Enzyme Structural Studies

The cysteine-specific electroactive label N-(2-ferrocenemethyl)maleiniide 24 was synthesized [39] and applied to label several enzymes containing cysteine residues either in their native sequence or introduced by site-directed mutagenesis. 

A cytochrome P450 j j mutant genetically engineered so as to introduce a surface cysteine residue at position 344 was labeled with the related compound N-ferro-cenyl maleimide 25. 

Cyclic voltammetry showed that there may be interactions between the iron center of the heme and the ferrocene reporter group [42]. 

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Pharmacophoric patterns have been proposed as the result of structure-activity studies, modeling studies, mechanistic studies, and enzyme structural studies. While two atom ("distance") and three atom ("triangle") pharmacophoric patterns have been proposed, we would not expect these to be as discriminating as more detailed patterns. Proposed pharmacophoric patterns have been reviewed by Kler,9 Korolkovas,10 and Gund.7 Some additional proposed patterns of drug pharmacophores and of complementary receptor maps are listed in Table I. 

A large family of these enzymes is now known, and their enzymology and structures have been reviewed. A number of crystal structures have been obtained for enzymes in this family, and in each case the mononuclear iron(II) center is coordinated by a His,His,Glu motif, also observed in the extradiol catechol dioxygenases, and in other nonheme iron-dependent enzymes. Structural studies on clavaminic acid synthase have indicated the structural basis for the separate hydroxylation and oxidative cyclization/ desaturation reactions catalyzed by this enzyme. ... 

The Protein Data Bank PDB ID 1A71 Colby T D Bahnson B J Chin J K Klinman J P Goldstein B M Active Site Modifications m a Double Mutant of Liver Alcohol Dehydrogenase Structural Studies of Two Enzyme Ligand Com plexes To be published... 

The isomerization of isopentenyl diphosphate to dimethylally diphos phate is catalyzed by JPP isomerase and occurs through a carbocation pathway Protonation of the IPP double bond by a hydrogen-bonded cysteine residue ir the enzyme gives a tertiary carbocation intermediate, which is deprotonated b a glutamate residue as base to yield DMAPP. X-ray structural studies on the enzyme show that it holds the substrate in an unusually deep, well-protectec pocket to shield the highly reactive carbocation from reaction with solvent 01 other external substances. 

Hen egg-white lysozyme catalyzes the hydrolysis of various oligosaccharides, especially those of bacterial cell walls. The elucidation of the X-ray structure of this enzyme by David Phillips and co-workers (Ref. 1) provided the first glimpse of the structure of an enzyme-active site. The determination of the structure of this enzyme with trisaccharide competitive inhibitors and biochemical studies led to a detailed model for lysozyme and its hexa N-acetyl glucoseamine (hexa-NAG) substrate (Fig. 6.1). These studies identified the C-O bond between the D and E residues of the substrate as the bond which is being specifically cleaved by the enzyme and located the residues Glu 37 and Asp 52 as the major catalytic residues. The initial structural studies led to various proposals of how catalysis might take place. Here we consider these proposals and show how to examine their validity by computer modeling approaches. 

A comparison of the structures of penicillin and Dalanyl-Dalanine (cf. structures 41 and 42) shows that there is a great deal of similarity between the two molecules. Penicillin is essentially an acylated cyclic dipeptide of Dcysteine and Dvaline (84). As such, it contains a peptide bond, that of the /3-lactam ring, that can acylate the enzyme. Labeling studies of the peptidoglycan transpeptidase of Bacillus subtilis indicate that radioactive penicillin reacts with a sulfhydryl group of a cysteine residue of the enzyme (86). 

Recently, the distribution of 2,3-dihydroxybenzoate decarboxylase has been found in a variety of fungal strains (unpubhshed data), and the carboxylation activity for catechol is confirmed by the reaction using resting cells (or cell-free extract) in the presence of 3M KHCO3. The detailed comparative studies of enzyme structures and catalytic properties between 2,3-dihydroxybenzoate decarboxylase and 3,4-dihyroxybenzoate decarboxylase might explain how the decarboxylases catalyze the regioselective carboxylation of catechol. 

Vijayalakshmi, J. Meyer, E. F. Kam, C.-M. Powers, J. C. Structural study of porcine pancreatic elastase complexed with 7-amino-3-(2-bromoethoxy)-4-chloroisocoumarin as a nonreactivable doubly covalent enzyme-inhibitor complex. Biochemistry 1991, 30, 2175-2183. 

The development of magnetic resonance techniques coupled with computer time averaging has made the study of enzyme structure and function by these techniques more fruitful. H NMR, 13C NMR and 19F NMR have been used successfully to determine the structure of B 12-compounds in solution. We are rapidly approaching the point where the structure and function of the B 12-coenzymes will be completely understood, and the need for the synthesis and study of simple Bi2-model compounds such as the cobaloximes (3) will be no longer necessary. However, even though studies on the chemistry of B 12-coenzymes is a necessary prerequisite to our understanding of their biochemical role, it is a wrong assumption to expect that the chemical properties of free coenzymes in aqueous solution should be duplicated in the enzymes. 

Wood, J.M., Brown, D. G. The Chemistry of Vitamin Bj2-Enzymes. Vol. 11, pp. 47-105. Wuthrich, K. Structural Studies of Hemes and Hemoproteins by Nuclear Magnetic Resonance Spectroscopy. Vol. 8, pp. 53-121. 

Enzyme structure may be studied by fluorescence spectroscopy [238-244]. Excitation in the 280-310 nm absorption bands of proteins, usually results in fluorescence from tryptophan (Trp) residues in the 310-390 nm region. The fluorescence from the Trp residues is a convenient marker for protein denaturation and large decreases or red-shifts in fluorescence are observed when proteins are denatured. These changes are most often due to the exposure of the Trp residues that are buried in the protein and may be due to the changes in the proximities of specific residues that may act as fluorescence quenchers. Fluorescence emission characterization of the immobilized... 

All compounds have a precise and often highly specific function to fulfil, and in animals many of them are concerned also with the protection of the body against agents of disease. The problems of immunity and of enzyme systems involve the consideration of protein-carbohydrate complexes so that structural studies in the group now need to be undertaken seriously. 

Since the first report on the ferrocene mediated oxidation of glucose by GOx [69], extensive solution-phase studies have been undertaken in an attempt to elucidate the factors controlling the mediator-enzyme interaction. Although the use of solution-phase mediators is not compatible with a membraneless biocatalytic fuel cell, such studies can help elucidate the relationship between enzyme structure, mediator size, structure and mobility, and mediation thermodynamics and kinetics. For example, comprehensive studies on ferrocene and its derivatives [70] and polypy-ridyl complexes of ruthenium and osmium [71, 72] as mediators of GOx have been undertaken. Ferrocenes have come to the fore as mediators to GOx, surpassing many others, because of factors such as their mediation efficiency, stability in the reduced form, pH independent redox potentials, ease of synthesis, and substitutional versatility. Ferrocenes are also of sufficiently small size to diffuse easily to the active site of GOx. However, solution phase mediation can only be used if the future biocatalytic fuel cell... 

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