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Abstract
High-quality crystals are essential to ensure high-resolution structural information. Protein crystals are controlled by many factors, such as pH, temperature, and the ion concentration of crystalline solutions. We previously reported the development of a device dedicated to protein crystallization. In the current study, we have further modified and improved our device. Exposure to external magnetic field leads to alignment of the crystal toward a preferred direction depending on the magnetization energy. Each material has different magnetic susceptibilities depending on the individual direction of their unit crystal cells. One of the strategies to acquire a large crystal entails controlling the nucleation rate. Furthermore, exposure of a crystal to a magnetic field may lead to new morphologies by affecting the crystal volume, shape, and quality.
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2
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Zhao H, Li Y, Zhu XQ. Thermodynamic Parameters of Elementary Steps for 3,5-Disubstituted 1,4-Dihydropyridines To Release Hydride Anions in Acetonitrile. ACS OMEGA 2018; 3:13598-13608. [PMID: 31458065 PMCID: PMC6645033 DOI: 10.1021/acsomega.8b01815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/09/2018] [Indexed: 06/10/2023]
Abstract
A series of 3,5-disubstituted 1,4-dihydropyridine derivatives including the derivative with two chiral centers, 6H (R2 = CH3, CH2Ph), as a new type of organic hydride source were synthesized and characterized. The thermodynamic driving forces (defined as enthalpy changes or standard redox potentials) of the 6 elementary steps for the organic hydrides to release hydride ions in acetonitrile were measured by isothermal titration calorimetry and electrochemical methods. The impacts of the substituents and functional groups bearing the N1 and C3/C5 positions on the thermodynamic driving forces of the 6 elementary steps were examined and analyzed. Moreover, the results showed that the reaction mechanism between the chiral organic hydride and activated ketone (ethyl benzoylformate) was identified as the concerted hydride transfer pathway based on the thermodynamic analysis platform. These valuable and crucial thermodynamic parameters will provide a broadly beneficial impact on the applications of 3,5-disubstituted 1,4-dihydropyridine derivatives in organic synthesis and pharmaceutical chemistry.
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Affiliation(s)
- Hui Zhao
- The
State Key Laboratory of Elemento-Organic Chemistry and Collaborative
Innovation Center of Chemical Science and Engineering (Tianjin), College
of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yang Li
- The
State Key Laboratory of Elemento-Organic Chemistry and Collaborative
Innovation Center of Chemical Science and Engineering (Tianjin), College
of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xiao-Qing Zhu
- The
State Key Laboratory of Elemento-Organic Chemistry and Collaborative
Innovation Center of Chemical Science and Engineering (Tianjin), College
of Chemistry, Nankai University, Tianjin 300071, P. R. China
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3
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Salehzadeh S, Maleki F. Where and How Does an Organic Molecule Having a C-X Bond Release X - Anion Like an Inorganic Compound? A Theoretical Study. J Phys Chem A 2018; 122:7598-7613. [PMID: 30200765 DOI: 10.1021/acs.jpca.8b07238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this research, at first, a comparative DFT study on hydride or fluoride release from a number of known orthoamides, their fluorine derivative having a central C-F bond and some simple organic compounds, is reported. The obtained data show that orthoamides release hydride or fluoride anions much easier than do other known organic compounds studied here. Interestingly, three simulated orthoamides having a central C-F bond, spontaneously and like an inorganic compound, release fluoride anion upon dissolving in polar solvents. The calculations confirmed that hyperconjugation interactions in the initial orthoamides facilitate the anion release from these compounds. However, the data clearly show that the proper overlap of an empty p orbital of the central carbon atom with adjacent lone-pair orbitals of nitrogen atoms ( lpN → lp*C or, in other words, the pπ-pπ interaction) in the resulting carbocations is a more important factor that must be taken into consideration when designing the hydride, fluoride, or other anion releasing agents. In addition, for the first time, a mechanism of hydride and fluoride removal from the orthoamides either through their reaction with BH3 and BF3 molecules, respectively, or upon their protonation is provided. To continue and for generalization of results to other groups attached to the central carbon atom of orthoamides, the reactions of H+ with orthoamides having the CH3, OH, CN, NH2, or C5H5 substituents were studied. The results showed that in all cases and in both gas and solution phases the above substituents easily leave the carbon atom as an anion and bond to H+. Thus, we have to conclude that upon the reaction of orthoamides with usual Lewis acids, many types of substituents on their central carbon atom can leave these compounds as anions.
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Affiliation(s)
- Sadegh Salehzadeh
- Department of Chemistry , Bu-Ali Sina University , Hamedan 65174 , Iran
| | - Farahnaz Maleki
- Department of Chemistry , Bu-Ali Sina University , Hamedan 65174 , Iran
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4
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Sapienza PJ, Lee AL. Widespread Perturbation of Function, Structure, and Dynamics by a Conservative Single-Atom Substitution in Thymidylate Synthase. Biochemistry 2016; 55:5702-5713. [PMID: 27649373 DOI: 10.1021/acs.biochem.6b00838] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TSase) is responsible for synthesizing the sole de novo source of dTMP in all organisms. TSase is a drug target, and as such, it has been well studied in terms of both structure and reaction mechanism. Cysteine 146 in Escherichia coli TSase is universally conserved because it serves as the nucleophile in the enzyme mechanism. Here we use the C146S mutation to probe the role of the sulfur atom in early events in the catalytic cycle beyond serving as the nucleophile. Surprisingly, the single-atom substitution severely decreases substrate binding affinity, and the unfavorable ΔΔG°bind is comprised of roughly equal enthalpic and entropic components at 25 °C. Chemical shifts in the free and dUMP-bound states show the mutation causes perturbations throughout TSase, including regions important for complex stability, in agreement with a less favorable enthalpy change. We measured the nuclear magnetic resonance methyl symmetry axis order parameter (S2axis), a proxy for conformational entropy, for TSase at all vertices of the dUMP binding/C146S mutation thermodynamic cycle and found that the calculated TΔΔS°conf is similar in sign and magnitude to the calorimetric TΔΔS°. Further, we ascribed minor resonances in wild-type-dUMP spectra to a state with a covalent bond between Sγ of C146 and C6 of dUMP and find S2axis values are unaffected by covalent bond formation, indicating this reaction step is neutral with respect to ΔS°conf. Lastly, the C146S mutation allowed us to measure cofactor analog binding by isothermal titration calorimetry without the confounding heat signature of covalent bond formation. Raltitrexed binds free and singly bound TSase with similar affinities, yet the two binding events have different enthalpy changes, providing further evidence of communication between the two active sites.
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Affiliation(s)
- Paul J Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Andrew L Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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5
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Singh P, Kumar A, Kaur S, Kaur J, Singh H. The bioinspired design of a reagent allows the functionalization of Cα-H of α,β-unsaturated carbonyl compounds via the Baylis-Hillman chemistry under ambient conditions. Chem Commun (Camb) 2016; 52:2936-9. [PMID: 26779574 DOI: 10.1039/c5cc08830e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A rationally designed reagent capable of affecting alkylation at Cα of α,β-unsaturated carbonyl compounds is reported. The reaction proceeded at room temperature without any additives. The pH and H-bond formation during the reaction play a key role in the working of the reagent.
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Affiliation(s)
- Palwinder Singh
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar-143005, India.
| | - Arun Kumar
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar-143005, India.
| | - Sukhmeet Kaur
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar-143005, India.
| | - Jagroop Kaur
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar-143005, India.
| | - Harpreet Singh
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar-143005, India.
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6
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Hori Y, Ida T, Mizuno M. A comparative theoretical study of the hydride transfer mechanisms during LiAlH 4 and LiBH 4 reductions. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2015.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Abeysinghe T, Hong B, Wang Z, Kohen A. Preserved hydride transfer mechanism in evolutionarily divergent thymidylate synthases. CURRENT TOPICS IN BIOCHEMICAL RESEARCH 2016; 17:19-30. [PMID: 28018055 PMCID: PMC5172458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Thymidylate synthase (TSase) catalyzes a hydride transfer in the last step of the de novo biosynthesis of the DNA nucleotide thymine. We compared two isozymes, namely, TSase from Escherichia coli (ecTSase) and TSase from Bacillus subtilis (bsTSase) that represent a case of divergent evolution. Interestingly, a highly conserved histidine (H147 of ecTSase) was proposed to serve a critical role in catalysis, but in bsTSase it is naturally substituted by valine (Val). Yet, bsTSase is more active than ecTSase, and the intrinsic kinetic isotope effects (KIEs) of both are temperature-independent, suggesting a similarly well-organized transition state (TS) for the catalyzed hydride transfer. To examine the role of that histidine (His) in TSase catalysis, we examined the kinetics of H147V ecTSase, which "bridges" between these two TSases. In contrast to both wild-type TSases, the single mutation results in deficient catalysis. The mutation leads to intrinsic KIEs that are temperature-dependent, indicating a substantial imperfection in its TS. The findings reveal two important features: a direct role of H147 in the hydride transfer step catalyzed by the ecTSase and the evolutionary compensation for its deficiency in bsTSase via extensive polymorphism across the protein. Very different active site residues are observed for these evolutionarily divergent isozymes, which result in a well-organized TS for both. It is suggested that evolutionary pressure compensated for the H to V substitution at the active site of bsTSase by polymorphism leading to a well-organized TS in both enzymes.
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Affiliation(s)
- Thelma Abeysinghe
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Baoyu Hong
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Genentech, South San Francisco, CA 94080, USA
| | - Zhen Wang
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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8
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Islam Z, Strutzenberg TS, Ghosh AK, Kohen A. Activation of Two Sequential H-transfers in the Thymidylate Synthase Catalyzed Reaction. ACS Catal 2015; 5:6061-6068. [PMID: 26576323 PMCID: PMC4643671 DOI: 10.1021/acscatal.5b01332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TSase) catalyzes the de novo biosynthesis of thymidylate, a precursor for DNA, and is thus an important target for chemotherapeutics and antibiotics. Two sequential C-H bond cleavages catalyzed by TSase are of particular interest: a reversible proton abstraction from the 2'-deoxy-uridylate substrate, followed by an irreversible hydride transfer forming the thymidylate product. QM/MM calculations of the former predicted a mechanism where the abstraction of the proton leads to formation of a novel nucleotide-folate intermediate that is not covalently bound to the enzyme (Wang, Z.; Ferrer, S.; Moliner, V.; Kohen, A. Biochemistry2013, 52, 2348-2358). Existence of such intermediate would hold promise as a target for a new class of drugs. Calculations of the subsequent hydride transfer predicted a concerted H-transfer and elimination of the enzymatic cysteine (Kanaan, N.; Ferrer, S.; Marti, S.; Garcia-Viloca, M.; Kohen, A.; Moliner, V. J. Am. Chem. Soc.2011, 133, 6692-6702). A key to both C-H activations is a highly conserved arginine (R166) that stabilizes the transition state of both H-transfers. Here we test these predictions by studying the R166 to lysine mutant of E. coli TSase (R166K) using intrinsic kinetic isotope effects (KIEs) and their temperature dependence to assess effects of the mutation on both chemical steps. The findings confirmed the predictions made by the QM/MM calculations, implicate R166 as an integral component of both reaction coordinates, and thus provide critical support to the nucleotide-folate intermediate as a new target for rational drug design.
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Affiliation(s)
- Zahidul Islam
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
| | | | - Ananda K. Ghosh
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
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9
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Singh P, Kumar A, Kaur S, Singh A. Thymidylate synthase inspired biomodel reagent for the conversion of uracil to thymine. Chem Commun (Camb) 2015; 51:9961-4. [PMID: 25997777 DOI: 10.1039/c5cc03312h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inspired by TSase catalysis for dUMP conversion to dTMP, a biomodel reagent is developed. The presence of NH2, Gly-(S)-Cys and (S)-oxiran methyl, at C5, C4 and N-10 of acridine, respectively, in addition to the pH of the reaction mixture, allows for good complementary inter- and intra-molecular interactions and chiral discrimination for the reagent to achieve conversion of uracil to thymine.
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Affiliation(s)
- Palwinder Singh
- Department of Chemistry, UGC Sponsored Centre for Advanced Studies, Guru Nanak Dev University, Amritsar-143005, India.
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10
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Khanna S, Kaur D, Kaur R. The saturated five-membered heterocyclic molecules as organic hydride donors: a computational study. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shweta Khanna
- Department of Chemistry; Guru Nanak Dev University; Amritsar 143005 India
| | - Damanjit Kaur
- Department of Chemistry; Guru Nanak Dev University; Amritsar 143005 India
| | - Rajinder Kaur
- Department of Chemistry; Guru Nanak Dev University; Amritsar 143005 India
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11
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Islam Z, Strutzenberg TS, Gurevic I, Kohen A. Concerted versus stepwise mechanism in thymidylate synthase. J Am Chem Soc 2014; 136:9850-3. [PMID: 24949852 PMCID: PMC4105062 DOI: 10.1021/ja504341g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymidylate synthase (TSase) catalyzes the intracellular de novo formation of thymidylate (a DNA building block) in most living organisms, making it a common target for chemotherapeutic and antibiotic drugs. Two mechanisms have been proposed for the rate-limiting hydride transfer step in TSase catalysis: a stepwise mechanism in which the hydride transfer precedes the cleavage of the covalent bond between the enzymatic cysteine and the product and a mechanism where both happen concertedly. Striking similarities between the enzyme-bound enolate intermediates formed in the initial and final step of the reaction supported the first mechanism, while QM/MM calculations favored the concerted mechanism. Here, we experimentally test these two possibilities using secondary kinetic isotope effect (KIE), mutagenesis study, and primary KIEs. The findings support the concerted mechanism and demonstrate the critical role of an active site arginine in substrate binding, activation of enzymatic nucleophile, and the hydride transfer studied here. The elucidation of this reduction/substitution sheds light on the critical catalytic step in TSase and may aid future drug or biomimetic catalyst design.
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Affiliation(s)
- Zahidul Islam
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242-1727, United States
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12
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Roston D, Islam Z, Kohen A. Isotope effects as probes for enzyme catalyzed hydrogen-transfer reactions. Molecules 2013; 18:5543-67. [PMID: 23673528 PMCID: PMC4342783 DOI: 10.3390/molecules18055543] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 11/16/2022] Open
Abstract
Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studies has changed our notion of how these enzymes exert their catalytic powers.
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Affiliation(s)
| | | | - Amnon Kohen
- Department of Chemistry, The University of Iowa, Iowa City, IA 52242, USA
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13
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Cheatum CM, Kohen A. Relationship of femtosecond-picosecond dynamics to enzyme-catalyzed H-transfer. Top Curr Chem (Cham) 2013; 337:1-39. [PMID: 23539379 PMCID: PMC4699684 DOI: 10.1007/128_2012_407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
At physiological temperatures, enzymes exhibit a broad spectrum of conformations, which interchange via thermally activated dynamics. These conformations are sampled differently in different complexes of the protein and its ligands, and the dynamics of exchange between these conformers depends on the mass of the group that is moving and the length scale of the motion, as well as restrictions imposed by the globular fold of the enzymatic complex. Many of these motions have been examined and their role in the enzyme function illuminated, yet most experimental tools applied so far have identified dynamics at time scales of seconds to nanoseconds, which are much slower than the time scale for H-transfer between two heavy atoms. This chemical conversion and other processes involving cleavage of covalent bonds occur on picosecond to femtosecond time scales, where slower processes mask both the kinetics and dynamics. Here we present a combination of kinetic and spectroscopic methods that may enable closer examination of the relationship between enzymatic C-H → C transfer and the dynamics of the active site environment at the chemically relevant time scale. These methods include kinetic isotope effects and their temperature dependence, which are used to study the kinetic nature of the H-transfer, and 2D IR spectroscopy, which is used to study the dynamics of transition-state- and ground-state-analog complexes. The combination of these tools is likely to provide a new approach to examine the protein dynamics that directly influence the chemical conversion catalyzed by enzymes.
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14
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Khan IA, Balaramnavar VM, Saxena AK. Identification and optimization of novel pyrimido-isoxazolidine and oxazine as selective hydride donors. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.09.105] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Experimental and theoretical studies of enzyme-catalyzed hydrogen-transfer reactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [PMID: 22607755 DOI: 10.1016/b978-0-12-398312-1.00006-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The mechanisms of enzyme-catalyzed reactions are medicinally important and present a fascinating intellectual challenge. Many experimental and theoretical techniques can shed light on these mechanisms, and here, we shall focus on the utility of kinetic isotope effects (KIEs) to study enzymatic reactions that involve hydrogen transfers. We will provide a short background on the prevailing models to interpret KIEs and then present more detailed reviews of two model enzymes: alcohol dehydrogenase and thymidylate synthase. These two examples provide a context to describe the types of experiments and theoretical calculations that drive this field forward and the kind of information each can furnish. We emphasize the importance of cooperation between experimentalists and theoreticians to continue the progress toward a comprehensive theory of enzyme catalysis.
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16
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Wang Z, Abeysinghe T, Finer-Moore JS, Stroud RM, Kohen A. A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase. J Am Chem Soc 2012; 134:17722-30. [PMID: 23034004 DOI: 10.1021/ja307859m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The role of protein flexibility in enzyme-catalyzed activation of chemical bonds is an evolving perspective in enzymology. Here we examine the role of protein motions in the hydride transfer reaction catalyzed by thymidylate synthase (TSase). Being remote from the chemical reaction site, the Y209W mutation of Escherichia coli TSase significantly reduces the protein activity, despite the remarkable similarity between the crystal structures of the wild-type and mutant enzymes with ligands representing their Michaelis complexes. The most conspicuous difference between these two crystal structures is in the anisotropic B-factors, which indicate disruption of the correlated atomic vibrations of protein residues in the mutant. This dynamically altered mutant allows a variety of small thiols to compete for the reaction intermediate that precedes the hydride transfer, indicating disruption of motions that preorganize the protein environment for this chemical step. Although the mutation causes higher enthalpy of activation of the hydride transfer, it only shows a small effect on the temperature dependence of the intrinsic KIE, suggesting marginal changes in the geometry and dynamics of the H-donor and -acceptor at the tunneling ready state. These observations suggest that the mutation disrupts the concerted motions that bring the H-donor and -acceptor together during the pre- and re-organization of the protein environment. The integrated structural and kinetic data allow us to probe the impact of protein motions on different time scales of the hydride transfer reaction within a complex enzymatic mechanism.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727, USA
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17
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Han X, Hao W, Zhu XQ, Parker VD. A Thermodynamic and Kinetic Study of Hydride Transfer of a Caffeine Derivative. J Org Chem 2012; 77:6520-9. [DOI: 10.1021/jo301042d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaozhen Han
- State Key Laboratory of Elemento-Organic
Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Weifang Hao
- Department of Chemistry and
Biochemistry, Utah State University, Logan,
Utah 84322, United States
| | - Xiao-Qing Zhu
- State Key Laboratory of Elemento-Organic
Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Vernon D. Parker
- Department of Chemistry and
Biochemistry, Utah State University, Logan,
Utah 84322, United States
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18
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19
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Zhu XQ, Li XT, Han SH, Mei LR. Conversion and Origin of Normal and Abnormal Temperature Dependences of Kinetic Isotope Effect in Hydride Transfer Reactions. J Org Chem 2012; 77:4774-83. [DOI: 10.1021/jo3005952] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiao-Qing Zhu
- State Key Laboratory
of Elemento-Organic Chemistry,
Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Xiu-Tao Li
- State Key Laboratory
of Elemento-Organic Chemistry,
Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Su-Hui Han
- State Key Laboratory
of Elemento-Organic Chemistry,
Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Lian-Rui Mei
- State Key Laboratory
of Elemento-Organic Chemistry,
Department of Chemistry, Nankai University, Tianjin 300071, China
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20
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Shi J, Huang XY, Wang HJ, Fu Y. Hydride Dissociation Energies of Six-Membered Heterocyclic Organic Hydrides Predicted by ONIOM-G4Method. J Chem Inf Model 2011; 52:63-75. [DOI: 10.1021/ci2001567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Shi
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
| | - Xiong-Yi Huang
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
| | - Hua-Jing Wang
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
| | - Yao Fu
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
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21
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Kanaan N, Ferrer S, Martí S, Garcia-Viloca M, Kohen A, Moliner V. Temperature dependence of the kinetic isotope effects in thymidylate synthase. A theoretical study. J Am Chem Soc 2011; 133:6692-702. [PMID: 21476498 PMCID: PMC3098132 DOI: 10.1021/ja1114369] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In recent years, the temperature dependence of primary kinetic isotope effects (KIE) has been used as indicator for the physical nature of enzyme-catalyzed H-transfer reactions. An interactive study where experimental data and calculations examine the same chemical transformation is a critical means to interpret more properly temperature dependence of KIEs. Here, the rate-limiting step of the thymidylate synthase-catalyzed reaction has been studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) simulations in the theoretical framework of the ensemble-averaged variational transition-state theory with multidimensional tunneling (EA-VTST/MT) combined with Grote-Hynes theory. The KIEs were calculated across the same temperature range examined experimentally, revealing a temperature independent behavior, in agreement with experimental findings. The calculations show that the H-transfer proceeds with ∼91% by tunneling in the case of protium and ∼80% when the transferred protium is replaced by tritium. Dynamic recrossing coefficients are almost invariant with temperature and in all cases far from unity, showing significant coupling between protein motions and the reaction coordinate. In particular, the relative movement of a conserved arginine (Arg166 in Escherichia coli ) promotes the departure of a conserved cysteine (Cys146 in E. coli ) from the dUMP by polarizing the thioether bond thus facilitating this bond breaking that takes place concomitantly with the hydride transfer. These promoting vibrations of the enzyme, which represent some of the dimensions of the real reaction coordinate, would limit the search through configurational space to efficiently find those decreasing both barrier height and width, thereby enhancing the probability of H-transfer by either tunneling (through barrier) or classical (over-the-barrier) mechanisms. In other words, the thermal fluctuations that are coupled to the reaction coordinate, together with transition-state geometries and tunneling, are the same in different bath temperatures (within the limited experimental range examined). All these terms contribute to the observed temperature independent KIEs in thymidylate synthase.
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Affiliation(s)
- Natalia Kanaan
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Silvia Ferrer
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - Mireia Garcia-Viloca
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
- Institute of Applied Radiation Chemistry, Technical University of Lodz, 90-924 Lodz, Poland
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22
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Wang Z, Kohen A. Thymidylate synthase catalyzed H-transfers: two chapters in one tale. J Am Chem Soc 2010; 132:9820-5. [PMID: 20575541 DOI: 10.1021/ja103010b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Examination of the nature of different bond activations along the same catalytic path is of general interest in chemistry and biology. In this report, we compare the physical nature of two sequential H-transfers in the same enzymatic reaction. Thymidylate synthase (TSase) catalyzes a complex reaction that involves many chemical transformations including two different C-H bond cleavages, a rate-limiting C-H-C hydride transfer and a non-rate-limiting C-H-O proton transfer. Although the large kinetic complexity imposes difficulties in studying the proton transfer catalyzed by TSase, we are able to experimentally extract the intrinsic kinetic isotope effects (KIEs) on both steps. In contrast with the hydride transfer, the intrinsic KIEs of the proton transfer are temperature dependent. The results are interpreted within the framework of the Marcus-like model. This interpretation suggests that TSase optimizes the donor-acceptor geometries for the slower and overall rate-limiting hydride transfer but not for the faster proton transfer.
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Affiliation(s)
- Zhen Wang
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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23
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Zhu XQ, Tan Y, Cao CT. Thermodynamic Diagnosis of the Properties and Mechanism of Dihydropyridine-Type Compounds as Hydride Source in Acetonitrile with “Molecule ID Card”. J Phys Chem B 2010; 114:2058-75. [DOI: 10.1021/jp911137p] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiao-Qing Zhu
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Yue Tan
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Chao-Tun Cao
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
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24
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Stojković V, Kohen A. Enzymatic H Transfers: Quantum Tunneling and Coupled Motion from Kinetic Isotope Effect Studies. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.163] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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RNA-assisted catalysis in a protein enzyme: The 2'-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase. Proc Natl Acad Sci U S A 2008; 105:17748-53. [PMID: 18997014 DOI: 10.1073/pnas.0804247105] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) join amino acids to 1 of 2 terminal hydroxyl groups of their cognate tRNAs, thereby contributing to the overall fidelity of protein synthesis. In class II histidyl-tRNA synthetase (HisRS) the nonbridging S(p)-oxygen of the adenylate is a potential general base for aminoacyl transfer. To test for conservation of this mechanism in other aaRSs and the role of terminal hydroxyls of tRNA in aminoacyl transfer, we investigated the class II Escherichia coli threonyl-tRNA synthetase (ThrRS). As with other class II aaRSs, the rate-determining step for ThrRS is amino acid activation. In ThrRS, however, the 2'-OH of A76 of tRNA(Thr) and a conserved active-site histidine (His-309) collaborate to catalyze aminoacyl transfer by a mechanism distinct from HisRS. Conserved residues in the ThrRS active site were replaced with alanine, and then the resulting mutant proteins were analyzed by steady-state and rapid kinetics. Nearly all mutants preferentially affected the amino acid activation step, with only a modest effect on aminoacyl transfer. By contrast, H309A ThrRS decreased transfer 242-fold and imposed a kinetic block to CCA accommodation. His-309 hydrogen bonds to the 2'-OH of A76, and substitution of the latter by hydrogen or fluorine decreased aminoacyl transfer by 763- and 94-fold, respectively. The proton relay mechanism suggested by these data to promote aminoacylation is reminiscent of the NAD(+)-dependent mechanisms of alcohol dehydrogenases and sirtuins and the RNA-mediated catalysis of the ribosomal peptidyl transferase center.
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26
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Calò S, Tondi D, Ferrari S, Venturelli A, Ghelli S, Costi MP. Constrained Dansyl Derivatives Reveal Bacterial Specificity of Highly Conserved Thymidylate Synthases. Chembiochem 2008; 9:779-90. [DOI: 10.1002/cbic.200700524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Jarmuła A, Dowierciał A, Rode W. A molecular modeling study of the interaction of 2'-fluoro-substituted analogues of dUMP/FdUMP with thymidylate synthase. Bioorg Med Chem Lett 2008; 18:2701-8. [PMID: 18362071 DOI: 10.1016/j.bmcl.2008.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 03/03/2008] [Accepted: 03/06/2008] [Indexed: 10/22/2022]
Abstract
Molecular dynamics simulations and free energy calculations are presented, exploring previously described experimentally studied interactions of a series of 2'-fluoro-substituted dUMP/FdUMP analogues with thymidylate synthase (TS). The results show the inhibitory behaviors of 2'-F-ara-UMP, 2',2''-diF-dUMP and 2',5-diF-ara-UMP to be dependent upon the binding positions and orientations adopted by the molecules of these compounds in the active site of TS. The binding mode of 2',5-diF-ara-UMP suggests a novel role of the active site residue Trp 80, stabilizing through hydrophobic stacking the binding position of the pyrimidine ring in 2',5-diF-ara-UMP.
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Affiliation(s)
- Adam Jarmuła
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warszawa, Poland.
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28
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Arvizu-Flores AA, Sugich-Miranda R, Arreola R, Garcia-Orozco KD, Velazquez-Contreras EF, Montfort WR, Maley F, Sotelo-Mundo RR. Role of an invariant lysine residue in folate binding on Escherichia coli thymidylate synthase: calorimetric and crystallographic analysis of the K48Q mutant. Int J Biochem Cell Biol 2008; 40:2206-17. [PMID: 18403248 PMCID: PMC2533807 DOI: 10.1016/j.biocel.2008.02.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 02/20/2008] [Accepted: 02/27/2008] [Indexed: 11/25/2022]
Abstract
Thymidylate synthase (TS) catalyzes the reductive methylation of deoxyuridine monophosphate (dUMP) using methylene tetrahydrofolate (CH(2)THF) as cofactor, the glutamate tail of which forms a water-mediated hydrogen bond with an invariant lysine residue of this enzyme. To understand the role of this interaction, we studied the K48Q mutant of Escherichia coli TS using structural and biophysical methods. The k(cat) of the K48Q mutant was 430-fold lower than wild-type TS in activity, while the K(m) for the (R)-stereoisomer of CH(2)THF was 300 microM, about 30-fold larger than K(m) from the wild-type TS. Affinity constants were determined using isothermal titration calorimetry, which showed that binding was reduced by one order of magnitude for folate-like TS inhibitors, such as propargyl-dideazafolate (PDDF) or compounds that distort the TS active site like BW1843U89 (U89). The crystal structure of the K48Q-dUMP complex revealed that dUMP binding is not impaired in the mutant, and that U89 in a ternary complex of K48Q-nucleotide-U89 was bound in the active site with subtle differences relative to comparable wild-type complexes. PDDF failed to form ternary complexes with K48Q and dUMP. Thermodynamic data correlated with the structural determinations, since PDDF binding was dominated by enthalpic effects while U89 had an important entropic component. In conclusion, K48 is critical for catalysis since it leads to a productive CH(2)THF binding, while mutation at this residue does not affect much the binding of inhibitors that do not make contact with this group.
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Affiliation(s)
- Aldo A. Arvizu-Flores
- Aquatic Molecular Biology Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, México 83000
| | - Rocio Sugich-Miranda
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Sonora, México
| | - Rodrigo Arreola
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF 04510
| | - Karina D. Garcia-Orozco
- Aquatic Molecular Biology Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, México 83000
| | | | - William R. Montfort
- Department of Biochemistry and Molecular Biophysics, The University of Arizona, Tucson, Arizona 85721, USA
| | - Frank Maley
- Wadsworth Center, New York State Department of Health, Albany, New York, 12201, USA
| | - Rogerio R. Sotelo-Mundo
- Aquatic Molecular Biology Laboratory, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, México 83000
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29
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Zhu XQ, Zhang MT, Yu A, Wang CH, Cheng JP. Hydride, Hydrogen Atom, Proton, and Electron Transfer Driving Forces of Various Five-Membered Heterocyclic Organic Hydrides and Their Reaction Intermediates in Acetonitrile. J Am Chem Soc 2008; 130:2501-16. [DOI: 10.1021/ja075523m] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiao-Qing Zhu
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Ming-Tian Zhang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Ao Yu
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Chun-Hua Wang
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Jin-Pei Cheng
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
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30
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Shi FQ, Li X, Xia Y, Zhang L, Yu ZX. DFT Study of the Mechanisms of In Water Au(I)-Catalyzed Tandem [3,3]-Rearrangement/Nazarov Reaction/[1,2]-Hydrogen Shift of Enynyl Acetates: A Proton-Transport Catalysis Strategy in the Water-Catalyzed [1,2]-Hydrogen Shift. J Am Chem Soc 2007; 129:15503-12. [DOI: 10.1021/ja071070+] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Hong B, Maley F, Kohen A. Role of Y94 in proton and hydride transfers catalyzed by thymidylate synthase. Biochemistry 2007; 46:14188-97. [PMID: 17999469 DOI: 10.1021/bi701363s] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymidylate synthase (TS) catalyzes the substitution of a carbon-bound proton in a uracil base by a methyl group to yield thymine in the de novo biosynthesis of this DNA base. The enzymatic mechanism involves making and breaking several covalent bonds. Traditionally, a conserved tyrosine (Y94 in Escherichia coli, Y146 in Lactobacillus casei, and Y135 in humans) was assumed to serve as the general base catalyzing the proton abstraction. That assumption was examined here by comparing the nature of the proton abstraction using wild-type (wt) E. coli TS (ecTS) and its Y94F mutant (with a turnover rate reduced by 2 orders of magnitude). A subsequent hydride transfer was also studied using the wt and Y94F. The physical nature of both H-transfer steps was examined by determining intrinsic kinetic isotope effects (KIEs). Surprisingly, the findings did not suggest a direct role for Y94 in the proton abstraction step. The effect of this mutation on the subsequent hydride transfer was examined by a comparison of the temperature dependency of the intrinsic KIE on both the wt and the mutant. The intrinsic KIEs for Y94F at physiological temperatures were slightly smaller than those for wt but, otherwise, were as temperature-independent, suggesting a perfectly preorganized reaction coordinate for both enzymes. At reduced temperatures, however, the KIE for the mutant increased with a decrease in temperature, indicating a poorly preorganized reaction coordinate. Other kinetic and structural properties were also compared, and the findings suggested that Y94 is part of a H-bond network that plays a critical role at a step between the proton and the hydride transfers, presumably the dissociation of H4folate from the covalently bound intermediate. The possibility that no single residue serves as the general base in question but, rather, that the whole network of H-bonds at the active site catalyzes proton abstraction is discussed.
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Affiliation(s)
- Baoyu Hong
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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