the last few years, single-molecule techniques such as force spectroscopy have improved in sensitivity and can today be used to detect forces in the pN range. In addition, these techniques can be used to investigate properties of single molecules close to physiological conditions. The challenges in the interpretation of the observations are aided by control experiments using well-characterised polysaccharides and by data provided by complementary methods. This field is expected to have increasing impact on the further advancement of the molecular understanding of the role of polysaccharides in various biological processes such as recognition and cell adhesion.
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Affiliation(s)
- Marit Sletmoen
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and Technology, NTNU, NO-7491 Trondheim, Norway
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Langan P, Nishiyama Y, Chanzy H. A Revised Structure and Hydrogen-Bonding System in Cellulose II from a Neutron Fiber Diffraction Analysis. J Am Chem Soc 1999. [DOI: 10.1021/ja9916254] [Citation(s) in RCA: 267] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. Langan
- Life Sciences Division, Los Alamos National Laboratory, MS-M888, Los Alamos New Mexico 87545, Graduate School of Agricultural and Life Science, The University of Tokyo, Yayoi, Tokyo 113, 8657 Japan, and Centre de Recherches sur les Macromolécules Végétales, CNRS, affiliated with the Joseph Fourier University of Grenoble, BP 53, 38041 Grenoble Cedex 9, France
| | - Y. Nishiyama
- Life Sciences Division, Los Alamos National Laboratory, MS-M888, Los Alamos New Mexico 87545, Graduate School of Agricultural and Life Science, The University of Tokyo, Yayoi, Tokyo 113, 8657 Japan, and Centre de Recherches sur les Macromolécules Végétales, CNRS, affiliated with the Joseph Fourier University of Grenoble, BP 53, 38041 Grenoble Cedex 9, France
| | - H. Chanzy
- Life Sciences Division, Los Alamos National Laboratory, MS-M888, Los Alamos New Mexico 87545, Graduate School of Agricultural and Life Science, The University of Tokyo, Yayoi, Tokyo 113, 8657 Japan, and Centre de Recherches sur les Macromolécules Végétales, CNRS, affiliated with the Joseph Fourier University of Grenoble, BP 53, 38041 Grenoble Cedex 9, France
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17
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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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Abstract
Water distributions around phosphate groups in 59 B-, A-, and Z-DNA crystal structures were analyzed. It is shown that the waters are concentrated in six hydration sites per phosphate and that the positions and occupancies of these sites are dependent on the conformation and type of nucleotide. The patterns of hydration that are characteristic of the backbone of the three DNA helical types can be attributed in part to the interactions of these hydration sites.
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Affiliation(s)
- B Schneider
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
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19
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Pope LH, Shotton MW, Forsyth T, Hughes DJ, Denny RC, Fuller W. Structural polymorphism in a tubercidin analogue of the DNA double helix. Biophys Chem 1998; 70:161-72. [PMID: 9540207 DOI: 10.1016/s0301-4622(97)00132-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A high-angle X-ray fibre diffraction study of a tubercidin analogue of the poly[d(A-T)].poly[d(A-T)] DNA double helix has been carried out using station 7.2 at the Daresbury Laboratory synchrotron radiation source. The polymer has been studied for a wide range of salt strengths and hydration conditions and exhibits conformational polymorphism that is quite distinct from that observed for the unmodified polymer. The replacement of deoxyadenosine by deoxytubercidin in the polynucleotide causes only slight alterations to the structure of A-DNA, but significantly alters the structure of the B conformation. Additionally, the modified polymer does not, in any conditions yet identified, adopt the D conformation. In conditions which would normally favour the D conformation of poly[d(A-T)].poly[d(A-T)], the modified polymer adopts an unusual conformation which is designated here as the K conformation. These observations are important for an understanding of major groove interactions involved in the stabilisation of particular DNA conformations and also more generally for an insight into the pharmacological activity of tubercidin which following its incorporation into nucleic acids may cause stereochemical distortions of the DNA double helix.
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Affiliation(s)
- L H Pope
- Physics Department, Keele University, Staffordshire, UK
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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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Cheatham TE, Kollman PA. Molecular Dynamics Simulations Highlight the Structural Differences among DNA:DNA, RNA:RNA, and DNA:RNA Hybrid Duplexes. J Am Chem Soc 1997. [DOI: 10.1021/ja963641w] [Citation(s) in RCA: 210] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Garcia AE, Hummer G, Soumpasis DM. Theoretical description of biomolecular hydration. Application to A-DNA. BASIC LIFE SCIENCES 1996; 64:299-308. [PMID: 9031515 DOI: 10.1007/978-1-4615-5847-7_26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG)5]2 and [d(C5G5)]2. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers (P. Langan et al. J. Biomol. Struct. Dyn., 10, 489 (1992)).
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Affiliation(s)
- A E Garcia
- Theoretical Biology and Biophysics Group, New Mexico 87545, USA
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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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Abstract
Ordered hydration sites were determined for the nucleotide bases in B-type conformations using the crystal structure data on 14 B-DNA decamer structures. A method of density representation was extended so that positions, occupancies, and distributions of the hydration sites were predicted around a B-DNA double helix by a method analogous to crystallographic refinement. The predicted hydration sites correctly reproduce the main features of hydration around the B-DNA dodecamer. In contrast to the previous observations, the newly available crystal data show the same extent of hydration of guanine and adenine, and of cytosine and thymine.
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Affiliation(s)
- B Schneider
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Abstract
The aqueous hydration of DNA is an important aspect of its structure, which is of direct relevance to mechanisms of radiation damage. We have made a quantitative analysis of solvent interactions within hydrogen bonding distance of polar atoms of oligonucleotides using 12 B-DNA oligonucleotide crystal structures. The distribution of water molecules around the four bases, the sugar residues and the phosphate groups were generated and analysed both qualitatively and quantitatively. These data have then been used in a knowledge-based method to generate the likely hydration sites around a canonical B-DNA conformation in order to generate models of use in track studies of radiation damage.
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Affiliation(s)
- Y Umrania
- Department of Crystallography, Birkbeck College, University of London, UK
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Krzyzaniak A, Barciszewski J, Fürste JP, Bald R, Erdmann VA, Sałański P, Jurczak J. A-Z-RNA conformational changes effected by high pressure. Int J Biol Macromol 1994; 16:159-62. [PMID: 7526896 DOI: 10.1016/0141-8130(94)90044-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This paper reports evidence obtained by circular dichroism (CD) spectroscopy measurements indicating that two oligoribonucleotide duplexes with the alternating purine-pyrimidine sequences r(GC)6 or r(AU)6 change their A-RNA conformation under high pressure. Under the high-pressure conditions at which B-Z-DNA transition easily occurs, RNA acquires a conformation which only differs slightly from that of A-RNA. However, exposure of r(GC)6 or r(AU)6 to high pressure (6 kbar) in the presence of 5 M NaCl causes a conformation change of both oligoribonucleotide duplexes from their A- to their Z-RNA form. The departure of RNA or DNA duplexes from their original conformations under high pressure depends on the water structure itself and involves displacing an active (structural) water molecule outside the nucleic acid molecules. Experiments carried out until now in many laboratories have shown that B-Z or A-Z transitions of DNA or RNA, respectively, do not depend on the conditions applied, but the common mechanism for these processes seems to be dehydration. This same effect can be observed either at high salt concentrations or in the presence of an alcohol or at high pressure. Our results also support the view that the higher stability of RNA compared with DNA duplexes is due to the strong interaction of the 2'-hydroxyl groups of RNA with water molecules.
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Affiliation(s)
- A Krzyzaniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań
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Schneider B, Cohen DM, Schleifer L, Srinivasan AR, Olson WK, Berman HM. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys J 1993; 65:2291-303. [PMID: 8312469 PMCID: PMC1225971 DOI: 10.1016/s0006-3495(93)81306-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A new method to analyze the distribution of water molecules around the bases in DNA is presented. This method relies on the notion of a "hydrated building block," which represents the joint observed hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using atomic coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calculated for water molecules in each hydrated building block using standard crystallographic procedures. The electron densities were fitted to obtain "average building blocks," which represent bases with waters only at average or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced.
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Affiliation(s)
- B Schneider
- Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08903
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