Biological enzymes, features

Combined quantum/classical treatment of molecular systems was introduced first in the pioneering paper of Warshel and Levitt. This paper contains the main features of the QM/MM approach widely used (with modifications) in other works on modeling organic systems. The authors considered a relatively large biological enzyme-substrate complex to study the mechanism of the lysozyme reaction of cleavage of hexasacharides with particular emphasis on factors that contribute to the stabilization of the carbonium ion intermediate. 

Quantitative Structure—Activity Relationships (QSAR). Quantitative Stmcture—Activity Relationships (QSAR) is the name given to a broad spectmm of modeling methods which attempt to relate the biological activities of molecules to specific stmctural features, and do so in a quantitative manner (see Enzyme INHIBITORS). The method has been extensively appHed. The concepts involved in QSAR studies and a brief overview of the methodology and appHcations are given here. 

Proteins are the indispensable agents of biological function, and amino acids are the building blocks of proteins. The stunning diversity of the thousands of proteins found in nature arises from the intrinsic properties of only 20 commonly occurring amino acids. These features include (1) the capacity to polymerize, (2) novel acid-base properties, (3) varied structure and chemical functionality in the amino acid side chains, and (4) chirality. This chapter describes each of these properties, laying a foundation for discussions of protein structure (Chapters 5 and 6), enzyme function (Chapters 14-16), and many other subjects in later chapters. 

Several features of these RNA enzymes, or ribozymes, lead to the realization that their biological efficiency does not challenge that achieved by proteins. First, RNA enzymes often do not fulfill the criterion of catalysis in vivo because they act only once in intramolecular events such as self-splicing. Second, the catalytic rates achieved by RNA enzymes in vivo and in vitro are... 

At the present time, the greatest importance of covalent hydration in biology seems to lie in the direction of understanding the action of enzymes. In this connection, the enzyme known as xanthine oxidase has been extensively investigated.This enzyme catalyzes the oxidation of aldehydes to acids, purines to hydroxypurines, and pteridines to hydroxypteridines. The only structural feature which these three substituents have in common is a secondary alcoholic group present in the covalently hydrated forms. Therefore it was logical to conceive of this group as the point of attack by the enzyme. 

Stereoselectivity, in particular, enantioselectivity, is the most important feature of enzymes. It should be stressed that enzymes are capable of recognizing any type of chirality of the substrates. It does not seem necessary to prove here how important the synthesis of sterically defined products is, because the differences in biological activity of particular stereoisomers of a given substance are well known. There are three approaches to the synthesis of enantiomerically enriched... 

The Qxo, or temperature coefficient, is the factor by which the rate of a biologic process increases for a 10 °C increase in temperature. For the temperatures over which enzymes are stable, the rates of most biologic processes typically double for a 10 °C rise in temperature (Qjo = 2). Changes in the rates of enzyme-catalyzed reactions that accompany a rise or fall in body temperature constitute a prominent survival feature for cold-blooded life forms such as lizards or fish, whose body temperatures are dictated by the external environment. However, for mammals and other homeothermic organisms, changes in enzyme reaction rates with temperature assume physiologic importance only in circumstances such as fever or hypothermia. 

Enzymes are highly active catalysts in many biological processes. A very important feature in the catalytic action of enzymes is their high selectivity. Any enzyme that is active toward a particular reaction involving a particular substrate is entirely inactive toward other reactions and toward other substrates. (Note that in biochemistry, a substrate is the substance undergoing reaction under the catalytic effect of the enzyme.)... 

Khan MTH (2007) Recent Advances on the Sugar-Derived Heterocycles and Their Precursors as Inhibitors Against Glycogen Phosphorylases (GP). 9 33-52 Khan MTH (2007) Heterocyclic Compounds Against the Enzyme Tyrosinase Essential for Melanin Production Biochemical Features of Inhibition. 9 119-138 Khan MTH (2007) Molecular Modeling of the Biologically Active Alkaloids. 10 75-98 Khan MTH, Ather A (2007) Microbial Transformation of Nitrogenous Compoimds. 10 99-122... 

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