Printing enzymatic reactions

We used relief and planographic printing methods to print the catalytic effect of an enzyme, but not the enzyme molecules, onto paper. Printing enzymatic reactions have applications in bioactive papers, low-cost diagnostics, anti-counterfeiting devices and advanced packaging materials. These methods can create novel printing effects on commodity surfaces for advanced applications.     

Density functional based parametrization of a valence bond method and its applications in quantum-classical molecular dynamics simulations of enzymatic reactions

An approximate valence bond (AVB) method was parametrized at a microscopic level for proton transfer and hydroxyanion nucleophilic reactions in enzyme catalytic processes. The method was applied to describe hydrolytic activity of phospholipase A₂. The AVB parametrization is based on density functional and conventional ab initio calculations calibrated with respect to experimental data in the gas phase. The method was used as a fast generator of the potential energy function in a quantum-classical molecular dynamics (QCMD) simulations describing atomic motions as well as propagation of the proton wave function in the enzyme active site. The protein environment surrounding the active site and solvent effects are included in the model via electrostatic interactions perturbing the original AVB Hamiltonian. © 1996 John Wiley & Sons, Inc.     

Computational modeling of enzymatic keto-enol isomerization reactions

Catalysis of proton abstraction from nonacidic carbon atoms adjacent to a carbonyl or carboxylate group is a fundamental reaction in enzymology that has been extensively studied during the last few decades. Enzymes catalyzing these reactions, which normally involve labile enolic intermediates, need to overcome large pK _a differences between the reacting groups as well as high intrinsic free-energy barriers. Here, we present an overview of results from recent computer simulation studies of keto-enol isomerization reactions catalyzed by the enzymes glyoxalase I, triosephopsphate isomerase and ketosteroid isomerase. For all three enzymes it is found that electrostatic stabilization of the transient enolate intermediates, either by charge–charge interactions or by hydrogen bonding, accounts for the main part of the activation free-energy barrier reduction. Another catalytic effect observed in all cases is the reduction of the reorganization energy by the enzyme active site. Some other factors that have been proposed to be important for these reactions are also discussed and evaluated. Received: 3 January 2002 / Accepted: 13 May 2002 / Published online: 29 July 2002     

Facile enzymatic aldol reactions with dihydroxyacetone in the presence of arsenate.

Aldol reactions of in situ formed dihydroxyacetone arsenate with different aldehydes were catalyzed by bacterial D-fructose-1,6-bisphosphate aldolase (FruA). Aldolases from bacteria were found to be much more stable and active than FruA from rabbit muscle. Arsenate acts as a phosphate mimic and can, in principle, be used in catalytic amounts. The use of inorganic arsenate and dihydroxyacetone afforded high yields with hydrophobic aldehydes. Cosolvents increased the solubility of hydrophobic aldehydes and afforded higher reaction rates and enzyme stability. Insight is given, for the first time, in the influence of arsenate on the stereoselectivity of the aldol reaction.     

Periodic and chaotic behavior of substrate-inhibited enzymatic reactions with hydrogen ions production

A two-compartment model of an enzyme system with substrate inhibition kinetics and hydrogen ion production is investigated. The model is used to study the bifurcation, instability, and chaotic behavior of the system. The investigation, although in a restricted region of the parameters’ space, has uncovered a good part of the rich dynamic characteristics of this system, including: period doubling sequences leading to chaos, banded chaos, fully developed chaos, interior crisis, tangent bifurcation leading to intermittency, periodic windows interrupting chaotic regions, and alternating periodic chaotic sequences. The results relate to the phenomena occurring in physiological experiments, such as the periodic stimulation of neural cells and the voltagegated ion channel dynamics.     

Predicting biotransformation potential from molecular structure

The program PASS-BioTransfo is presented, which is capable of predicting many classes of biotransformation for chemical compounds. A particular class of biotransformation is defined by the chemical transformation type and may additionally include the name of the enzyme involved in a transformation. An evaluation of the approach is presented, using biotransformations taken from the databases Metabolite (MDL) and Metabolism (Accelrys), respectively. When trained with biotransformations from Metabolite, PASS-BioTransfo predicts 1927 classes of biotransformation; the average accuracy estimated in LOO cross-validation is about 88%. After training with the biotransformations from the Metabolism database, 178 classes of biotransformation are predicted with an average accuracy of about 85%. The results of cross-prediction with several training and evaluation sets are presented and discussed.     

Understanding dynamic disorder fluctuations in single-molecule enzymatic reactions

Single-molecule studies of enzymatic reactions reveal fluctuations in the reaction rate, which cannot be explained by classic Markovian dynamics. This dynamic disorder is attributed to slow transitions in enzyme conformations that take place over timescales longer than reaction cycle times. In this review we summarize current theoretical models for reaction kinetics in fluctuating, single enzyme systems. Also examined are some of the implications of single-molecule fluctuations for reaction rates in systems such as cells or biosensors that contain a moderate number of molecular copies. We conclude that the dynamic disorder in single-molecule enzyme systems is well-described by available models. However, more work is required to study the effect of single-molecule fluctuations on finite systems over limited periods of time.     

Electrophilic and nucleophilic enzymatic cascade reactions in biosynthesis

The biosynthesis of cyclic terpenoids and polyethers involves enzyme-initiated cascade reactions for ring formation. While the former are obtained by electrophilic cascades through carbenium ions as intermediates, cyclic polyethers are formed by nucleophilic cascade reactions of (poly)epoxide precursors. These mechanistically complementary pathways follow common principles via (i) triggering of the cascade by forming a reactive intermediate ('initiation'), (ii) sequential 'proliferation' of the cyclization and finally (iii) 'termination' of the cascade. As analyzed in this concept paper, the multiplicity of precursors, combined with various initiation and termination routes and kinetically favored or disfavored cyclization modes accounts for the enormous diversity in cyclic terpenoid and polyether scaffolds. Although the essential role of enzymes in the triggering of these cascades is reasonably well understood, remarkably little is known about their influence in proliferation reactions, especially those implying kinetically disfavored (anti-Markovnikov and anti-Baldwin) routes. Mechanistic analysis of enzymatic cascade reactions provides biomimetic strategies for natural product synthesis.     

酶催化脱保护方法及在生物有机化学中的应用

系统地介绍和评述了近年来氨基、羧基、巯基和羟基等到基团的酶催化脱保护方法的进展。由于酶催化脱保护方法具有反应条件温和(中性,水溶液)、选择性和专一性高、副反应少等到优点,故在多肽缀合物、糖等敏感多官能团化合物的研究中有很广阔的应用前景。     

Model for solvent viscosity effect on enzymatic reactions

The solvent viscosity dependence for enzymatic reactions is discussed. We suggest the interpretation of the phenomenon that requires neither a modification of the Kramers’ theory nor that of the Stokes law. We assume that an enzyme solution is an ensemble of samples with different values of the viscosity for the movement of the system along the reaction coordinate. We quantify the extent of this difference by some parameter, introduce heterogeneity in our system with the help of a distribution over this parameter and find the solution of the integral equation for the function of the distribution. All parameters of the model are related to experimentally observable values. The meaning of fractional exponents appears to be the characteristic for the behavior of the distribution. Our approach yields the existence of the limit value for the fractional power exponent with the decrease of cosolvent molecular weight in agreement with known experimental data.     

氯分子束与钛表面激光化学反应动力学

本文采用飞行时间质谱技术测定了在紫外(355nm), 可见(560nm)和近代红外(1064nm)脉冲激光作用下, 氯分子束与Ti表面反应产物的质量分布和速度分布。所得结果表明, 不同波长激光诱导反应的主要产物相同, 有Ti, TiCl, TiCl3和TiCl4。在高能量密度的紫外激光作用下, 首次测得具有很高动能的原生Ti+。各种含Ti氯化物的飞行时间谱, 能满意地用单组分或多组分Maxwell-Boltzmann公式拟合和分析。上述激光诱导气-固表面反应的机理主要由氯分子在Ti表面上的解离吸附,吸附态氯原子在表面上生成TiClx(X=1～4)的连串反应以及激光诱导脱附所组成。近红外激光主要引起热脱附, 而紫外激光的作用还原可能有非热脱附过程。     

Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions

The mechanism of thiamin diphosphate-dependent enzymatic reactions is discussed, concentrating on two enzymes involved in decarboxylating pyruvic acid, the yeast pyruvate decarboxylase and the pyruvate dehydrogenase multienzyme complex from Escherichia coli. The availability of high-resolution X-ray structures for several thiamin diphosphate-dependent enzymes, the use of site-specifically substituted protein variants (resulting from site-directed mutagenesis), the development of model reactions for the various putative intermediates, and the application of new mechanistic tools in solution have all contributed to a much better understanding of the role of the protein component in catalysis. Perhaps the most important advance in our understanding of these mechanisms concerns the role of the 4'-aminopyrimidine component of the coenzyme, widely ignored prior to the publication of the X-ray results. The current view is that the two aromatic rings both contribute to catalysis, perhaps carrying out an intramolecular proton transfer to initiate the various reactions, an ability that makes this coenzyme virtually unique among coenzymes.     

Predicting rate constants of OH radical reactions with organic substances: advances for oxygenated organics through a molecular orbital HF/6-31G** approach

The molecular orbital OH (MOOH) approach is a perturbational quantum chemical method to predict rate constants of OH radical reactions with organic compounds. Going beyond previous AM1 parameterizations, a first ab initio implementation employing the HF/6-31G** level of calculation has been developed. For a set of 799 organic compounds with experimental rate constants, k _OH, varying over more than six orders of magnitude, the new MOOH-HF method is superior to both MOOH-AM1 and Atkinson’s increment scheme, yielding a predictive squared correlation coefficient (q ²) of 0.95 and a root-mean-square error of 0.29 log units. For oxygenated compounds, MOOH-HF shows significant improvements over MOOH-AM1, which holds in particular for aldehydes and ketones. The discussion includes detailed comparative analyses of the model performances for individual compound classes.     

The explanation of high specificity of discriminating optical isomers in enzymatic reactions by the molecular anvil model of enzyme

The molecular anvil model of enzyme is proposed and applied to explain high specificity of discriminating optical isomers in enzymatic reactions. The molecular anvil is a mechanism which can accumulate energy from two interacting molecules and produce locally a high energy spot called anvil site. Two conditions neccessary for formation of the molecular anvil are described. For a pair of enzyme and substrate molecules these two conditions are considered to be satisfied. Assuming proper shapes and sizes for molecules of optical isomers and a hole on the surface of the enzyme molecule into which the optical isomers can fit and also assuming Lenard-Jones 12-6 type potential for each pair of interacting molecular sites. The amount of energy accumulated at the anvil site is calculated. Following the assumption that the total reactivity is determined by binding process and chemical process in which the accumulated energy at the anvil site is utilized to enhance the reaction, total reactivities for L- and D-isomers are calculated and the values of specificity of discriminating L-isomer from D-isomer are derived for various values of interaction energy. It is shown that the molecular anvil plays an important role in elevating specificity as well as producing high catalytic power of enzyme.