Catalytic Structure-Function

Catalytic Structure-Function Relationships in Heme Peroxidases Ann M. English and George Tsaprailis... 

CATALYTIC STRUCTURE-FUNCTION RELATIONSHIPS IN HEME PEROXIDASES... 

Living systems contain thousands of different enzymes As we have seen all are structurally quite complex and no sweeping generalizations can be made to include all aspects of enzymic catalysis The case of carboxypeptidase A illustrates one mode of enzyme action the bringing together of reactants and catalytically active functions at the active site... 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

Apart from mode of action and kinetics of wild type enzymes structure function relationships of these industrially important enzymes is of high interest to provide the necessary knowledge for genetic engineering of desired properties. As a first approach the identification of catalytically important residues was addressed in conjunction with the elucidation of the three dimensional structure [15]. 

The condensation reactions described above are unique in yet another sense. The conversion of an amine, a basic residue, to a neutral imide occurs with the simultaneous creation of a carboxylic acid nearby. In one synthetic event, an amine acts as the template and is converted into a structure that is the complement of an amine in size, shape and functionality. In this manner the triacid 15 shows high selectivity toward the parent triamine in binding experiments. Complementarity in binding is self-evident. Cyclodextrins for example, provide a hydrophobic inner surface complementary to structures such as benzenes, adamantanes and ferrocenes having appropriate shapes and sizes 12) (cf. 1). Complementary functionality has been harder to arrange in macrocycles the lone pairs of the oxygens of crown ethers and the 7t-surfaces of the cyclo-phanes are relatively inert13). Catalytically useful functionality such as carboxylic acids and their derivatives are available for the first time within these new molecular clefts. 

T. Yamamoto, T. Murauyama, Z.-H. Zhou, T. Ito, T. Fukuda, Y. Yoneda, F. Begum, T. Ikeda, S. Sasaki, H. Takezoe, A. Fukuda, and K. Kubota, -ir-Conjugated poly(pyridine-2,5-diyl), poly(2,2 -bipyridine-5,5 -diyl), and their alkyl derivatives. Preparation, linear structure, function as a ligand to form their transition metal complexes, catalytic reactions, //-type electrically conducting properties, optical properties, and alignment on substrates, J. Am. Chem. Soc., 116 4832-4845,... 

Since the first successful examples of tailored antibodies that catalyze chemical transformations, great attention has been drawn to this field of research. In the last two decades, a large number of antibodies that are able to catalyze a variety of chemical processes have been investigated and the mechanism of those abzymes has greatly been elucidated thanks to structural studies. Indeed, a good number of three-dimensional structures were solved during the past few years, which made it possible to elucidate the mechanism whereby the catalytic antibodies function. 

Herschlag s group continued its study of structure-function relationships in the hammerhead ribozyme using a base-rescue biochemical method. This method substitutes other atoms or molecules for bases at critical catalytic or structural positions and tests whether catalytic activity is lost. If so, the RNA bases (U, A, G, C) or a modified base (for instance, deazaguanine or 2-aminopurine substituted for guanine) is added to the solution to ascertain... 

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