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Khorosheva EI, Sharapova SA, Kuramshina GM. Quantum-Chemical Modeling of Interaction between the Most Stable Methylamine-Pyridoxal-5'-Phosphate Tautomers and Water: Structure and Properties of Monohydrates and Dihydrates. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s003602442011014x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Davydova IB, Senyavin VM, Zefirova ON, Kuramshina GM. Vibrational Spectra and Stable Conformations of Methyl 6-Methoxy-2,3,4,9-Tetrahydro-1H-1,4-Ethanocarbazole-3-Carboxylate. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420110047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Davydova IB, Senyavin VM, Zefirova ON, Kuramshina GM. Vibrational Spectra and Stable Conformations of (1RS, 5RS, 6SR)-6-Methoxycarbonylamino-(5'-methoxyindolo[2,3-b])bicyclo[3.2.1]oct-2-en. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s0036024419080077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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The molecular structure of 4-piperidinemethanol in gas, solutions, and solid state: spectral and theoretical investigations. Struct Chem 2019. [DOI: 10.1007/s11224-019-01296-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tsendra O, Boese AD, Isayev O, Gorb L, Scott AM, Hill FC, Ilchenko MM, Lobanov V, Leszczynska D, Leszczynski J. Adsorption of nitrogen-containing compounds on hydroxylated α-quartz surfaces. RSC Adv 2019; 9:36066-36074. [PMID: 35540615 PMCID: PMC9074934 DOI: 10.1039/c9ra07130j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/27/2019] [Indexed: 12/04/2022] Open
Abstract
Adsorption energies of various nitrogen-containing compounds (specifically, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAn), and 3-nitro-1,2,4-triazole-5-one (NTO)) on the hydroxylated (001) and (100) α-quartz surfaces are computed. Different density functionals are utilized and both periodic as well as cluster approaches are applied. From the adsorption energies, partition coefficients on the considered α-quartz surfaces are derived. While TNT and DNT are preferably adsorbed on the (001) surface of α-quartz, NTO is rather located on both α-quartz surfaces. Adsorption energies of different nitrogen-containing compounds on two hydroxylated (001) and (100) quartz surfaces are computed.![]()
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Affiliation(s)
- Oksana Tsendra
- Interdisciplinary Nanotoxicity Center
- Department of Chemistry and Biochemistry
- Jackson State University
- Jackson
- USA
| | - A. Daniel Boese
- Institute of Chemistry, Physical and Theoretical Chemistry
- University of Graz
- 8010 Graz
- Austria
| | - Olexandr Isayev
- UNC Eshelman School of Pharmacy
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Leonid Gorb
- HX5, LLC
- Vicksburg
- USA
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
| | | | - Frances C. Hill
- U. S. Army Engineer Research and Development Center (ERDC)
- Vicksburg
- USA
| | - Mykola M. Ilchenko
- Institute of Molecular Biology and Genetics
- National Academy of Sciences of Ukraine
- Kyiv 03143
- Ukraine
| | - Victor Lobanov
- Chuiko Institute of Surface Chemistry
- National Academy of Sciences of Ukraine
- Kyiv 03164
- Ukraine
| | - Danuta Leszczynska
- Department of Civil and Environmental Engineering
- Jackson State University
- Jackson
- USA
| | - Jerzy Leszczynski
- Interdisciplinary Nanotoxicity Center
- Department of Chemistry and Biochemistry
- Jackson State University
- Jackson
- USA
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Kuramshina GM, Vakula OA, Vakula NI, Majouga AG, Senyavin VM, Gorb LG, Leszczynski J. Conformations, vibrational spectra and force field of 1-methyl-2-(2′-pyridyl)benzimidazole: experimental data and density functional theory investigation in comparison with 2-(2′-pyridyl)benzimidazole. Struct Chem 2015. [DOI: 10.1007/s11224-015-0693-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Fujiwara SI, Sawada K, Amisaki T. Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions. J Mol Graph Model 2014; 51:158-67. [PMID: 24929814 DOI: 10.1016/j.jmgm.2014.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 01/05/2023]
Abstract
The modified nucleotide base 7,8-dihydro-8-oxo-guanine (8-oxo-G) is one of the major sources of spontaneous mutagenesis. Nucleotide-sanitizing enzymes, such as the MutT homolog-1 (MTH1) and nudix-type motif 5 (NUDT5), selectively remove 8-oxo-G from the cellular pool of nucleotides. Previous studies showed that, although the syn conformation generally predominates in purine nucleotides with a bulky substituent at the 8-position, 8-oxo-dGMP binds to both MTH1 and NUDT5 in the anti conformation. This study was initiated to investigate the possibility that 8-oxo-dGMP itself may adopt the anti conformation. Molecular dynamics simulations of mononucleotides (dGMP, 8-oxo-dGMP) in aqueous solution were performed. 8-oxo-dGMP adopted the anti conformation as well as the syn conformation, and the proportion of adopting the anti conformation increased in the presence of metal ions. When 8-oxo-dGMP was in the anti conformation, a metal ion was located between the oxygen atom of phosphate and the oxygen atom at the 8-position of 8-oxo-G. The types of stable anti conformations of 8-oxo-dGMP differed, depending on the ionic radii and charges of coexisting ions. These data suggested a role for metal ions, other than as cofactors for the hydrolysis of the di- and tri-phosphate forms of mononucleotides; that the metal ions help retain the anti conformation of the N-glycosidic torsion angle of 8-oxo-dGMP to promote the binding between the 8-oxo-G deoxynucleotide and the nucleotide-sanitizing enzymes.
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Affiliation(s)
- Shin-Ichi Fujiwara
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan.
| | - Kenichiro Sawada
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
| | - Takashi Amisaki
- Department of Biological Regulation, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago 683-8503, Japan
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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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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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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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