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Abstract
Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.
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2
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Gorb L, Pekh A, Nyporko A, Ilchenko M, Golius A, Zubatiuk T, Zubatyuk R, Dubey I, Hovorun DM, Leszczynski J. Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study. J Phys Chem B 2020; 124:9343-9353. [DOI: 10.1021/acs.jpcb.0c06154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Anatolii Pekh
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Alexey Nyporko
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Mykola Ilchenko
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Anastasiia Golius
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Tetiana Zubatiuk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Roman Zubatyuk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Igor Dubey
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
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3
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Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments. J Mol Model 2018; 24:46. [DOI: 10.1007/s00894-018-3589-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
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4
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Smith DA, Holroyd LF, van Mourik T, Jones AC. A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure. Phys Chem Chem Phys 2017; 18:14691-700. [PMID: 27186599 DOI: 10.1039/c5cp07816d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5'-position and each of the natural bases in the 3'-position are examined, together with the analogous 5'-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
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Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Anita C Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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5
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Poltev VI, Anisimov VM, Sanchez C, Deriabina A, Gonzalez E, Garcia D, Rivas F, Polteva NA. Analysis of the conformational features of Watson–Crick duplex fragments by molecular mechanics and quantum mechanics methods. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916020160] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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6
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Zubatiuk T, Kukuev MA, Korolyova AS, Gorb L, Nyporko A, Hovorun D, Leszczynski J. Structure and Binding Energy of Double-Stranded A-DNA Mini-helices: Quantum-Chemical Study. J Phys Chem B 2015; 119:12741-9. [DOI: 10.1021/acs.jpcb.5b04644] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tetiana Zubatiuk
- Division
of Functional Materials Chemistry, SSI “Institute for Single
Crystals”, National Academy of Science of Ukraine, Kharkiv 61001, Ukraine
| | - Maxim A. Kukuev
- Division
of Functional Materials Chemistry, SSI “Institute for Single
Crystals”, National Academy of Science of Ukraine, Kharkiv 61001, Ukraine
| | - Alexandra S. Korolyova
- Department
of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Leonid Gorb
- Department
of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03143, Ukraine
| | - Alexey Nyporko
- Department
of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Dmytro Hovorun
- Department
of Molecular Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv 03143, Ukraine
| | - Jerzy Leszczynski
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
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7
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Anisimov VM, Bauer GH, Chadalavada K, Olson RM, Glenski JW, Kramer WTC, Aprà E, Kowalski K. Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures. J Chem Theory Comput 2014; 10:4307-16. [DOI: 10.1021/ct500404c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victor M. Anisimov
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Gregory H. Bauer
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Kalyana Chadalavada
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Ryan M. Olson
- Cray, Inc., 380 Jackson
Street, St.
Paul, Minnesota 55101, United States
| | - Joseph W. Glenski
- Cray, Inc., 380 Jackson
Street, St.
Paul, Minnesota 55101, United States
| | - William T. C. Kramer
- National
Center for Supercomputing Applications, University of Illinois at Urbana−Champaign, 1205 West Clark Street, MC-257, Urbana, Illinois 61801, United States
| | - Edoardo Aprà
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, K8-91, Richland, Washington 99352, United States
| | - Karol Kowalski
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, K8-91, Richland, Washington 99352, United States
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8
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Zubatiuk TA, Shishkin OV, Gorb L, Hovorun DM, Leszczynski J. B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study. Phys Chem Chem Phys 2014; 15:18155-66. [PMID: 24065071 DOI: 10.1039/c3cp51584b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report the results of the first comprehensive DFT study on the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid duplexes. The ability of mini-helixes to preserve the conformation of B-DNA in the gas phase and under the influence of such factors as: solvent, uncompensated charge, and counter-ions was evaluated using M06-2X functional with 6-31G(d,p) basis set. The accuracy of the models was ascertained based on their ability to reproduce key structural features of natural B-DNA. Analysis of the helicity suggests that the helical conformations adopt geometrical parameters which are close to those of the B-DNA form. The torsion angles fall somewhere between the values observed for BI/BII conformational classes. The comparative analysis of parameters of isolated Watson-Crick base pairs versus B-DNA-like conformations indicates the same tendency of base-pair polarization and hydration. Specifically, effects of polarization of nucleobases in continuum type dielectric medium mimicking water are stronger than those caused by the presence of backbone. Polar environment as well as the presence of counterions stabilizes duplexes, facilitating helix formation. Substantial conformational changes of nucleotides upon duplex formation decrease the binding energy. In spite of structural and energetic changes, the placement of a mini-helix into the gas phase does not lead to significant disruption of the structure. On the contrary, the duplex preserves its helicity and the strands remain bound.
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Affiliation(s)
- Tetiana A Zubatiuk
- Division of Functional Materials Chemistry, SSI "Institute for Single Crystals" National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv, 61001, Ukraine
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9
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Poltev V, Anisimov VM, Danilov VI, Garcia D, Sanchez C, Deriabina A, Gonzalez E, Rivas F, Polteva N. The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures. Biopolymers 2014; 101:640-50. [DOI: 10.1002/bip.22432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/23/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Valeri Poltev
- Autonomous University of Puebla; Puebla 72570 Mexico
| | | | | | | | | | | | | | | | - Nina Polteva
- Institute of Theoretical and Experimental Biophysics RAS; Pushchino 142290 Russia
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10
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Lenz SAP, Kellie JL, Wetmore SD. Glycosidic bond cleavage in deoxynucleotides: effects of solvent and the DNA phosphate backbone in the computational model. J Phys Chem B 2012; 116:14275-84. [PMID: 23167947 DOI: 10.1021/jp3096677] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Density functional theory (B3LYP) was employed to examine the hydrolysis of the canonical 2'-deoxynucleotides in varied environments (gas phase or water) using different computational models for the sugar residue (methyl or phosphate group at C5') and nucleophile (water activated through full or partial proton abstraction). Regardless of the degree of nucleophile activation, our results show that key geometrical parameters along the reaction pathway are notably altered upon direct inclusion of solvent effects in the optimization routine, which leads to significant changes in the reaction energetics and better agreement with experiment. Therefore, despite the wide use of gas-phase calculations in the literature, small model computational work, as well as large-scale enzyme models, that strive to understand nucleotide deglycosylation must adequately describe the environment. Alternatively, although inclusion of the phosphate group at C5' also affects the geometries of important stationary points, the effects cancel to yield unchanged deglycosylation barriers, and therefore smaller computational models can be used to estimate the energy associated with nucleotide deglycosylation, with the 5' phosphate group included if full (geometric) details of the reaction are desired. Hydrogen-bonding interactions with the nucleobase can significantly reduce the barrier to deglycosylation, which supports suggestions that discrete hydrogen-bonding interactions with active-site amino acid residues can play a significant role in enzyme-catalyzed nucleobase excision. Taken together with previous studies, the present work provides vital clues about the components that must be included in future studies of the deglycosylation of isolated noncanonical nucleotides, as well as the corresponding enzyme-catalyzed reactions.
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Affiliation(s)
- Stefan A P Lenz
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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11
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Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys 2012; 14:15257-77. [PMID: 23072945 DOI: 10.1039/c2cp41987d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.
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12
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Mládek A, Šponer JE, Kulhánek P, Lu XJ, Olson WK, Šponer J. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J Chem Theory Comput 2012; 8:335-347. [PMID: 22712001 PMCID: PMC3375708 DOI: 10.1021/ct200712b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Folded RNA molecules are shaped by an astonishing variety of highly conserved noncanonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms - 5'-GpU-3', ApA, and UpC - via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader's atoms-in-molecules analysis reveals that the N2(G)…O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5'-ribose sugar (G) is in the C2'-endo form and the 3'-sugar (U) in the C3'-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2'…O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2'…O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Thus, the observed structural and evolutionary patterns of the dinucleotide platforms can be accounted for, to a large extent, by their intrinsic properties as described by modern QM calculations. In contrast, we show that the dinucleotide platform is not properly described in the course of atomistic explicit-solvent simulations. Our work also gives methodological insights into QM calculations of experimental RNA backbone geometries. Such calculations are inherently complicated by rather large data and refinement uncertainties in the available RNA experimental structures, which often preclude reliable energy computations.
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Affiliation(s)
- Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Wilma K. Olson
- Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers - The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jiřĺ Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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14
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Millen AL, Kamenz BL, Leavens FMV, Manderville RA, Wetmore SD. Conformational flexibility of C8-phenoxylguanine adducts in deoxydinucleoside monophosphates. J Phys Chem B 2011; 115:12993-3002. [PMID: 21942470 DOI: 10.1021/jp2057332] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
M06-2X/6-31G(d,p) is used to calculate the structure of all natural deoxydinucleoside monophosphates with G in the 5' or 3' position, the anti or syn conformation, and each natural (A, C, G, T) base in the corresponding flanking position. When the ortho or para C8-phenoxyl-2'-deoxyguanosine (C8-phenoxyl-dG) adduct replaces G in each model, there is little change in the relative base-base orientation or backbone conformation. However, the orientation of the C8-phenoxyl group can be characterized according to the position (5' versus 3'), conformation (anti versus syn), and isomer (ortho versus para) of damage. Although the degree of coplanarity between the phenoxyl ring and G base in the ortho adduct is highly affected by the sequence since the hydroxyl group can interact with neighboring bases, the para adduct generally does not exhibit discrete interactions with flanking bases. For both adducts, steric clashes between the phenoxyl group and the backbone or flanking base destabilize the anti conformation preferred by the natural nucleotide and thereby result in a clear preference for the syn conformation regardless of the sequence or position. This contrasts the conclusions drawn from smaller (nucleoside, nucleotide) models previously used in the literature, which stresses the importance of using models that address the steric constraints present due to the surrounding environment. Since replication errors for other C8-dG bulky adducts have been linked to a preference for the syn conformation, our findings provide insight into the possible mutagenicity of phenolic adducts.
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Affiliation(s)
- Andrea L Millen
- Department of Chemistry, University of Lethbridge, Lethbridge, Alberta, Canada
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15
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Churchill CDM, Wetmore SD. Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA. Phys Chem Chem Phys 2011; 13:16373-83. [PMID: 21842033 DOI: 10.1039/c1cp21689a] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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16
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Mahalakshmi A, Shenbagarathai R. Homology modeling of Cry10Aa toxin from B. thuringiensis israelensis and B. thuringiensis subsp. LDC-9. J Biomol Struct Dyn 2011; 28:363-78. [PMID: 20919752 DOI: 10.1080/07391102.2010.10507366] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A three dimensional model was developed for Cry10Aa protein sequence of B. thuringiensis LDC-9 and B. thuringiensis israelensis that has not been solved empirically by X-ray crystallography or NMR. Homology modeling was employed for the structure prediction using Cry2Aa as template protein, a high-resolution X-ray crystallography structure. The model predicted for the B. thuringiensis LDC-9 Cry10Aa protein reveals a partial N-terminal domain only due to its partial sequence of 104 amino acids. B. thuringiensis israelensis Cry10Aa model contains three domains such as domain I, a bundle of eight alpha helices with the central relatively hydrophobic helix surrounded by amphipathic helices while domain II and III contain mostly beta-sheets. Significant structural differences within domain II in this model among all Cry protein structures indicates that it is involved in recognition and binding to cell surfaces. Comparison of B. thuringiensis israelensis predicted structure with available experimentally determined Cry structures reveals identical folds. The distribution of electrostatic potential on the surface of the molecules in the model is non-uniform and identifies one side of the alpha-helical domain as negatively charged indicating orientation of toxic molecules toward the cell membrane during the initial binding with a cell surface receptor. The collective knowledge of Cry toxin structures will lead to a more critical understanding of the structural basis for receptor binding and pore formation, as well as allowing the scope of diversity to be better appreciated. This model will serve as a starting point for the design of mutagenesis experiments aimed to improve the toxicity and to provide a new tool for the elucidation of the mechanism of action of these mosquitocidal proteins.
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Affiliation(s)
- A Mahalakshmi
- PG and Research Department of Zoology and Biotechnology, Lady Doak College, Madurai-625 002, TamilNadu, India.
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Bhargavi K, Chaitanya PK, Ramasree D, Vasavi M, Murthy DK, Uma V. Homology Modeling and Docking Studies of Human Bcl-2L10 Protein. J Biomol Struct Dyn 2010; 28:379-91. [DOI: 10.1080/07391102.2010.10507367] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Aman MJ, Karauzum H, Bowden MG, Nguyen TL. Structural model of the pre-pore ring-like structure of Panton-Valentine leukocidin: providing dimensionality to biophysical and mutational data. J Biomol Struct Dyn 2010; 28:1-12. [PMID: 20476791 DOI: 10.1080/073911010010524952] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Panton-Valentine leukocidin (PVL) is a bipartite toxin that plays an important role in the pathogenesis of methicillin-resistant Staphylococcus aureus. Recent clinical data suggest a correlation between PVL and severe cases of S. aureus pneumonia. A clear understanding of the structure and function of PVL is critical to the development of novel, effective treatments. Here, we report an all-atom model of the macromolecular structure of Panton-Valentine leukocidin in its octameric, pre-pore conformation that confirms and extends our understanding of the toxin's mechanism of action.
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Affiliation(s)
- M Javad Aman
- Integrated BioTherapeutics, Inc., Germantown, MD 20876, USA.
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Borkar A, Ghosh I, Bhattacharyya D. Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach. J Biomol Struct Dyn 2010; 27:695-712. [DOI: 10.1080/07391102.2010.10508582] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Millen AL, Manderville RA, Wetmore SD. Conformational Flexibility of C8-Phenoxyl-2′-deoxyguanosine Nucleotide Adducts. J Phys Chem B 2010; 114:4373-82. [DOI: 10.1021/jp911993f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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DFT study of minimal fragments of nucleic acid single chain for explication of sequence dependence of DNA duplex conformation. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.03.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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