Structures and Enzymatic Mechanisms

Hadzi, D., M. Hodoscek, D. Turk, and V. Harb. 1988. Theoretical Investigations of Structure and Enzymatic Mechanisms of Aspartyl Protcinascs Part 2. Ab initio calculations on some possible initial steps of proteolysis. J. Mol. Struct. (Theochem) 181, 71-80. 

S proteasomes are ubiquitous and essential in eukaryotes (Heinemeyer 2000) ubiquitous but not essential in archaea (Ruepp et al. 1998) and rare and non-essential in bacteria (Knipfer and Shrader 1997 Ete Mot et al. 1999). Because of ist relative simplicity the proteasome from the archaeon Thermoplasma acidophilum (Dahlmann et al. 1989) has played a pivotal role in resolving the structure and enzymatic mechanism of 20S proteasomes (see for example Hegerl et al. 1991 Grziwa et al. 1991 Piihler et al. 1992 Zwickl et al. 1992 Jap et al. 1993). 

Wilson BA, Collier RJ (1992) Diphtheria toxin and Pseudomonas aeruginosa exotoxin A Active-site structure and enzymatic mechanism. In Curr. Top. Microbiol. Immunol. 175 27-41. 

Despite the apparent simplicity of their molecular structure, the metabolism of these agents is chemically so complex, and their routes of bioactivation and inactivation so intimately intertwined, that a detailed and coherent picture of their behavior in the body is not available. The presentation to follow considers first their in vivo de-esterification, and only then the nonen-zymatic and enzymatic mechanisms postulated to be involved. 

R., Huber, R., Bode, W., Demuth, H.-U., and Beandstettee, H. The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism. Proe. Natl. Acad. Sd. USA 2003, 100, 5063-5068. 

Structure, assembly and enzymatic mechanism of the 20S complex have been elucidated, but the functional organization of the 26S proteasome is... 

ROP of p-lactones is highly prone to numerous side reactions, such as transester-fication, chain-transfer or multiple hydrogen transfer reactions (proton or hydride). Specifically, the latter often causes unwanted functionalities such as crotonate and results in loss over molecular weight control. Above all, backbiting decreases chain length, yielding macrocyclic structures. All these undesired influences are dependent on the reaction conditions such as applied initiator or catalyst, temperature, solvent, or concentration. The easiest way to suppress these side reactions is the coordination of the reactive group to a Lewis acid in conjunction with mild conditions [71]. p-BL can be polymerized cationically and enzymatically but, due to the mentioned facts, the coordinative insertion mechanism is the most favorable. Whereas cationic and enzymatic mechanisms share common mechanistic characteristics, the latter method offers not only the possibility to influence... 

Zamaraev el al. [2] have concluded that there are deep analogies in the structure and the mechanism of active sites in homogeneous, heterogeneous and enzymatic systems the reason is the coincidence of unitypical active site properties in different systems and qualitatively equal types of the environmental influence on the mechanism of the rate of the key stage of catalysis . 

NMR spectroscopy has so far been suited for non-invasive investigation of biochemical structures, fluxes through pathways, distribution of marker-nuclei among various cellular components and enzymatic mechanisms rather than for quantitative determination of small molecules. Biochemical applications have involved NMR spectroscopy mainly for structural determination of complex molecules, e.g. [27,180], as well as inside the cells, i.e. in vivo [184,189]. In biotechnology, the potential of determining intracellular components without cell disruption is increasingly used for in vivo studies of metabolism, e.g. [15,55,88, 121,146,197,250-252,271,335], and effectors [419]. 

The terms mimicking enzymatic processes or chemical models of enzymes have no monosemantic and exact definitions. In some cases mimicking involves preceding a specific fast chemical reaction catalyzed by an enzyme in mild conditions. In other cases, attempts to construct chemical structures similar to an enzyme active site and to imitate different steps of an enzymatic process are made. Depending on the knowledge of the detailed structure and action mechanism of a target enzyme, starting positions of chemist are also diverse. 

Previous detailed analysis of existing data on the structure and action mechanism of an enzyme, together with the experience and chemical intuition of the investigator, allow the composition a realistic working program which could provide optimal conditions for each stage of the enzymatic processes. 

The importance of reactions 1-3 in the biosphere is clear. However, relatively little is known about the catalytic mechanisms of these reactions, particularly reactions 2 and 3. In order to better understand the catalytic mechanisms of these enzymes, it is important to establish the correlation between metal site structure and enzymatic function. X-ray absorption spectroscopy is one of the premier tools for determining the local structural environment of metalloprotein metal sites. In the following, we summarize our results using X-ray absorption spectroscopy to characterize the structure of the Mn active site environments in manganese catalase and in the OEC and show how these structural results can be used to deduce details of the catalytic mechanism of these enzymes. 

The enzymatic depolymerization of chitin by chitinases has been investigated for a few decades. Chitinases, a class of glycosyl hydrolyases, have been found in a variety of organisms ranging from bacteria to animals. Chitinases belong to two major families of carbohydrate enzymes, family 18 and family 19, based on the amino acid sequences (CAZY http //www.cazy.org). Both families of enzymes differ in their amino acid sequences, three-dimensional structures, and catalytic mechanisms (Fukamizo 2000). Prior to the family classification, plant chitinases are divided into five classes on the basis of their primary structures. Classes 1,11, and IV chitinases are included in family 19, whereas classes III and V belong to family 18. 

T. C. Bruice and S. I Benkovic, Bioorganic Mechanisms, Vol. 1, W. A. Benjamin, New brk, 1966, pp. 1-258 W. P. Jencks, Catalysis in Chemistry and Enzymology, McGraw-Hill, New York, 1969 M. L. Bender, Mechanisms of Homogeneous Catalysis from Protons to Proteins, Wiley-Interscience, New York, 1971 C. Walsh, Enzymatic Reaction Mechanisms, W. H. Freeman, San Francisco, 1979 A. Fersht, Enzyme Structure and Mechanism, 2nd ed., W. H. Freeman, New York, 1985. 

Kinetics is the branch of science concerned with the rates of chemical reactions. The study of enzyme kinetics addresses the biological roles of enzymatic catalysts and how they accomplish their remarkable feats. In enzyme kinetics, we seek to determine the maximum reaction velocity that the enzyme can attain and its binding affinities for substrates and inhibitors. Coupled with studies on the structure and chemistry of the enzyme, analysis of the enzymatic rate under different reaction conditions yields insights regarding the enzyme s mechanism of catalytic action. Such information is essential to an overall understanding of metabolism. 

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