51
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López-Canut V, Ruiz-Pernía JJ, Castillo R, Moliner V, Tuñón I. Hydrolysis of Phosphotriesters: A Theoretical Analysis of the Enzymatic and Solution Mechanisms. Chemistry 2012; 18:9612-21. [DOI: 10.1002/chem.201103615] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 04/26/2012] [Indexed: 11/06/2022]
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52
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Theoretical investigation of astacin proteolysis. J Inorg Biochem 2012; 111:70-9. [DOI: 10.1016/j.jinorgbio.2012.02.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/06/2011] [Accepted: 02/07/2012] [Indexed: 11/19/2022]
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53
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Bigley AN, Raushel FM. Catalytic mechanisms for phosphotriesterases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:443-53. [PMID: 22561533 DOI: 10.1016/j.bbapap.2012.04.004] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/31/2012] [Accepted: 04/13/2012] [Indexed: 01/04/2023]
Abstract
Phosphotriesters are one class of highly toxic synthetic compounds known as organophosphates. Wide spread usage of organophosphates as insecticides as well as nerve agents has lead to numerous efforts to identify enzymes capable of detoxifying them. A wide array of enzymes has been found to have phosphotriesterase activity including phosphotriesterase (PTE), methyl parathion hydrolase (MPH), organophosphorus acid anhydrolase (OPAA), diisopropylfluorophosphatase (DFP), and paraoxonase 1 (PON1). These enzymes differ widely in protein sequence and three-dimensional structure, as well as in catalytic mechanism, but they also share several common features. All of the enzymes identified as phosphotriesterases are metal-dependent hydrolases that contain a hydrophobic active site with three discrete binding pockets to accommodate the substrate ester groups. Activation of the substrate phosphorus center is achieved by a direct interaction between the phosphoryl oxygen and a divalent metal in the active site. The mechanistic details of the hydrolytic reaction differ among the various enzymes with both direct attack of a hydroxide as well as covalent catalysis being found. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.
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Affiliation(s)
- Andrew N Bigley
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
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54
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Multiligand zinc(II) hydroxide complexes: Zn(OH)2X2Y and Zn(OH)2X1,2Y2; X=H2O, CH3OH and Y=NH3, C5H5N. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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55
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Ai YJ, Liao RZ, Chen SL, Hua WJ, Fang WH, Luo Y. Repair of DNA Dewar photoproduct to (6-4) photoproduct in (6-4) photolyase. J Phys Chem B 2011; 115:10976-82. [PMID: 21834563 DOI: 10.1021/jp204128k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.
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Affiliation(s)
- Yue-Jie Ai
- Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden
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56
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Siegbahn PE, Himo F. The quantum chemical cluster approach for modeling enzyme reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.13] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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57
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The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis. Biochem J 2011; 432:565-73. [PMID: 20868365 DOI: 10.1042/bj20101054] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The OP (organophosphate)-degrading enzyme from Agrobacterium radiobacter (OpdA) is a binuclear metallohydrolase able to degrade highly toxic OP pesticides and nerve agents into less or non-toxic compounds. In the present study, the effect of metal ion substitutions and site-directed mutations on the catalytic properties of OpdA are investigated. The study shows the importance of both the metal ion composition and a hydrogen-bond network that connects the metal ion centre with the substrate-binding pocket using residues Arg254 and Tyr257 in the mechanism and substrate specificity of this enzyme. For the Co(II) derivative of OpdA two protonation equilibria (pKa1 ~5; pKa2 ~10) have been identified as relevant for catalysis, and a terminal hydroxide acts as the likely hydrolysis-initiating nucleophile. In contrast, the Zn(II) and Cd(II) derivatives only have one relevant protonation equilibrium (pKa ~4-5), and the μOH is the proposed nucleophile. The observed mechanistic flexibility may reconcile contrasting reaction models that have been published previously and may be beneficial for the rapid adaptation of OP-degrading enzymes to changing environmental pressures.
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58
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Park JM, Boero M. Protonation of a hydroxide anion bridging two divalent magnesium cations in water probed by first-principles metadynamics simulation. J Phys Chem B 2010; 114:11102-9. [PMID: 20695500 DOI: 10.1021/jp102991f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The protonation of a hydroxide anion (OH(-)) located between two magnesium cations (Mg(2+)) in aqueous solution has been investigated by first-principles metadynamics simulation. We observe that the complex Mg(2+)-OH(-)-Mg(2+) is stabilized by the coparticipation of the hydroxide anion to the first hydration shells of both the Mg(2+) cations. Contrary to the cases of OH(-) in pure water, the transfer of protons in the presence of the divalent metal ions turns out to be a slow chemical event. This can be ascribed to the decreased proton affinity of the bridging OH(-). Metadynamics simulation, used to overcome the difficulty of the long time scale required by the protonation of the bridging OH(-), has shown that the system possesses a great stability on the reactant state, characterized by a bioctahedral (6,6) solvation structure around the two Mg(2+) cations. The exploration of the free energy landscape shows that this stable bioctahedral configuration converts into a lower coordinated (5,6) structure, leading to a proton transfer from a water molecule belonging to the first solvation shell of the Mg(2+) ion having the lower coordination to the bridging OH(-); the free energy barrier for the protonation reaction is 11 kcal/mol, meaning that the bridging hydroxide is a weak base. During the proton transfer, the bridging OH(-) reverts to an H(2)O molecule, and this breaks the electrostatic coupling of the two Mg(2+) ions, which depart independently with their own hydration shells, one of which is entirely formed by water molecules. The second one carries the newly created OH(-). Our results show that the flexibility in the metal coordination plays a crucial role in both the protonation process of the bridging OH(-) and the separation of the metal cations, providing useful insight into the nature of proton transfer in binuclear divalent metal ions, with several biological implications, such as, for instance, transesterification of catalytic RNA.
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Affiliation(s)
- Jung Mee Park
- Department of Chemistry, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Korea.
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59
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Ugwumba IN, Ozawa K, Xu ZQ, Ely F, Foo JL, Herlt AJ, Coppin C, Brown S, Taylor MC, Ollis DL, Mander LN, Schenk G, Dixon NE, Otting G, Oakeshott JG, Jackson CJ. Improving a natural enzyme activity through incorporation of unnatural amino acids. J Am Chem Soc 2010; 133:326-33. [PMID: 21162578 DOI: 10.1021/ja106416g] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial phosphotriesterases catalyze hydrolysis of the pesticide paraoxon with very fast turnover rates and are thought to be near to their evolutionary limit for this activity. To test whether the naturally evolved turnover rate could be improved through the incorporation of unnatural amino acids and to probe the role of peripheral active site residues in nonchemical steps of the catalytic cycle (substrate binding and product release), we replaced the naturally occurring tyrosine amino acid at position 309 with unnatural L-(7-hydroxycoumarin-4-yl)ethylglycine (Hco) and L-(7-methylcoumarin-4-yl)ethylglycine amino acids, as well as leucine, phenylalanine, and tryptophan. Kinetic analysis suggests that the 7-hydroxyl group of Hco, particularly in its deprotonated state, contributes to an increase in the rate-limiting product release step of substrate turnover as a result of its electrostatic repulsion of the negatively charged 4-nitrophenolate product of paraoxon hydrolysis. The 8-11-fold improvement of this already highly efficient catalyst through a single rationally designed mutation using an unnatural amino acid stands in contrast to the difficulty in improving this native activity through screening hundreds of thousands of mutants with natural amino acids. These results demonstrate that designer amino acids provide easy access to new and valuable sequence and functional space for the engineering and evolution of existing enzyme functions.
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Affiliation(s)
- Isaac N Ugwumba
- Commonwealth Scientific and Industrial Research Organization, Black Mountain, Canberra, Australia
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60
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Ma Y, Sun Q, Zhang H, Peng L, Yu JG, Smith SC. The mechanism of cyclization in chromophore maturation of green fluorescent protein: a theoretical study. J Phys Chem B 2010; 114:9698-705. [PMID: 20593847 DOI: 10.1021/jp1039817] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An intriguing aspect of the green fluorescent protein (GFP) is the autocatalytic post-translational modification that results in the formation of its chromophore. Numerous experimental and theoretical studies indicate that cyclization is the first and the most important step in the maturation process. In this work, two proposed mechanisms for the cyclization were investigated by using the hybrid density functional theory method B3LYP. Cluster models corresponding to the two mechanisms proposed by Wachter et al. [J. Biol. Chem. 2005, 280, 26248-26255] are constructed on the basis of the X-ray crystal structure (PDB entry 2AWJ) and corresponding reaction path potential energy profiles for the two cyclization mechanisms are presented. Our results suggest that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 alpha-carbon. Moreover, Arg96 fulfills the role of stabilizing the enolate moiety, and Glu222 plays the role of a general base. The formation of the cyclized product is found to be 16.0 and 18.6 kcal/mol endothermic with respect to the two models, which is in agreement with experimental observation.
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Affiliation(s)
- Yingying Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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61
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Liao RZ, Yu JG, Himo F. Phosphate mono- and diesterase activities of the trinuclear zinc enzyme nuclease P1--insights from quantum chemical calculations. Inorg Chem 2010; 49:6883-8. [PMID: 20604512 DOI: 10.1021/ic100266n] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclease P1 is a trinuclear zinc enzyme that catalyzes the hydrolysis of single-stranded DNA and RNA. Density functional calculations are used to elucidate the reaction mechanism of this enzyme with a model of the active site designed on the basis of the X-ray crystal structure. 2-Tetrahydrofuranyl phosphate and methyl 2-tetrahydrofuranyl phosphate substrates are used to explore the phosphomonoesterase and phosphodiesterase activities of this enzyme, respectively. The calculations reveal that for both activities, a bridging hydroxide performs an in-line attack on the phosphorus center, resulting in inversion of the configuration. Simultaneously, the P-O bond is cleaved, and Zn2 stabilizes the negative charge of the leaving alkoxide anion and assists its departure. All three zinc ions, together with Arg48, provide electrostatic stabilization to the penta-coordinated transition state, thereby lowering the reaction barrier.
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Affiliation(s)
- Rong-Zhen Liao
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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62
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Georgieva P, Himo F. Quantum chemical modeling of enzymatic reactions: the case of histone lysine methyltransferase. J Comput Chem 2010; 31:1707-14. [PMID: 20082388 DOI: 10.1002/jcc.21458] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods.
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Affiliation(s)
- Polina Georgieva
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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63
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Liao RZ, Yu JG, Himo F. Reaction Mechanism of the Trinuclear Zinc Enzyme Phospholipase C: A Density Functional Theory Study. J Phys Chem B 2010; 114:2533-40. [PMID: 20121060 DOI: 10.1021/jp910992f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Rong-Zhen Liao
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Jian-Guo Yu
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
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64
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Sevastik R, Whitman CP, Himo F. Reaction mechanism of cis-3-chloroacrylic acid dehalogenase: a theoretical study. Biochemistry 2009; 48:9641-9. [PMID: 19725565 DOI: 10.1021/bi900879a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The reaction mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) is studied using the B3LYP density functional theory method. This enzyme catalyzes the hydrolytic dehalogenation of cis-3-chloroacrylic acid to yield malonate semialdehyde and HCl. The uncatalyzed reaction is first considered, and excellent agreement is found between the calculated barrier and the measured rate constant. The enzymatic reaction is then studied with an active site model consisting of 159 atoms. The results suggest an alternative mechanism for cis-CaaD catalysis and different roles for some active site residues in this mechanism.
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Affiliation(s)
- Robin Sevastik
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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65
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Zhang X, Wu R, Song L, Lin Y, Lin M, Cao Z, Wu W, Mo Y. Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase. J Comput Chem 2009; 30:2388-401. [PMID: 19353598 PMCID: PMC2754597 DOI: 10.1002/jcc.21238] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Combined QM(PM3)/MM molecular dynamics simulations together with QM(DFT)/MM optimizations for key configurations have been performed to elucidate the enzymatic catalysis mechanism on the detoxification of paraoxon by phosphotriesterase (PTE). In the simulations, the PM3 parameters for the phosphorous atom were reoptimized. The equilibrated configuration of the enzyme/substrate complex showed that paraoxon can strongly bind to the more solvent-exposed metal ion Zn(beta), but the free energy profile along the binding path demonstrated that the binding is thermodynamically unfavorable. This explains why the crystal structures of PTE with substrate analogues often exhibit long distances between the phosphoral oxygen and Zn(beta). The subsequent SN2 reaction plays the key role in the whole process, but controversies exist over the identity of the nucleophilic species, which could be either a hydroxide ion terminally coordinated to Zn(alpha) or the micro-hydroxo bridge between the alpha- and beta-metals. Our simulations supported the latter and showed that the rate-limiting step is the distortion of the bound paraoxon to approach the bridging hydroxide. After this preparation step, the bridging hydroxide ion attacks the phosphorous center and replaces the diethyl phosphate with a low barrier. Thus, a plausible way to engineer PTE with enhanced catalytic activity is to stabilize the deformed paraoxon. Conformational analyses indicate that Trp131 is the closest residue to the phosphoryl oxygen, and mutations to Arg or Gln or even Lys, which can shorten the hydrogen bond distance with the phosphoryl oxygen, could potentially lead to a mutant with enhanced activity for the detoxification of organophosphates.
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Affiliation(s)
- Xin Zhang
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Ruibo Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Lingchun Song
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Yuchun Lin
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
| | - Menghai Lin
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Zexing Cao
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Wei Wu
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
- Department of Chemistry, College of Chemistry and Chemical Engineering, the State Key Laboratory for Physical Chemistry of Solid States, Center for Theoretical Chemistry, Xiamen University, Xiamen, Fujian 361005, P. R. China
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66
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Yang L, Liao RZ, Yu JG, Liu RZ. DFT study on the mechanism of Escherichia coli inorganic pyrophosphatase. J Phys Chem B 2009; 113:6505-10. [PMID: 19366250 DOI: 10.1021/jp810003w] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli inorganic pyrophosphatase (E-PPase) is a tetranuclear divalent metal dependent enzyme that catalyzes the reversible interconversion of pyrophosphate (PPi) and orthophosphate (Pi), with Mg(2+) conferring the highest activity. In the present work, the reaction mechanism of E-PPase is investigated using the hybrid density functional theory (DFT) method B3LYP with a large model of the active site. Our calculated results shed further light on the detailed reaction mechanism. In particular, the important residue Asp67, either protonated or unprotonated, was taken into account in the present calculations. Our calculations indicated that a protonated Asp67 is crucial for the reverse reaction to take place; however, it is lost sight of in the forward reaction. The bridging hydroxide is shown to be capable of performing nucleophilic in-line attack on the substrate from its bridging position in the presence of four Mg(2+) ions. During the catalysis, the roles of the four magnesium ions are suggested to provide a necessary conformation of the active site, facilitate the nucleophile formation and substrate orientation, and stabilize the trigonal bipyramid transition state, thereby lowering the barrier for the nucleophilic attack.
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Affiliation(s)
- Ling Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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67
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Liao RZ, Himo F, Yu JG, Liu RZ. Theoretical Study of the RNA Hydrolysis Mechanism of the Dinuclear Zinc Enzyme RNase Z. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900202] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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68
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Reaction mechanism of the binuclear zinc enzyme glyoxalase II – A theoretical study. J Inorg Biochem 2009; 103:274-81. [DOI: 10.1016/j.jinorgbio.2008.10.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2008] [Revised: 10/14/2008] [Accepted: 10/20/2008] [Indexed: 11/18/2022]
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69
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Liao RZ, Yu JG, Himo F. Reaction Mechanism of the Dinuclear Zinc Enzyme N-Acyl-l-homoserine Lactone Hydrolase: A Quantum Chemical Study. Inorg Chem 2009; 48:1442-8. [PMID: 19159270 DOI: 10.1021/ic801531n] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rong-Zhen Liao
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Jian-Guo Yu
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
| | - Fahmi Himo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden, and College of Chemistry, Beijing Normal University, Beijing, 100875, People’s Republic of China
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70
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A quantum mechanics study on the reaction mechanism of chalcone formation from p-coumaroyl-CoA and malonyl-CoA catalyzed by chalcone synthase. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0495-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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71
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Georgieva P, Himo F. Density functional theory study of the reaction mechanism of the DNA repairing enzyme alkylguanine alkyltransferase. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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72
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Kim J, Tsai PC, Chen SL, Himo F, Almo SC, Raushel FM. Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase. Biochemistry 2008; 47:9497-504. [PMID: 18702530 DOI: 10.1021/bi800971v] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial phosphotriesterase (PTE) from Pseudomonas diminuta catalyzes the hydrolysis of organophosphate esters at rates close to the diffusion limit. X-ray diffraction studies have shown that a binuclear metal center is positioned in the active site of PTE and that this complex is responsible for the activation of the nucleophilic water from solvent. In this paper, the three-dimensional structure of PTE was determined in the presence of the hydrolysis product, diethyl phosphate (DEP), and a product analogue, cacodylate. In the structure of the PTE-diethyl phosphate complex, the DEP product is found symmetrically bridging the two divalent cations. The DEP displaces the hydroxide from solvent that normally bridges the two divalent cations in structures determined in the presence or absence of substrate analogues. One of the phosphoryl oxygen atoms in the PTE-DEP complex is 2.0 A from the alpha-metal ion, while the other oxygen is 2.2 A from the beta-metal ion. The two metal ions are separated by a distance of 4.0 A. A similar structure is observed in the presence of cacodylate. Analogous complexes have previously been observed for the product complexes of isoaspartyl dipeptidase, d-aminoacylase, and dihydroorotase from the amidohydrolase superfamily of enzymes. The experimentally determined structure of the PTE-diethyl phosphate product complex is inconsistent with a recent proposal based upon quantum mechanical/molecular mechanical simulations which postulated the formation of an asymmetrical product complex bound exclusively to the beta-metal ion with a metal-metal separation of 5.3 A. This structure is also inconsistent with a chemical mechanism for substrate hydrolysis that utilizes the bridging hydroxide as a base to abstract a proton from a water molecule loosely associated with the alpha-metal ion. Density functional theory (DFT) calculations support a reaction mechanism that utilizes the bridging hydroxide as the direct nucleophile in the hydrolysis of organophosphate esters by PTE.
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Affiliation(s)
- Jungwook Kim
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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73
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Dyguda-Kazimierowicz E, Sokalski WA, Leszczynski J. Gas-Phase Mechanisms of Degradation of Hazardous Organophosphorus Compounds: Do They Follow a Common Pattern of Alkaline Hydrolysis Reaction As in Phosphotriesterase? J Phys Chem B 2008; 112:9982-91. [DOI: 10.1021/jp800386f] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Edyta Dyguda-Kazimierowicz
- Department of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Jackson State University, Jackson, Mississippi, 39217
| | - W. Andrzej Sokalski
- Department of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Jackson State University, Jackson, Mississippi, 39217
| | - Jerzy Leszczynski
- Department of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland, and Jackson State University, Jackson, Mississippi, 39217
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74
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Liao RZ, Yu JG, Raushel FM, Himo F. Theoretical investigation of the reaction mechanism of the dinuclear zinc enzyme dihydroorotase. Chemistry 2008; 14:4287-92. [PMID: 18366031 DOI: 10.1002/chem.200701948] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The reaction mechanism of the dinuclear zinc enzyme dihydroorotase was investigated by using hybrid density functional theory. This enzyme catalyzes the reversible interconversion of dihydroorotate and carbamoyl aspartate. Two reaction mechanisms in which the important active site residue Asp250 was either protonated or unprotonated were considered. The calculations establish that Asp250 must be unprotonated for the reaction to take place. The bridging hydroxide is shown to be capable of performing nucleophilic attack on the substrate from its bridging position and the role of Zn(beta) is argued to be the stabilization of the tetrahedral intermediate and the transition state leading to it, thereby lowering the barrier for the nucleophilic attack. It is furthermore concluded that the rate-limiting step is the protonation of the amide nitrogen by Asp250 coupled with C-N bond cleavage, which is consistent with previous experimental findings from isotope labeling studies.
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Affiliation(s)
- Rong-Zhen Liao
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, 10691 Stockholm, Sweden
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75
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Hopmann KH, Himo F. Cyanolysis and Azidolysis of Epoxides by Haloalcohol Dehalogenase: Theoretical Study of the Reaction Mechanism and Origins of Regioselectivity. Biochemistry 2008; 47:4973-82. [DOI: 10.1021/bi800001r] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kathrin H. Hopmann
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Fahmi Himo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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76
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Leopoldini M, Marino T, Toscano M. Theoretical investigation of the catalytic mechanism of the protein arginine deiminase 4 enzyme. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0433-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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77
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Chen SL, Fang WH, Himo F. Technical aspects of quantum chemical modeling of enzymatic reactions: the case of phosphotriesterase. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0430-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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78
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Chen SL, Marino T, Fang WH, Russo N, Himo F. Peptide Hydrolysis by the Binuclear Zinc Enzyme Aminopeptidase from Aeromonas proteolytica: A Density Functional Theory Study. J Phys Chem B 2008; 112:2494-500. [DOI: 10.1021/jp710035j] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shi-Lu Chen
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Tiziana Marino
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Wei-Hai Fang
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Nino Russo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Fahmi Himo
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova SE-10691 Stockholm, Sweden, Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite-Centro d'Eccellenza MURST, Università della Calabria, I-87030 Arcavacata di Rende (CS), Italy, and College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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79
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Jackson CJ, Foo JL, Kim HK, Carr PD, Liu JW, Salem G, Ollis DL. In Crystallo Capture of a Michaelis Complex and Product-binding Modes of a Bacterial Phosphotriesterase. J Mol Biol 2008; 375:1189-96. [DOI: 10.1016/j.jmb.2007.10.061] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Revised: 10/19/2007] [Accepted: 10/24/2007] [Indexed: 10/22/2022]
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80
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Wong KY, Gao J. The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations. Biochemistry 2007; 46:13352-69. [PMID: 17966992 DOI: 10.1021/bi700460c] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations employing combined quantum mechanical and molecular mechanical (QM/MM) potentials have been carried out to investigate the reaction mechanism of the hydrolysis of paraoxon by phosphotriesterase (PTE). We used a dual-level QM/MM approach that synthesizes accurate results from high-level electronic structure calculations with computational efficiency of semiempirical QM/MM potentials for free energy simulations. In particular, the intrinsic (gas-phase) energies of the active site in the QM region are determined by using density functional theory (B3LYP) and second-order Møller-Plesset perturbation theory (MP2) and the molecular dynamics free energy simulations are performed by using the mixed AM1:CHARMM potential. The simulation results suggest a revised mechanism for the phosphotriester hydrolysis mechanism by PTE. The reaction free energy profile is mirrored by structural motions of the binuclear metal center in the active site. The two zinc ions occupy a compact conformation with an average zinc-zinc distance of 3.5 +/- 0.1 A in the Michaelis complex, whereas it is elongated to 5.3 +/- 0.3 A at the transition state and product state. The substrate is loosely bound to the more exposed zinc ion (Znbeta2+) at an average distance of 3.8 A +/- 0.3 A. The P=O bond of the substrate paraoxon is activated by adopting a tight coordination to the Znbeta2+, releasing the coordinate to the bridging hydroxide ion and increasing its nucleophilicity. It was also found that a water molecule enters into the binding pocket of the loosely bound binuclear center, originally occupied by the nucleophilic hydroxide ion. We suggest that the proton of this water molecule is taken up by His254 at low pH or released to the solvent at high pH, resulting in a hydroxide ion that pulls the Znbeta2+ ion closer to form the compact configuration and restores the resting state of the enzyme.
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Affiliation(s)
- Kin-Yiu Wong
- Department of Chemistry and Minnesota Supercomputing Institute, University of Minnesota, Smith Hall, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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