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Effects of Physical and Chemical Factors on the Structure of Gluten, Gliadins and Glutenins as Studied with Spectroscopic Methods. Molecules 2021; 26:molecules26020508. [PMID: 33478043 PMCID: PMC7835854 DOI: 10.3390/molecules26020508] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 11/17/2022] Open
Abstract
This review presents applications of spectroscopic methods, infrared and Raman spectroscopies in the studies of the structure of gluten network and gluten proteins (gliadins and glutenins). Both methods provide complimentary information on the secondary and tertiary structure of the proteins including analysis of amide I and III bands, conformation of disulphide bridges, behaviour of tyrosine and tryptophan residues, and water populations. Changes in the gluten structure can be studied as an effect of dough mixing in different conditions (e.g., hydration level, temperature), dough freezing and frozen storage as well as addition of different compounds to the dough (e.g., dough improvers, dietary fibre preparations, polysaccharides and polyphenols). Additionally, effect of above mentioned factors can be determined in a common wheat dough, model dough (prepared from reconstituted flour containing only wheat starch and wheat gluten), gluten dough (lack of starch), and in gliadins and glutenins. The samples were studied in the hydrated state, in the form of powder, film or in solution. Analysis of the studies presented in this review indicates that an adequate amount of water is a critical factor affecting gluten structure.
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2
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Liu Y, Ren X, He L. A DFT study of energetic and structural properties of a full turn of A-form DNA under relaxed and stretching conditions. J Chem Phys 2019; 151:215102. [DOI: 10.1063/1.5129716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Yue Liu
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Xinguo Ren
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Lixin He
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
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3
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Zacharias M. Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2019; 58:5967-5972. [DOI: 10.1002/anie.201900935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Martin Zacharias
- Physics Department T38Technical University of Munich 85748 Garching Germany
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4
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Zacharias M. Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Martin Zacharias
- Physics Department T38Technical University of Munich 85748 Garching Germany
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5
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Kar S, Katti DR, Katti KS. Fourier transform infrared spectroscopy based spectral biomarkers of metastasized breast cancer progression. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 208:85-96. [PMID: 30292907 DOI: 10.1016/j.saa.2018.09.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 06/08/2023]
Abstract
Breast cancer is a global health issue and the second leading cause of cancer death in women. Breast cancer tends to migrate to bone and causes bone metastases which is ultimately the cause of death. Here, we report the use of FTIR to identify spectral biomarkers of cancer progression on 3D in vitro model of breast cancer bone metastasis. Our results indicate that the following spectral biomarkers can monitor cancer progression, for example, lipids (CH2 asymmetric/CH2 symmetric stretch), Amide I/Amide II, and RNA/DNA. Principal component analysis also confirmed the involvement of protein, lipids and nucleic acids in cancer progression on sequential culture. The collective observations from this study suggest successful application of FTIR as a non-invasive and accurate method to identify biochemical changes in cancer cells during the progression of breast cancer bone metastasis.
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Affiliation(s)
- Sumanta Kar
- Department of Civil and Environmental Engineering, CIE 201, NDSU, Fargo, ND 58104, United States of America
| | - Dinesh R Katti
- Department of Civil and Environmental Engineering, CIE 201, NDSU, Fargo, ND 58104, United States of America
| | - Kalpana S Katti
- Department of Civil and Environmental Engineering, CIE 201, NDSU, Fargo, ND 58104, United States of America.
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6
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Chandra GK, Eklouh-Molinier C, Fere M, Angiboust JF, Gobinet C, Van-Gulick L, Jeannesson P, Piot O. Probing in Vitro Ribose Induced DNA-Glycation Using Raman Microspectroscopy. Anal Chem 2015; 87:2655-64. [DOI: 10.1021/acs.analchem.5b00182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Goutam Kumar Chandra
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Christophe Eklouh-Molinier
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Michael Fere
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Jean-François Angiboust
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Cyril Gobinet
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Laurence Van-Gulick
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Pierre Jeannesson
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
| | - Olivier Piot
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, CNRS UMR 7369 MEDyC, UFR de Pharmacie, SFR CAP Santé, 51096 Reims Cedex, France
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7
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Shi W, Jia Y, Xu S, Li Z, Fu Y, Wei M, Shi S. A chiroptical switch based on DNA/layered double hydroxide ultrathin films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12916-12922. [PMID: 25285378 DOI: 10.1021/la502968z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A highly oriented film was fabricated by layer-by-layer self-assembly of DNA and MgAl-layered double hydroxide nanosheets, and its application in chiroptical switch was demonstrated via intercalation and deintercalation of an achiral molecule into the DNA cavity. DNA molecules are prone to forming an ordered and dispersive state in the interlayer region of rigid layered double hydroxide (LDH) nanosheets as confirmed by scanning electron microscopy and atomic force microscopy. The induced chiroptical ultrathin film (UTF) is achieved via the intercalation of an achiral chromophore [5,10,15,20-tetrakis(4-N-methylpyridyl)porphine tetra(p-toluenesulfonate) (TMPyP)] into the spiral cavity of DNA stabilized in the LDH matrix [denoted as TMPyP-(DNA/LDH)20]. Fluorescence and circular dichroism spectroscopy are utilized to testify the intercalation of TMPyP into (DNA/LDH)20 UTF that involves two steps: the electrostatic binding of TMPyP onto the surface of (DNA/LDH)20 followed by intercalation into base pairs of DNA. In addition, the TMPyP-(DNA/LDH)20 UTF exhibits good reversibility and repeatability in induced optical chirality, based on the intercalation and deintercalation of TMPyP by alternate exposure to HCl and NH3/H2O vapor, which can be potentially used as a chiroptical switch in data storage.
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Affiliation(s)
- Wenying Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing 100029, P. R. China
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8
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Jangir DK, Mehrotra R. Raman spectroscopic evaluation of DNA adducts of a platinum containing anticancer drug. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:386-389. [PMID: 24810023 DOI: 10.1016/j.saa.2014.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 03/30/2014] [Accepted: 04/04/2014] [Indexed: 06/03/2023]
Abstract
Mechanistic understanding of the interaction of drugs with their target molecules is important for better understanding of their mode of action and to improve their efficacy. Carboplatin is a platinum containing anticancer drug, used to treat different type of tumors. In the present work, we applied Raman spectroscopy to study the interaction of carboplatin with DNA at molecular level using different carboplatin-DNA molar ratios. These Raman spectroscopic results provide comprehensive understanding on the carboplatin-DNA interactions and indicate that DNA cross-linked adducts formed by carboplatin are similar to cisplatin adducts. The results indicate that guanine N7 and adenine N7 are the putative sites for carboplatin interaction. It is observed that carboplatin has some affinity toward cytosine in DNA. Phosphate sugar backbone of DNA showed conformation perturbation in DNA which were easily sensible at higher concentrations of carboplatin. Most importantly, carboplatin interaction induces intermediate A- and B-DNA conformations at the cross-linking sites.
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Affiliation(s)
- Deepak K Jangir
- Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110012, India
| | - Ranjana Mehrotra
- Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110012, India.
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9
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Suresh G, Priyakumar UD. DNA–RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids. Phys Chem Chem Phys 2014; 16:18148-55. [DOI: 10.1039/c4cp02478h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A gradual increase in the deoxypyrimidine content in DNA–RNA hybrids leads to B- to A-form nucleic acid transition. Possible factors that govern nuclease activity on hybrid duplexes are presented.
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Affiliation(s)
- Gorle Suresh
- Centre for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology
- Hyderabad 500 032, India
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10
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Chu WT, Zheng QC. Conformational changes of enzymes and DNA in molecular dynamics: influenced by pH, temperature, and ligand. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 92:179-217. [PMID: 23954102 DOI: 10.1016/b978-0-12-411636-8.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Protein conformation, which has been a research hotspot for human diseases, is an important factor of protein properties. Recently, a series of approaches have been utilized to investigate the conformational changes under different conditions. Some of them have gained promising achievements, but it is still deficient in the detail researches at the atomic level. In this chapter, a series of computational examples of protein conformational changes under different pH environment, temperature, and ligand binding are described. We further show some useful methods, such as constant pH molecular dynamics simulations, molecular docking, and molecular mechanics Poisson-Boltzmann surface area/generalized Born surface area calculations. In comparison with the experimental results, the methods mentioned above are reasonable to detect and predict the interaction between residue and residue, residue and DNA, and residue and ligand. Additionally, some crucial interactions that cause protein conformational changes are discovered and discussed in this chapter. In summary, our work can give penetrating information to understand the pH-, temperature-, and ligand-induced conformational change mechanisms.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, PR China
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11
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Valle-Orero J, Wildes A, Garden JL, Peyrard M. Purification of A-Form DNA Fiber Samples by the Removal of B-Form DNA Residues. J Phys Chem B 2013; 117:1849-56. [DOI: 10.1021/jp311199f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jessica Valle-Orero
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Andrew Wildes
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Jean-Luc Garden
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP
166, 38042 Grenoble cedex 9, France
| | - Michel Peyrard
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée
d’Italie, 69364 Lyon Cedex 07, France
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12
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Takeuchi H. Raman spectral marker of tryptophan conformation: Theoretical basis and extension to a wider range of torsional angle. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.03.075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Chen L, Zheng QC, Yu LY, Chu WT, Zhang JL, Xue Q, Zhang HX, Sun CC. Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis. J Biomol Struct Dyn 2012; 30:716-27. [PMID: 22731116 DOI: 10.1080/07391102.2012.689702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480 K) and MM-PBSA at 300 and 360 K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, P.R. China
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14
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Sun Q, Xiong J, Lu J, Xu S, Li Y, Zhong XP, Gao GK, Liu HQ. Secretory TAT-peptide-mediated protein transduction of LIF receptor α-chain distal cytoplasmic motifs into human myeloid HL-60 cells. Braz J Med Biol Res 2012; 45:913-20. [PMID: 22714809 PMCID: PMC3854185 DOI: 10.1590/s0100-879x2012007500101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 05/29/2012] [Indexed: 11/22/2022] Open
Abstract
The distal cytoplasmic motifs of leukemia inhibitory factor receptor α-chain (LIFRα-CT3) can independently induce intracellular myeloid differentiation in acute myeloid leukemia (AML) cells by gene transfection; however, there are significant limitations in the potential clinical use of these motifs due to liposome-derived genetic modifications. To produce a potentially therapeutic LIFRα-CT3 with cell-permeable activity, we constructed a eukaryotic expression pcDNA3.0-TAT-CT3-cMyc plasmid with a signal peptide (ss) inserted into the N-terminal that codes for an ss-TAT-CT3-cMyc fusion protein. The stable transfection of Chinese hamster ovary (CHO) cells via this vector and subsequent selection by Geneticin resulted in cell lines that express and secrete TAT-CT3-cMyc. The spent medium of pcDNA3.0-TAT-CT3-cMyc-transfected CHO cells could be purified using a cMyc-epitope-tag agarose affinity chromatography column and could be detected via SDS-PAGE, with antibodies against cMyc-tag. The direct administration of TAT-CT3-cMyc to HL-60 cell culture media caused the enrichment of CT3-cMyc in the cytoplasm and nucleus within 30 min and led to a significant reduction of viable cells (P < 0.05) 8 h after exposure. The advantages of using this mammalian expression system include the ease of generating TAT fusion proteins that are adequately transcripted and the potential for a sustained production of such proteins in vitro for future AML therapy.
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Affiliation(s)
- Q Sun
- Department of Hyperbaric Medicine, No 401 Hospital of PLA, Qingdao, China
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15
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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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16
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Priyakumar UD, Harika G, Suresh G. Molecular simulations on the thermal stabilization of DNA by hyperthermophilic chromatin protein Sac7d, and associated conformational transitions. J Phys Chem B 2010; 114:16548-57. [PMID: 21086967 DOI: 10.1021/jp101583d] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of DNA at higher growth temperatures. It is capable of binding DNA nonspecifically, and is responsible for the increase in the melting temperature of DNA in the bound form up to 85 °C. Molecular dynamics (MD) simulations were performed at different temperatures on two protein-DNA complexes of Sac7d. Various structural and energetic parameters were calculated to examine the DNA stability and to investigate the conformational changes in DNA and the protein-DNA interactions. Room temperature simulations indicated very good agreement with the experimental structures. The protein structure is nearly unchanged at both 300 and 360 K, and only up to five base pairs of the DNA are stabilized by Sac7d at 360 K. However, the MD simulations on DNA alone systems show that they lose their helical structures at 360 K further supporting the role of Sac7d in stabilizing the oligomers. At higher temperatures (420 and 480 K), DNA undergoes denaturation in the presence and the absence of the protein. The DNA molecules were found to undergo B- to A-form transitions consistent with experimental studies, and the extent of these transitions are examined in detail. The extent of sampling B- and A-form regions was found to show temperature and sequence dependence. Multiple MD simulations yielded similar results validating the proposed model. Interaction energy calculations corresponding to protein-DNA binding indicates major contribution due to DNA backbone, explaining the nonspecific interactions of Sac7d.
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Affiliation(s)
- U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India.
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17
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van Dijk M, Bonvin AMJJ. Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance. Nucleic Acids Res 2010; 38:5634-47. [PMID: 20466807 PMCID: PMC2943626 DOI: 10.1093/nar/gkq222] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The intrinsic flexibility of DNA and the difficulty of identifying its interaction surface have long been challenges that prevented the development of efficient protein-DNA docking methods. We have demonstrated the ability our flexible data-driven docking method HADDOCK to deal with these before, by using custom-built DNA structural models. Here we put our method to the test on a set of 47 complexes from the protein-DNA docking benchmark. We show that HADDOCK is able to predict many of the specific DNA conformational changes required to assemble the interface(s). Our DNA analysis and modelling procedure captures the bend and twist motions occurring upon complex formation and uses these to generate custom-built DNA structural models, more closely resembling the bound form, for use in a second docking round. We achieve throughout the benchmark an overall success rate of 94% of one-star solutions or higher (interface root mean square deviation ≤4 A and fraction of native contacts >10%) according to CAPRI criteria. Our improved protocol successfully predicts even the challenging protein-DNA complexes in the benchmark. Finally, our method is the first to readily dock multiple molecules (N > 2) simultaneously, pushing the limits of what is currently achievable in the field of protein-DNA docking.
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Affiliation(s)
- Marc van Dijk
- Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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18
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Improving real-time measurement of H/D exchange using a FTIR biospectroscopic probe. Anal Bioanal Chem 2008; 393:1289-95. [DOI: 10.1007/s00216-008-2535-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 11/13/2008] [Accepted: 11/18/2008] [Indexed: 10/21/2022]
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19
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Spectroscopic and molecular dynamics evidence for a sequential mechanism for the A-to-B transition in DNA. Biophys J 2008; 95:257-72. [PMID: 18326653 DOI: 10.1529/biophysj.107.117606] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The A-to-B form transition has been examined in three DNA duplexes, d(CGCGAATTCGCG)(2), d(CGCGAATTGCGC), and d(CGCAAATTTCGC), using circular dichroism spectroscopy, ultraviolet resonance Raman (UVRR) spectroscopy, and molecular dynamics (MD) simulation. Circular dichroism spectra confirm that these molecules adopt the A form under conditions of reduced water activity. UVRR results, obtained under similar conditions, suggest that the transition involves a series of intermediate forms between A and B. Cooperative and distinct transitions were observed for the bases and the sugars. Independent MD simulations on d(CGCGAATTCGCG)(2) show a spontaneous change from the A to B form in aqueous solution and describe a kinetic model that agrees well with UVRR results. Based on these observations, we predict that the mechanism of the transition involves a series of A/B hybrid forms and is sequential in nature, similar to previous crystallographic studies of derivatized duplexes. A simulation in which waters were restrained in the major groove of B DNA shows a rapid, spontaneous change from B to A at reduced water activity. These results indicate that a quasiergodic sampling of the solvent distribution may be a problem in going from B to A at reduced water activity in the course of an MD simulation.
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20
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Vrána O, Masek V, Drazan V, Brabec V. Raman spectroscopy of DNA modified by intrastrand cross-links of antitumor cisplatin. J Struct Biol 2007; 159:1-8. [PMID: 17321149 DOI: 10.1016/j.jsb.2007.01.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 01/16/2007] [Accepted: 01/17/2007] [Indexed: 11/30/2022]
Abstract
Raman spectroscopy was employed to characterize the perturbations to DNA conformation induced in DNA by two different intrastrand adducts of antitumor cis-diamminedichloroplatinum(II) (cisplatin), namely by its 1,2-GG or 1,3-GTG intrastrand cross-links. We examined short deoxyribooligonucleotide duplexes containing single, site-specific cross-link by Raman spectroscopy and assigned the spectral alterations to conformational changes induced in DNA by 1,2-GG or 1,3-GTG intrastrand CLs determined earlier by other biochemical and biophysical methods. The results confirmed significant perturbations to the B-form DNA backbone due to the intrastrand lesions and that several nucleotides changed their conformation from C2'-endo to C3'-endo. Evidence for a partial transition from B- to A-form was found in several regions of the Raman spectra as well. The spectra also confirmed the different and more extensive distortion induced in B-DNA by 1,3-GTG in comparison with 1,2-GG intrastrand CLs, consistent with their already known high resolution structures. The results of the present work demonstrate that Raman spectroscopy represents a suitable tool to provide insights into structural factors involved in the mechanisms underlying antitumor effects of platinum drugs.
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Affiliation(s)
- Oldrich Vrána
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ-61265 Brno, Czech Republic
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Elsawy KM, Hodgson MK, Caves LSD. The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA. Nucleic Acids Res 2005; 33:5749-62. [PMID: 16214808 PMCID: PMC1253833 DOI: 10.1093/nar/gki888] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A multivariate analysis of the backbone and sugar torsion angles of dinucleotide fragments was used to construct a 3D principal conformational subspace (PCS) of DNA duplex crystal structures. The potential energy surface (PES) within the PCS was mapped for a single-strand dinucleotide model using an empirical energy function. The low energy regions of the surface encompass known DNA forms and also identify previously unclassified conformers. The physical determinants of the conformational landscape are found to be predominantly steric interactions within the dinucleotide backbone, with medium-dependent backbone-base electrostatic interactions serving to tune the relative stability of the different local energy minima. The fidelity of the PES to duplex DNA properties is validated through a correspondence to the conformational distribution of duplex DNA crystal structures and the reproduction of observed sequence specific propensities for the formation of A-form DNA. The utility of the PES is demonstrated through its succinct and accurate description of complex conformational processes in simulations of duplex DNA. The study suggests that stereochemical considerations of the nucleic acid backbone play a role in determining conformational preferences of DNA which is analogous to the role of local steric interactions in determining polypeptide secondary structure.
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Affiliation(s)
- Karim M. Elsawy
- Department of Biology, University of YorkYork YO10 5YW, UK
- Department of Chemistry, University of YorkYork YO10 5YW, UK
| | | | - Leo S. D. Caves
- Department of Biology, University of YorkYork YO10 5YW, UK
- To whom correspondence should be addressed. Tel: +44 1904 328619; Fax: +44 1904 328505;
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Nauwelaerts K, Lescrinier E, Sclep G, Herdewijn P. Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides. Nucleic Acids Res 2005; 33:2452-63. [PMID: 15863723 PMCID: PMC1087899 DOI: 10.1093/nar/gki538] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties. In order to study the conformation of cyclohexenyl nucleosides by NMR, the HexRot program was developed to calculate conformations from scalar coupling constants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the thermodynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between 2H3 (N-type) and 2H3 (S-type) is 1.8 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleoside (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 4–20 kJ/mol). The flexibility of the cyclohexenyl nucleoside was demonstrated by the fast equilibrium between two conformational states that was observed in a CeNA-U monomer, combined with the 2H3 conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the 2H3 conformation when incorporated in a d(5′-GCGT*GCG-3′)/d(5′-CGCACGC-3′) duplex, as determined by the NMR spectroscopy. This represents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences.
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Affiliation(s)
| | | | | | - Piet Herdewijn
- To whom correspondence should be addressed. Tel: +32 16 337387; Fax: +32 16 337340;
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Chen CY, Ko TP, Lin TW, Chou CC, Chen CJ, Wang AHJ. Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d. Nucleic Acids Res 2005; 33:430-8. [PMID: 15653643 PMCID: PMC546169 DOI: 10.1093/nar/gki191] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (∼60°) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant–DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (∼50°). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (∼80°). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower Tm values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA.
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Affiliation(s)
- Chin-Yu Chen
- Institute of Biological ChemistryTaipei 115, Taiwan
- Department of Chemistry, National Taiwan UniversityTaipei 106, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological ChemistryTaipei 115, Taiwan
| | - Ting-Wan Lin
- Institute of Biological ChemistryTaipei 115, Taiwan
| | - Chia-Cheng Chou
- Institute of Biological ChemistryTaipei 115, Taiwan
- Core Facility for Protein X-ray Crystallography, Academia SinicaTaipei 115, Taiwan
| | - Chun-Jung Chen
- Biology Group, National Synchrotron Radiation Research CenterHsinchu 30077, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological ChemistryTaipei 115, Taiwan
- Core Facility for Protein X-ray Crystallography, Academia SinicaTaipei 115, Taiwan
- To whom correspondence should be addressed at Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan. Tel: +886 2 2788 1918; Fax: +886 2 2788 2043;
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