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Brzeski J, Wyrzykowski D, Makowska J. Application of a modern theoretical approach to the study of the interaction of KR-12 peptides derived from human cathelicidins with Cu(II) ions. Dalton Trans 2024; 53:9942-9951. [PMID: 38809157 DOI: 10.1039/d4dt01027b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The human cationic antimicrobial protein (hCAP) corresponding to the overlapping sequences of 151-162 of hCAP named KR-12 peptide is the smallest portion of the only type of human Cathelicidin, which has been shown to be modifiable into a more effective antimicrobial. In this study, an in silico analysis, supported by potentiometric titration and isothermal titration calorimetry techniques, was performed to identify potential Cu(II) binding sites of KR-12. The analysis of the presented data at the given theoretical level (GFN2-xTB/ALPB) revealed which peptide chain fragments are involved in the most favourable KR-12-Cu(II) binding mode. Based on a quantum chemical approach, the most favourable coordination modes of Cu(II) to peptides are proposed together with the discussion of the chemical nature of the interactions. The presented results demonstrated that KR-12 interacts with metal ions mostly via the main chain's oxygen atoms; however, the two types of amino acids that are expected to be vital for the interaction of Cu(II) are D (aspartic acid) and R29 (arginine). It was demonstrated that in order to explain the complexity of the interaction process in peptide-metal ion systems, the use of theoretical methods is sometimes necessary to explain the details of the experimental results and provide an in-depth understanding of these dynamic systems.
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Affiliation(s)
- Jakub Brzeski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Dariusz Wyrzykowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
| | - Joanna Makowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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2
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Brzeski J. On the influence of pnictogen bonding on acidity. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Boychuk BTA, Rebecca Jeong YE, Wetmore SD. Assessment of the Accuracy of DFT-Predicted Li +-Nucleic Acid Binding Energies. J Chem Theory Comput 2021; 17:5392-5408. [PMID: 34339194 DOI: 10.1021/acs.jctc.1c00401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding how lithium interacts with complex biosystems is crucial for uncovering the roles of this alkali metal in biology and designing extraction techniques for battery production and environmental remediation. In this light, fundamental information about Li+ binding to nucleic acids is required. Herein, a new database of Li+-nucleic acid interactions is presented that contains CCSD(T)/CBS benchmark energies for all nucleobase and phosphate binding locations. Furthermore, the performance of 54 DFT functionals in combination with three triple-zeta (TZ) basis sets (6-311+G(3df,2p), aug-cc-pVTZ, and def2-TZVPP) is tested. The results identify a range of functionals across different families (B2-PLYP, PBE-QIDH, ωB97, ωB97X-D, MN15, B3PW91, B97-2, TPSS, BP86-D3(BJ), and PBE) that can accurately describe coordinated Li+-nucleic acid interactions, with the average mean percent error (AMPE) across binding positions and basis sets being below 2%. Nevertheless, only three functionals tested (B2-PLYP, PBE-QIDH, and ωB97X-D) preserve this accuracy for metal cation-π interactions, suggesting that caution is warranted when choosing a functional to describe a diverse range of Li+-nucleic acid complexes. Removal of counterpoise corrections has very little impact on the reliability of most functionals, while the effect of empirical dispersion corrections varies depending on the functional choice and interaction type. While increasing the basis set to quadruple-zeta quality had little impact on the AMPE, the accuracy of double-zeta basis sets varies with family. Importantly, DFT methods reproduce the CCSD(T)/CBS trend in the preferred binding position for a given nucleic acid component and the global trend across components (phosphate ≫ G > C ≫ A ∼ T = U), as well as the geometries of the metal-nucleic acid complexes. The overall top performing functional is PBE-QIDH, which results in deviations from CCSD(T)/CBS values as small as ∼0.1 kcal/mol for nucleobase contacts and ∼1 kcal/mol for phosphate interactions. The most accurate DFT methods identified in the present work are recommended for future investigations of lithium interactions in larger nucleic acid systems to provide insights into the biological roles of this metal and the design of novel biosensing strategies.
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Affiliation(s)
- Briana T A Boychuk
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ye Eun Rebecca Jeong
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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4
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Wu RR, Chen Y, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2'-deoxyguanosine and guanosine. Phys Chem Chem Phys 2016; 18:2968-80. [PMID: 26740232 DOI: 10.1039/c5cp05738h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental and theoretical investigations suggest that hydrolysis of N-glycosidic bonds generally involves a concerted SN2 or a stepwise SN1 mechanism. While theoretical investigations have provided estimates for the intrinsic activation energies associated with N-glycosidic bond cleavage reactions, experimental measurements to validate the theoretical studies remain elusive. Here we report experimental investigations for N-glycosidic bond cleavage of the protonated guanine nucleosides, [dGuo+H](+) and [Guo+H](+), using threshold collision-induced dissociation (TCID) techniques. Two major dissociation pathways involving N-glycosidic bond cleavage, resulting in production of protonated guanine or the elimination of neutral guanine are observed in competition for both [dGuo+H](+) and [Guo+H](+). The detailed mechanistic pathways for the N-glycosidic bond cleavage reactions observed are mapped via electronic structure calculations. Excellent agreement between the measured and B3LYP calculated activation energies and reaction enthalpies for N-glycosidic bond cleavage of [dGuo+H](+) and [Guo+H](+) in the gas phase is found indicating that these dissociation pathways involve stepwise E1 mechanisms in analogy to the SN1 mechanisms that occur in the condensed phase. In contrast, MP2 is found to significantly overestimate the activation energies and slightly overestimate the reaction enthalpies. The 2'-hydroxyl substituent is found to stabilize the N-glycosidic bond such that [Guo+H](+) requires ∼25 kJ mol(-1) more than [dGuo+H](+) to activate the glycosidic bond.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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5
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Sowlati-Hashjin S, Wetmore SD. Computational Investigation of Glycosylase and β-Lyase Activity Facilitated by Proline: Applications to FPG and Comparisons to hOgg1. J Phys Chem B 2014; 118:14566-77. [PMID: 25415645 DOI: 10.1021/jp507783d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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6
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Chen M, Lee JK. Computational Studies of the Gas-Phase Thermochemical Properties of Modified Nucleobases. J Org Chem 2014; 79:11295-300. [DOI: 10.1021/jo502058w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mu Chen
- Department of Chemistry and
Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Jeehiun K. Lee
- Department of Chemistry and
Chemical Biology Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States
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7
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Stasyuk OA, Szatyłowicz H, Krygowski TM. Effect of H-bonding and complexation with metal ions on the π-electron structure of adenine tautomers. Org Biomol Chem 2014; 12:456-66. [DOI: 10.1039/c3ob41653d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Kellie JL, Wilson KA, Wetmore SD. Standard role for a conserved aspartate or more direct involvement in deglycosylation? An ONIOM and MD investigation of adenine-DNA glycosylase. Biochemistry 2013; 52:8753-65. [PMID: 24168684 DOI: 10.1021/bi401310w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
8-Oxoguanine (OG) is one of the most frequently occurring forms of DNA damage and is particularly deleterious since it forms a stable Hoogsteen base pair with adenine (A). The repair of an OG:A mispair is initiated by adenine-DNA glycosylase (MutY), which hydrolyzes the sugar-nucleobase bond of the adenine residue before the lesion is processed by other proteins. MutY has been proposed to use a two-part chemical step involving protonation of the adenine nucleobase, followed by SN1 hydrolysis of the glycosidic bond. However, differences between a recent (fluorine recognition complex, denoted as the FLRC) crystal structure and the structure on which most mechanistic conclusions have been based to date (namely, the lesion recognition complex or LRC) raise questions regarding the mechanism used by MutY and the discrete role of various active-site residues. The present work uses both molecular dynamics (MD) and quantum mechanical (ONIOM) models to compare the active-site conformational dynamics in the two crystal structures, which suggests that only the understudied FLRC leads to a catalytically competent reactant. Indeed, all previous computational studies on MutY have been initiated from the LRC structure. Subsequently, for the first time, various mechanisms are examined with detailed ONIOM(M06-2X:PM6) reaction potential energy surfaces (PES) based on the FLRC structure, which significantly extends the mechanistic picture. Specifically, our work reveals that the reaction proceeds through a different route than the commonly accepted mechanism and the catalytic function of various active-site residues (Geobacillus stearothermophilus numbering). Specifically, contrary to proposals based on the LRC, E43 is determined to solely be involved in the initial adenine protonation step and not the deglycosylation reaction as the general base. Additionally, a novel catalytic role is proposed for Y126, whereby this residue plays a significant role in stabilizing the highly charged active site, primarily through interactions with E43. More importantly, D144 is found to explicitly catalyze the nucleobase dissociation step through partial nucleophilic attack. Although this is a more direct role than previously proposed for any other DNA glycosylase, comparison to previous work on other glycosylases justifies the larger contribution in the case of MutY and allows us to propose a unified role for the conserved Asp/Glu in the DNA glycosylases, as well as other enzymes that catalyze nucleotide deglycosylation reactions.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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9
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Umadevi V, Senthilkumar L, Kolandaivel P. Theoretical investigations on the hydrogen bonding of nitrile isomers with H2O, HF, NH3and H2S. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.777840] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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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Kellie JL, Wetmore SD. Mechanistic and conformational flexibility of the covalent linkage formed during β-lyase activity on an AP-site: application to hOgg1. J Phys Chem B 2012; 116:10786-97. [PMID: 22877319 DOI: 10.1021/jp306344g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The β/δ-lyase activity of bifunctional glycosylases on damaged nucleotides in DNA involves the formation of a covalent linkage between the protein (lysine or N-terminal proline) and DNA (C1' of the damaged nucleotide). In the present study, the conformational and mechanistic flexibility of the cross-link is examined. Repair of 8-oxoguanine damage by hOgg1 is considered as a representative system, and the glycosylase through β-lyase steps are investigated using density functional theory. (PCM/SMD)-M06-2X/6-311+G(2df,2p)//PCM-B3LYP/6-31G(d) energetics were determined for eight unique mechanisms differing in the conformation of the imine linkage (E/Z), the proton (pro-S/R) abstracted during elimination, and whether the ring-opening step is base catalyzed. This initial study used a model system limited to the damaged nucleoside 3'-monophosphate and a model nucleophile to investigate this series of complex reaction steps. The great flexibility exhibited by the linkage and clustered β-elimination energetics indicate sterics will play a large role in predicting the preferred lyase mechanism for a given enzyme. The stationary points identified herein can be overlaid into a protein structure to assist in generating initial guesses for large model systems. By comparing the characterized geometries and enzyme active sites, methods for catalysis of the various chemical steps can be identified, and these possibilities are discussed in detail for hOgg1. Interestingly, the most stable structure on the potential energy surface occurs before elimination of the 3'-phosphate. Hydrolysis of the protein-DNA cross-link at this point would yield an AP-site, which provides support for the recently observed monofunctional activity of hOgg1.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
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12
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Stasyuk OA, Szatyłowicz H, Krygowski TM. Effect of the H-bonding on aromaticity of purine tautomers. J Org Chem 2012; 77:4035-45. [PMID: 22448684 DOI: 10.1021/jo300406r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four tautomers of purine (1-H, 3-H, 7-H, and 9-H) and their equilibrium H-bonded complexes with F(-) and HF for acidic and basic centers, respectively, were optimized by means of the B3LYP/6-311++G(d,p) level of theory. Purine tautomer stability increases in the following series: 1-H < 3-H < 7-H < 9-H, consistent with increasing aromaticity. Furthermore, the presence of a hydrogen bond with HF does not change this order. For neutral H-bonded complexes, the strongest and the weakest intermolecular interactions occur (-14.12 and -10.49 kcal/mol) for less stable purine tautomers when the proton acceptor is located in the five- and six-membered rings, respectively. For 9-H and 7-H tautomers the order is reversed. The H-bond energy for the imidazole complex with HF amounts to -14.03 kcal/mol; hence, in the latter case, the fusion of imidazole to pyrimidine decreases its basicity. The ionic H-bonds of N(-)···HF type are stronger by ~10 kcal/mol than the neutral N···HF intermolecular interactions. The hydrogen bond N(-)···HF energies in pyrrole and imidazole are -32.28 and -30.03 kcal/mol, respectively, and are substantially stronger than those observed in purine complexes. The aromaticity of each individual ring and of the whole molecule for all tautomers in ionic complexes is very similar to that observed for the anion of purine. This is not the case for neutral complexes and purine as a reference. The N···HF bonds perturb much more the π-electron structure of five-membered rings than that of the six-membered ones. The H-bonding complexes for 7-H and 9-H tautomers are characterized by higher aromaticity and a much lower range of HOMA variability.
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Affiliation(s)
- Olga A Stasyuk
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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13
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Kellie JL, Navarro-Whyte L, Carvey MT, Wetmore SD. Combined effects of π-π stacking and hydrogen bonding on the (N1) acidity of uracil and hydrolysis of 2'-deoxyuridine. J Phys Chem B 2012; 116:2622-32. [PMID: 22296509 DOI: 10.1021/jp2121627] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
M06-2X/6-31+G(d,p) is used to study the simultaneous effects of π-π stacking interactions with phenylalanine (modeled as benzene) and hydrogen bonding with small molecules (HF, H(2)O, and NH(3)) on the N1 acidity of uracil and the hydrolytic deglycosylation of 2'-deoxyuridine (dU) (facilitated by fully (OH(-)) or partially (HCOO(-)···H(2)O) activated water). When phenylalanine is complexed with isolated uracil, the proton affinity of all acceptor sites significantly increases (by up to 28 kJ mol(-1)), while the N1 acidity slightly decreases (by ~6 kJ mol(-1)). When small molecules are hydrogen bound to uracil, addition of the phenylalanine ring can increase or decrease the acidity of uracil depending on the number and nature (acidity) of the molecules bound. Furthermore, a strong correlation between the effects of π-π stacking on the acidity of U and the dU deglycosylation reaction energetics is found, where the hydrolysis barrier can increase or decrease depending on the nature and number of small molecules bound, the nucleophile considered (which dictates the negative charge on U in the transition state), and the polarity of the (bulk) environment. These findings emphasize that the catalytic (or anticatalytic) role of the active-site aromatic amino acid residues is highly dependent on the situation under consideration. In the case of uracil-DNA glycosylase (UNG), which catalyzes the hydrolytic excision of uracil from DNA, the type of discrete hydrogen-bonding interactions with U, the nature of the nucleophile, and the anticipated weak, nonpolar environment in the active site suggest that phenylalanine will be slightly anticatalytic in the chemical step, and therefore experimentally observed contributions to catalysis may entirely result from associated structural changes that occur prior to deglycosylation.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada
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14
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Vícha J, Demo G, Marek R. Platinum-Modified Adenines: Unprecedented Protonation Behavior Revealed by NMR Spectroscopy and Relativistic Density-Functional Theory Calculations. Inorg Chem 2012; 51:1371-9. [DOI: 10.1021/ic201595e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Jan Vícha
- National Center for Biomolecular Research, Faculty
of Science and Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech
Republic
| | - Gabriel Demo
- National Center for Biomolecular Research, Faculty
of Science and Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech
Republic
| | - Radek Marek
- National Center for Biomolecular Research, Faculty
of Science and Central European Institute of Technology-CEITEC, Masaryk University, Kamenice 5/A4, CZ-62500 Brno, Czech
Republic
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15
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Hamm ML, Parker AJ, Steele TWE, Carman JL, Parish CA. Oligonucleotide incorporation and base pair stability of 9-deaza-2'-deoxyguanosine, an analogue of 8-oxo-2'-deoxyguanosine. J Org Chem 2010; 75:5661-9. [PMID: 20669985 DOI: 10.1021/jo1010763] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
9-Deaza-2'-deoxyguanosine (CdG) is a C-nucleoside and an analogue of the abundant promutagen 8-oxo-2'-deoxyguanosine (OdG). Like 2'-deoxyguanosine (dG), CdG should form a stable base pair with dC, but similar to OdG, CdG contains an N7-hydrogen that should allow it to also form a relatively stable base pair with dA. In order to further investigate the base pairing of CdG, it was incorporated into DNA and paired with either dC or dA. Melting studies revealed CdG:dC base pairs are less stable than dG:dC base pairs, while CdG:dA base pairs are less stable than OdG:dA base pairs. In order to gain a deeper understanding of these results, quantum studies on model structures of nucleoside monomers and base pairs were performed, the results of which indicate that (i) CdG:dC base pairs are likely destabilized relative to dG:dC as a result of structural constraints imposed by the C-nucleotide character of CdG, and (ii) CdG:dA base pairs may be less stable than OdG:dA base pairs, at least in part, because of a third long-range interaction that is possible in OdG:dA but not in CdG:dA.
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Affiliation(s)
- Michelle L Hamm
- Department of Chemistry, University of Richmond, Gottwald Science Center, Richmond, Virginia 23173, USA.
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16
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Kumar N, Shukla P, Mishra P. Reactions of the OOH radical with guanine: Mechanisms of formation of 8-oxoguanine and other products. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Shim EJ, Przybylski JL, Wetmore SD. Effects of nucleophile, oxidative damage, and nucleobase orientation on the glycosidic bond cleavage in deoxyguanosine. J Phys Chem B 2010; 114:2319-26. [PMID: 20095611 DOI: 10.1021/jp9113656] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deglycosylation of nucleotides occurs during many essential biological processes, including DNA repair, and is initiated by a variety of nucleophiles. In the present work, density functional theory (B3LYP) was used to investigate the thermodynamics and kinetics of the glycosidic bond cleavage reaction in the model nucleoside forms of guanine and its major oxidation product, 8-oxoguanine. Base excision facilitated by four different nucleophiles (hydroxyl anion (fully activated water), formate-water complex (partially activated water), lysine, and proline) was considered, which spans nucleophiles involved in a collection of spontaneous and enzyme-catalyzed processes. Because some enzymes that catalyze deglycosylation can accommodate more than one orientation of the base with respect to the sugar moiety, the effects of the (anti/syn) base orientation on the barrier height were also considered. We find that the nucleophile has a very large effect on the overall (gas-phase) reaction energetics. Although this effect decreases in different (polar) environments, the nucleophile has the greatest influence on the overall reaction as compared to whether the base is damaged or to the base orientation. Furthermore, the effects are significant in environments that most closely resemble (nonpolar) enzymatic active sites. Our results provide a greater understanding of the relative effects of the nucleophile, damage to the nucleobase, and the nucleobase orientation with respect to the sugar moiety on the deglycosylation pathway, which provide qualitative explanations for relative base excision rates observed in some biological systems.
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Affiliation(s)
- Eun Jung Shim
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada
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18
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Riley KE, Pitoňák M, Černý J, Hobza P. On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations. J Chem Theory Comput 2009; 6:66-80. [PMID: 26614320 DOI: 10.1021/ct900376r] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H···π interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFT-SAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.
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Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Michal Pitoňák
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Jiří Černý
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Pavel Hobza
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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19
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Zhachkina A, Liu M, Sun X, Amegayibor FS, Lee JK. Gas-Phase Thermochemical Properties of the Damaged Base O6-Methylguanine versus Adenine and Guanine. J Org Chem 2009; 74:7429-40. [DOI: 10.1021/jo901479m] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Anna Zhachkina
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Min Liu
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Xuejun Sun
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - F. Sedinam Amegayibor
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
| | - Jeehiun K. Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901
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20
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Millen AL, Wetmore SD. Glycosidic bond cleavage in deoxynucleotides — A density functional study. CAN J CHEM 2009. [DOI: 10.1139/v09-024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Density functional theory was used to study the glycosidic bond cleavage in deoxynucleotides with the main goal to determine the effects of the nucleobase, hydrogen bonding with the nucleobase, and the (bulk) environment on the reaction energetics. Since direct glycosidic bond cleavage is a high-energy process, two nucleophile models were considered (HCOO–···H2O and HO–), which represent different stages of activation of a water nucleophile. The glycosidic bond cleavage barriers were found to decrease, while the reaction exothermicity increases, with an increase in the nucleobase acidity. The gas-phase barriers and reaction energies for bond cleavage in all deoxynucleotides were found to be significantly affected by hydrogen-bonding interactions with the nucleobase (by up to 30 kJ mol–1 depending on the nucleophile). Although the barriers increase and reaction energies become less exothermic in enzymatic and aqueous environments, the effects of the bulk environment are similar in the presence and absence of small molecules bound to the nucleobase. Therefore, the effects of hydrogen bonding with the bases are approximately the same in all environments. Our results suggest that hydrogen bonding with the nucleobase may play an important role in the glycosidic bond cleavage in both pyrimidine and purine nucleotides in a variety of environments.
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Affiliation(s)
- Andrea L. Millen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
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21
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Jayatilaka N, Nelson WH. Guanine radical reaction processes: a computational description of proton transfer in X-irradiated 9-ethylguanine single crystals. J Phys Chem B 2009; 112:16908-16. [PMID: 19367818 DOI: 10.1021/jp806262d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational methods based on DFT procedures have been used to investigate proton-transfer processes in irradiated 9-ethylguanine crystals. Previous experimental results from X-irradiation and study of this system at 10 K found significant concentrations of two main products, R1, formed by N7-hydrogenation of the purine ring, and R2, the primary one-electron oxidation product (Jayatilaka, N.; Nelson, W. H. J. Phys. Chem. B 2007, 111, 7887). The objective of this work is to describe the processes leading to these products using computational methods that take into account molecular packing and bulk dielectric properties. The basic concept is that a proton will transfer following ionization if the net electronic energy of the system, consisting of the donor plus the acceptor plus any intervening molecules, becomes lower. Three approaches were used to investigate this concept, two based on energies computed for single molecules and one based on energies computed for two-molecule clusters arranged as in the crystals. The results are that the methods successfully predict the observed behavior, that it is energetically favorable on one-electron reduction for proton H1 to transfer from a neutral molecule to N7 of the neighbor, forming the N7-hydrogenated product, and that there is virtually no energy advantage for a proton to transfer upon one-electron oxidation. The results also support the proposal that the C8 H-addition radical, found only upon irradiation at 300 K, was the product of intramolecular transfer of the H7 proton to C8 in a process apparently requiring sufficient thermal energy for activation. Finally, the computations predict hyperfine couplings and tensors in very good agreement with those from experiment, thereby providing additional evidence for the success of the computations in describing the experimental observations.
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Affiliation(s)
- Nayana Jayatilaka
- Department of Physics and Astronomy, Georgia State University, P.O. Box 4106, Atlanta, Georgia 30302-4106, USA
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22
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Rutledge LR, Durst HF, Wetmore SD. Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions. J Chem Theory Comput 2009; 5:1400-10. [DOI: 10.1021/ct800567q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Holly F. Durst
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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23
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Rutledge LR, Wetmore SD. Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking. J Chem Theory Comput 2008; 4:1768-80. [DOI: 10.1021/ct8002332] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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24
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Park HS, Nam SH, Song JK, Park SM, Ryu S. Density Functional Study of Intradimer Proton Transfers in Hydrated Adenine Dimer Ions, A2+(H2O)n (n = 0−2). J Phys Chem A 2008; 112:9023-30. [DOI: 10.1021/jp801238b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hye Sun Park
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Sang Hwan Nam
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Jae Kyu Song
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Seung Min Park
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Seol Ryu
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
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25
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Rutledge LR, Durst HF, Wetmore SD. Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases. Phys Chem Chem Phys 2008; 10:2801-12. [DOI: 10.1039/b718621e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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26
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Wolstenholme DJ, Weigand JJ, M Cameron E, Cameron TS. The progression of strong and weak hydrogen bonds in a series of ethylenediammonium dithiocyanate derivatives—a new bonding protocol for macromolecules? Phys Chem Chem Phys 2008; 10:3569-77. [PMID: 18548163 DOI: 10.1039/b800108a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- David J Wolstenholme
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, CanadaB3H 4J3.
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27
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Mirzaei M, Hadipour NL. An investigation of hydrogen-bonding effects on the nitrogen and hydrogen electric field gradient and chemical shielding tensors in the 9-methyladenine real crystalline structure: a density functional theory study. J Phys Chem A 2007; 110:4833-8. [PMID: 16599452 DOI: 10.1021/jp0600920] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen-bonding effects in the real crystalline structure of 9-methyladenine, 9-MA, were studied using calculated electric field gradient, EFG, and chemical shielding, CS, tensors for nitrogen and hydrogen nuclei via density functional theory. The calculations were carried out at the B3LYP and B3PW91 levels with the 6-311++G basis set via the Gaussian 98 package. Nuclear quadrupole coupling constants, C(Q), and asymmetry parameters, eta(Q), are reported for (14)N and (2)H. The chemical shielding anisotropy, Deltasigma, and chemical shielding isotropy, sigma(iso), are also reported for (15)N and (1)H. The difference between the calculated parameters of the monomer and heptameric layer-like cluster 9-MA shows how much H-bonding interactions affect the EFG and CS tensors of each nucleus. This result indicates that N(10) (imino nitrogen) has a major role in H-bonding interactions, whereas that of N(9) is negligible. There is good agreement between the present calculated parameters and reported experimental data. Although some discrepancies were observed, this could be attributed to the different conditions which were applied for calculation and the experiments.
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Affiliation(s)
- Mahmoud Mirzaei
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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28
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García-Teran JP, Castillo O, Luque A, García-Couceiro U, Beobide G, Roman P. Molecular recognition of adeninium cations on anionic metal-oxalato frameworks: an experimental and theoretical analysis. Inorg Chem 2007; 46:3593-602. [PMID: 17375914 DOI: 10.1021/ic062448s] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactions of adenine with water-soluble oxalato complexes at acidic pH give the compounds (1H,9H-ade)2[Cu(ox)2(H2O)] (1) [H2ade=adeninium cation (1+), ox=oxalato ligand (2-)] and (3H,7H-ade)2[M(ox)2(H2O)2].2H2O [M(II)=Co (2), Zn (3)]. The X-ray single crystal analyses show that the supramolecular architecture of all compounds is built up of anionic sheets of metal-oxalato-water complexes and ribbons of cationic nucleobases among them to afford lamellar inorganic-organic hybrid materials. The molecular recognition process between the organic and the inorganic frameworks determines the isolated tautomeric form of the adeninium cation found in the crystal structures: the canonical 1H,9H for compound 1, and the first solid-state characterized 3H,7H-adeninium tautomer for compounds 2 and 3. Density functional theory calculations have been performed to study the stability of the protonated nucleobase forms and their hydrogen-bonded associations by comparing experimental and theoretical results.
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Affiliation(s)
- Juan P García-Teran
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado 644, E-48080 Bilbao, Spain
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29
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Millen AL, Archibald LAB, Hunter KC, Wetmore SD. A kinetic and thermodynamic study of the glycosidic bond cleavage in deoxyuridine. J Phys Chem B 2007; 111:3800-12. [PMID: 17388517 DOI: 10.1021/jp063841m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Density functional theory was used to study the thermodynamics and kinetics for the glycosidic bond cleavage in deoxyuridine. Two reaction pathways were characterized for the unimolecular decomposition in vacuo. However, these processes are associated with large reaction barriers and highly endothermic reaction energies, which is in agreement with experiments that suggest a (water) nucleophile is required for the nonenzymatic glycosidic bond cleavage. Two (S(N)1 and S(N)2) reaction pathways were characterized for direct hydrolysis of the glycosidic bond by a single water molecule; however, both pathways also involve very large barriers. Activation of the water nucleophile via partial proton abstraction steadily decreases the barrier and leads to a more exothermic reaction energy as the proton affinity of the molecule interacting with water increases. Indeed, our data suggests that the barrier heights and reaction energies range from that for hydrolysis by water to that for hydrolysis by the hydroxyl anion, which represents the extreme of (full) water activation (deprotonation). Hydrogen bonds between small molecules (hydrogen fluoride, water, or ammonia) and the nucleobase were found to further decrease the barrier and overall reaction energy but not to the extent that the same hydrogen-bonding interactions increase the acidity of the nucleobase. Our results suggest that the nature of the nucleophile plays a more important role in reducing the barrier to glycosidic bond cleavage than the nature of the small molecule bound, and models with more than one hydrogen fluoride molecule interacting with the nucleobase provide further support for this conclusion. Our results lead to a greater fundamental understanding of the effects of the nucleophile, activation of the nucleophile, and interactions with the nucleobase for this important biological reaction.
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Affiliation(s)
- Andrea L Millen
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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30
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Hunter KC, Wetmore SD. Environmental Effects on the Enhancement in Natural and Damaged DNA Nucleobase Acidity Because of Discrete Hydrogen-Bonding Interactions. J Phys Chem A 2007; 111:1933-42. [PMID: 17302396 DOI: 10.1021/jp066641j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present study uses density functional theory to carefully consider the effects of the environment on the enhancement in (natural and damaged) DNA nucleobase acidities because of multiple hydrogen-bonding interactions. Although interactions with one small molecule can increase the acidity of the nucleobases by up to 60 kJ mol-1 in the gas phase, the maximum increase in enzymatic-like environments is expected to be approximately 40 kJ mol-1, which reduces to approximately 30 kJ mol-1 in water. Furthermore, the calculated (simultaneous) effects of two, three, or four molecules are increasingly less than the sum of the individual (additive) effects with an increase in the number and acidity of the small molecules bound or the dielectric constant of the solvent. Regardless of these trends, our calculations reveal that additional hydrogen-bonding interactions will have a significant effect on nucleobase acidity in a variety of environments, where the exact magnitude of the effect depends on the properties of the small molecule bound, the nucleobase binding site, and the solvent. The maximum increase in nucleobase acidity because of interactions with up to four small molecules is approximately 80 kJ mol-1 in enzymatic-like environments (or 65 kJ mol-1 in water). These results suggest that hydrogen-bonding interactions likely play an important role in many biological processes by changing the physical and chemical properties of the nucleobases.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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31
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Hunter KC, Millen AL, Wetmore SD. Effects of Hydrogen-Bonding and Stacking Interactions with Amino Acids on the Acidity of Uracil. J Phys Chem B 2007; 111:1858-71. [PMID: 17256895 DOI: 10.1021/jp066902p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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32
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Viudez AJ, Madueño R, Pineda T, Blázquez M. Stabilization of Gold Nanoparticles by 6-Mercaptopurine Monolayers. Effects of the Solvent Properties. J Phys Chem B 2006; 110:17840-7. [PMID: 16956270 DOI: 10.1021/jp062165l] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
6-Mercaptopurine-coated gold nanoparticles (6MP-AuNPs) have been prepared by modification of the nanoparticle surface with 6MP upon displacement of the protective layer of citrate anions. The modification has been studied by UV-vis and FTIR spectroscopies. A study of the stability of these 6MP-AuNPs in aqueous solutions as a function of ionic strength and pH has shown the importance of the charges on the stabilization. The protonation of N9 of the 6MP molecules brings about a sudden flocculation phenomenon. However, the flocculation is reversible upon changing the pH to values where the molecules become newly charged. Evidence of the competence between the interaction of capping solvent molecules and the attractive forces between particles is also shown in this paper.
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Affiliation(s)
- Alfonso J Viudez
- Departamento de Química Física y Termodinamica Aplicada, Universidad de Córdoba, Campus de Rabanales, Ed. Marie Curie, E-14071 Córdoba, Spain
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33
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Hydrogen-bonding between cytosine and water: Computational evidence for a ring-opened complex. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.02.092] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hunter KC, Rutledge LR, Wetmore SD. The Hydrogen Bonding Properties of Cytosine: A Computational Study of Cytosine Complexed with Hydrogen Fluoride, Water, and Ammonia. J Phys Chem A 2005; 109:9554-62. [PMID: 16866407 DOI: 10.1021/jp0527709] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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