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Rasouli Z, Ghavami R. Facile Approach to Fabricate a Chemical Sensor Array Based on Nanocurcumin-Metal Ions Aggregates: Detection and Identification of DNA Nucleobases. ACS OMEGA 2020; 5:19331-19341. [PMID: 32803026 PMCID: PMC7424583 DOI: 10.1021/acsomega.0c00593] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/07/2020] [Indexed: 05/04/2023]
Abstract
Here, a three-channel absorbance sensor array based on the nanocurcumin-metal ion (NCur-MI) aggregates is designed for the detection and identification of deoxyribonucleic acid nucleobases (DNA NBs) for the first time. For this purpose, the binding affinities of some of MIs (i.e., Co2+, Cr3+, Cu2+, Fe2+, Fe3+, Hg2+, Mn2+, Ni2+, V3+, and Zn2+) to the NCur to induce the aggregation were evaluated under various experimental conditions. Further studies reveal that in the presence of DNA NBs, the aggregates of NCur-Co2+, NCur-Ni2+, and NCur-Zn2+ show the diverse absorbance responses to the deaggregation of NCur depending on the binding affinity of each of DNA NBs to the metal ions Co2+, Ni2+, and Zn2+. These responses are distinguishable from one another. Thus, clear differentiation among the DNA NBs is achieved by linear discriminant analysis and hierarchical clustering analysis to generate clustering maps. The discriminatory capacity of the sensor array for the identification of the DNA NBs is tested in the ranges of 2.4-16 and 5.6-10.4 μM. Furthermore, a mixed set of the DNA NBs was prepared for multivariate multicomponent analysis. Finally, the practicability of the sensor array is confirmed by the discrimination of the DNA NBs in an animal DNA sample. It should be noted that the proposed array is the first example to fabricate an NCur-based sensor array for the simultaneous detection of DNA NBs.
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Affiliation(s)
- Zolaikha Rasouli
- Chemometrics Laboratory, Chemistry
Department, Faculty of Science, University
of Kurdistan, P.O. Box 416, Sanandaj 66177-15175, Iran
| | - Raouf Ghavami
- Chemometrics Laboratory, Chemistry
Department, Faculty of Science, University
of Kurdistan, P.O. Box 416, Sanandaj 66177-15175, Iran
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2
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Andrić JM, Stanković IM, Zarić SD. Binding of metal ions and water molecules to nucleic acid bases: the influence of water molecule coordination to a metal ion on water-nucleic acid base hydrogen bonds. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:301-309. [PMID: 32830651 DOI: 10.1107/s2052520619001999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/04/2019] [Indexed: 06/11/2023]
Abstract
The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.
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Affiliation(s)
- Jelena M Andrić
- Innovation center of the Faculty of Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | | | - Snežana D Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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3
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Xu P, Guidez EB, Bertoni C, Gordon MS. Perspective:Ab initioforce field methods derived from quantum mechanics. J Chem Phys 2018. [DOI: 10.1063/1.5009551] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, USA
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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4
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Mujtaba M, Kaya M, Akyuz L, Erdonmez D, Akyuz B, Sargin I. Detailed adsorption mechanism of plasmid DNA by newly isolated cellulose from waste flower spikes of Thypa latifolia using quantum chemical calculations. Int J Biol Macromol 2017; 102:914-923. [PMID: 28457957 DOI: 10.1016/j.ijbiomac.2017.04.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 11/19/2022]
Affiliation(s)
- Muhammad Mujtaba
- Department of Biotechnology and Molecular Biology, Faculty of Science and Letters, Aksaray University, 68100 Aksaray, Turkey.
| | - Murat Kaya
- Department of Biotechnology and Molecular Biology, Faculty of Science and Letters, Aksaray University, 68100 Aksaray, Turkey
| | - Lalehan Akyuz
- Aksaray University, Technical Vocational School, Department of Chemistry Technology, 68100 Aksaray, Turkey
| | - Demet Erdonmez
- Department of Biology, Faculty of Science and Letters Aksaray University, 68100 Aksaray, Turkey
| | - Bahar Akyuz
- Department of Biotechnology and Molecular Biology, Faculty of Science and Letters, Aksaray University, 68100 Aksaray, Turkey
| | - Idris Sargin
- Department of Biotechnology and Molecular Biology, Faculty of Science and Letters, Aksaray University, 68100 Aksaray, Turkey
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5
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Kučerka N, Dushanov E, Kholmurodov KT, Katsaras J, Uhríková D. Calcium and Zinc Differentially Affect the Structure of Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3134-3141. [PMID: 28277666 DOI: 10.1021/acs.langmuir.6b03228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Interactions of calcium (Ca2+) and zinc (Zn2+) cations with biomimetic membranes made of dipalmitoylphosphatidylcholine (DPPC) were studied by small angle neutron diffraction (SAND). Experiments show that the structure of these lipid bilayers is differentially affected by the two divalent cations. Initially, both Ca2+ and Zn2+ cause DPPC bilayers to thicken, while further increases in Ca2+ concentration result in the bilayer thinning, eventually reverting to having the same thickness as pure DPPC. The binding of Zn2+, on the other hand, causes the bilayers to swell to a maximum thickness, and the addition of more Zn2+ does not result in a further thickening of the membrane. Agreement between our results obtained using oriented planar membranes and those from vesicular samples implies that the effect of cations on bilayer thickness is the result of electrostatic interactions, rather than geometrical constraints due to bilayer curvature. This notion is further reinforced by MD simulations. Finally, the radial distribution functions reveal a strong interaction between Ca2+ and the phosphate oxygens, while Zn2+ shows a much weaker binding specificity.
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Affiliation(s)
- Norbert Kučerka
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava , 83232 Bratislava, Slovakia
| | | | | | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Daniela Uhríková
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava , 83232 Bratislava, Slovakia
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Gresh N, Sponer JE, Devereux M, Gkionis K, de Courcy B, Piquemal JP, Sponer J. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics. J Phys Chem B 2015; 119:9477-95. [DOI: 10.1021/acs.jpcb.5b01695] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Nohad Gresh
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Judit E. Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Mike Devereux
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH 4056, Switzerland
| | - Konstantinos Gkionis
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
| | - Benoit de Courcy
- Chemistry & Biology, Nucleo(s)tides & Immunology for Therapy (CBNIT), CNRS UMR8601, Université Paris Descartes, PRES Sorbonne Paris Cité, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jean-Philip Piquemal
- Laboratoire
de Chimie Théorique, Sorbonne Universités, UPMC, Paris 6, case courrier
137, 4, place Jussieu, Paris, F75252, France
- Laboratoire
de Chimie Théorique, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, Paris, F75252, France
| | - Jiri Sponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska,
135, 612 65 Brno, Czech Republic
- CEITEC − Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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8
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Divalent Metal Cations in DNA–Phospholipid Binding. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-12-418698-9.00004-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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9
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10
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Wu Y, Wang H, Lin Y, Gao S, Zhang F. Hydrogen-bonded proton transfer in the hydrated adenine–thymine anion. CAN J CHEM 2013. [DOI: 10.1139/cjc-2013-0162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The proton transfer processes of microhydrated adenine–thymine anions are studied using density functional theory with the B3LYP method and DZP++ basis set. The microhydration effects on the geometrical structures, adsorption site, and the proton transfer reaction of the adenine–thymine anion are investigated. The site N10 atom of the adenine moiety has a larger proton affinity than the site O24 atom of thymine, which facilitates the proton H26 transfers from the N25 site of thymine to the N10 site of adenine. Therefore, the first single-proton transfer pathway (SPT1) is found for the all of the monohydrated adenine–thymine anions (AN4T)−·H2O, (AN13T)−·H2O, (ATO24)−·H2O, and (ATO28)−·H2O and tetrahydrated adenine–thymine anions (AT)−·4H2O. The proton H9 at the N7 site of adenine is also found to transfer to the O24 site of thymine for (AN4T)−·H2O and (AN13T)−·H2O in the gas phase. The double-proton transferred pathway is found when one water molecule interacts with the O28 atom of thymine. The reactant structures before the proton transfer are more stable than the product structures, and the structural changes mainly occur in thymine. The reaction energies of the microhydrated adenine–thymine anion in the gas phase and in the aqueous environment predict that the proton transfer process of the microhydrated adenine–thymine anion are more favorable in the gas phase than in aqueous solution.
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Affiliation(s)
- Yingxi Wu
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Hongyan Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Yuexia Lin
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Simin Gao
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Feng Zhang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
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11
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Xiao S, Wang L, Liu Y, Lin X, Liang H. Theoretical investigation of the proton transfer mechanism in guanine-cytosine and adenine-thymine base pairs. J Chem Phys 2012. [DOI: 10.1063/1.4766319] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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12
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Liang LJ, Huang CZ. Spectral study on the unique enhanced fluorescence of guanosine triphosphate by zinc ions. Talanta 2012; 104:198-203. [PMID: 23597910 DOI: 10.1016/j.talanta.2012.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 11/26/2022]
Abstract
Binding effect of guanosine triphosphate (GTP) with metal ions is involved in many biologically important processes, and so its investigation has been one interesting research focus for many chemical and biochemical research groups. In this contribution, we presented the unique fluorescence recovery and enhancement of GTP induced by Zn(II) based on the spectrofluorometric method. When excited at 280 nm, GTP is hardly fluorescent at the alkaline condition. However, the presence of Zn(II) caused an obvious fluorescence emission of GTP at 346 nm, and the binding molar ratio between GTP and Zn(II) had been proved to be 1. The investigations of binding property of various nucleotides with metal ions demonstrated that this fluorescence recovery and enhancement of GTP with Zn(II) was highly specific, which could successfully discriminate GTP from other structurally similar nucleotides including GDP and GMP. Furthermore, similar fluorescence response of the bacterial alarmone ppGpp to Zn(II) had also been identified.
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Affiliation(s)
- Li Jiao Liang
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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13
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Liang LJ, Zhen SJ, Zhao XJ, Huang CZ. A ratiometric fluorescence recognition of guanosine triphosphate on the basis of Zn(II) complex of 1,4-bis(imidazol-1-ylmethyl) benzene. Analyst 2012; 137:5291-6. [PMID: 23013938 DOI: 10.1039/c2an35743g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
As one vital member among the family of phosphates, guanosine triphosphate (GTP) not only plays a very important role in many critical biological processes but also closely associates with definite pathological states. Based on the ratiometric fluorescence response of the zinc complex of 1,4-bis(imidazol-1-ylmethyl) benzene (bix) in this contribution, a highly selective recognition of GTP has been successfully developed. The fluorescence of bix-Zn(II) at 289 nm decreased in the presence of GTP with the appearance of one new emission band at 341 nm, resulting in ratiometric fluorescence changes with the concentration of GTP. With that, ratiometric fluorescence recognition for GTP could be effectively established, and so GTP could be successfully discriminated from other structurally similar anions, including ATP and PPi. Furthermore, bix-Zn(II) also has a ratiometric fluorescence response to DNA sequences containing guanine.
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Affiliation(s)
- Li Jiao Liang
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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14
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Uhríková D, Kučerka N, Lengyel A, Pullmannová P, Teixeira J, Murugova T, Funari SS, Balgavý P. Lipid bilayer – DNA interaction mediated by divalent metal cations: SANS and SAXD study. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/351/1/012011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Gasbarri C, Angelini G, Fontana A, De Maria P, Siani G, Giannicchi I, Cort AD. Kinetics of demetallation of a zinc–salophen complex into liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:747-52. [DOI: 10.1016/j.bbamem.2011.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/07/2011] [Accepted: 10/18/2011] [Indexed: 01/10/2023]
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16
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Cerón-Carrasco JP, Jacquemin D. Influence of Mg2+ on the Guanine-Cytosine Tautomeric Equilibrium: Simulations of the Induced Intermolecular Proton Transfer. Chemphyschem 2011; 12:2615-23. [DOI: 10.1002/cphc.201100264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/28/2011] [Indexed: 01/01/2023]
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17
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Lengyel A, Uhríková D, Klacsová M, Balgavý P. DNA condensation and its thermal stability influenced by phospholipid bilayer and divalent cations. Colloids Surf B Biointerfaces 2011; 86:212-7. [DOI: 10.1016/j.colsurfb.2011.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 03/30/2011] [Accepted: 04/01/2011] [Indexed: 10/18/2022]
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18
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Roux C, Bhatt F, Foret J, de Courcy B, Gresh N, Piquemal JP, Jeffery CJ, Salmon L. The reaction mechanism of type I phosphomannose isomerases: new information from inhibition and polarizable molecular mechanics studies. Proteins 2011; 79:203-20. [PMID: 21058398 DOI: 10.1002/prot.22873] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Type I phosphomannose isomerases (PMIs) are zinc-dependent metalloenzymes involved in the reversible isomerization of D-mannose 6-phosphate (M6P) and D-fructose 6-phosphate (F6P). 5-Phospho-D-arabinonohydroxamic acid (5PAH), an inhibitor endowed with nanomolar affinity for yeast (Type I) and Pseudomonas aeruginosa (Type II) PMIs (Roux et al., Biochemistry 2004; 43:2926-2934), strongly inhibits human (Type I) PMI (for which we report an improved expression and purification procedure), as well as Escherichia coli (Type I) PMI. Its K(i) value of 41 nM for human PMI is the lowest value ever reported for an inhibitor of PMI. 5-Phospho-D-arabinonhydrazide, a neutral analogue of the reaction intermediate 1,2-cis-enediol, is about 15 times less efficient at inhibiting both enzymes, in accord with the anionic nature of the postulated high-energy reaction intermediate. Using the polarizable molecular mechanics, sum of interactions between fragments ab initio computed (SIBFA) procedure, computed structures of the complexes between Candida albicans (Type I) PMI and the cyclic substrate β-D-mannopyranose 6-phosphate (β-M6P) and between the enzyme and the high-energy intermediate analogue inhibitor 5PAH are reported. Their analysis allows us to identify clearly the nature of each individual active site amino acid and to formulate a hypothesis for the overall mechanism of the reaction catalyzed by Type I PMIs, that is, the ring-opening and isomerization steps, respectively. Following enzyme-catalyzed ring-opening of β-M6P by zinc-coordinated water and Gln111 ligands, Lys136 is identified as the probable catalytic base involved in proton transfer between the two carbon atoms C1 and C2 of the substrate D-mannose 6-phosphate.
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Affiliation(s)
- Céline Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, ICMMO, Univ Paris-Sud, UMR 8182, Orsay F-91405, France
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Šponer J, Šponer JE, Petrov AI, Leontis NB. Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B 2010; 114:15723-41. [PMID: 21049899 PMCID: PMC4868365 DOI: 10.1021/jp104361m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches. The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Anton I. Petrov
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
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20
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Ebrahimi A, Habibi Khorassani SM, Delarami H, Esmaeeli H. The effect of CH3, F and NO2 substituents on the individual hydrogen bond energies in the adenine-thymine and guanine-cytosine base pairs. J Comput Aided Mol Des 2010; 24:409-16. [PMID: 20352295 DOI: 10.1007/s10822-010-9348-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Accepted: 03/18/2010] [Indexed: 11/29/2022]
Abstract
The substituent effects on the geometrical parameters and the individual hydrogen bond (HB) energies of base pairs such as X-adenine-thymine (X-A-T), X-thymine-adenine (X-T-A), X-guanine-cytosine (X-G-C), and X-cytosine-guanine (X-C-G) have been studied by the quantum mechanical calculations at the B3LYP and MP2 levels with the 6-311++G(d,p) basis set. The electron withdrawing (EW) substituents (F and NO(2)) increase the total binding energy (DeltaE) of X-G-C derivatives and the electron donating (ED) substituent (CH(3)) decreases it when they are introduced in the 8 and 9 positions of G. The effects of substituents are reversed when they are located in the 1, 5, and 6 positions of C, with exception of CH(3) in the 1 position and F in the 5 position, which in both cases the DeltaE value decreases negligibly small. With minor exceptions (X=8-CH(3), 8-F, and 9-NO(2)), both ED and EW substituents increase slightly the DeltaE values of X-A-T derivatives. The individual HB energies (E (HB)s) have been estimated using electron densities that calculated at the hydrogen bond critical points (HBCPs) by the atoms in molecules (AIM) method. Most of changes of individual HBs are in consistent with the ED/EW nature of substituents and the role of atoms entered H-bonding. The remarkable change is observed for NO(2) substituted derivative in each case.
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Affiliation(s)
- A Ebrahimi
- Department of Chemistry, University of Sistan & Baluchestan, PO Box 98135-674, Zahedan, Iran.
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21
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Oliva R, Cavallo L. Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs. J Phys Chem B 2010; 113:15670-8. [PMID: 19921955 DOI: 10.1021/jp906847p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We performed MP2 calculations to elucidate the structure and energetics of the Mg(2+), Mn(2+), and Co(2+) hexahydrated aquaions, and the effect of the metal binding to the N7 atom of (i) a single guanine, (ii) a guanine involved in a Watson-Crick pair, and (iii) a guanine involved in a reverse Watson-Crick base pair. Our comparative analysis of the three aquaions indicates a clear inverse correlation between the radius of the cation and the binding energy, that indeed increases in the order Mn(2+) < Co(2+) < Mg(2+). The trend in the binding energies of the pentahydrated cations to the N7 atom of the guanine is instead Mg(2+) < Mn(2+) < Co(2+), suggesting a rather different bonding scheme that, for the two transition metals, involves back-donation from the aromatic ring of the guanine to their empty d orbitals. In the gas phase, the three hydrated metals significantly stabilize both G-C base pair geometries, Watson-Crick and reverse Watson-Crick, we investigated. Inclusion of a continuous solvent model, however, remarkably reduces this additional stabilization, which becomes almost negligible in the case of the Mg(2+) cation coordinated to the guanine in the standard Watson-Crick geometry. Conversely, all three metal ions sensibly stabilize the reverse Watson-Crick geometry, also in water. Our results are supported by a screening of the structures available in the Protein Data Bank, which clearly indicates that the two transition metals we investigated have a tendency greater than Mg(2+) to coordinate to the N7 atom of guanines, and that there is no clear correlation between the number of guanines in experimental structures with a metal bound to N7 atom and their involvement in Watson-Crick base pairs.
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Affiliation(s)
- Romina Oliva
- Dipartimento di Scienze Applicate, Università di Napoli Parthenope, I-80143 Naples, Italy
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Andrushchenko V, Bour P. Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: experimental and theoretical study. J Phys Chem B 2009; 113:283-91. [PMID: 19063657 DOI: 10.1021/jp8058678] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+) cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm(-1) band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region ( approximately 800-1200 cm(-1)), but also notable frequency shifts of the carbonyl vibrations. The Cu(2+) and Zn(2+) ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu(2+) binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610, Praha 6, Czech Republic
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23
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Salsbury FR, Crowder MW, Kingsmore SF, Huntley JJA. Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor. J Mol Model 2008; 15:133-45. [PMID: 19039608 DOI: 10.1007/s00894-008-0410-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 07/19/2008] [Indexed: 11/28/2022]
Abstract
The beta-lactam-based antibiotics are among the most prescribed and effective antibacterial agents. Widespread use of these antibiotics, however, has created tremendous pressure for the emergence of resistance mechanisms in bacteria. The most common cause of antibiotic resistance is bacterial production of actamases that efficiently degrade antibiotics. The metallo-beta-lactamases are of particular clinical concern due to their transference between bacterial strains. We used molecular dynamics (MD) simulations to further study the conformational changes that occur due to binding of an inhibitor to the dicanzinc metallo-beta-lactamase from Bacteroides fragilis. Our studies confirm previous findings that the major flap is a major source of plasticity within the active site, therefore its dynamic response should be considered in drug development. However, our results also suggest the need for care in using MD simulations in evaluating loop mobility, both due to relaxation times and to the need to accurately model the zinc active site. Our study also reveals two new robust responses to ligand binding. First, there are specific localized changes in the zinc active site--a local loop flip--due to ligand intercalation that may be critical to the function of this enzyme. Second, inhibitor binding perturbs the dynamics throughout the protein, without otherwise perturbing the enzyme structure. These dynamic perturbations radiate outward from the active site and their existence suggests that long-range communication and dynamics may be important in the activity of this enzyme.
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Affiliation(s)
- Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston Salem, NC 27109, USA.
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24
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Noguera M, Bertran J, Sodupe M. Cu2+/+ cation coordination to adenine--thymine base pair. Effects on intermolecular proton-transfer processes. J Phys Chem B 2008; 112:4817-25. [PMID: 18358032 DOI: 10.1021/jp711982g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Intermolecular proton-transfer processes in the Watson & Crick adenine-thymine Cu+ and Cu2+ cationized base pairs have been studied using the density functional theory (DFT) methods. Cationized systems subject to study are those resulting from cation coordination to the main basic sites of the base pair, N7 and N3 of adenine and O2 of thymine. For Cu+ coordinated to N7 or N3 of adenine, only the double proton-transferred product is found to be stable, similarly to the neutral system. However, when Cu+ interacts with thymine, through the O2 carbonyl atom, the single proton transfer from thymine to adenine becomes thermodynamically spontaneous, and thus rare forms of the DNA bases may spontaneously appear. For Cu2+ cation, important effects on proton-transfer processes appear due to oxidation of the base pair, which stabilizes the different single proton-transfer products. Results for hydrated systems show that the presence of the water molecules interacting with the metal cation (and their mode of coordination) can strongly influence the ability of Cu2+ to induce oxidation on the base pair.
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Affiliation(s)
- Marc Noguera
- Departament de Química, Universitat Autónoma de Barcelona, Bellaterra 08193, Spain
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25
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Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput 2007; 3:1960-1986. [PMID: 18978934 PMCID: PMC2367138 DOI: 10.1021/ct700134r] [Citation(s) in RCA: 279] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université René-Descartes, 45, rue des Saints-Pères, 75006 Paris, France, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, and Laboratoire de Chimie Théorique, Université Pierre-et-Marie-Curie, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, 75252 Paris, France
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26
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Soteras I, Curutchet C, Bidon-Chanal A, Dehez F, Ángyán JG, Orozco M, Chipot C, Luque FJ. Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations. J Chem Theory Comput 2007; 3:1901-13. [DOI: 10.1021/ct7001122] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ignacio Soteras
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
| | - Carles Curutchet
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
| | - Axel Bidon-Chanal
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
| | - François Dehez
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
| | - János G. Ángyán
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
| | - Modesto Orozco
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
| | - Christophe Chipot
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
| | - F. Javier Luque
- Departament de Fisicoquímica and Institut de Biomedicina, Facultat de Farmàcia, Universitat de Barcelona, Avgda, Diagonal 643, Barcelona 08028, Spain, Équipe de Dynamique des Assemblages Membranaires, Unité Mixte de Recherche CNRS/UHP 7565 and Équipe Modélisation Quantique et Cristallographique, LCM3B UMR 7036, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France, Departament de Bioquímica i Biología Molecular, Facultat de Química, Universitat de Barcelona, c/. Martí i Franqués 1, 08028,
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27
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On the interactions of hydrated metal cations (Mg2+, Mn2+, Ni2+, Zn2+) with guanine–cytosine Watson–Crick and guanine–guanine reverse-Hoogsteen DNA base pairs. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Roux C, Gresh N, Perera LE, Piquemal JP, Salmon L. Binding of 5-phospho-D-arabinonohydroxamate and 5-phospho-D-arabinonate inhibitors to zinc phosphomannose isomerase from Candida albicans studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2007; 28:938-57. [PMID: 17253648 DOI: 10.1002/jcc.20586] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Type I phosphomannose isomerase (PMI) is a Zn-dependent metalloenzyme involved in the isomerization of D-fructose 6-phosphate to D-mannose 6-phosphate. One of our laboratories has recently designed and synthesized 5-phospho-D-arabinonohydroxamate (5PAH), an inhibitor endowed with a nanomolar affinity for PMI (Roux et al., Biochemistry 2004, 43, 2926). By contrast, the 5-phospho-D-arabinonate (5PAA), in which the hydroxamate moiety is replaced by a carboxylate one, is devoid of inhibitory potency. Subsequent biochemical studies showed that in its PMI complex, 5PAH binds Zn(II) through its hydroxamate moiety rather than through its phosphate. These results have stimulated the present theoretical investigation in which we resort to the SIBFA polarizable molecular mechanics procedure to unravel the structural and energetical aspects of 5PAH and 5PAA binding to a 164-residue model of PMI. Consistent with the experimental results, our theoretical studies indicate that the complexation of PMI by 5PAH is much more favorable than by 5PAA, and that in the 5PAH complex, Zn(II) ligation by hydroxamate is much more favorable than by phosphate. Validations by parallel quantum-chemical computations on model of the recognition site extracted from the PMI-inhibitor complexes, and totaling up to 140 atoms, showed the values of the SIBFA intermolecular interaction energies in such models to be able to reproduce the quantum-chemistry ones with relative errors < 3%. On the basis of the PMI-5PAH SIBFA energy-minimized structure, we report the first hypothesis of a detailed view of the active site of the zinc PMI complexed to the high-energy intermediate analogue inhibitor, which allows us to identify active site residues likely involved in the proton transfer between the two adjacent carbons of the substrates.
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Affiliation(s)
- Celine Roux
- Laboratoire de Chimie Bioorganique et Bioinorganique, CNRS-UMR 8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay, Bâtiment 420, Université Paris-Sud XI, 15 rue Georges Clémenceau, 91405 Orsay, France
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29
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Pye CC, Corbeil CR, Rudolph WW. An ab initio investigation of zinc chloro complexes. Phys Chem Chem Phys 2006; 8:5428-36. [PMID: 17119651 DOI: 10.1039/b610084h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of geometry, frequency, and energy calculations of chloroaquazinc(II) complexes were carried out at up to the MP2/6-31+G* level. A thorough examination of all species up to and including hexacoordinate species, and with up to six chlorides, was carried out. The structures of the complexes are compared with experimental data where available. The solution chemistry of zinc(II) in the presence of chloride is discussed, and Raman spectra of zinc perchlorate with increasing amount of chloride are presented.
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Affiliation(s)
- Cory C Pye
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia, Canada B3H 3C3.
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30
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Gresh N, Piquemal JP, Krauss M. Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. J Comput Chem 2005; 26:1113-30. [PMID: 15934064 DOI: 10.1002/jcc.20244] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first-order contributions, electrostatic (E(MTP)), and short-range repulsion (E(rep)), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, E(MTP) is augmented with a penetration component, E(pen), which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. E(pen) is fit in a limited number of selected Zn(II)-mono-ligated complexes so that the sum of E(MTP) and E(pen) reproduces the Coulomb contribution E(c) from an ab initio Hartree-Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, E(rep) is expressed by a S(2)/R term now augmented with an S(2)/R(2) one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion E(exch) from ab initio energy decomposition, and no longer as previously the difference between (E(c) + E(exch)) and E(MTP). Along with the reformulation of the first-order contributions, a limited recalibration of the second-order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and beta-lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term-to-term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, FRE 2718 CNRS, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France.
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31
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Poater J, Sodupe M, Bertran * J, Solà * M. Hydrogen bonding and aromaticity in the guanine–cytosine base pair interacting with metal cations (M = Cu+, Ca2+and Cu2+). Mol Phys 2005. [DOI: 10.1080/00268920512331316238] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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32
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Sun L, Bu Y. Marked Variations of Dissociation Energy and H-Bond Character of the Guanine-Cytosine Base Pair Induced by One-Electron Oxidation and Li+ Cation Coupling. J Phys Chem B 2004; 109:593-600. [PMID: 16851051 DOI: 10.1021/jp0459817] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The variation of dissociation energy and H-bond character of the G-C cation and the Li-GC cation have been investigated by employing density functional theory (B3LYP) with the 6-31+G* basis set. The one-electron oxidation and the coupling of Li(+) to the guanine-cytosine base pair can strengthen the interaction between guanine and cytosine. The interaction of the cation Li(+) with guanine is attractive and is attributed to the polarization of the H-bonds between G-C that enhances G-C interaction. The cooperativity of the three H-bonds in the GC and Li-GC cations is different from that in the neutral GC base pair. The proton-transfer process between N(1) of the guanine and N(3) of the cytosine can occur in the GC cation and the Li-GC cation. The geometries of the transition state are out of plane, especially for the transition state of the Li-GC cation. The analysis of the activation energy for the proton-transfer process shows that the GC(+) before and after proton transfer can exist simultaneously in the gas phase, but for the Li-GC(+) system, the Li-GC(+) without proton transfer is the dominating species in the gas phase.
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Affiliation(s)
- Lixiang Sun
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China
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33
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Sponer J, Jurecka P, Hobza P. Accurate interaction energies of hydrogen-bonded nucleic acid base pairs. J Am Chem Soc 2004; 126:10142-51. [PMID: 15303890 DOI: 10.1021/ja048436s] [Citation(s) in RCA: 374] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. The study presents reference ab initio structures and interaction energies of selected base pairs with binding energies ranging from -5 to -47 kcal/mol. The molecular structures are obtained using the RI-MP2 (resolution of identity MP2) method with extended cc-pVTZ basis set of atomic orbitals. The RI-MP2 method provides results essentially identical with the standard MP2 method. The interaction energies are calculated using the Complete Basis Set (CBS) extrapolation at the RI-MP2 level. For some base pairs, Coupled-Cluster corrections with inclusion of noniterative triple contributions (CCSD(T)) are given. The calculations are compared with selected medium quality methods. The PW91 DFT functional with the 6-31G basis set matches well the RI-MP2/CBS absolute interaction energies and reproduces the relative values of base pairing energies with a maximum relative error of 2.6 kcal/mol when applied with Becke3LYP-optimized geometries. The Becke3LYP DFT functional underestimates the interaction energies by few kcal/mol with relative error of 2.2 kcal/mol. Very good performance of nonpolarizable Cornell et al. force field is confirmed and this indirectly supports the view that H-bonded base pairs are primarily stabilized by electrostatic interactions.
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Affiliation(s)
- Jirí Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
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34
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Madurga S, Vilaseca E. Solvent Effect on the Conformational Equilibrium of 1,2-Dichloroethane in Water. The Role of Solute Polarization. J Phys Chem A 2004. [DOI: 10.1021/jp0491358] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergio Madurga
- Departament de Química Física i Centre Especial de Recerca en Química Teòrica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, 08028-Barcelona, Catalunya, Spain
| | - Eudald Vilaseca
- Departament de Química Física i Centre Especial de Recerca en Química Teòrica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, 08028-Barcelona, Catalunya, Spain
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35
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Gresh N, Shi GB. Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation. J Comput Chem 2004; 25:160-8. [PMID: 14648615 DOI: 10.1002/jcc.10312] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have explored the conformation-dependent interaction energy of the triphosphate moiety, a key constituent of ATP and GTP, with a closed-shell divalent cation, Zn2+, used as a probe. This was done using the SIBFA polarizable molecular mechanics procedure. We have resorted to a previously developed approach in which triphosphate is built out from its elementary constitutive fragments, and the intramolecular, interfragment, interaction energies are computed simultaneously with their intermolecular interactions with the divalent cation. This approach has enabled reproduction of the values of the intermolecular interaction energies from ab initio quantum-chemistry with relative errors <3%. It was extended to the complex of a nonhydrolyzable analog of ATP with the active site of a bacterial enzyme having two Mg2+ cations as cofactors. We obtained following energy-minimization a very close overlap of the ATP analog over its position from X-ray crystallography. For models of the ATP analog-enzyme complex encompassing up to 169 atoms, the values of the SIBFA interaction energies were found to match their DFT counterparts with relative errors of <2%.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université René-Descartes, 4, Avenue de l'Observatoire, 75006, Paris, France.
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36
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Šponer JE, Sychrovský V, Hobza P, Šponer J. Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids. Phys Chem Chem Phys 2004. [DOI: 10.1039/b404306p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Sychrovský V, Sponer J, Hobza P. Theoretical Calculation of the NMR Spin−Spin Coupling Constants and the NMR Shifts Allow Distinguishability between the Specific Direct and the Water-Mediated Binding of a Divalent Metal Cation to Guanine. J Am Chem Soc 2003; 126:663-72. [PMID: 14719966 DOI: 10.1021/ja036942w] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The calculated intermolecular and intramolecular indirect NMR spin-spin coupling constants and NMR shifts were used for the discrimination between the inner-shell and the outer-shell binding motif of hydrated divalent cations Mg(2+) or Zn(2+) with a guanine base. The intermolecular coupling constants (1)J(X,O6) and (1)J(X,N7) (X = Mg(2+), Zn(2+)) can be unambiguously assigned to the specific inner-shell binding motif of the hydrated cation either with oxygen O6 or with nitrogen N7 of guanine. The calculated coupling constants (1)J(Mg,O6) and (1)J(Zn,O6) were 6.2 and -17.5 Hz, respectively, for the inner-shell complex of cation directly interacting with oxygen O6 of guanine. For the inner-shell coordination of the cation at nitrogen N7, the calculated coupling constants (1)J(Mg,N7) and (1)J(Zn,N7) were 5.6 and -36.5 Hz, respectively. When the binding of the cation is water-mediated, the coupling constant is zero. To obtain reliable shifts in NMR parameters, hydrated guanine was utilized as the reference state. The calculated change of NMR spin-spin coupling constants due to the hydration and coordination of the cation with guanine is caused mainly by the variation of Fermi-contact coupling contribution while the variation of diamagnetic spin-orbit, paramagnetic spin-orbit, and spin-dipolar coupling contributions is small. The change of s-character of guanine sigma bonding, sigma antibonding, and lone pair orbitals upon the hydration and cation coordination (calculated using the Natural Bond Orbital analysis) correlates with the variation of the Fermi-contact term. The calculated NMR shifts delta(N7) of -15.3 and -12.2 ppm upon the coordination of Mg(2+) and Zn(2+) ion are similar to the NMR shift of 19.6 ppm toward the high field measured by Tanaka for N7 of guanine upon the coordination of the Cd(2+) cation (Tanaka, Y.; Kojima, C.; Morita, E. H.; Kasai. Y.; Yamasaki, K.; Ono, A.; Kainosho, M.; Taira, K. J. Am. Chem. Soc. 2002, 124, 4595-4601). The present data indicate that measurements of NMR intermolecular coupling constants may be used to discriminate between the specific inner- and outer-shell binding of divalent cations to nucleobases in DNA and RNA.
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Affiliation(s)
- Vladimír Sychrovský
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, 182 23, Prague 8, Czech Republic
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Dal Peraro M, Vila AJ, Carloni P. Substrate binding to mononuclear metallo-β-lactamase from Bacillus cereus. Proteins 2003; 54:412-23. [PMID: 14747990 DOI: 10.1002/prot.10554] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Structure and dynamics of substrate binding (cefotaxime) to the catalytic pocket of the mononuclear zinc-beta-lactamase from Bacillus cereus are investigated by molecular dynamics simulations. The calculations, which are based on the hydrogen-bond pattern recently proposed by Dal Peraro et al. (J Biol Inorg Chem 2002; 7:704-712), are carried out for both the free and the complexed enzyme. In the resting state, active site pattern and temperature B-factors are in agreement with crystallographic data. In the complexed form, cefotaxime is accommodated into a stable orientation in the catalytic pocket within the nanosecond timescale, interacting with the enzyme zinc-bound hydroxide and the surrounding loops. The beta-lactam ring remains stable and very close to the hydroxide nucleophile agent, giving a stable representation of the productive enzyme-substrate complex.
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Affiliation(s)
- Matteo Dal Peraro
- International School for Advanced Studies, SISSA and INFM-DEMOCRITOS, Trieste, Italy
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39
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Noguera M, Bertran J, Sodupe M. A Quantum Chemical Study of Cu2+ Interacting with Guanine−Cytosine Base Pair. Electrostatic and Oxidative Effects on Intermolecular Proton-Transfer Processes. J Phys Chem A 2003. [DOI: 10.1021/jp036573q] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marc Noguera
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193
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40
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Ledecq M, Lebon F, Durant F, Giessner-Prettre C, Marquez A, Gresh N. Modeling of Copper(II) Complexes with the SIBFA Polarizable Molecular Mechanics Procedure. Application to a New Class of HIV-1 Protease Inhibitors. J Phys Chem B 2003. [DOI: 10.1021/jp0354604] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Ledecq
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Florence Lebon
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - François Durant
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Claude Giessner-Prettre
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Antonio Marquez
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
| | - Nohad Gresh
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium, Laboratoire de Chimie Théorique, UMR7615, Université Pierre & Marie Curie, 4, place Jussieu, 75252 Paris, France, Departamento de Qimica Fisica, Facultad de Qimica, Universitad de Sevilla, E-41012 Sevilla, Spain, and Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Université Rene Descartes, 4, avenue de l'Observatoire, 75006 Paris,
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41
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Gresh N, Šponer JE, Špačková N, Leszczynski J, Šponer J. Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5‘-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA. J Phys Chem B 2003. [DOI: 10.1021/jp022659s] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Judit E. Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Nad'a Špačková
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jerzy Leszczynski
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
| | - Jiři Šponer
- Laboratoire de Pharmacochimie Moléculaire et Structurale, FRE 2463 CNRS, U266 INSERM, Faculté de Pharmacie de Paris, Université René-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, Institute of Biophysics, Academy of Sciences of the Czech Republic, National Center for Biomolecular Research, Kralovopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and J
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42
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Moroni F, Famulari A, Raimondi M, Sabat M. Stabilization of the Noncomplementary Guanine−Adenine Base Pairs by Zn(II) Ions. An ab Initio SCF-MI Study. J Phys Chem B 2003. [DOI: 10.1021/jp026315d] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Federico Moroni
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
| | - Antonino Famulari
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
| | - Mario Raimondi
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
| | - Michal Sabat
- Dipartimento di Chimica Fisica ed Elettrochimica and Centro CNR-CSRSRC, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy, and Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904
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43
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Rulíšek L, Šponer J. Outer-Shell and Inner-Shell Coordination of Phosphate Group to Hydrated Metal Ions (Mg2+, Cu2+, Zn2+, Cd2+) in the Presence and Absence of Nucleobase. The Role of Nonelectrostatic Effects. J Phys Chem B 2003. [DOI: 10.1021/jp027058f] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lubomír Rulíšek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
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44
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Krauss M, Gresh N, Antony J. Binding and Hydrolysis of Ampicillin in the Active Site of a Zinc Lactamase. J Phys Chem B 2003. [DOI: 10.1021/jp027097r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Krauss
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland, Laboratoire de Pharmacochimie Moleculaire, U 266 INSERM, FRE 2463 CNRS, Universite Rene-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, and Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
| | - N. Gresh
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland, Laboratoire de Pharmacochimie Moleculaire, U 266 INSERM, FRE 2463 CNRS, Universite Rene-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, and Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
| | - J. Antony
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland, Laboratoire de Pharmacochimie Moleculaire, U 266 INSERM, FRE 2463 CNRS, Universite Rene-Descartes, 4, Avenue de l'Observatoire, 75006 Paris, France, and Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
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45
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Muñoz J, Gelpí JL, Soler-López M, Subirana JA, Orozco M, Luque FJ. Can Divalent Metal Cations Stabilize the Triplex Motif? Theoretical Study of the Interaction of the Hydrated Mg2+ Cation with the G−G·C Triplet. J Phys Chem B 2002. [DOI: 10.1021/jp026096w] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jordi Muñoz
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - J. L. Gelpí
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Montserrat Soler-López
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Juan A. Subirana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Modesto Orozco
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - F. Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
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46
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Binder H, Zschörnig O. The effect of metal cations on the phase behavior and hydration characteristics of phospholipid membranes. Chem Phys Lipids 2002; 115:39-61. [PMID: 12047897 DOI: 10.1016/s0009-3084(02)00005-1] [Citation(s) in RCA: 230] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To characterize the specificity of ion binding to phospholipids in terms of headgroup structure, hydration and lyotropic phase behavior we studied 1-palmitoyl-2-oleoyl-phosphatidylcholine as a function of relative humidity (RH) at 25 degrees C in the presence and absence of Li+, Na+, K+, Be2+, Mg2+, Ca2+, Sr2+, Ba2+, Zn2+ and Cu2+ ions by means of infrared (IR) spectroscopy. All divalent cations and Li+ shift the gel-to-liquid crystalline phase transition towards bigger RH values indicating stabilization of the gel state. The observed shift correlates in a linearly fashion with the electrostatic solvation free energy for most of the ions in water that in turn, is inversely related to the ionic radius. This interesting result was interpreted in terms of the excess chemical potential of mixing of hydrated ions and lipids. Calcium, zinc and partially lithium, cause a positive deviation from the linear relationship. IR spectral analysis shows that the carbonyl groups become more accessible to the water in the presence of Mg2+, Ca2+, Sr2+ and Ba2+ probably because of their involvement into the hydration shell of the ions. In contrast, Be2+, Zn2+ and Cu2+ dehydrate the carbonyl groups at small and medium RH. The ability of the lipid to take up water is distinctly reduced in the presence of Zn2+ and, partially, of Cu2+ meaning that the headgroups have become less hydrophilic. The binding mode of Be2+ to lipid headgroups involves hydrolyzed water. Polarized IR spectra show that complex formation of the phosphate groups with divalent ions gives rise to conformational changes and immobilization of the headgroups. The results are discussed in terms of the lyotropic Hofmeister series and of fusogenic activity of the ionic species.
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Affiliation(s)
- Hans Binder
- Department of Medicine, Institute of Medical Physics and Biophysics, University of Leipzig, Liebigstr. 27, Leipzig, Germany.
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47
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Abstract
This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C [bond] H...O interbase contacts, sugar-base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed.
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Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejskova 3, 182 23 Prague, Czech Republic.
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Affiliation(s)
- Anton S. Petrov
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Gene Lamm
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - George R. Pack
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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49
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Martínez JM, Elmroth SK, Kloo L. Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study. J Am Chem Soc 2001; 123:12279-89. [PMID: 11734028 DOI: 10.1021/ja0108786] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of sodium counterion presence and chain length on the structure and dynamics of single DNA strands of polythymidylate were studied by means of molecular dynamics simulations. The importance of the base-base stacking phenomenon increases with the chain length and partially reduces the flexibility of the strand. Sodium ions directly interact with the phosphate groups and keto oxygens of the thymine bases, complexes showing lifetimes below 400 ps. Simultaneous phosphate and keto complexes were observed for one of the sodium ions with lifetimes around 1 ns. The implications of such complexes in the folding process experienced by the strand are considered. Structurally, cation inner- and outer-sphere complexes were observed in the coordination of phosphate groups. For the inner-sphere complexes, the structural information retrieved from the simulations is in very good agreement with experimental data. The diffusion properties of the sodium ions also reflect both types of coordination modes.
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Affiliation(s)
- J M Martínez
- Department of Inorganic Chemistry, Royal Institute of Technology, Stockholm S-10044, Sweden
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50
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Šponer JE, Glahé F, Leszczynski J, Lippert B, Šponer J. How Nucleobases Rotate When Bonded to a Metal Ion: Detailed View from an Ab Initio Quantum Chemical Study of a Cytosine Complex of trans-a2PtII. J Phys Chem B 2001. [DOI: 10.1021/jp012795h] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judit E. Šponer
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Frank Glahé
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Bernhard Lippert
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
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