National Institute of Standards and Technology における超伝導研究及び生活

■ Abstract Apoptosis is a genetically programmed, morphologically distinct form of cell death that can be triggered by a variety of physiological and pathological stimuli. Studies performed over the past 10 years have demonstrated that proteases play critical roles in initiation and execution of this process. The caspases, a family of cysteine-dependent aspartate-directed proteases, are prominent among the death proteases. Caspases are synthesized as relatively inactive zymogens that become activated by scaffold-mediated transactivation or by cleavage via upstream proteases in an intracellular cascade. Regulation of caspase activation and activity occurs at several different levels: ( a) Zymogen gene transcription is regulated; ( b) antiapoptotic members of the Bcl-2 family and other cellular polypeptides block proximity-induced activation of certain procaspases; and ( c) certain cellular inhibitor of apoptosis proteins (cIAPs) can bind to and inhibit active caspases. Once activated, caspases cleave a variety of intracellular polypeptides, including major structural elements of the cytoplasm and nucleus, components of the DNA repair machinery, and a number of protein kinases. Collectively, these scissions disrupt survival pathways and disassemble important architectural components of the cell, contributing to the stereotypic morphological and biochemical changes that characterize apoptotic cell death.

Mammalian caspases: structure ,a ctivation ,s ubstrates, and functions during apoptosis

Oxidative Nucleobase Modifications Leading to Strand Scission

Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefficient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by specific enzymes, are identified and quantified by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.

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How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations

▪ Abstract This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.

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Quantum mechanical methods for enzyme kinetics

The O2-dependent oxidation of urate catalyzed by urate oxidase has been examined in order to identify the immediate product of the enzymatic reaction Specifically labeled [13C]urates were utilized as substrates, and the time courses were monitored by 13C NMR On the basis of chemical shift values and 18O labeling, the product of the reaction was identified as 5-hydroxyisourate This identification was substantiated by calculation of the 13C NMR spectrum of 5-hydroxyisourate using ab initio density functional theory methods The predominant tautomers of urate and allantoin in aqueous solution were identified from 13C NMR titration data; the ionization behavior of urate and 5-hydroxyisourate were also examined by computational methods The nonenzymatic pathway for production of allantoin from 5-hydroxyisourate was delineated; the reaction proceeds by the hydrolysis of the N1−C6 bond, followed by an unusual 1,2-carboxylate shift and decarboxylation to form allantoin

Identification of the True Product of the Urate Oxidase Reaction

The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for the sp(3) carbon and oxygen atoms were refined using Monte Carlo simulations of bulk liquids. The resulting force field predicts conformer energies and torsional barriers of alkanes, alcohols, ethers, and hemiacetals with an overall RMS deviation of 0.40 kcal/mol as compared to reference data. Densities of 19 bulk liquids are predicted with an average error of 1.1%, and heats of vaporization are reproduced within 2.4% of experimental values. The force field was used to perform conformational analysis of smaller analogs of the macrocyclic polyketide drug FK506. Structures that adopted low-energy conformations similar to that of bound FK506 were identified. The results show that a linker of four ketide units constitutes the shortest effector domain that allows binding of the ketide drugs to FKBP proteins. It is proposed that the exact chemical makeup of the effector domain has little influence on the conformational preference of tetraketides.

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Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

The oxidation of urate catalyzed by soybean urate oxidase was studied under single-turnover conditions using stopped-flow absorbance and fluorescence spectrophotometry. Two discrete enzyme-bound intermediates were observed; the first intermediate to form had an absorbance maximum at 295 nm and was assigned to a urate dianion species; the second intermediate had an absorbance maximum at 298 nm and is believed to be urate hydroperoxide. These data are consistent with a catalytic mechanism that involves formation of urate hydroperoxide from O2 and the urate dianion, collapse of the peroxide to form dehydrourate, and hydration of dehydrourate to form the observed product, 5-hydroxyisourate. The rate of formation of the first intermediate was too fast to measure accurately at 20 degreesC; the second intermediate formed with a rate constant of 32 s-1 and decayed with a rate constant of 6.6 s-1. The product of the reaction, 5-hydroxyisourate, is fluorescent, and its release from the active site occurred with a rate constant of 31 s-1.

Spectroscopic characterization of intermediates in the urate oxidase reaction.

The kinetic mechanism of urate oxidase isolated from soybean root nodules has been determined by initial velocity kinetic studies monitoring oxygen uptake, in order to avoid potential artifacts in ...

Kinetic mechanism and cofactor content of soybean root nodule urate oxidase.

Conformational analysis of three small alcohols—ethanol, propanol, and isopropanol—was carried out by systematically improving the basis set and the level of electron correlation. Correlation energy contributions to conformational energies are strongly basis-set-dependent but accurate energy contributions can be obtained by extrapolation to the basis-set limit. At the basis-set limit, second- and third-order electron correlation effects play a significant role for rotations around the CCOH, HCCO, and CCCO bonds. Specifically, second- and third-order correlation effects strongly stabilize structures in which the hydroxylic hydrogen eclipses with the adjacent carbon; a lesser stabilization is present in structures where the CCOH moiety is in the gauche form. Fourth-order correlation effects to the CCOH rotation are small due to a partial cancellation of the singles, doubles, and quadruples contribution by the triples contribution. Electron correlation significantly lowers barriers for methyl-group rotations in ethanol and isopropanol, and in these cases the fourth-order correlation effects are noticeable. The relatively large overall importance of third-order correlation energy contributions raises a concern that the inability to accurately estimate this slowly converging contribution may become a limiting factor when highly accurate conformational energies in larger molecules are sought.

Kalju Kahn

Papers

Identification of the True Product of the Urate Oxidase Reaction

Parameterization of OPLS–AA force field for the conformational analysis of macrocyclic polyketides

Spectroscopic characterization of intermediates in the urate oxidase reaction.

Kinetic mechanism and cofactor content of soybean root nodule urate oxidase.

Focal-point conformational analysis of ethanol, propanol, and isopropanol