Dynamic enzyme-catalyzed

Based on the previous publications, azo dye can be reduced by azoreductase-catalyzed reduction under anaerobic conditions. But still there is a speculation whether bacterial flavin reductases are responsible for the azo reductase activity observed with bacterial cell extracts. In a published report, it is reported that flavin reductases are indeed able to act as azo reductases [24]. Bacteria produce extracellular oxidative enzymes, which are relatively nonspecific enzymes catalyzing the oxidation of a variety of dyes. It was reported that so many diverse groups of bacteria play a role in decolorization. It has been also reported that mixed microbial community could reduce various azo dyes, and members of the y-proteabacteria and sulfate reducing bacteria (SRB) were found to be prominent members of mixed bacterial population by using molecular methods to determine the microbial population dynamics [1],... 

In this chapter, a short introduction to DFT and to its implementation in the so-called ab initio molecular dynamics (AIMD) method will be given first. Then, focusing mainly on our own work, applications of DFT to such fields as the definition of structure-activity relationships (SAR) of bioactive compounds, the interpretation of the mechanism of enzyme-catalyzed reactions, and the study of the physicochemical properties of transition metal complexes will be reviewed. Where possible, a case study will be examined, and other applications will be described in less detail. 

Quantum Mechanical Dynamical Effects for an Enzyme Catalyzed Proton Transfer Reaction... 

Zhu, Y-.Z., Fow, K.L., Chuah, G.K. and Jaenicke, S., Dynamic kinetic resolution of secondary alcohols combining enzyme-catalyzed transesterification and zeolite-catalyzed racemisation. Chem. Eur. J. 2007, 13, 541. 

Enantioselective and Diastereoselective Enzyme-catalyzed Dynamic Kinetic Resolution of an Unsaturated Ketone... 

Enzymes may be used either directly for chiral synthesis of the desired enantiomer of the amino acid itself or of a derivative from which it can readily be prepared, or for kinetic resolution. Resolution of a racemate may remove the unwanted enantiomer, leaving the intended product untouched, or else the reaction may release the desired enantiomer from a racemic precursor. In either case the apparent disadvantage is that the process on its own can only yield up to 50% of the target compound. However, in a number of processes the enzyme-catalyzed kinetic resolution is combined with a second process that re-racemizes the unwanted enantiomer. This may be chemical or enzymatic, and in the latter case, the combination of two simultaneous enzymatic reactions can produce a smooth dynamic kinetic resolution leading to 100% yield. 

The reversibility of hydrogen transfer reactions has been exploited for the racemi-zation of alcohols and amines. By coupling the racemization process with an enantioselective enzyme-catalyzed acylation reaction, it has been possible to achieve dynamic kinetic resolution reactions. The combination of lipases or... 

TTie diversity in the type of Fe-S clusters associated with these enzymes, catalyzing apparently simple hydration and/or dehydration reactions, is striking. Taken together, these results suggest that some of the Fe-S clusters that have been assigned redox roles in various enzymes may actually be functioning as catalytic groups. Clearly the field of Fe-S proteins, which a decade ago seemed to be well understood, has developed into a dynamic and fertile area for future research endeavors. 

Upon use of structurally modified variants as internal standards for the particular analytes, the relative quantificahon of oligonucleotides, peptides, and small proteins was demonstrated [44]. The potential of the ILM to allow quantitative analyses of peptides without the use of internal standards was presented recently [43]. Linear correlahons between peptide amount and signal intensities could be found upon applicahon of increased matrix-to-analyte ratios between 25,000 and 250,000 (mokmol). The dynamic range of linearity thus spanned one order of magnitude. Unfortunately, the importance of the M/A ratio prevents the use of this method in samples with unknown orders of concentration, for example, in a proteomics environment. On the other hand, the method is applicable for the screening of enzyme-catalyzed reactions because the starting concentrahons of the peptides are generally known in such assays. 

The enzyme-catalyzed regio- and enantioselective reduction of a- and/or y-alkyl-substituted p,5-diketo ester derivatives would enable the simultaneous introduction of up to four stereogenic centers into the molecule by two consecutive reduction steps through dynamic kinetic resolution with a theoretical maximum yield of 100%. Although the dynamic kinetic resolution of a-substituted P-keto esters by chemical [14] or biocatalytic [15] reduction has proven broad applicability in stereoselective synthesis, the corresponding dynamic kinetic resolution of 2-substituted 1,3-diketones is rarely found in the literature [16]. 

During the past few years great efforts have been made to overcome the 50% threshold of enzyme-catalyzed KRs. Among the methods developed, deracemization processes have attracted considerable attention. Deracemizations are processes during which a racemate is converted into a non-racemic product in 100% theoretical yield without intermediate separation of materials [5]. This chapter aims to provide a summary of chemoenzymatic dynamic kinetic resolutions (DKRs) and chemoenzymatic cyclic deracemizations. 

The combination of Ru complex-catalyzed stereomutation of secondary alcohols with enzyme-catalyzed enantioselective acylation is an efficient procedure to obtain chiral acyloxy compounds with excellent optical purity from a variety of racemic secondary alcohols via dynamic kinetic resolution [112]. 

Enzyme-catalyzed reactions, which are characteristically reversible under physiologic conditions, are ideally suited to the generation of dynamic combinatorial libraries. Many enzymes with broad specificity (required for library diversity) are already commercially available, and the application of modem techniques in directed evolution may be expected to increase their number. 

Structural studies of the oxy-Cope catalytic antibody system reinforce the idea that conformational dynamics of both protein and substrate are intimately intertwined with enzyme catalysis, and consideration of these dynamics is essential for complete understanding of biologically catalyzed reactions. Indeed, recent single molecule kinetic studies of enzyme-catalyzed reactions also suggest that different conformations of proteins are associated with different catalytic rates (Xie and Lu, 1999). In addition, a number of enzymes are known to undergo conformational changes on binding of substrate (Koshland, 1987) that lead to enhanced catalysis two examples are hexokinase (Anderson and Steitz, 1975 Dela-Fuente and Sols, 1970) and triosephosphate isomerase (Knowles, 1991). 

Another illustration of the power of molecular dynamics simulation can be drawn from the sphere of enzyme catalysis. Many enzyme-catalyzed reactions proceed at a rate that depends on the diffusion-limited association of the substrate with the active site. Sharp et al. [28] have carried out Brownian dynamics simulations of the association of superoxide anions with superoxide dismutase (SOD). The active center in SOD is a positively charged copper atom. The distribution of charge over the enzyme is not uniform, and so an electric field is produced. Using their model, Sharp et al. [28] have shown that the electric field enhances the association of the substrate with the enzyme by a factor of 30 or more. Their calculations also predict correctly the response of the association rate to changes in ionic strength and amino... 

Turner, N. J. 2004. Enzyme catalyzed deracemization and dynamic kinetic resolution reactions. Curr. Op. Chem. Biol., 8(2), 114-119. 

A completely different enzyme-catalyzed synthesis of cyanohydrins is the lipase-catalyzed dynamic kinetic resolution (see also Chapter 6). The normally undesired, racemic base-catalyzed cyanohydrin formation is used to establish a dynamic equilibrium. This is combined with an irreversible enantioselective kinetic resolution via acylation. For the acylation, lipases are the catalysts of choice. The overall combination of a dynamic carbon-carbon bond forming equilibrium and a kinetic resolution in one pot gives the desired cyanohydrins protected as esters with 100% yield [19-22]. 

The above examples demonstrate the DSR concept as a useful approach to generate and interrogate simultaneously complex systems for different applications. A range of reversible reactions, in particular carbon-carbon bond-formation transformations, was used to demonstrate dynamic system formation in both organic and aqueous solutions. By applying selection pressures, the optimal constituents were subsequently selected and amplified from the dynamic system by irreversible processes under kinetic control. The DSR technique can be used not only for identification purposes, but also for evaluation of the specificities of selection pressures in one-pot processes. The nature of the selection pressure applied leads to two fundamentally different classes external selection pressures, exemplified by enzyme-catalyzed resolution, and internal selection pressures, exemplified by transformation- and/or crystallization-induced resolution. Future endeavors in this area include, for example, the exploration of more complex dynamic systems, multiple resolution schemes, and variable systemic control. 

Kuhn, B. Kollman, P. A. QM—FE and molecular dynamics calculations on catechol O-methyltransferase Eree energy of activation in the enzyme and in aqueous solution and regioselectivity of the enzyme-catalyzed reaction, J. Am. Chem. Soc. 2000,122, 2586-2596. 

This article will describe the different chemical strategies used by enzymes to achieve rate acceleration in the reactions that they catalyze. The concept of transition state stabilization applies to all types of catalysts. Because enzyme-catalyzed reactions are contained within an active site of a protein, proximity effects caused by the high effective concentrations of reactive groups are important for enzyme-catalyzed reactions, and, depending on how solvent-exposed the active site is, substrate desolvation may be important also. Examples of acid-base catalysis and covalent (nucleophilic) catalysis will be illustrated as well as examples of "strain" or substrate destabilization, which is a type of catalysis observed rarely in chemical catalysis. Some more advanced topics then will be mentioned briefly the stabilization of reactive intermediates in enzyme active sites and the possible involvement of protein dynamics and hydrogen tunneling in enzyme catalysis. 

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