1
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Tevonyan LL, Bazhulina NP, Kaluzhny DN. Enhancement of intrinsic guanine fluorescence by protonation in DNA of various structures. Biochimie 2024; 222:101-108. [PMID: 38447859 DOI: 10.1016/j.biochi.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/24/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
Understanding the diversity of DNA structure and functions in biology requires tools to study this biomolecule selectively and thoroughly. Fluorescence methods are powerful technique for non-invasive research. Due to the low quantum yield, the intrinsic fluorescence of nucleotides has not been considered for use in the detection and differentiation of nucleic acid bases. Here, we have studied the influence of protonation of nucleotides on their fluorescence properties. We show that protonation of ATP and GTP leads to enhanced intrinsic fluorescence. Fluorescence enhancement at acidic pH has been observed for double-stranded DNA and single-stranded oligonucleotides. The formation of G4 secondary structures apparently protected certain nucleotides from protonation, resulting in less pronounced fluorescence enhancement. Furthermore, acid-induced depurination under protonation was less noticeable in G4 structures than in double-stranded and single-stranded DNA. We show that changes in the intrinsic fluorescence of guanine can be used as a sensitive sensor for changes in the structure of the DNA and for the protonation of specific nucleotides.
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Affiliation(s)
- Liana L Tevonyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov st., 119991, Moscow, Russia; Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, 141701, Moscow Region, Russia
| | - Natalia P Bazhulina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov st., 119991, Moscow, Russia
| | - Dmitry N Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov st., 119991, Moscow, Russia.
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2
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Hartman JD, Harper JK. Improving the accuracy of GIPAW chemical shielding calculations with cluster and fragment corrections. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2022; 122:101832. [PMID: 36198253 DOI: 10.1016/j.ssnmr.2022.101832] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Ab initio methods for predicting NMR parameters in the solid state are an essential tool for assigning experimental spectra and play an increasingly important role in structural characterizations. Recently, a molecular correction (MC) technique has been developed which combines the strengths of plane-wave methods (GIPAW) with single molecule calculations employing Gaussian basis sets. The GIPAW + MC method relies on a periodic calculation performed at a lower level of theory to model the crystalline environment. The GIPAW result is then corrected using a single molecule calculation performed at a higher level of theory. The success of the GIPAW + MC method in predicting a range of NMR parameters is a result of the highly local character of the tensors underlying the NMR observable. However, in applications involving strong intermolecular interactions we find that expanding the region treated at the higher level of theory more accurately captures local many-body contributions to the N15 NMR chemical shielding (CS) tensor. We propose alternative corrections to GIPAW which capture interactions between adjacent molecules at a higher level of theory using either fragment or cluster-based calculations. Benchmark calculations performed on N15 and C13 data sets show that these advanced GIPAW-corrected calculations improve the accuracy of chemical shielding tensor predictions relative to existing methods. Specifically, cluster-based N15 corrections show a 24% and 17% reduction in RMS error relative to GIPAW and GIPAW + MC calculations, respectively. Comparing the benchmark data sets using multiple computational models demonstrates that N15 CS tensor calculations are significantly more sensitive to intermolecular interactions relative to C13. However, fragment and cluster-based corrections that include direct hydrogen bond partners are sufficient for optimizing the accuracy of GIPAW-corrected methods. Finally, GIPAW-corrected methods are applied to the particularly challenging NMR spectral assignment of guanosine dihydrate which contains two guanosine molecules in the asymmetric unit.
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Affiliation(s)
- Joshua D Hartman
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
| | - James K Harper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, United States.
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3
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Liu Y, Munsayac A, Hall I, Keane SC. Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA. J Mol Biol 2022; 434:167688. [PMID: 35717998 PMCID: PMC9474619 DOI: 10.1016/j.jmb.2022.167688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/22/2022]
Abstract
The miR-17 ∼ 92a polycistron, also known as oncomiR-1, is commonly overexpressed in multiple cancers and has several oncogenic properties. OncomiR-1 encodes six constituent microRNAs (miRs), each enzymatically processed with different efficiencies. However, the structural mechanism that regulates this differential processing remains unclear. Chemical probing of oncomiR-1 revealed that the Drosha cleavage sites of pri-miR-92a are sequestered in a four-way junction. NPSL2, an independent stem loop element, is positioned just upstream of pri-miR-92a and sequesters a crucial part of the sequence that constitutes the basal helix of pri-miR-92a. Disruption of the NPSL2 hairpin structure could promote the formation of a pri-miR-92a structure that is primed for processing by Drosha. Thus, NPSL2 is predicted to function as a structural switch, regulating pri-miR-92a processing. Here, we determined the solution structure of NPSL2 using solution NMR spectroscopy. This is the first high-resolution structure of an oncomiR-1 element. NPSL2 adopts a hairpin structure with a large, but highly structured, apical and internal loops. The 10-bp apical loop contains a pH-sensitive A+·C mismatch. Additionally, several adenosines within the apical and internal loops have elevated pKa values. The protonation of these adenosines can stabilize the NPSL2 structure through electrostatic interactions. Our study provides fundamental insights into the secondary and tertiary structure of an important RNA hairpin proposed to regulate miR biogenesis.
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Affiliation(s)
- Yaping Liu
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/YapingLiu5
| | - Aldrex Munsayac
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Ian Hall
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/ihallu14
| | - Sarah C Keane
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA.
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4
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Ashwood B, Sanstead PJ, Dai Q, He C, Tokmakoff A. 5-Carboxylcytosine and Cytosine Protonation Distinctly Alter the Stability and Dehybridization Dynamics of the DNA Duplex. J Phys Chem B 2020; 124:627-640. [PMID: 31873021 DOI: 10.1021/acs.jpcb.9b11510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Applications associated with nucleobase protonation events are grounded in their fundamental impact on DNA thermodynamics, structure, and hybridization dynamics. Of the canonical nucleobases, N3 protonation of cytosine (C) is the most widely utilized in both biology and nanotechnology. Naturally occurring C derivatives that shift the N3 pKa introduce an additional level of tunability. The epigenetic nucleobase 5-carboxylcytosine (caC) presents a particularly interesting example since this derivative forms Watson-Crick base pairs of similar stability and displays pH-dependent behavior over the same range as the canonical nucleobase. However, the titratable group in caC corresponds to the exocyclic carboxyl group rather than N3, and the implications of these divergent protonation events toward DNA hybridization thermodynamics, kinetics, and base pairing dynamics remain poorly understood. Here, we study the pH dependence of these physical properties using model oligonucleotides containing C and caC with FTIR and temperature-jump IR spectroscopy. We demonstrate that N3 protonation of C completely disrupts duplex stability, leading to large shifts in the duplex/single-strand equilibrium, a reduction in the cooperativity of melting, and an acceleration in the rate of duplex dissociation. In contrast, while increasing 5-carboxyl protonation in caC-containing duplexes induces an increase in base pair fluctuations, the DNA duplex can tolerate substantial protonation without significant perturbation to the duplex/single-strand equilibrium. However, 5-carboxyl protonation has a large impact on hybridization kinetics by reducing the transition state free energy. Our thermodynamic and kinetic analysis provides new insight on the impact of two divergent protonation mechanisms in naturally occurring nucleobases on the biophysical properties of DNA.
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5
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Wang Z, Zheng Y, Zheng Y, Xue XS, Ji P. A Systematic Theoretical Study on the Acidities for Cations of Ionic Liquids in Dimethyl Sulfoxide. J Phys Chem A 2018; 122:5750-5755. [DOI: 10.1021/acs.jpca.8b02265] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhen Wang
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
- State Key Laboratory on Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yongjun Zheng
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Yong Zheng
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Xiao-Song Xue
- School of Chemical and Environmental Engineering, Anyang Institute of Technology, Anyang 455000, China
- State Key Laboratory on Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pengju Ji
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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6
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Rivera-Márquez KI, Godoy-Alcántar C, Claudio-Catalán MÁ, Medrano F. Adenine nucleotide recognition by spiramycin and some of its aromatic derivatives. J INCL PHENOM MACRO 2016. [DOI: 10.1007/s10847-016-0654-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Chen YL, Wu DY, Tian ZQ. Theoretical Investigation on the Substituent Effect of Halogen Atoms at the C8 Position of Adenine: Relative Stability, Vibrational Frequencies, and Raman Spectra of Tautomers. J Phys Chem A 2016; 120:4049-58. [PMID: 27243104 DOI: 10.1021/acs.jpca.6b03604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have theoretically investigated the substituent effect of adenine at the C8 position with a substituent X = H, F, Cl, and Br by using the density functional theory (DFT) at the B3LYP/6-311+G(d, p) level. The aim is to study the substituent effect of halogen atoms on the relative stability, vibrational frequencies, and solvation effect of tautomers. Our calculated results show that for substituted adenine molecules the N9H8X tautomer to be the most stable structure in gas phase at the present theoretical level. Here N9H8X denotes the hydrogen atom binds to the N9 position of imidazole ring and X denotes H, F, Cl, and Br atoms. The influence of the induced attraction of the fluorine substituent is significantly larger than chlorine and bromine ones. The halogen substituent effect has a significant influence on changes of vibrational frequencies and Raman intensities.
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Affiliation(s)
- Yan-Li Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - De-Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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8
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Wu RR, He CC, Hamlow LA, Nei YW, Berden G, Oomens J, Rodgers MT. N3 Protonation Induces Base Rotation of 2'-Deoxyadenosine-5'-monophosphate and Adenosine-5'-monophosphate. J Phys Chem B 2016; 120:4616-24. [PMID: 27138137 DOI: 10.1021/acs.jpcb.6b04052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) action spectroscopy experiments combined with theoretical calculations are performed to investigate the stable gas-phase conformations of the protonated adenine mononucleotides, [pdAdo+H](+) and [pAdo+H](+). Conformations that are present in the experiments are elucidated via comparative analyses of the experimental IRMPD spectra and the B3LYP/6-311+G(d,p) IR spectra predicted for the conformers optimized at this level of theory. N3 protonation is preferred as it induces base rotation, which allows a strong hydrogen bond to be formed between the excess proton of adenine and the phosphate moiety. In contrast, both N1 and N7 protonation are predicted to be >35 kJ/mol less favorable than N3 protonation. Only N3 protonated conformers are present in the experiments in measurable abundance. Both the low-energy conformers computed and the experimental IRMPD spectra of [pdAdo+H](+) and [pAdo+H](+) indicate that the 2'-hydroxyl moiety does not significantly impact the structure of the most stable conformer or the IRMPD spectral profile of [pAdo+H](+) vs that of [pdAdo+H](+). However, the 2'-hydroxyl leads to a 3-fold enhancement in the IRMPD yield of [pAdo+H](+) in the fingerprint region. Comparison of present results to those reported in a previous IRMPD study of the analogous protonated adenine nucleosides allows the effects of the phosphate moiety on the gas-phase conformations to be elucidated.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - C C He
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - L A Hamlow
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - Y-W Nei
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - G Berden
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University , Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - J Oomens
- FELIX Laboratory, Institute for Molecules and Materials, Radboud University , Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam , 1090 GD Amsterdam, The Netherlands
| | - M T Rodgers
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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9
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Wu RR, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated adenine nucleosides: N3 protonation induces base rotation and enhances N-glycosidic bond stability. Phys Chem Chem Phys 2016; 18:16021-32. [DOI: 10.1039/c6cp01445c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
N3 protonation induces base rotation and stabilizes the syn orientation of the adenine nucleobase of [dAdo+H]+ and [Ado+H]+via formation of a strong intramolecular N3H+⋯O5′ hydrogen-bonding interaction, which in turn influences the mechanisms and energetics for N-glycosidic bond cleavage.
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Affiliation(s)
- R. R. Wu
- Department of Chemistry
- Wayne State University
- Detroit
- USA
| | - M. T. Rodgers
- Department of Chemistry
- Wayne State University
- Detroit
- USA
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10
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Semenov VA, Samultsev DO, Krivdin LB. Theoretical and experimental study of 15N NMR protonation shifts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:433-441. [PMID: 25891386 DOI: 10.1002/mrc.4231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/22/2015] [Accepted: 02/05/2015] [Indexed: 06/04/2023]
Abstract
A combined theoretical and experimental study revealed that the nature of the upfield (shielding) protonation effect in 15N NMR originates in the change of the contribution of the sp(2)-hybridized nitrogen lone pair on protonation resulting in a marked shielding of nitrogen of about 100 ppm. On the contrary, for amine-type nitrogen, protonation of the nitrogen lone pair results in the deshielding protonation effect of about 25 ppm, so that the total deshielding protonation effect of about 10 ppm is due to the interplay of the contributions of adjacent natural bond orbitals. A versatile computational scheme for the calculation of 15N NMR chemical shifts of protonated nitrogen species and their neutral precursors is proposed at the density functional theory level taking into account solvent effects within the supermolecule solvation model.
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Affiliation(s)
- Valentin A Semenov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, Irkutsk Oblast, 664033, Russia
| | - Dmitry O Samultsev
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, Irkutsk Oblast, 664033, Russia
| | - Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Favorsky St. 1, Irkutsk, Irkutsk Oblast, 664033, Russia
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11
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Halder A, Halder S, Bhattacharyya D, Mitra A. Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study. Phys Chem Chem Phys 2015; 16:18383-96. [PMID: 25070186 DOI: 10.1039/c4cp02541e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protonated nucleobases have significant roles in facilitating catalytic functions of RNA, and in stabilizing different structural motifs. Reported pKa values of nucleobase protonation suggest that the population of neutral nucleobases is 10(3)-10(4) times higher than that of protonated nucleobases under physiological conditions (pH ∼ 7.4). Therefore, a molecular level understanding of various putative roles of protonated nucleobases cannot be achieved without addressing the question of how their occurrence propensities and stabilities are related to the free energy costs associated with the process of protonation under physiological conditions. With water as the proton donor, we use advanced QM methods to evaluate the site specific protonation propensities of nucleobases in terms of their associated free energy changes (ΔGprot). Quantitative follow up on the energetics of base pair formation and database search for evaluating their occurrence frequencies, reveal a lack of correlation between base pair stability and occurrence propensities on the one hand, and ease of protonation on the other. For example, although N7 protonated adenine (ΔGprot = 40.0 kcal mol(-1)) is found to participate in stable base pairing, base pairs involving N7 protonated guanine (ΔGprot = 36.8 kcal mol(-1)), on geometry optimization, converge to a minima where guanine transfers its extra proton to its partner base. Such observations, along with examples of weak base pairs involving N3 protonation of cytosine (ΔGprot = 37.0 kcal mol(-1)) are rationalized by analysing the protonation induced charge redistributions which are found to significantly influence, both positively and negatively, the hydrogen bonding potentials of different functional sites of individual nucleobases. Protonation induced charge redistribution is also found to strongly influence (i) the aromatic character of the rings of the participating bases and (ii) hydrogen bonding potential of the free edges of the protonated base pair. Comprehensive analysis of a non-redundant RNA crystal structure dataset further reveals that, while availability of stabilization possibilities determine the feasibility of occurrence of protonated bases, their occurrence context and specific functional roles are important factors determining their occurrence propensities.
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Affiliation(s)
- Antarip Halder
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad 500032, India.
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12
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Munday JC, Tagoe DNA, Eze AA, Krezdorn JAM, Rojas López KE, Alkhaldi AAM, McDonald F, Still J, Alzahrani KJ, Settimo L, De Koning HP. Functional analysis of drug resistance-associated mutations in the Trypanosoma brucei adenosine transporter 1 (TbAT1) and the proposal of a structural model for the protein. Mol Microbiol 2015; 96:887-900. [PMID: 25708978 PMCID: PMC4755147 DOI: 10.1111/mmi.12979] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2015] [Indexed: 02/01/2023]
Abstract
The Trypanosoma brucei aminopurine transporter P2/TbAT1 has long been implicated in the transport of, and resistance to, the diamidine and melaminophenyl arsenical classes of drugs that form the backbone of the pharmacopoeia against African trypanosomiasis. Genetic alterations including deletions and single nucleotide polymorphisms (SNPs) have been observed in numerous strains and clinical isolates. Here, we systematically investigate each reported mutation and assess their effects on transporter function after expression in a tbat1(-/-) T. brucei line. Out of a set of six reported SNPs from a reported 'resistance allele', none significantly impaired sensitivity to pentamidine, diminazene or melarsoprol, relative to the TbAT1-WT allele, although several combinations, and the deletion of the codon for residue F316, resulted in highly significant impairment. These combinations of SNPs, and ΔF316, also strongly impaired the uptake of [(3)H]-adenosine and [(3)H]-diminazene, identical to the tbat1(-/-) control. The TbAT1 protein model predicted that residues F19, D140 and F316 interact with the substrate of the transporter. Mutation of D140 to alanine resulted in an inactive transporter, whereas the mutation F19A produced a transporter with a slightly increased affinity for [(3)H]-diminazene but reduced the uptake rate. The results presented here validate earlier hypotheses of drug binding motifs for TbAT1.
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Affiliation(s)
- Jane C Munday
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
- Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, UK
| | - Daniel N A Tagoe
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Anthonius A Eze
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Medical Biochemistry, College of Medicine, University of Nigeria, Enugu Campus, Enugu, Nigeria
| | - Jessica A M Krezdorn
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Karla E Rojas López
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Abdulsalam A M Alkhaldi
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Biology, College of Science, Aljouf University, Sakaka, Saudi Arabia
| | - Fiona McDonald
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Jennifer Still
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Khalid J Alzahrani
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
- Faculty of Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Luca Settimo
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
- Department of Chemistry and Chemical Biology, 417 Egan Research Center, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Harry P De Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
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13
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Pedersen SØ, Støchkel K, Byskov CS, Baggesen LM, Nielsen SB. Gas-phase spectroscopy of protonated adenine, adenosine 5'-monophosphate and monohydrated ions. Phys Chem Chem Phys 2013; 15:19748-52. [PMID: 24141603 DOI: 10.1039/c3cp53742k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microsolvation of chromophore ions commonly has large effects on their electronic structure and as a result on their optical absorption spectra. Here spectroscopy of protonated adenine (AdeH(+)) and its complex with one water molecule isolated in vacuo was done using a home-built mass spectrometer in combination with a tuneable pulsed laser system. Experiments also included the protonated adenosine 5'-monophosphate nucleotide (AMPH(+)). In the case of bare AdeH(+) ions, one-photon absorption leads to four dominant fragment ions corresponding to ammonium and ions formed after loss of either NH3, HCN, or NH2CN. The yields of these were measured as a function of the wavelength of the light from 210 nm to 300 nm, and they were combined to obtain the total photoinduced dissociation at each wavelength (i.e., action spectrum). A broad band between 230 nm and 290 nm and the tail of a band with maximum below 210 nm (high-energy band) are seen. In the case of AdeH(+)(H2O), the dominant dissociation channel after photoexcitation in the low-energy band was simply loss of H2O while photodissociation of protonated AMP revealed two dominant dissociation channels associated with the formation of either AdeH(+) or loss of H3PO4. The action spectra of AdeH(+), AdeH(+)(H2O), and AMPH(+) are almost identical in the 230-290 nm region, and they resemble the absorption spectrum of protonated adenine in aqueous solution recorded at low pH. Hence from our work it is firmly established that the lowest-energy transitions are independent of the surroundings.
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Affiliation(s)
- Sara Øvad Pedersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
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14
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Bankura A, Klein ML, Carnevale V. Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics. Chem Phys 2013; 422:156-164. [PMID: 25914436 PMCID: PMC4407280 DOI: 10.1016/j.chemphys.2013.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nε positions of the imidazole group to estimate the pKa's. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.
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Affiliation(s)
- Arindam Bankura
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Michael L. Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
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15
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Lanucara F, Crestoni ME, Chiavarino B, Fornarini S, Hernandez O, Scuderi D, Maitre P. Infrared spectroscopy of nucleotides in the gas phase 2. The protonated cyclic 3′,5′-adenosine monophosphate. RSC Adv 2013. [DOI: 10.1039/c3ra41117f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Quantitative Study of the Interaction between ATP and Aromatic Amines in Aqueous Solution. J SOLUTION CHEM 2012. [DOI: 10.1007/s10953-012-9865-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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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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18
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Sarangi MK, Bhattacharyya D, Basu S. Influence of 2′-Deoxy Sugar Moiety on Excited-State Protonation Equilibrium of Adenine and Adenosine with Acridine inside SDS Micelles: A Time-Resolved Study with Quantum Chemical Calculations. Chemphyschem 2012; 13:525-34. [DOI: 10.1002/cphc.201100763] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Indexed: 11/10/2022]
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19
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Kelly DN, Schwartz CP, Uejio JS, Duffin AM, England AH, Saykally RJ. Communication: Near edge x-ray absorption fine structure spectroscopy of aqueous adenosine triphosphate at the carbon and nitrogen K-edges. J Chem Phys 2011; 133:101103. [PMID: 20849154 DOI: 10.1063/1.3478548] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the nitrogen and carbon K-edges was used to study the hydration of adenosine triphosphate in liquid microjets. The total electron yield spectra were recorded as a function of concentration, pH, and the presence of sodium, magnesium, and copper ions (Na(+)/Mg(2+)/Cu(2+)). Significant spectral changes were observed upon protonation of the adenine ring, but not under conditions that promote π-stacking, such as high concentration or presence of Mg(2+), indicating that NEXAFS is insensitive to the phenomenon. Intramolecular inner-sphere association of Cu(2+) did create observable broadening of the nitrogen spectrum, whereas outer-sphere association with Mg(2+) did not.
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Affiliation(s)
- Daniel N Kelly
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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20
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Devine SM, Scammells PJ. Synthesis and Utility of 2-Halo-O6-(benzotriazol-1-yl)-Functionalized Purine Nucleosides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001395] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Gillerman I, Fischer B. Investigations into the origin of the molecular recognition of several adenosine deaminase inhibitors. J Med Chem 2010; 54:107-21. [PMID: 21138280 DOI: 10.1021/jm101286g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inhibitors of adenosine deaminase (ADA, EC 3.5.4.4) are potential therapeutic agents for the treatment of various health disorders. Several highly potent inhibitors were previously identified, yet they exhibit unacceptable toxicities. We performed a SAR study involving a series of C2 or C8 substituted purine-riboside analogues with a view to discover less potent inhibitors with a lesser toxicity. We found that any substitution at C8 position of nebularine resulted in total loss of activity toward calf intestinal ADA. However, several 2-substituted-adenosine, 8-aza-adenosine, and nebularine analogues exhibited inhibitory activity. Specifically, 2-Cl-purine riboside, 8-aza-2-thiohexyl adenosine, 2-thiohexyl adenosine, and 2-MeS-purine riboside were found to be competitive inhibitors of ADA with K(i) values of 25, 22, 6, and 3 μM, respectively. We concluded that electronic parameters are not major recognition determinants of ADA but rather steric parameters. A C2 substituent which fits ADA hydrophobic pocket and improves H-bonding with the enzyme makes a good inhibitor. In addition, a gg rotamer about C4'-C5' bond is apparently an important recognition determinant.
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Affiliation(s)
- Irina Gillerman
- Department of Chemistry, Gonda-Goldschmied Medical Research Center, Bar-Ilan University, Ramat-Gan, Israel
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22
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Shishkin OV, Dopieralski P, Palamarchuk GV, Latajka Z. Rotation around the glycosidic bond as driving force of proton transfer in protonated 2′-deoxyriboadenosine monophosphate (dAMP). Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.03.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Abstract
It has normally been assumed that ribonucleotides arose on the early Earth through a process in which ribose, the nucleobases, and phosphate became conjoined. However, under plausible prebiotic conditions, condensation of nucleobases with ribose to give beta-ribonucleosides is fraught with difficulties. The reaction with purine nucleobases is low-yielding and the reaction with the canonical pyrimidine nucleobases does not work at all. The reasons for these difficulties are considered and an alternative high-yielding synthesis of pyrimidine nucleotides is discussed. Fitting the new synthesis to a plausible geochemical scenario is a remaining challenge but the prospects appear good. Discovery of an improved method of purine synthesis, and an efficient means of stringing activated nucleotides together, will provide underpinning support to those theories that posit a central role for RNA in the origins of life.
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24
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Study of the protonation (methylation) position and tautomeric structure of thiopyrimidine derivatives by 2D 1H—15H NMR HSQC/HMBC. Experimental approach and theoretical modeling. Russ Chem Bull 2010. [DOI: 10.1007/s11172-009-0008-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Song Z, Parker KJ, Enoh I, Zhao H, Olubajo O. Elucidation of spermidine interaction with nucleotide ATP by multiple NMR techniques. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48:123-128. [PMID: 19960498 PMCID: PMC2909874 DOI: 10.1002/mrc.2554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Interaction of polyamines with nucleotides plays a key role in many biological processes. Here we use multiple NMR techniques to characterize interaction of spermidine with adenosine 5'-triphosphate (ATP). Two-dimensional (1)H-(15)N spectra obtained from gs-HMBC experiments at varied pH show significant shift of N-1 peak around pH 2.0-7.0 range, suggesting that spermidine binds to N-1 site of ATP base. The binding facilitates N-1 deprotonation, shifting its pK(a) from 4.3 to 3.4. By correlating (15)N and (31)P chemical shift data, it is clear that spermidine is capable of concurrently binding to ATP base and phosphate sites around pH 4.0-7.0. The self-diffusion constants derived from (1)H PFG-diffusion measurements provide evidence that binding of spermidine to ATP is in 1:1 ratio, and pH variations do not induce significant nucleotide self-association in our samples. (31)P spectral analysis suggests that at neutral pH, Mg(2+) ion competes with spermidine and shows stronger binding to ATP phosphates. From (31)P kinetic measurements of myosin-catalyzed ATP hydrolysis, it is found that binding of spermidine affects the stability and reactivity of ATP. These NMR results are important for advancing the studies on nucleotide-polyamine interaction and its impact on nucleotide structures and activities under varied conditions.
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Affiliation(s)
- Zhiyan Song
- Department of Natural Sciences, Savannah State University, Savannah, GA 31404, USA.
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26
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Urban M, Joubert N, Hocek M, Alexander RE, Kuchta RD. Herpes simplex virus-1 DNA primase: a remarkably inaccurate yet selective polymerase. Biochemistry 2009; 48:10866-81. [PMID: 19835416 DOI: 10.1021/bi901476k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herpes simplex virus-1 primase misincorporates the natural NTPs at frequencies of around one error per 30 NTPs polymerized, making it one of the least accurate polymerases known. We used a series of nucleotide analogues to further test the hypothesis that primase requires Watson-Crick hydrogen bond formation to efficiently polymerize a NTP. Primase could not generate base pairs containing a complete set of hydrogen bonds in an altered arrangement (isoguanine.isocytosine) and did not efficiently polymerize dNTPs completely incapable of forming Watson-Crick hydrogen bonds opposite templating bases incapable of forming Watson-Crick hydrogen bonds. Similarly, primase did not incorporate most NTPs containing hydrophobic bases incapable of Watson-Crick hydrogen bonding opposite natural template bases. However, 2-pyridone NTP and 4-methyl-2-pyridone NTP provided striking exceptions to this rule. The effects of removing single Watson-Crick hydrogen bonding groups from either the NTP or templating bases varied from almost no effect to completely blocking polymerization depending both on the parental base pair (G.C vs A.T/U) and which base pair of the growing primer (second, third, or fourth) was examined. Thus, primase does not absolutely need to form Watson-Crick hydrogen bonds to efficiently polymerize a NTP. Additionally, we found that herpes primase can misincorporate nucleotides both by misreading the template and by a primer-template slippage mechanism. The mechanistic and biological implications of these results are discussed.
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Affiliation(s)
- Milan Urban
- Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, Colorado 80309, USA
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27
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Studies on the coordination chemistry of methylated xanthines and their imidazolium salts. Part 1: benzyl derivatives. TRANSIT METAL CHEM 2009. [DOI: 10.1007/s11243-009-9310-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Jongh LAD, Strasser CE, Raubenheimer HG, Cronje S. Imine coordinated 2-aminoazole complexes of (CO)5Cr(0) and (CO)5W(0), verification by structural characterisation. Polyhedron 2009. [DOI: 10.1016/j.poly.2009.07.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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29
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Nilapwar S, Williams E, Fu C, Prodromou C, Pearl LH, Williams MA, Ladbury JE. Structural-thermodynamic relationships of interactions in the N-terminal ATP-binding domain of Hsp90. J Mol Biol 2009; 392:923-36. [PMID: 19631219 DOI: 10.1016/j.jmb.2009.07.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/13/2009] [Accepted: 07/14/2009] [Indexed: 11/28/2022]
Abstract
Despite its importance as a target in anti-cancer therapeutics and the numerous rational-based inhibitor design efforts aimed at it, there are only limited data available on structural-thermodynamic relationships of interactions of the N-terminal ATP-binding domain of Hsp90 (N-Hsp90). Here, we redress this by presenting an investigation of binding of nucleotides and ansamycin compounds to this domain. Interactions of nucleotides with N-Hsp90 are relatively weak (>10 microM) and are strongly enthalpy driven over the temperature range 10-25 degrees C. Geldanamycin (GA) and its analogues 17-AAG [17-(allylamino)-17-demethoxy-GA] and 17-DMAG (17-N,N-dimethylaminoethylamino-17-demethoxy-GA) bind more strongly and have a dominant favourable enthalpic contribution over the temperature range investigated. We investigated the temperature dependence of the enthalpic contribution to binding. We found that while the ansamycin compounds have the commonly observed negative value, the nucleotides show a negligible or even a positive DeltaC(p) of binding. These data represent the first observation of a single binding site for which interactions with different ligands result in both negative and positive DeltaC(p) values. By addressing the likely impact of the potential contributions from protein-ligand interactions, we are able to attribute the anomalous DeltaC(p) for the nucleotides largely to a change in the conformation of the domain structure and local motion in the lid region of N-Hsp90 with the concomitant exposure of hydrophobic amino acid side chains.
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Affiliation(s)
- Sanjay Nilapwar
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
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30
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Cherepanov AV, Doroshenko EV, Matysik J, de Vries S, De Groot HJM. A view on phosphate ester photochemistry by time-resolved solid state NMR. Intramolecular redox reaction of caged ATP. Phys Chem Chem Phys 2008; 10:6820-8. [PMID: 19015786 DOI: 10.1039/b806677a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The light-driven intramolecular redox reaction of adenosine-5'-triphosphate-[P3-(1-(2-nitrophenyl)-ethyl)]ester (caged ATP) has been studied in frozen aqueous solution using time-resolved solid state NMR spectroscopy under continuous illumination conditions. Cleavage of the phosphate ester bond leads to 0.3, 1.36, and 6.06 ppm downfield shifts of the alpha-, beta-, and gamma-phosphorus resonances of caged ATP, respectively. The observed rate of ATP formation is 2.4 +/- 0.2 h(-1) at 245 K. The proton released in the reaction binds to the triphosphate moiety of the nascent ATP, causing the upfield shifts of the 31P resonances. Analyses of the reaction kinetics indicate that bond cleavage and proton release are two sequential processes in the solid state, suggesting that the 1-hydroxy,1-(2-nitrosophenyl)-ethyl carbocation intermediate is involved in the reaction. The beta-phosphate oxygen atom of ATP is protonated first, indicating its proximity to the reaction center, possibly within hydrogen bonding distance. The residual linewidth kinetics are interpreted in terms of chemical exchange processes, hydrogen bonding of the beta-phosphate oxygen atom and evolution of the hydrolytic equilibrium at the triphosphate moiety of the nascent ATP. Photoreaction of caged ATP in situ gives an opportunity to study structural kinetics and catalysis of ATP-dependent enzymes by NMR spectroscopy in rotating solids.
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Affiliation(s)
- Alexey V Cherepanov
- Biophysical Organic Chemistry/Solid State NMR group, Leiden Institute of Chemistry, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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31
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Romanova IP, Larionova OA, Balandina AA, Latypov SK, Mustafina AR, Skripacheva VV, Zverev VV, Sinyashin OG. Proton-acceptor properties of azahomofullerene and fullerenoaziridine containing a cyanuric acid fragment. RUSS J GEN CHEM+ 2008. [DOI: 10.1134/s1070363208030201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Kozlov AV, Semenov VE, Mikhailov AS, Aganov AV, Smith MB, Reznik VS, Latypov SK. Preferential Protonation and Methylation Site of Thiopyrimidine Derivatives in Solution: NMR Data. J Phys Chem B 2008; 112:3259-67. [DOI: 10.1021/jp710952r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Artem V. Kozlov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Vyacheslav E. Semenov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Anatoliy S. Mikhailov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Albert V. Aganov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Michael B. Smith
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Vladimir S. Reznik
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
| | - Shamil K. Latypov
- Institute of Organic and Physical Chemistry, Arbuzov Str. 8, Kazan, 420088, Russian Federation, Kazan State University, Kazan, 420008, Russian Federation, and University of Connecticut, 55 North Eagleville Road, 4-60, Storrs, Connecticut 06269-3060
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33
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Chen X, Syrstad EA, Nguyen MT, Gerbaux P, Turecek F. Adenine radicals in the gas phase: an experimental and computational study of hydrogen atom adducts to adenine. J Phys Chem A 2007; 109:8121-32. [PMID: 16834198 DOI: 10.1021/jp0529725] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The elusive hydrogen atom adduct to the N-1 position in adenine, which is thought to be the initial intermediate of chemical damage, was specifically generated in the gas phase and characterized by neutralization-reionization mass spectrometry. The N-1 adduct, 1,2-dihydroaden-2-yl radical (1), was generated by femtosecond electron transfer to N-1-protonated adenine that was selectively produced by electrospray ionization of adenine in aqueous-methanol solution. Radical 1 is an intrinsically stable species in the gas phase that undergoes specific loss of the N-1-hydrogen atom to form adenine, but does not isomerize to the more stable C-2 adduct, 1,2-dihydroaden-1-yl radical (5). Radicals 1 that are formed in the fifth and higher electronically excited states of DeltaE > or = 2.5 eV can also undergo ring-cleavage dissociations resulting in expulsion of HCN. The relative stabilities, dissociation, and transition state energies for several hydrogen atom adducts to adenine have been established computationally at highly correlated levels of theory. Transition state theory calculations of 298 K rate constants in the gas phase, including quantum tunnel corrections, indicate the branching ratios for H-atom additions to C-8, C-2, N-3, N-1, and N-7 positions in adenine as 0.68, 0.20, 0.08, 0.03, and 0.01, respectively. The relative free energies of adenine radicals in aqueous solution point to the C-8 adduct as the most stable tautomer, which is predicted to be the predominating (>99.9%) product at thermal equilibrium in solution at 298 K.
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Affiliation(s)
- Xiaohong Chen
- Department of Chemistry, Bagley Hall, Box 351700, University of Washington, Seattle, WA 98195-1700, USA
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34
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Fu Y, Liu L, Wang YM, Li JN, Yu TQ, Guo QX. Quantum-chemical predictions of redox potentials of organic anions in dimethyl sulfoxide and reevaluation of bond dissociation enthalpies measured by the electrochemical methods. J Phys Chem A 2007; 110:5874-86. [PMID: 16640384 DOI: 10.1021/jp055682x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A first-principle theoretical protocol was developed that could predict the absolute pK(a) values of over 250 structurally unrelated compounds in DMSO with a precision of 1.4 pK(a) units. On this basis we developed the first theoretical protocol that could predict the standard redox potentials of over 250 structurally unrelated organic anions in DMSO with a precision of 0.11 V. Using the two new protocols we systematically reevaluated the bond dissociation enthalpies (BDEs) measured previously by the electrochemical methods. It was confirmed that for most compounds the empirical equation (BDE = 1.37 pK(HA) + 23.1E(o) + constant) was valid. The constant in this equation was determined to be 74.0 kcal/mol, compared to 73.3 kcal/mol previously reported. Nevertheless, for a few compounds the empirical equation could not be used because the solvation energy changed dramatically during the bond cleavage, which resulted from the extraordinary change of dipole moment during the reaction. In addition, we found 40 compounds (mostly oximes and amides) for which the experimental values were questionable by over 5 kcal/mol. Further analyses revealed that all these questionable BDEs could be explained by one of the three following reasons: (1) the experimental pK(a) value is questionable; (2) the experimental redox potential is questionable; (3) the solvent effect cannot be neglected. Thus, by developing practical theoretical methods and utilizing them to solve realistic problems, we hope to demonstrate that ab initio theoretical methods can now be developed to make not only reliable, but also useful, predictions for solution-phase organic chemistry.
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Affiliation(s)
- Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei.
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35
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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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36
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Harki DA, Graci JD, Edathil JP, Castro C, Cameron CE, Peterson BR. Synthesis of a universal 5-nitroindole ribonucleotide and incorporation into RNA by a viral RNA-dependent RNA polymerase. Chembiochem 2007; 8:1359-62. [PMID: 17600792 PMCID: PMC2194811 DOI: 10.1002/cbic.200700160] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel A. Harki
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
| | - Jason D. Graci
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Jocelyn P. Edathil
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
| | - Christian Castro
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Craig E. Cameron
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Blake R. Peterson
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
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37
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Laxer A, Gottlieb HE, Fischer B. Molecular recognition of adenosine deaminase: 15N NMR studies. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 26:161-80. [PMID: 17365795 DOI: 10.1080/15257770601112713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The elucidation of the molecular recognition of adenosine deaminase (ADA), the interpretation of the catalytic mechanism, and the design of novel inhibitors are based mostly on data obtained for the crystalline state of the enzyme. To obtain evidence for molecular recognition of the physiologically relevant soluble enzyme, we studied its interactions with the in situ formed inhibitor, 6-OH-purine riboside (HDPR), by 1D-15N- and 2D-(1H-15N)- NMR using the labeled primary inhibitor [15N4]-PR. We synthesized both [15N4]-PR and an [15N4]-HDPR model, from relatively inexpensive 15N sources. The [15N4]-HDPR model was used to simulate H-bonding and possible Zn2+-coordination of HDPR with ADA. We also explored possible ionic interactions between PR and ADA by 15N-NMR monitored pH-titrations of [15N4]-PR. Finally, we investigated the [15N4]-PR-ADA 1:1 complex by 2D-(1H-15N) NMR. We found that HDPR recognition determinants in ADA do not include any ionic-interactions. HDPR N1 H is an H-bond acceptor, and not an H-bond donor. Despite the proximity of N7 to the Zn2+-ion, no coordination occurs; instead, N7 is an H-bond acceptor. We found an overall agreement between the crystallographic data for the crystallized ADA:HDPR complex and the 15N-NMR signals for the corresponding soluble complex. This finding justifies the use of ADA's crystallographic data for the design of novel inhibitors.
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Affiliation(s)
- Avital Laxer
- Department of Chemistry, Gonda-Goldschmied Medical Research Center, Bar-Ilan University, Ramat-Gan, Israel
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Zhang B, Muller-Steffner H, Schuber F, Potter BVL. Nicotinamide 2-fluoroadenine dinucleotide unmasks the NAD+ glycohydrolase activity of Aplysia californica adenosine 5'-diphosphate ribosyl cyclase. Biochemistry 2007; 46:4100-9. [PMID: 17341094 DOI: 10.1021/bi061933w] [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: 11/29/2022]
Abstract
ADP-ribosyl cyclases catalyze the transformation of nicotinamide adenine dinucleotide (NAD+) into the calcium-mobilizing nucleotide second messenger cyclic adenosine diphosphoribose (cADP-ribose) by adenine N1-cyclization onto the C-1' ' position of NAD+. The invertebrate Aplysia californica ADP-ribosyl cyclase is unusual among this family of enzymes by acting exclusively as a cyclase, whereas the other members, such as CD38 and CD157, also act as NAD+ glycohydrolases, following a partitioning kinetic mechanism. To explore the intramolecular cyclization reaction, the novel nicotinamide 2-fluoroadenine dinucleotide (2-fluoro-NAD+) was designed as a sterically very close analogue to the natural substrate NAD+, with only an electronic perturbation at the critical N1 position of the adenine base designed to impede the cyclization reaction. 2-Fluoro-NAD+ was synthesized in high yield via Lewis acid catalyzed activation of the phosphoromorpholidate derivative of 2-fluoroadenosine 5'-monophosphate and coupling with nicotinamide 5'-monophosphate. With 2-fluoro-NAD+ as substrate, A. californica ADP-ribosyl cyclase exhibited exclusively a NAD+ glycohydrolase activity, catalyzing its hydrolytic transformation into 2-fluoro-ADP-ribose, albeit at a rate ca. 100-fold slower than for the cyclization of NAD+ and also, in the presence of methanol, into its methanolysis product beta-1' '-O-methyl 2-fluoro-ADP-ribose with a preference for methanolysis over hydrolysis of ca. 100:1. CD38 likely converted 2-fluoro-NAD+ exclusively into the same product. We conclude that A. californica ADP-ribosyl cyclase can indeed be classified as a multifunctional enzyme that also exhibits a classical NAD+ glycohydrolase function. This alternative pathway that remains, however, kinetically cryptic when using NAD+ as substrate can be unmasked with a dinucleotide analogue whose conversion into the cyclic derivative is blocked. 2-Fluoro-NAD+ is therefore a useful molecular tool allowing dissection of the kinetic scheme for this enzyme.
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Affiliation(s)
- Bo Zhang
- Wolfson Laboratory of Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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Sharon E, Lévesque SA, Munkonda MN, Sévigny J, Ecke D, Reiser G, Fischer B. Fluorescent N2,N3-epsilon-adenine nucleoside and nucleotide probes: synthesis, spectroscopic properties, and biochemical evaluation. Chembiochem 2006; 7:1361-74. [PMID: 16871613 PMCID: PMC5218839 DOI: 10.1002/cbic.200600070] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Indexed: 11/06/2022]
Abstract
N1,N(6)-ethenoadenine, epsilon-A, nucleos(t)ides have been previously applied as fluorescent probes in numerous biochemical systems. However, these epsilon-A analogues lack the H-bonding capability of adenine. To improve the fluorescence characteristics while preserving the H-bonding pattern required for molecular recognition, we designed a novel probe: N(2),N3-etheno-adenosine, (N(2),N3-epsilon-A). Here, we describe four novel syntheses of the target epsilon-nucleoside and related analogues. These methods are short, facile, and provide the product regiospecifically. In addition, we report the absorption and emission spectra of N(2),N3-epsilon-A and the dependence of the spectral features on the pH and polarity of the medium. Specifically, maximum emission of N(2),N3-epsilon-A in water is observed at 420 nm (phi=0.03, excitation at 290 nm). The biochemical relevance of the new probe was evaluated with respect to the P2Y(1) receptor and NTPDases 1 and 2. N(2),N3-epsilon-ATP was found to be almost equipotent with ATP at the P2Y(1) receptor and was hydrolyzed by NTPDases 1 and 2 at about 80 % of the rate of ATP. Furthermore, protein binding does not seem to shift the fluorescence of N(2),N3-epsilon-ATP. Based on the fluorescence and full recognition by ATP-binding proteins, we propose N(2),N3-epsilon-ATP and related nucleo(s)tides as unique probes for the investigation of adenine nucleo(s)tide-binding proteins as well as for other biochemical applications.
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Affiliation(s)
- Einat Sharon
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900 (Israel)
| | - Sébastien A. Lévesque
- Centre de Recherche en Rhumatologie et Immunologie, Université Laval, 2705 boulevard Laurier, T1-49, Sainte-Foy, Québec, G1V 4G2 (Canada)
| | - Mercedes N. Munkonda
- Centre de Recherche en Rhumatologie et Immunologie, Université Laval, 2705 boulevard Laurier, T1-49, Sainte-Foy, Québec, G1V 4G2 (Canada)
| | - Jean Sévigny
- Centre de Recherche en Rhumatologie et Immunologie, Université Laval, 2705 boulevard Laurier, T1-49, Sainte-Foy, Québec, G1V 4G2 (Canada)
| | - Denise Ecke
- Institute for Neurobiochemistry, Faculty of Medicine, Otto von Guericke University, Leipzigerstrasse 44, 39120 Magdeburg (Germany)
| | - Georg Reiser
- Institute for Neurobiochemistry, Faculty of Medicine, Otto von Guericke University, Leipzigerstrasse 44, 39120 Magdeburg (Germany)
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900 (Israel)
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Bernasconi L, Baerends EJ, Sprik M. Long-Range Solvent Effects on the Orbital Interaction Mechanism of Water Acidity Enhancement in Metal Ion Solutions: A Comparative Study of the Electronic Structure of Aqueous Mg and Zn Dications. J Phys Chem B 2006; 110:11444-53. [PMID: 16771418 DOI: 10.1021/jp0609941] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We study the dissociation of water coordinated to a divalent metal ion center, M2+ = Mg2+, Zn2+ using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. First, the proton affinity of a coordinated OH- group is computed from gas-phase Mg2+(H2O)5(OH-), which yields a relative higher gas-phase acidity for a Zn2+-coordinated as compared to a Mg2+-coordinated water molecule, DeltapKa(gp) = 5.3. We explain this difference on the basis of a gain in stabilization energy of the Zn2+(H2O)5(OH-) system arising from direct orbital interaction between the coordinated OH- and the empty 4s state of the cation. Next, we compute the acidity of coordinated water molecules in solution using free-energy thermodynamic integration with constrained AIMD. This approach yields pKa Mg2+ = 11.2 and pKa Zn2+ = 8.4, which compare favorably to experimental data. Finally, we examine the factors responsible for the apparent decrease in the relative Zn2+-coordinated water acidity in going from the gas-phase (DeltapKa(gp) = 5.3) to the solvated (DeltapKa = 2.8) regime. We propose two simultaneously occurring solvation-induced processes affecting the relative stability of Zn2+(H2O)5(OH-), namely: (a) reduction of the Zn 4s character in solution states near the bottom of the conduction band; (b) hybridization between OH- orbitals and valence-band states of the solvent. Both effects contribute to hindering the OH- --> Zn2+ charge transfer, either by making it energetically unfavorable or by delocalizing the ligand charge density over several water molecules.
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Affiliation(s)
- Leonardo Bernasconi
- Theoretische Chemie, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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41
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Berti PJ, McCann JAB. Toward a detailed understanding of base excision repair enzymes: transition state and mechanistic analyses of N-glycoside hydrolysis and N-glycoside transfer. Chem Rev 2006; 106:506-55. [PMID: 16464017 DOI: 10.1021/cr040461t] [Citation(s) in RCA: 211] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Paul J Berti
- Department of Chemistry, McMaster University, Hamilton, Ontario, Canada.
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De Stefano C, Milea D, Pettignano A, Sammartano S. Modeling ATP protonation and activity coefficients in NaClaq and KClaq by SIT and Pitzer equations. Biophys Chem 2006; 121:121-30. [PMID: 16488529 DOI: 10.1016/j.bpc.2005.12.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Revised: 12/22/2005] [Accepted: 12/26/2005] [Indexed: 10/25/2022]
Abstract
The acid-base properties of Adenosine 5'-triphosphate (ATP) in NaCl and KCl aqueous solutions at different ionic strengths (0<I/mol L(-1)<or=5 for NaCl(aq), 0<I/mol L(-1)<or=3 for KCl(aq)) and at t=25 degrees C were investigated. A selection of literature data on ATP protonation constants and on activity isopiestic coefficients was performed, together with new potentiometric measurements (by ISE-H(+), glass electrode). Both literature and new experimental data were used to model the dependence on ionic strength and ionic medium of ATP protonation by SIT (Specific ion Interaction Theory) and Pitzer equations. In addition to values of first and second ATP protonation constants in NaCl(aq) and KCl(aq) at different ionic strengths, stability constants of NaATP(3-) and KATP(3-) complexes, SIT interaction coefficients and Pitzer parameters were calculated, together with protonation constants at infinite dilution: log (T)K(1)(H)=p(T)K(a2)=7.656+/-0.010 and log (T)K(2)(H)=p(T)K(a1)=4.561+/-0.006 (in the molar concentration scale, +/-95% confidence interval). Both SIT and Pitzer approaches give satisfactory results.
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Affiliation(s)
- Concetta De Stefano
- Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Università di Messina, Salita Sperone, 31, I-98166 Messina, Vill. S. Agata, Italy
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43
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Ramirez-Aguilar KA, Moore CL, Kuchta RD. Herpes simplex virus 1 primase employs watson-crick hydrogen bonding to identify cognate nucleoside triphosphates. Biochemistry 2006; 44:15585-93. [PMID: 16300408 DOI: 10.1021/bi0513711] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We utilized NTP analogues containing modified bases to probe the mechanism of NTP selection by the primase activity of the herpes simplex virus 1 helicase-primase complex. Primase readily bound NTP analogues of varying base shape, hydrophobicity, and hydrogen-bonding capacity. Remarkably, primase strongly discriminated against incorporating virtually all of the analogues, even though this enzyme misincorporates natural NTPs at frequencies as high as 1 in 7. This included analogues with bases much more hydrophobic than a natural base (e.g., 4- and 7-trifluoromethylbenzimidazole), a base of similar hydrophobicity as a natural base but with the Watson-Crick hydrogen-bonding groups in unusual positions (7-beta-d-guanine), bases shaped almost identically to the natural bases (4-aminobenzimidazole and 4,6-difluorobenzimidazole), bases shaped very differently than a natural base (e.g., 5- and 6-trifluoromethylbenzimidazole), and bases capable of forming just one Watson-Crick hydrogen bond with the template base (purine and 4-aminobenzimidazole). The only analogues that primase readily polymerized into primers (ITP and 3-deaza-ATP) were those capable of forming Watson-Crick hydrogen bonds with the template base. Thus, herpes primase appears to require the formation of Watson-Crick hydrogen bonds in order to efficiently polymerize a NTP. In contrast to primase's narrow specificity for NTP analogues, the DNA-dependent NTPase activity associated with the herpes primase-helicase complex exhibited very little specificity with respect to NTPs containing unnatural bases. The implications of these results with respect to the mechanism of the helicase-primase and current fidelity models are discussed.
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Bhattacharya S, Vemula PK. Effect of Heteroatom Insertion at the Side Chain of 5-Alkyl-1H-tetrazoles on Their Properties as Catalysts for Ester Hydrolysis at Neutral pH. J Org Chem 2005; 70:9677-85. [PMID: 16292794 DOI: 10.1021/jo050775w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Herein we introduce tetrazole and its suitably designed derivatives as powerful ester-cleaving reagents. By first performing a detailed ab initio computational study, we found that, in the side chain of 5-alkyl-1H-tetrazoles, introduction of a heteroatom (e.g., N, O, or S at the alpha-position of the tetrazole ring) raises the charge on the tetrazole nucleus significantly. All calculations have been performed using restricted Hartree-Fock (RHF) and hybrid ab initio/DFT (B3LYP) methods employing 6-31G* and 6-31+G* basis sets. To estimate the nucleophilicity of these reagents, the charges on conjugate bases of various tetrazole derivatives have been calculated using natural population (NBO) analysis in gas phase and in water. Free energy of protonation (fep) of the 1H-tetrazole derivatives (1-7), free energy of solvation, deltaG(aq), and the corresponding pKa values have been calculated by self-consistent reaction field (SCRF) methods applying the polarized continuum model (PCM). Since the calculation indicates that incorporation of heteroatom leads to enhanced nucleophilicity in their deprotonated anionic tetrazole forms, a series of 5-substituted 1H-tetrazole derivatives have been synthesized. These compounds indeed catalyze the hydrolysis of p-nitrophenyl diphenyl phosphate (PNPDPP) and p-nitrophenyl hexanoate (PNPH) efficiently in cationic cetyl trimethylammonium bromide (CTABr) micelles at pH 7.0 and 25 degrees C. The pseudo-first-order rate constants (k(obs)) were determined for each catalyst against both substrates. The experimental and theoretical results show that, to achieve better k(obs) values for the cleavage of PNPDPP and PNPH under micellar conditions, charge on the N- atom (nucleophile) of conjugate base is important. Replacing the alpha-CH2 in alkyl substituent with S (3), NH (4), or O (5) enhances the accumulation of charge on N- in conjugate bases of tetrazoles and subsequently increases their intrinsic nucleophilic reactivity toward hydrolytic reactions. Significantly large rate enhancements were observed for the cleavage of PNPDPP and PNPH at pH 7.0 in the presence of catalytic system 5/CTABr over background (only CTABr). Tetrazole 4 (alpha-isomer) showed 4-5-fold superior reactivity over 6 (beta-isomer) under identical conditions. Natural charges obtained from NBO analysis (B3LYP/6-31+G*) are -0.94 and -0.852 on N- in the conjugate bases of 4 and 6, respectively. This also predicts that 4 is a better nucleophile than 6. All the newly synthesized tetrazole derivatives in micellar media display true catalytic properties by cleaving several fold excess of substrates.
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Affiliation(s)
- Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, India 560 012.
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Turecek F, Chen X. Protonated adenine: tautomers, solvated clusters, and dissociation mechanisms. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1713-26. [PMID: 16099164 DOI: 10.1016/j.jasms.2005.06.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Revised: 06/01/2005] [Accepted: 06/01/2005] [Indexed: 05/04/2023]
Abstract
Ab initio and density functional theory calculations at the B3-MP2 and CCSD(T)/6-311 + G(3df,2p) levels of theory are reported that address the protonation of adenine in the gas phase, water clusters, and bulk aqueous solution. The calculations point to N-1-protonated adenine (1+) as the thermodynamically most stable cationic tautomer in the gas phase, water clusters, and bulk solution. This strongly indicates that electrospray ionization of adenine solutions produces tautomer 1+ with a specificity calculated as 97-90% in the 298-473 K temperature range. The mechanisms for elimination of hydrogen atoms and ammonia from 1+ have also been studied computationally. Ion 1+ is calculated to undergo fast migrations of protons among positions N-1, C-2, N-3, N-10, N-7, and C-8 that result in an exchange of five hydrogens before loss of a hydrogen atom forming adenine cation radical at 415 kJ mol(-1) dissociation threshold energy. The elimination of ammonia is found to be substantially endothermic requiring 376-380 kJ mol(-1) at the dissociation threshold and depending on the dissociation pathway. The overall dissociation is slowed by the involvement of ion-molecule complexes along the dissociation pathways. The competing isomerization of 1+ proceeds by a sequence of ring opening, internal rotations, imine flipping, ring closures, and proton migrations to effectively exchange the N-1 and N-10 atoms in 1+, so that either can be eliminated as ammonia. This mechanism explains the previous N-1/N-10 exchange upon collision-induced dissociation of protonated adenine.
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Affiliation(s)
- Frantisek Turecek
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
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McConnell TL, Wheaton CA, Hunter KC, Wetmore SD. Effects of Hydrogen Bonding on the Acidity of Adenine, Guanine, and Their 8-Oxo Derivatives. J Phys Chem A 2005; 109:6351-62. [PMID: 16833978 DOI: 10.1021/jp0509919] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density-functional theory. The binding strengths of the neutral and (N9) anionic complexes are considered for a variety of purine binding sites. The effects of hydrogen-bonding interactions on the (N9) acidity of the purine derivatives are considered as a function of the molecule bound and the binding site. It is found that hydrogen-bonding interactions with one molecule can increase the acidity of purine derivatives by up to 60 kJ mol(-1). The (calculated) simultaneous effects of up to four molecules on the acidity of the purine derivatives are also considered. Our data suggest that the effects of more than one molecule on the acidity of the purines are generally less than the sum of the individual (additive) effects, where the magnitude of the deviation from additivity increases with the number, as well as the acidity, of molecules bound. Nevertheless, the increase in the acidity due to additional hydrogen-bonding interactions is significant, where the effect of two, three, or four hydrogen-bonding interactions can be as large as approximately 95, 115, and 130 kJ mol(-1), respectively. The present study provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.
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Affiliation(s)
- Tom L McConnell
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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Sharon E, Zündorf G, Lévesque SA, Beaudoin AR, Reiser G, Fischer B. Fluorescent epsilon-ATP analogues for probing physicochemical properties of proteins. Synthesis, biochemical evaluation, and sensitivity to properties of the medium. Bioorg Med Chem 2005; 12:6119-35. [PMID: 15519157 DOI: 10.1016/j.bmc.2004.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Accepted: 09/06/2004] [Indexed: 10/26/2022]
Abstract
Despite the significance of the elucidation of proteins' physicochemical parameters to understand various molecular phenomena, direct methods for measuring these parameters are not readily available. Here, we propose the use of 8-[p-amino-Ph]-epsilon-ATP, 3b, as a fluorescent probe for the elucidation of physicochemical parameters of binding sites in certain proteins. We synthesized novel fluorescent nucleotide analogues based on an extension of the epsilon-ATP scaffold. These analogues bear a primary or tertiary p-amino-phenyl moiety on the etheno-bridge. We explored the recognition of the fluorescent analogues by the target proteins: P2Y(1)-receptor (P2Y(1)-R) and NTPDase1. Based on the high affinity to the P2Y(1)-R (EC(50) 100nM), 3b proved a suitable probe for the investigation of this receptor. Next, we elucidated the dependencies of the absorption and emission spectra of 3b on environmental parameters, for establishing correlation equations. These equations will help determine the properties of the ATP-binding site from the spectral data of the protein-bound 3b. For this purpose, the sensitivity of the probe to acidity, dielectricity, H-bonding, viscosity, and to correlation between these parameters was determined. Thus, the pH-dependence of 3b emission intensity is bell shaped. At pH2.8 the quantum yield (phi) is enhanced 150-fold, as compared to neutral pH. The basic nitrogen atoms of 3b were assigned and pK(a) values were determined. A linear relationship was found between log phi and log viscosity, however, emission maxima (lambda(max)) remained constant. A linear relationship was found between both phi and lambda(max) and dielectricity, as measured in protic or aprotic solvents of comparable viscosity. pK(a)-like values were measured in acid-titrated alcohols with varying dielectricity but comparable viscosity, or with varying viscosity but comparable dielectricity. An inverse relationship and a linear relationship were found between the pK(a) values of 3b and the medium dielectricity and viscosity, respectively. These correlations help the calibration of properties of a protein ATP-binding site.
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Affiliation(s)
- Einat Sharon
- Department of Chemistry, Gonda-Goldschmied Medical Research Center, Bar-Ilan University, Ramat-Gan 52900, Israel
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Mäki J, Tähtinen P, Kronberg L, Klika KD. Restricted rotation/tautomeric equilibrium and determination of the site and extent of protonation in bi-imidazole nucleosides by multinuclear NMR and GIAO-DFT calculations. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.840] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Kumar VP, Ganguly B, Bhattacharya S. Computational Study on Hydroxybenzotriazoles as Reagents for Ester Hydrolysis. J Org Chem 2004; 69:8634-42. [PMID: 15575739 DOI: 10.1021/jo049539w] [Citation(s) in RCA: 37] [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
1-Hydroxybenzotriazole (1) and several of its derivatives (2-5) demonstrate potent esterolytic activity toward activated esters such as p-nitrophenyl diphenyl phosphate (PNPDPP) and p-nitrophenyl hexanoate (PNPH) in cationic micelles at pH 8.2 and 25 degrees C. The deprotonated anionic forms of such reagents act as reactive species in the hydrolysis of ester. To rationalize the origin of their nucleophilic character, a detailed ab initio/DFT computational study has been performed on 1-5 along with additional hydroxybenzotriazole derivatives (6-13). The geometries of 1-hydroxybenzotriazoles (1-13) and their corresponding bases are discussed in detail. All calculations were carried out using different methods, i.e., restricted Hartree-Fock (RHF) and hybrid ab initio/DFT (B3LYP) using 6-31G and 6-31+G basis sets. Free energy of protonation ("fep") of the 1-hydroxybenzotriazoles (1-13), free energy of solvation DeltaG(aq), and the corresponding pK(a) values have been calculated. Solvation-free energies were calculated using density functional theory and the polarizable continuum model. In addition, to examine the reliability of calculated fep, benzaldehyde oxime (14) and 2-methyl propionaldehyde oxime (15) have been computed as reference systems using different methods and basis sets, the experimental feps of which are known. Our experimental finding shows that the compound 4 is the most effective catalyst for the hydrolytic cleavages of PNPDPP and PNPH. This has been predicted from our calculated fep, pK(a), and natural charge analysis results as well. In general, the introduction of electron-withdrawing substituents on 1-hydroxybenzotriazoles facilitates the lowering of pK(a) and fep. As the pK(a) values are lowered, a greater percentage of such hydroxybenzotriazoles remain in their deprotonated, anionic forms at pH 8.2. Since the anionic forms are nucleophilic, pK(a) lowering should enhance their ester cleaving capacity. However, such substitution also decreases the charge density on the catalytically active oxido atom (O(7)). Taking these two factors together, the derivatives are only modestly better nucleophiles in comparison to the parent 1-hydroxybenzotriazole. Interestingly, the introduction of electron-donating groups does not significantly enhance the charge accumulation on the oxido atom (O(7)) of 1-hydroxybenzotriazoles.
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Affiliation(s)
- V Praveen Kumar
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, India 560 012
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50
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Moore CL, Zivkovic A, Engels JW, Kuchta RD. Human DNA primase uses Watson-Crick hydrogen bonds to distinguish between correct and incorrect nucleoside triphosphates. Biochemistry 2004; 43:12367-74. [PMID: 15379576 DOI: 10.1021/bi0490791] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human DNA primase synthesizes short RNA primers that DNA polymerase alpha further elongates. Primase readily misincorporates the natural NTPs and will generate a wide variety of mismatches. In contrast, primase exhibited a remarkable resistance to polymerizing NTPs containing unnatural bases. This included bases whose shape was almost identical to the natural bases (4-aminobenzimidazole and 4,6-difluorobenzimidazole), bases shaped very differently than a natural base [e.g., 5- and 6-(trifluoromethyl)benzimidazole], bases much more hydrophobic than a natural base [e.g., 4- and 7-(trifluoromethyl)benzimidazole], bases of similar hydrophobicity as a natural base but with the Watson-Crick hydrogen-bonding groups in unusual positions (7-beta-D-guanine), and bases capable of forming only one Watson-Crick hydrogen bond with the template base (purine and 4-aminobenzimidazole). Primase only polymerized NTP analogues containing bases capable of forming hydrogen bonds between the equivalent of both N-1 and the exocyclic group at C-6 of a purine NTP (2-fluoroadenine, 2-chloroadenine, 3-deazaadenine, and hypoxanthine) and N-3 and the exocyclic group at C-4 of a pyrimidine. These data indicate that human primase requires the formation of Watson-Crick hydrogen bonds in order to polymerize a NTP, a situation very different than what is observed with some DNA polymerases. The implications of these results with respect to current theories of how polymerases discriminate between right and wrong (d)NTPs are discussed.
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Affiliation(s)
- Chad L Moore
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
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