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Fontecilla-Camps JC. The Complex Roles of Adenosine Triphosphate in Bioenergetics. Chembiochem 2022; 23:e202200064. [PMID: 35353443 DOI: 10.1002/cbic.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/16/2022] [Indexed: 11/09/2022]
Abstract
ATP is generally defined as the "energy currency" of the cell. Its phosphoanhydride P-O bonds are often considered to be "high energy" linkages that release free energy when broken, and its hydrolysis is described as "strongly exergonic". However, breaking bonds cannot release energy and ATP hydrolysis in motor and active transport proteins is not "strongly exergonic". So, the relevance of ATP resides elsewhere. As important as the nucleotide are the proteins that undergo functionally relevant conformational changes upon both ATP binding and release of ADP and inorganic phosphate. ATP phosphorylates proteins for signaling, active transport, and substrates in condensation reactions. The ensuing dephosphorylation has different consequences in each case. In signaling and active transport the phosphate group is hydrolyzed whereas in condensation reactions the phosphoryl fragment acts as a dehydrating agent. As it will be discussed in this article, ATP does much more than simply contribute free energy to biological processes.
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2
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Alabugin IV, Kuhn L, Krivoshchapov NV, Mehaffy P, Medvedev MG. Anomeric effect, hyperconjugation and electrostatics: lessons from complexity in a classic stereoelectronic phenomenon. Chem Soc Rev 2021; 50:10212-10252. [PMID: 34542133 DOI: 10.1039/d1cs00564b] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the interplay of multiple components (steric, electrostatic, stereoelectronic, dispersive, etc.) that define the overall energy, structure, and reactivity of organic molecules can be a daunting task. The task becomes even more difficult when multiple approaches based on different physical premises disagree in their analysis of a multicomponent molecular system. Herein, we will use a classic conformational "oddity", the anomeric effect, to discuss the value of identifying the key contributors to reactivity that can guide chemical predictions. After providing the background related to the relevant types of hyperconjugation and a brief historic outline of the origins of the anomeric effect, we outline variations of its patterns and provide illustrative examples for the role of the anomeric effect in structure, stability, and spectroscopic properties. We show that the complete hyperconjugative model remains superior in explaining the interplay between structure and reactivity. We will use recent controversies regarding the origin of the anomeric effect to start a deeper discussion relevant to any electronic effect. Why are such questions inherently controversial? How to describe a complex quantum system using a model that is "as simple as possible, but no simpler"? What is a fair test for such a model? Perhaps, instead of asking "who is right and who is wrong?" one should ask "why do we disagree?". Stereoelectronic thinking can reconcile quantum complexity with chemical intuition and build the conceptual bridge between structure and reactivity. Even when many factors contribute to the observed structural and conformational trends, electron delocalization is a dominating force when the electronic demand is high (i.e., bonds are breaking as molecules distort from their equilibrium geometries). In these situations, the role of orbital interactions increases to the extent where they can define reactivity. For example, negative hyperconjugation can unleash the "underutilized" stereoelectronic power of unshared electrons (i.e., the lone pairs) to stabilize a developing positive charge at an anomeric carbon. This analysis paves the way for the broader discussion of the omnipresent importance of negative hyperconjugation in oxygen-containing functional groups. From that point of view, the stereoelectronic component of the anomeric effect plays a unique role in guiding reaction design.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation. .,Lomonosov Moscow State University, Leninskie Gory 1 (3), Moscow, 119991, Russian Federation
| | - Patricia Mehaffy
- Department of Chemistry and Biochemistry, Florida State University, USA.
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation. .,A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova St., 119991 Moscow, Russian Federation
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3
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Alabugin IV, Kuhn L, Medvedev MG, Krivoshchapov NV, Vil' VA, Yaremenko IA, Mehaffy P, Yarie M, Terent'ev AO, Zolfigol MA. Stereoelectronic power of oxygen in control of chemical reactivity: the anomeric effect is not alone. Chem Soc Rev 2021; 50:10253-10345. [PMID: 34263287 DOI: 10.1039/d1cs00386k] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although carbon is the central element of organic chemistry, oxygen is the central element of stereoelectronic control in organic chemistry. Generally, a molecule with a C-O bond has both a strong donor (a lone pair) and a strong acceptor (e.g., a σ*C-O orbital), a combination that provides opportunities to influence chemical transformations at both ends of the electron demand spectrum. Oxygen is a stereoelectronic chameleon that adapts to the varying situations in radical, cationic, anionic, and metal-mediated transformations. Arguably, the most historically important stereoelectronic effect is the anomeric effect (AE), i.e., the axial preference of acceptor groups at the anomeric position of sugars. Although AE is generally attributed to hyperconjugative interactions of σ-acceptors with a lone pair at oxygen (negative hyperconjugation), recent literature reports suggested alternative explanations. In this context, it is timely to evaluate the fundamental connections between the AE and a broad variety of O-functional groups. Such connections illustrate the general role of hyperconjugation with oxygen lone pairs in reactivity. Lessons from the AE can be used as the conceptual framework for organizing disjointed observations into a logical body of knowledge. In contrast, neglect of hyperconjugation can be deeply misleading as it removes the stereoelectronic cornerstone on which, as we show in this review, the chemistry of organic oxygen functionalities is largely based. As negative hyperconjugation releases the "underutilized" stereoelectronic power of unshared electrons (the lone pairs) for the stabilization of a developing positive charge, the role of orbital interactions increases when the electronic demand is high and molecules distort from their equilibrium geometries. From this perspective, hyperconjugative anomeric interactions play a unique role in guiding reaction design. In this manuscript, we discuss the reactivity of organic O-functionalities, outline variations in the possible hyperconjugative patterns, and showcase the vast implications of AE for the structure and reactivity. On our journey through a variety of O-containing organic functional groups, from textbook to exotic, we will illustrate how this knowledge can predict chemical reactivity and unlock new useful synthetic transformations.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Leah Kuhn
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Michael G Medvedev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation.,A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilova St., 119991 Moscow, Russian Federation
| | - Nikolai V Krivoshchapov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation.,Lomonosov Moscow State University, Leninskie Gory 1 (3), Moscow, 119991, Russian Federation
| | - Vera A Vil'
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Ivan A Yaremenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Patricia Mehaffy
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| | - Meysam Yarie
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65167, Iran
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., 119991 Moscow, Russian Federation
| | - Mohammad Ali Zolfigol
- Department of Organic Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65167, Iran
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4
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Synthesis and characterizations of fluorophosphoryl diazide and diisocyanate. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2020.109694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Unusual resistance of cobalt bis dicarbollide phosphate and phosphorothioate bridged esters towards alkaline hydrolysis: The “metallacarborane effect”. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Lu X, Duchimaza-Heredia J, Cui Q. Analysis of Density Functional Tight Binding with Natural Bonding Orbitals. J Phys Chem A 2019; 123:7439-7453. [PMID: 31373822 DOI: 10.1021/acs.jpca.9b05072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The description of chemical bonding by the density functional tight binding (DFTB) model is analyzed using natural bonding orbitals (NBOs) and compared to results from density functional theory (B3LYP/aug-cc-pVTZ) calculations. Several molecular systems have been chosen to represent fairly diverse bonding scenarios that include standard covalent bonds, hypervalent interactions, multicenter bonds, metal-ligand interactions (with and without the pseudo-Jahn-Teller effect), and through-space donor-acceptor interactions. Overall, the results suggest that DFTB3/3OB provides physically sound descriptions for the different bonding scenarios analyzed here, as reflected by the general agreement between DFTB3 and B3LYP NBO properties, such as the nature of the NBOs, the magnitudes of natural charges and bond orders, and the dominant donor-acceptor interactions. The degree of ligand-to-metal charge transfer and the ionic nature of pentavalent phosphate are overestimated, likely reflecting the minimal-basis nature of DFTB3/3OB. Moreover, certain orbital interactions, such as geminal interactions, are observed to be grossly overestimated by DFTB3 for hypervalent phosphate and several transition metal compounds that involve copper and nickel. The study indicates that results from NBO analysis can be instructive for identifying electronic structure descriptions at the approximate quantum-mechanical level that require improvement and thus for guiding the systematic improvement of these methods.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
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7
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Takahashi H, Umino S, Miki Y, Ishizuka R, Maeda S, Morita A, Suzuki M, Matubayasi N. Drastic Compensation of Electronic and Solvation Effects on ATP Hydrolysis Revealed through Large-Scale QM/MM Simulations Combined with a Theory of Solutions. J Phys Chem B 2017; 121:2279-2287. [PMID: 28222598 DOI: 10.1021/acs.jpcb.7b00637] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy, ΔGhyd, of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd. It was revealed that the electronic-state contribution in ΔGhyd is largely negative (favorable) upon hydrolysis, due to the reduction of electrostatic repulsion accompanying the breakage of the P-O bond. In contrast, the solvation effect was found to be strongly more favorable on the reactant side. Thus, we showed that a drastic compensation of the two opposite effects takes place, leading to the modest value of ΔGhyd at each number of excess electrons examined. The computational analyses were also conducted for pyrophosphate ions (PPi), and the parallelism between the ATP and PPi hydrolyses was confirmed. Classical molecular dynamics simulation was further carried out to discuss the effect of the solvent environment; the insensitivity of ΔGhyd to the number of excess electrons was seen to hold in solvent water and ethanol.
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Affiliation(s)
- Hideaki Takahashi
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Satoru Umino
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Yuji Miki
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Ryosuke Ishizuka
- Department of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Shu Maeda
- Department of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Akihiro Morita
- Department of Chemistry, Graduate School of Science, Tohoku University , Sendai, Miyagi 980-8578, Japan
| | - Makoto Suzuki
- Department of Materials Processing, Graduate School of Engineering, Tohoku University , Sendai, Miyagi 980-8579, Japan
| | - Nobuyuki Matubayasi
- Department of Chemical Engineering, Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
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8
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Foster CA, West AH. Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. Proteins 2016; 85:155-176. [PMID: 27802580 PMCID: PMC5242315 DOI: 10.1002/prot.25207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023]
Abstract
Two‐component signaling (TCS) is the primary means by which bacteria, as well as certain plants and fungi, respond to external stimuli. Signal transduction involves stimulus‐dependent autophosphorylation of a sensor histidine kinase and phosphoryl transfer to the receiver domain of a downstream response regulator. Phosphorylation acts as an allosteric switch, inducing structural and functional changes in the pathway's components. Due to their transient nature, phosphorylated receiver domains are challenging to characterize structurally. In this work, we provide a methodology for simulating receiver domain phosphorylation to predict conformations that are nearly identical to experimental structures. Using restrained molecular dynamics, phosphorylated conformations of receiver domains can be reliably sampled on nanosecond timescales. These simulations also provide data on conformational dynamics that can be used to identify regions of functional significance related to phosphorylation. We first validated this approach on several well‐characterized receiver domains and then used it to compare the upstream and downstream components of the fungal Sln1 phosphorelay. Our results demonstrate that this technique provides structural insight, obtained in the absence of crystallographic or NMR information, regarding phosphorylation‐induced conformational changes in receiver domains that regulate the output of their associated signaling pathway. To our knowledge, this is the first time such a protocol has been described that can be broadly applied to TCS proteins for predictive purposes. Proteins 2016; 85:155–176. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Clay A Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
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9
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Gong D, Pan W, Zhu T, Chen H, Zhou Z, Jiang F, Hu Y, Zhang X. Polymerization of 1,3-butadiene catalyzed by a thermal robust, high selective and active iron catalyst: An applicable recipe for producing syndiotactic 1,2-polybutadiene. POLYMER 2016. [DOI: 10.1016/j.polymer.2016.06.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Liz DG, Manfredi AM, Medeiros M, Montecinos R, Gómez-González B, Garcia-Rio L, Nome F. Supramolecular phosphate transfer catalysis by pillar[5]arene. Chem Commun (Camb) 2016; 52:3167-70. [DOI: 10.1039/c5cc10214f] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester destabilization inside pillar[5]arene due to disrupting the H-bonding to water speed its hydrolysis reaction.
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Affiliation(s)
- Daiane G. Liz
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Alex M. Manfredi
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Michelle Medeiros
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Rodrigo Montecinos
- Facultad de Química
- Pontificia Universidad Católica de Chile
- Santiago
- Chile
| | - Borja Gómez-González
- Departamento de Química Física
- Centro de Investigaciónen Química Biológica y Materiales Moleculares (CIQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Luis Garcia-Rio
- Departamento de Química Física
- Centro de Investigaciónen Química Biológica y Materiales Moleculares (CIQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Faruk Nome
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
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11
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Strieter ER, Andrew TL. Restricting the ψ Torsion Angle Has Stereoelectronic Consequences on a Scissile Bond: An Electronic Structure Analysis. Biochemistry 2015; 54:5748-56. [PMID: 26332921 DOI: 10.1021/acs.biochem.5b00845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein motion is intimately linked to enzymatic catalysis, yet the stereoelectronic changes that accompany different conformational states of a substrate are poorly defined. Here we investigate the relationship between conformation and stereoelectronic effects of a scissile amide bond. Structural studies have revealed that the C-terminal glycine of ubiquitin and ubiquitin-like proteins adopts a syn (ψ ∼ 0°) or gauche (ψ ∼ ±60°) conformation upon interacting with deubiquitinases/ubiquitin-like proteases. We used hybrid density functional theory and natural bond orbital analysis to understand how the stereoelectronic effects of the scissile bond change as a function of φ and ψ torsion angles. This led to the discovery that when ψ is between 30° and -30° the scissile bond becomes geometrically and electronically deformed. Geometric distortion occurs through pyramidalization of the carbonyl carbon and amide nitrogen. Electronic distortion is manifested by a decrease in the strength of the donor-acceptor interaction between the amide nitrogen and antibonding orbital (π*) of the carbonyl. Concomitant with the reduction in nN → π* delocalization energy, the sp(2) hybrid orbital of the carbonyl carbon becomes richer in p-character, suggesting the syn configuration causes the carbonyl carbon hybrid orbitals to adopt a geometry reminiscent of a tetrahedral-like intermediate. Our work reveals important insights into the role of substrate conformation in activating the reactive carbonyl of a scissile bond. These findings have implications for designing potent active site inhibitors based on the concept of transition state analogues.
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Affiliation(s)
- Eric R Strieter
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Trisha L Andrew
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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12
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Abstract
Historically, the chemistry of phosphate transfer-a class of reactions fundamental to the chemistry of Life-has been discussed almost exclusively in terms of the nucleophile and the leaving group. Reactivity always depends significantly on both factors; but recent results for reactions of phosphate triesters have shown that it can also depend strongly on the nature of the nonleaving or "spectator" groups. The extreme stabilities of fully ionised mono- and dialkyl phosphate esters can be seen as extensions of the same effect, with one or two triester OR groups replaced by O(-). Our chosen lead reaction is hydrolysis-phosphate transfer to water: because water is the medium in which biological chemistry takes place; because the half-life of a system in water is an accepted basic index of stability; and because the typical mechanisms of hydrolysis, with solvent H2O providing specific molecules to act as nucleophiles and as general acids or bases, are models for reactions involving better nucleophiles and stronger general species catalysts. Not least those available in enzyme active sites. Alkyl monoester dianions compete with alkyl diester monoanions for the slowest estimated rates of spontaneous hydrolysis. High stability at physiological pH is a vital factor in the biological roles of organic phosphates, but a significant limitation for experimental investigations. Almost all kinetic measurements of phosphate transfer reactions involving mono- and diesters have been followed by UV-visible spectroscopy using activated systems, conveniently compounds with good leaving groups. (A "good leaving group" OR* is electron-withdrawing, and can be displaced to generate an anion R*O(-) in water near pH 7.) Reactivities at normal temperatures of P-O-alkyl derivatives-better models for typical biological substrates-have typically had to be estimated: by extended extrapolation from linear free energy relationships, or from rate measurements at high temperatures. Calculation is free from these limitations, able to handle very slow reactions as readily as very fast ones, and capable of predicting rate constants with levels of accuracy acceptable to the experimentalist. We present an updated overview of phosphate transfer, with particular reference to the mechanisms of the reactions of alkyl derivatives and triesters. The intention is to present a holistic (not comprehensive!) overview of the reactivity of typical phosphate esters, in terms familiar to the working chemist, at a level sufficient to support informed predictions of reactivity for structures of interest.
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Affiliation(s)
- Anthony J. Kirby
- University Chemical Laboratory, Cambridge CB2 1EW, United Kingdom
| | - Faruk Nome
- Departamento
de Química, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-900 Brazil
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13
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Ning Y, Gao M, Zheng K, Zhang Z, Zhou J, Hao X, Cao R. Phosphate monoester hydrolysis at tricopper site: The advantage and disadvantage of closely assembled trimetallic active sites. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcata.2015.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Mermer A, Lis T, Starynowicz P. Charge density distribution and theoretical analysis of low and high energy phosphate esters. RSC Adv 2015. [DOI: 10.1039/c5ra12605c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
There is a strict relation between the energy of hydrolysis of phosphate esters and the extent of interactions between the p ester oxygen lone pair and the antibonding orbitals of the rest of the molecule. Its impact on experimental charge density distribution is analyzed.
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Affiliation(s)
- Adrian Mermer
- Wydział Chemii
- Uniwersytet Wrocławski
- 50-383 Wrocław
- Poland
| | - Tadeusz Lis
- Wydział Chemii
- Uniwersytet Wrocławski
- 50-383 Wrocław
- Poland
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15
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Summerton JC, Martin GM, Evanseck JD, Chapman MS. Common hydrogen bond interactions in diverse phosphoryl transfer active sites. PLoS One 2014; 9:e108310. [PMID: 25238155 PMCID: PMC4169622 DOI: 10.1371/journal.pone.0108310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/27/2014] [Indexed: 11/18/2022] Open
Abstract
Phosphoryl transfer reactions figure prominently in energy metabolism, signaling, transport and motility. Prior detailed studies of selected systems have highlighted mechanistic features that distinguish different phosphoryl transfer enzymes. Here, a top-down approach is developed for comparing statistically the active site configurations between populations of diverse structures in the Protein Data Bank, and it reveals patterns of hydrogen bonding that transcend enzyme families. Through analysis of large samples of structures, insights are drawn at a level of detail exceeding the experimental precision of an individual structure. In phosphagen kinases, for example, hydrogen bonds with the O3β of the nucleotide substrate are revealed as analogous to those in unrelated G proteins. In G proteins and other enzymes, interactions with O3β have been understood in terms of electrostatic favoring of the transition state. Ground state quantum mechanical calculations on model compounds show that the active site interactions highlighted in our database analysis can affect substrate phosphate charge and bond length, in ways that are consistent with prior experimental observations, by modulating hyperconjugative orbital interactions that weaken the scissile bond. Testing experimentally the inference about the importance of O3β interactions in phosphagen kinases, mutation of arginine kinase Arg280 decreases kcat, as predicted, with little impact upon KM.
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Affiliation(s)
- Jean C. Summerton
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Gregory M. Martin
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
| | - Jeffrey D. Evanseck
- Center for Computational Sciences and the Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Michael S. Chapman
- Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health and Science University, Portland, Oregon, United States of America
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16
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Brandão TAS. Linear correlation between effective charge and bond length sensitivity to electronic effects in phosphoryl, sulfonyl, and sulfuryl compounds. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tiago A. S. Brandão
- Departamento de Química, ICEX; Universidade Federal de Minas Gerais; Belo Horizonte Minas Gerais 31270-901, Brazil
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17
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Summerton JC, Evanseck JD, Chapman MS. Hyperconjugation-mediated solvent effects in phosphoanhydride bonds. J Phys Chem A 2012; 116:10209-17. [PMID: 23009395 DOI: 10.1021/jp306607k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory and natural bond orbital analysis are used to explore the impact of solvent on hyperconjugation in methyl triphosphate, a model for "energy rich" phosphoanhydride bonds, such as found in ATP. As expected, dihedral rotation of a hydroxyl group vicinal to the phosphoanhydride bond reveals that the conformational dependence of the anomeric effect involves modulation of the orbital overlap between the donor and acceptor orbitals. However, a conformational independence was observed in the rotation of a solvent hydrogen bond. As one lone pair orbital rotates away from an optimal antiperiplanar orientation, the overall magnitude of the anomeric effect is compensated approximately by the other lone pair as it becomes more antiperiplanar. Furthermore, solvent modulation of the anomeric effect is not restricted to the antiperiplanar lone pair; hydrogen bonds involving gauche lone pairs also affect the anomeric interaction and the strength of the phosphoanhydride bond. Both gauche and anti solvent hydrogen bonds lengthen nonbridging O-P bonds, increasing the distance between donor and acceptor orbitals and decreasing orbital overlap, which leads to a reduction of the anomeric effect. Solvent effects are additive with greater reduction in the anomeric effect upon increasing water coordination. By controlling the coordination environment of substrates in an active site, kinases, phosphatases, and other enzymes important in metabolism and signaling may have the potential to modulate the stability of individual phosphoanhydride bonds through stereoelectronic effects.
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Affiliation(s)
- Jean C Summerton
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Mail Code L224, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239-3098, USA
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18
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Hong J, Yoshida N, Chong SH, Lee C, Ham S, Hirata F. Elucidating the Molecular Origin of Hydrolysis Energy of Pyrophosphate in Water. J Chem Theory Comput 2012; 8:2239-46. [DOI: 10.1021/ct300099e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jooyeon Hong
- Department of Chemistry, Sookmyung Women’s University, Cheongpa-ro 47-gil
100, Yongsan-Ku, Seoul 140-742, Korea
| | - Norio Yoshida
- Department of Chemistry, Faculty
of Sciences, Kyusyu University, Fukuoka
812-8581, Japan
| | - Song-Ho Chong
- Department of Chemistry, Sookmyung Women’s University, Cheongpa-ro 47-gil
100, Yongsan-Ku, Seoul 140-742, Korea
| | - Chewook Lee
- Department of Chemistry, Sookmyung Women’s University, Cheongpa-ro 47-gil
100, Yongsan-Ku, Seoul 140-742, Korea
| | - Sihyun Ham
- Department of Chemistry, Sookmyung Women’s University, Cheongpa-ro 47-gil
100, Yongsan-Ku, Seoul 140-742, Korea
| | - Fumio Hirata
- Department
of Theoretical Molecular
Science, Institute for Molecular Science, Okazaki 444-8585, Japan
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19
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Glaves R, Mathias G, Marx D. Mechanistic insights into the hydrolysis of a nucleoside triphosphate model in neutral and acidic solution. J Am Chem Soc 2012; 134:6995-7000. [PMID: 22468651 DOI: 10.1021/ja2101533] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleoside triphosphate hydrolysis is an essential component of all living systems. Despite extensive research, the exact modus and mechanism of this ubiquitous reaction still remain elusive. In this work, we examined the detailed hydrolysis mechanisms of a model nucleoside triphosphate in acidic and neutral solution by means of ab initio simulations. The timescale of the reaction was accessed through use of an accelerated sampling method, metadynamics. Both hydrolyses were found to proceed via different mechanisms; the acidic system reacted by means of concerted general acid catalysis (found to be a so-called D(N)A(N)A(H)D(xh) mechanism), whereas the neutral system reacted by way of a different mechanism (namely, D(N)*A(N)D(xh)A(H)). A neighboring water molecule took on the role of a general base in both systems, which has not been seen before but is a highly plausible reaction path, meaning that substrate-assisted catalysis was not observed in the bulk water environment.
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Affiliation(s)
- Rachel Glaves
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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20
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Rudbeck ME, Nilsson Lill SO, Barth A. Influence of the molecular environment on phosphorylated amino acid models: a density functional theory study. J Phys Chem B 2012; 116:2751-7. [PMID: 22303954 DOI: 10.1021/jp206414d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A protein environment can affect the structure and charge distribution of substrate molecules. Here, the structure and partial charges were studied for different phosphorylated amino acid models in varying environments using density functional theory. The three systems investigated, acetyl phosphate, methyl phosphate, and p-tolyl phosphate are representative models for aspartyl phosphate, serine or threonine phosphate, and tyrosine phosphate, respectively. Combined with the CPCM continuum model, explicit HF and H(2)O molecules were added in order to model environmental effects and interactions that may occur in a protein matrix. We show how the different interactions affect the scissile P-O(R) bond and that the elongation can be explained by an anomeric effect. An increasing scissile bond length will result in transfer of negative charge to the leaving group and in a widening of the angle between the terminal oxygens of the phosphate molecule, features that can expose the phosphate group to attacking nucleophiles. Lastly, calculations were performed on the active site of the Ca(2+)-ATPase E2P intermediate, which provide an example of how a protein environment facilitates the formation of a destabilized ground state.
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Affiliation(s)
- Maria E Rudbeck
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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21
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Ramanathan N, Sundararajan K, Kar BP, Viswanathan KS. Conformations of Trimethyl Phosphite: A Matrix Isolation Infrared and ab Initio Study. J Phys Chem A 2011; 115:10059-68. [DOI: 10.1021/jp205368k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N. Ramanathan
- Chemistry Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
| | - K. Sundararajan
- Chemistry Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
| | - Bishnu Prasad Kar
- Chemistry Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
| | - K. S. Viswanathan
- Chemistry Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603 102, India
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22
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Focus on phosphoaspartate and phosphoglutamate. Amino Acids 2010; 40:1035-51. [DOI: 10.1007/s00726-010-0738-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/27/2010] [Indexed: 11/26/2022]
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23
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Harvey JS, Giuffredi GT, Gouverneur V. Diastereoselective Synthesis of P-Stereogenic Heterocycles via Enyne Ring-Closing Metathesis. Org Lett 2010; 12:1236-9. [DOI: 10.1021/ol100098c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James Stephen Harvey
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Guy T. Giuffredi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Véronique Gouverneur
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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24
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Yang Y, Cui Q. The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state. J Phys Chem A 2009; 113:12439-46. [PMID: 19534504 PMCID: PMC2783400 DOI: 10.1021/jp902949f] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combined quantum mechanical/molecular mechanical (QM/MM) calculations with density functional theory are employed to analyze two issues related to the hydrolysis activity of adenosine triphosphate (ATP) in myosin. First, we compare the geometrical properties and electronic structure of ATP in the open (post-rigor) and closed (pre-powerstroke) active sites of the myosin motor domain. Compared to both solution and the open active site cases, the scissile P(gamma)-O(3beta) bond of ATP in the closed active site is shown to be substantially elongated. Natural bond orbital (NBO) analysis clearly shows that this structural feature is correlated with the stronger anomeric effects in the closed active site, which involve charge transfers from the lone pairs in the nonbridging oxygen in the gamma-phosphate to the antibonding orbital of the scissile bond. However, an energetic analysis finds that the ATP molecule is not significantly destabilized by the P(gamma)-O(3beta) bond elongation. Therefore, despite the notable perturbations in the geometry and electronic structure of ATP as its environment changes from solution to the hydrolysis-competent active site, ground-state destabilization is unlikely to play a major role in enhancing the hydrolysis activity in myosin. Second, two-dimensional potential energy maps are used to better characterize the energetic landscape near the hydrolysis transition state. The results indicate that the transition-state region is energetically flat and a range of structures representative of different mechanisms according to the classical nomenclature (e.g., "associative", "dissociative", and "concerted") are very close in energy. Therefore, at least in the case of ATP hydrolysis in myosin, the energetic distinction between different reaction mechanisms following the conventional nomenclature is likely small. This study highlights the importance of (i) explicitly evaluating the relevant energetic properties for determining whether a factor is essential to catalysis and (ii) broader explorations of the energy landscape beyond saddle points (even on free-energy surface) for characterizing the molecular mechanism of catalysis.
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Affiliation(s)
- Yang Yang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave, Madison, WI 53706
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25
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Gong D, Dong W, Hu Y, Bi J, Zhang X, Jiang L. Syndiotactically enriched 1,2-selective polymerization of 1,3-butadiene initiated by iron catalysts based on a new class of donors. POLYMER 2009. [DOI: 10.1016/j.polymer.2009.10.060] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Khan MAS, Kesharwani MK, Bandyopadhyay T, Ganguly B. Solvolysis of chemical warfare agent VX is more efficient with hydroxylamine anion: A computational study. J Mol Graph Model 2009; 28:177-82. [DOI: 10.1016/j.jmgm.2009.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 06/16/2009] [Accepted: 06/19/2009] [Indexed: 10/20/2022]
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27
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Michielssens S, Tien Trung N, Froeyen M, Herdewijn P, Tho Nguyen M, Ceulemans A. Hydrolysis of aspartic acid phosphoramidate nucleotides: a comparative quantum chemical study. Phys Chem Chem Phys 2009; 11:7274-85. [PMID: 19672539 DOI: 10.1039/b906020k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
L-Aspartic acid has recently been found to be a good leaving group during HIV reverse transcriptase catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. This showed that L-Asp is a good mimic for the pyrophosphate moiety of deoxyadenosine triphosphate. The present work explores the thermochemistry and mechanism for hydrolysis of several models for L-aspartic-dAMP using B3LYP/DGDZVP, MP2/6-311++G** and G3MP2 level of theory. The effect of the new compound is gradually investigated: starting from a simple methyl amine leaving group up to the aspartic acid leaving group. The enzymatic environment was mimicked by involving two Mg(2+) ions and some important active site residues in the reaction. All reactions are compared to the corresponding O-coupled leaving group, which is methanol for methyl amine and malic acid for aspartic acid. With methyl amine as a leaving group a tautomeric associative or tautomeric dissociative mechanism is preferred and the barrier is lower than the comparable mechanism with methanol as a leaving group. The calculations on the aspartic acid in the enzymatic environment show that qualitatively the mechanism is the same as for triphosphate but the barrier for hydrolysis by the associative mechanism is higher for L-aspartic-dAMP than for L-malic-dAMP and pyrophosphate.
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Affiliation(s)
- Servaas Michielssens
- Katholieke Universiteit Leuven, Department of Chemistry and LMCC-Mathematical Modeling and Computational Science Center, Leuven, Belgium.
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