Substrate specificity mechanisms

Gefflaut, T., Blonski, C., Perie, J., and Willson, M., Class I aldolases Substrate specificity, mechanism, inhibitors and structural aspects. Prog. Biophys. Mol. Biol. 1995,63 (3), 301-340. 

The metal substrate evidently affords a huge ( 10 and even as high as 10 [84, 85]) increase in the cross-section for Raman scattering of the adsorbate. There are two broad classes of mechanisms which are said to contribute to this enhancenient [, and Ml- The first is based on electromagnetic effects and the second on cheniicaT effects. Of these two classes the fomier is better understood and, for the most part, the specific mechanisms are agreed upon the latter is more complicated and is less well understood. SERS enhancenient can take place in either physisorbed or chemisorbed situations, with the chemisorbed case typically characterized by larger Raman frequency shifts from the bulk phase. 

Catalysis (qv) refers to a process by which a substance (the catalyst) accelerates an otherwise thermodynamically favored but kiaeticahy slow reaction and the catalyst is fully regenerated at the end of each catalytic cycle (1). When photons are also impHcated in the process, photocatalysis is defined without the implication of some special or specific mechanism as the acceleration of the prate of a photoreaction by the presence of a catalyst. The catalyst may accelerate the photoreaction by interaction with a substrate either in its ground state or in its excited state and/or with the primary photoproduct, depending on the mechanism of the photoreaction (2). Therefore, the nondescriptive term photocatalysis is a general label to indicate that light and some substance, the catalyst or the initiator, are necessary entities to influence a reaction (3,4). The process must be shown to be truly catalytic by some acceptable and attainable parameter. Reaction 1, in which the titanium dioxide serves as a catalyst, may be taken as both a photocatalytic oxidation and a photocatalytic dehydrogenation (5). 

Engineering Substrate Specificity. Although the serine proteases use a common catalytic mechanism, the enzymes have a wide variety of substrate specificities. For example, the natural variant subtiHsins of B. amyloliquefaciens (subtiHsin BPN J and B. licheniformis (subtiHsin Carlsberg) possess very similar stmctures and sequences where 86 of 275 amino acids are identical, but have different catalytic efficiencies, toward tetraamino acid -nitroanilide substrates (67). 

Since the locus of failure can clearly distinguish between adhesive and cohesive failures, the following discussion separates loss of adherence into loss of adhesion and loss of cohesion. In the loss of cohesion it is the polysiloxane network that degrades, which can be dealt with independently of the substrate. The loss of adhesion, however, is dependent on the cure chemistry of the silicone, the chemical and physical properties of the substrates, and the specific mechanisms of adhesion involved. 

Uptake of LCFAs across the lipid-bilayer of most mammalian cells occurs through both a passive diffusion of LCFAs and a protein-mediated LCFA uptake mechanism. At physiological LCFA concentrations (7.5 nM) the protein-mediated, saturable, substrate-specific, and hormonally regulated mechanism of fatty acids accounts for the majority (>90%) of fatty acid uptake by tissues with high LCFA metabolism and storage such as skeletal muscle, adipose tissue, liver,... 

Rhinoviruses, which represent the single major cause of common cold, belong to the family of picornavimses that harbors many medically relevant pathogens. Inhibitors of the 3C protease, a cysteine protease, have shown good antiviral potential. Several classes of compounds were designed based on the known substrate specificity of the enzyme. Mechanism-based, irreversible Michael-acceptors were shown to be both potent inhibitors of the purified enzyme and to have antiviral activity in infected cells. 

Finally, if the phosphorylation of myosin is the activation mechanism, then dephosphorylation is likely to be the deactivation mechanism, and so it seems. However, there are several myosin phosphatases in smooth muscle cells and they have some range of substrate specificities. Thus, there are several possible candidates for a regulatory role. 

Clearly, the control of gene expression at the transcriptional level is a key regulatory mechanism controlling carotenogenesis in vivo. However, post-transcriptional regulation of carotenoid biosynthesis enzymes has been found in chromoplasts of the daffodil. The enzymes phytoene synthase (PSY) and phytoene desaturase (PDS) are inactive in the soluble fraction of the plastid, but are active when membrane-bound (Al-Babili et al, 1996 Schledz et al, 1996). The presence of inactive proteins indicates that a post-translational regulation mechanism is present and is linked to the redox state of the membrane-bound electron acceptors. In addition, substrate specificity of the P- and e-lycopene cyclases may control the proportions of the p, P and P, e carotenoids in plants (Cunningham et al, 1996). 

Redmond, T.M. et al.. Identification, expression, and substrate specificity of a mammalian beta-carotene 15,15-dioxygenase, J. Biol. Chem., 276, 6560, 2001. Leuenberger, M.G., Engeloch-Jarret, C., and Woggon, W.D., The reaction mechanism of the enzyme-catalyzed central cleavage of beta-carotene to retinal, Ang. Chem. Int. Ed., 40, 2614, 2001. 

Although the absolute configurations of the products are opposite to that of antiinflammatory active compounds, and the substrate specificity is rather restricted as to the steric bulkiness around the reaction center, the enzyme system of A. bronchisepticus was proved to have a unique reactivity. Thus, detailed studies on the isolated enzyme were expected to elucidate some new interesting mechanism of the new type of decarboxylation. Thus, the enzyme was purified. (The enzyme is now registered as EC 4.1.1.76.) The molecular mass was about 24kDa. The enzyme was named as arylmalonate decarboxylase (AMDase), as the rate of the decarboxylation of phenylmalonic acid was faster than that of the a-methyl derivative. ... 

Facilitated transport combines some properties of both mechanisms discussed above. This type of transport is carrier mediated so that there is substrate specificity, a transport maximum, and competitive inhibition. However, facilitated transport is not energy-dependent and is unable to transport a substrate against a concentration gradient. 

In this chapter we have seen that enzymatic catalysis is initiated by the reversible interactions of a substrate molecule with the active site of the enzyme to form a non-covalent binary complex. The chemical transformation of the substrate to the product molecule occurs within the context of the enzyme active site subsequent to initial complex formation. We saw that the enormous rate enhancements for enzyme-catalyzed reactions are the result of specific mechanisms that enzymes use to achieve large reductions in the energy of activation associated with attainment of the reaction transition state structure. Stabilization of the reaction transition state in the context of the enzymatic reaction is the key contributor to both enzymatic rate enhancement and substrate specificity. We described several chemical strategies by which enzymes achieve this transition state stabilization. We also saw in this chapter that enzyme reactions are most commonly studied by following the kinetics of these reactions under steady state conditions. We defined three kinetic constants—kai KM, and kcJKM—that can be used to define the efficiency of enzymatic catalysis, and each reports on different portions of the enzymatic reaction pathway. Perturbations... 

Ziegler, D.M. (2002) An overview of the mechanism, substrate specificities, and structure of FMOs. Drug... 

Changes in transporter proteins by high-frequency genetic mutation mechanisms, while maintaining transport activity, helps to evade the host s immune response, and in cases where the substrate specificity is changed, helps the microorganism to adapt to new iron sources. 

Although kinetic evidence for prior equilibrium inclusion was not obtained, competitive inhibition by cyclohexanol and apparent substrate specificity once again provide strong support for this mechanism. Since the rate of the catalytic reaction is strictly proportional to the concentration of the ionized hydroxamate function (kinetic and spectrophotometric p/Cas are identical within experimental error and are equal to 8.5), the reaction probably proceeds by a nucleophilic mechanism to produce an acyl intermediate. Although acyl derivatives of N-alkylhydroxamic acids are exceptionally labile in aqueous solution, deacylation is nevertheless the ratedetermining step of the overall hydrolysis (Gruhn and Bender, 1969). 

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