Catalytic mechanism active site region

Perhaps enzyme-substrate recognition and interaction are facilitated by an oscillating active site Its correlated motion could position more readily and reliably the catalytically essential groups of atoms. Recognition of the substrate could be visualized as a nonlinear resonance phenomenon, perhaps providing the mechanism of energy transfer from the entatic active site region to the substrate. An off-resonance condition could characterize an enzyme-inhibitor interaction. 

Proteases are classified according to their catalytic mechanism. There are serine, cysteine, aspartic, and metalloproteases. This classification is determined through reactivity toward inhibitors that act on particular amino acid residues in the active site region of the enzyme. The serine proteases are widely distributed among microbes. The enzymes have a reactive serine residue in the active site and are generally inhibited by DFP or PMSF. They... 

Genetic methods provide a powerful approach to the biosynthetic introduction of redox groups [including cysteine residues as well as unnatural redox active amino acids (79)] into proteins. As an example, a disulfide bridge inserted across the active site of T4 lysozyme has been used to create a redox mechanism for regulating enzyme activity (SO). Oxidation of the cysteines to form the disulfide closes the active site region, whereas reduction exposes the active site and restores catalytic activity. 

The understanding of the catalytic function of enzymes is a prime objective in biomolecular science. In the last decade, significant developments in computational approaches have made quantum chemistry a powerful tool for the study of enzymatic mechanisms. In all applications of quantum chemistry to proteins, a key concept is the active site, i.e. a local region where the chemical reactivity takes place. The concept of the active site makes it possible to scale down large enzymatic systems to models small enough to be handled by accurate quantum chemistry methods. 

In the ONIOM(QM MM) scheme as described in Section 2.2, the protein is divided into two subsystems. The QM region (or model system ) contains the active-site selection and is treated by quantum mechanics (here most commonly the density functional B3LYP [31-34]). The MM region (referred to as the real system ) is treated with an empirical force field (here most commonly Amber 96 [35]). The real system contains the surrounding protein (or selected parts of it) and some solvent molecules. To analyze the effects of the protein on the catalytic reactions, we have in general compared the results from ONIOM QM MM models with active-site QM-only calculations. Such comparisons make it possible to isolate catalytic effects originating from e.g. the metal center itself from effects of the surrounding protein matrix. 

The catalytic subunit C of PKA consists of two domains, one composed mostly of a-helices and one of /3-strands, which are connected by a small hnker region. The ATP binding site is located deep in the active site between the two domains the binding site of the larger substrate is at the mouth of the pocket (Color Plate 4). A flexible activation loop is postulated to function as a door for the active site and is beheved to be directly involved in regulating PKA. PKA has a disordered or random binding mechanism. When the door is open, both the substrate and ATP have unhindered access to the active site and the binding of one does not influence the other. ... 

An 80- to 90-residue N-terminal propeptide domain contains a cysteine whose -S group binds to the active site zinc, screening it from potential substrates. The central catalytic domain is followed by a hinge region and a C-terminal domain that resembles the serum iron binding and transporting hemopexin.427/436 The mechanism of action is probably similar to that of thermolysin.430... 

Well-defined peptides of known sequence have been used to shed light on the mechanism of catalysis in the epoxidation of enones with hydrogen peroxide [91, 93-95]. The peptide sequences of the catalysts have been systematically varied and correlated with catalytic activity and selectivity. From the many variations investigated it was concluded (i) that the N-terminal region of the peptides harbors the catalytically active site, and that (ii) a helical conformation is required for the peptide catalysts to be active. The latter conclusion is supported both by the dependence of catalytic activity on chain-length and by IR investigations [91, 94]. NMR data that might aid further elucidation of catalyst structure, interaction with the substrate enones, etc., are, unfortunately, not yet available. 

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