基礎講座 電気泳動(Electrophoresis)

We analysed the roles and distribution of metal ions in enzymatic catalysis using available public databases and our new resource Metal-MACiE (http://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html). In Metal-MACiE, a database of metal-based reaction mechanisms, 116 entries covering 21% of the metal-dependent enzymes and 70% of the types of enzyme-catalysed chemical transformations are annotated according to metal function. We used Metal-MACiE to assess the functions performed by metals in biological catalysis and the relative frequencies of different metals in different roles, which can be related to their individual chemical properties and availability in the environment. The overall picture emerging from the overview of Metal-MACiE is that redox-inert metal ions are used in enzymes to stabilize negative charges and to activate substrates by virtue of their Lewis acid properties, whereas redox-active metal ions can be used both as Lewis acids and as redox centres. Magnesium and zinc are by far the most common ions of the first type, while calcium is relatively less used. Magnesium, however, is most often bound to phosphate groups of substrates and interacts with the enzyme only transiently, whereas the other metals are stably bound to the enzyme. The most common metal of the second type is iron, which is prevalent in the catalysis of redox reactions, followed by manganese, cobalt, molybdenum, copper and nickel. The control of the reactivity of redox-active metal ions may involve their association with organic cofactors to form stable units. This occurs sometimes for iron and nickel, and quite often for cobalt and molybdenum.

Metal ions in biological catalysis: from enzyme databases to general principles

Heterogeneous single-site catalysts consist of isolated, well-defined, active sites that are spatially separated in a given solid and, ideally, structurally identical. In this review, the potential of metal–organic frameworks (MOFs) and covalent organic frameworks (COFs) as platforms for the development of heterogeneous single-site catalysts is reviewed thoroughly. In the first part of this article, synthetic strategies and progress in the implementation of such sites in these two classes of materials are discussed. Because these solids are excellent playgrounds to allow a better understanding of catalytic functions, we highlight the most important recent advances in the modelling and spectroscopic characterization of single-site catalysts based on these materials. Finally, we discuss the potential of MOFs as materials in which several single-site catalytic functions can be combined within one framework along with their potential as powerful enzyme-mimicking materials. The review is wrapped up with our personal vision on future research directions.

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Metal–organic and covalent organic frameworks as single-site catalysts

1. Scope of Article and Previous Related Reviews 5346 2. Introduction 5346 2.1. Destruction 5347 2.2. Sensing 5347 2.3. Historical Context 5348 2.3.1. Brief History and Molecular Structure 5348 2.4. Related Compounds and Nomenclature 5348 2.4.1. Phosphorus(V) Parent Compounds and Fundamental Chemistry 5348 2.4.2. Pesticides 5349 2.4.3. Simulants 5349 2.4.4. Decomposition Products 5350 2.5. Toxicology 5351 2.5.1. Acetylcholine Esterase (AChE) Inhibition 5351 2.5.2. Endocannabinoid System Activation 5352 2.6. Critical Needs To Decontaminate and Detect 5353 2.7. Treaties and Conventions 5354 3. Stockpile Destruction 5355 3.1. Agent Storage 5355 3.2. Protection Protocols and Logistics 5355 3.3. Background 5355 3.4. Methods Currently Employed 5355 3.4.1. Incineration 5355 3.4.2. Neutralization by Base Hydrolysis 5356 4. Decomposition Reactions 5357 4.1. Hydrolysis 5357 4.2. Autocatalytic Hydrolysis or Hydrolysis Byproducts 5358 4.3. Use of Peroxide 5359 4.4. Oxidation with Bleach and Related Reagents 5360 4.5. Alkoxide as Nucleophile 5360 4.5.1. Basic Media 5360 4.5.2. Metal-Catalyzed Reactions 5361 4.5.3. Metal-Assisted Reactions 5363 4.5.4. Biotechnological Degradation 5363 4.5.5. Cyclodextrin-Assisted Reactions 5370 4.6. Halogen as the Nucleophile 5370 4.6.1. Use of BrOx 5370 4.6.2. Use of Other Halogens 5371 4.6.3. Use of Group 13 Chelates 5371 4.7. Surface Chemistry 5371 4.7.1. Bare Metals and Solid Nanoparticles 5371 4.7.2. Metal Oxides 5371 4.7.3. Representative Elements 5372 4.7.4. d-Block (Groups 4 10) 5373 4.7.5. Solid Metal Oxides of Group 3 and the Lanthanides 5375 4.7.6. Porous Silicon and Related Systems 5375 4.7.7. Zeolites 5375 4.7.8. Comparative IR Data 5375 4.8. Other Types of Systems 5375 5. Decontamination 5376 5.1. Overview: Ability to React with All Types of Agents, Ease of Application, and Compatibility with Treated Objects 5376 6. Agent Fate and Disposal 5378 6.1. Indoor 5378 6.2. Concrete and Construction Surfaces 5378 6.3. Landfills 5379 7. Sensing and Detection 5379 7.1. Possible Metal Ion Binding Modes in Solution 5379 7.1.1. Early Reports of Phosph(on)ate [R3PdO 3 3 3M nþ] Interactions (R= Alkyl, Alkoxyl) 5380 7.1.2. Coordination Chemistry of Downstream Non-P-Containing Products of Decomposition 5380 7.2. Colorimetric Detection 5381 7.3. Chemiluminescence: Fluorescence and Phosphorescence 5382 7.3.1. Lanthanide-Based Catalysts 5382 7.3.2. Organometallic-Based Sensors 5382 7.3.3. Organic Design 5382 7.3.4. Biologically-Based Luminescence Detection 5382 7.3.5. Polymer and Bead Supports 5382 7.4. Porous Silicon 5383 7.5. Carbon Nanotubes 5383

Destruction and Detection of Chemical Warfare Agents

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.

Phosphotriesterase (PTE) from Pseudomonas diminuta is a zinc metalloenzyme that hydrolyzes a variety of organophosphorus compounds. The kinetic parameters of Zn/Zn PTE, Cd/Cd PTE, and a mixed-metal Zn/Cd hybrid PTE were obtained with a variety of substrates to determine the role of each metal ion in binding and catalysis. pH-rate profiles for the hydrolysis of diethyl p-nitrophenyl phosphate (I) and diethyl p-chlorophenyl phosphate (II) demonstrated that the ionization of a single group in the pH range of 5−10 was critical for substrate turnover. The pKa values determined from the kinetic assays were dependent on the identity of the metal ion that occupied the α site within the binuclear metal center. These results suggest that the hydrolytic nucleophile is activated as a hydroxide via the ionization of a water molecule attached to the α-metal ion. The kinetic constants for the hydrolysis of II and diethyl p-chlorophenyl thiophosphate (IV) were determined for the metal substituted forms of PTE. The kineti...

https://www.chem.tamu.edu/rgroup/raushel/publications/P195-Biochemistry-Phosphotriesterase-2004.pdf

Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase.

With the emergence of sequences and even structures for proteins of unknown function, structure-based prediction of enzyme activity has become a pragmatic as well as an interesting question. Here we investigate a method to predict substrates for enzymes of known structure by docking high-energy intermediate forms of the potential substrates. A database of such high-energy transition-state analogues was created from the KEGG metabolites. To reduce the number of possible reactions to consider, we restricted ourselves to enzymes of the amidohydrolase superfamily. We docked each metabolite into seven different amidohydrolases in both the ground-state and the high-energy intermediate forms. Docking the high-energy intermediates improved the discrimination between decoys and substrates significantly over the corresponding standard ground-state database, both by enrichment of the true substrates and by geometric fidelity. To test this method prospectively, we attempted to predict the enantioselectivity of a set ...

Predicting substrates by docking high-energy intermediates to enzyme structures.

Organophosphorus compounds include many synthetic, neurotoxic substances that are commonly used as insecticides. The toxicity of these compounds is due to their ability to inhibit the enzyme acetylcholine esterase. Some of the most toxic organophosphates have been adapted for use as chemical warfare agents; the most well-known are GA, GB, GD, GF, VX, and VR. All of these compounds contain a chiral phosphorus center, with the SP enantiomers being significantly more toxic than the RP enantiomers. Phosphotriesterase (PTE) is an enzyme capable of detoxifying these agents, but the stereochemical preference of the wild-type enzyme is for the RP enantiomers. A series of enantiomerically pure chiral nerve agent analogues containing the relevant phosphoryl centers found in GB, GD, GF, VX, and VR has been developed. Wild-type and mutant forms of PTE have been tested for their ability to hydrolyze this series of compounds. Mutant forms of PTE with significantly enhanced, as well as relaxed or reversed, stereoselecti...

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Stereoselective Hydrolysis of Organophosphate Nerve Agents by the Bacterial Phosphotriesterase

Glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a nonspecific diesterase that enables Escherichia coli to utilize alkyl phosphodiesters, such as diethyl phosphate, as the sole phosphorus source. The catalytic properties of GpdQ were determined, and the best substrate found was bis(p-nitrophenyl) phosphate with a kcat/Km value of 6.7 x 10(3) M-1 s-1. In addition, the E. aerogenes diesterase was tested as a catalyst for the hydrolysis of a series of phosphonate monoesters which are the hydrolysis products of the highly toxic organophosphonate nerve agents sarin, soman, GF, VX, and rVX. Among the phosphonate monoesters tested, the hydrolysis product of rVX, isobutyl methyl phosphonate, was the best substrate with a kcat/Km value of 33 M-1 s-1. The ability of GpdQ to hydrolyze the phosphonate monoesters provides an alternative selection strategy in the search of enhanced variants of the bacterial phosphotriesterase (PTE) for the hydrolysis of organophosphonate nerve agents. This investigation demonstrated that the previously reported activity of GpdQ toward the hydrolysis of methyl demeton-S is due to the presence of a diester contaminant in the commercial material. Furthermore, it was shown that GpdQ is capable of hydrolyzing a close analogue of EA 2192, the most toxic and persistent degradation product of the nerve agent VX.

https://www.chem.tamu.edu/rgroup/raushel/publications/P227-Biochemistry-Phosphodiesterase-2007.pdf

Characterization of a phosphodiesterase capable of hydrolyzing EA 2192, the most toxic degradation product of the nerve agent VX

Dihydroorotase (DHO) is a zinc metalloenzyme that functions in the pathway for the biosynthesis of pyrimidine nucleotides by catalyzing the reversible interconversion of carbamoyl aspartate and dihydroorotate. A chemical mechanism was proposed on the basis of an analysis of the effects of pH, metal substitution, solvent isotope effects, mutant proteins, and alternative substrates on the enzyme-catalyzed reaction. The pH-rate profiles for the hydrolysis of dihydroorotate or thiodihydroorotate demonstrated that a single group from the enzyme must be unprotonated for maximal catalytic activity. Conversely, the pH-rate profiles for the condensation of carbamoyl aspartate to dihydroorotate showed that a single group from the enzyme must be protonated for maximal catalytic activity. The native zinc ions within the active site of DHO were substituted with cobalt or cadmium by reconstitution of the apoenzyme with divalent cations in the presence of bicarbonate. The ionizations observed in the pH-rate profiles were dependent on the specific metal ion bound to the active site. Mutation of the residue (Asp-250) that hydrogen bonds to the bridging hydroxide (or water) resulted in the loss of catalytic activity. These results are consistent with the formation of a hydroxide bridge between the two divalent cations that functions as the nucleophile during the hydrolysis of dihydroorotate. In addition, Asp-250 is postulated to shuttle the proton from the bridging hydroxide to the leaving group amide during hydrolysis of dihydroorotate. The X-ray crystal structure of DHO showed that the exocyclic alpha-carboxylate of dihydroorotate is bound to the protein via electrostatic interactions with Arg-20, Asn-44, and His-254. Mutation of these residues resulted in the loss of catalytic activity, indicating that these residues are critical for substrate recognition. The thio analogue of dihydroorotate was found to be a good substrate of the enzyme. A comprehensive chemical mechanism for DHO was proposed on the basis of the experimental findings in this study and the X-ray crystal structure.

Yingchun Li

Papers

Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase.

Predicting substrates by docking high-energy intermediates to enzyme structures.

Stereoselective Hydrolysis of Organophosphate Nerve Agents by the Bacterial Phosphotriesterase

Characterization of a phosphodiesterase capable of hydrolyzing EA 2192, the most toxic degradation product of the nerve agent VX

Mechanism of the dihydroorotase reaction