Substrate binding determinants

Left side of Fig. 4 shows a ribbon model of the catalytic (C-) subunit of the mammalian cAMP-dependent protein kinase. This was the first protein kinase whose structure was determined [35]. Figure 4 includes also a ribbon model of the peptide substrate, and ATP (stick representation) with two manganese ions (CPK representation). All kinetic evidence is consistent with a preferred ordered mechanism of catalysis with ATP binding proceeding substrate binding. 

Figure 4.8 The active site in all a/p barrels is in a pocket formed by the loop regions that connect the carboxy ends of the p strands with the adjacent a helices, as shown schematically in (a), where only two such loops are shown, (b) A view from the top of the barrel of the active site of the enzyme RuBisCo (ribulose bisphosphate carboxylase), which is involved in CO2 fixation in plants. A substrate analog (red) binds across the barrel with the two phosphate groups, PI and P2, on opposite sides of the pocket. A number of charged side chains (blue) from different loops as welt as a Mg ion (yellow) form the substrate-binding site and provide catalytic groups. The structure of this 500 kD enzyme was determined to 2.4 A resolution in the laboratory of Carl Branden, in Uppsala, Sweden. (Adapted from an original drawing provided by Bo Furugren.)...

Molecular characteristics of luciferase. A molecule of the luciferase of G. polyedra comprises three homologous domains (Li et al., 1997 Li and Hastings, 1998). The full-length luciferase (135 kDa) and each of the individual domains are most active at pH 6.3, and they show very little activity at pH 8.0. Morishita et al. (2002) prepared a recombinant Pyrocystis lunula luciferase consisting of mainly the third domain. This recombinant enzyme catalyzed the light emission of luciferin (luminescence A.max 474 nm) and the enzyme was active at pH 8.0. The recombinant enzyme of the third domain of G. polyedra luciferase was crystallized and its X-ray structure was determined (Schultz et al., 2005). A -barrel pocket putatively for substrate binding and catalysis was identified in the structure, and... 

Both enzymes belong to the family of a,p-hydrolases." The active site of MeHNL is located inside the protein and connected to the outside through a small channel, which is covered by the bulky amino acid tryptophane 128." It was possible to obtain the crystal structure of the complex with the natural substrate acetone cyanohydrin with the mutant SerSOAla of MeHNL. This complex allowed the determination of the mode of substrate binding in the active site." A summary of 3D structures of known HNLs was published recently." " ... 

Second, P-gp differs from other transporters in that it recognizes its substrates when dissolved in the lipid membrane [52], and not when dissolved in aqueous solution. The site of recognition and binding has been shown to be located in the membrane leaflet facing the cytosol [53, 54], This implies that the membrane concentration of the substrate, Csm, determines activation [57]. Since the nature of a molecular interaction is strongly influenced by the solvent, the lipid membrane must be taken into account as the solvent for the SAR analysis of P-gp. Under certain conditions, the effect of additional solvents or excipients (used to apply hydrophobic substrates or inhibitors) on the lipid membrane and/or on the transporter must also be considered. Lipophilicity of substrates has long been known to play an important role in P-gp-substrate interactions nevertheless, the correlation of the octanol/water partition coefficients with the concentration of half-maximum... 

Marcus, S.L., and Balbinder, E. (1972) Use of affinity matrices in determining steric requirements for substrate binding Binding of anthranilate 5-phosphoribosyl-pyrophosphate phosphoribosyltransferase from Salmonella typhimurium to Sepharose-anthranilate derivatives. Anal. Biochem. 48, 448-459. 

Recent investigations have reported that, at least for some plant LOXs, a combined version of both models may explain the underlying reactions because the inverse orientation of the substrate is determined by the space available in the substrate-binding pocket. 

Flavan-3,4-diols FIavan-3,4-diols, also known as leucoanthocyanidins, are not particularly prevalent in the plant kingdom, instead being themselves precursors of flavan-3-ols (catechins), anthocyanidins, and condensed tannins (proanthocyanidins) (see Fig. 5.4). Flavan-3,4-diols are synthesized from dihydroflavonol precursors by the enzyme dihydroflavonol 4-reductase (DFR), through an NADPH-dependent reaction (Anderson and Markham 2006). The substrate binding affinity of DFR is paramount in determining which types of downstream anthocyanins are synthesized, with many fruits and flowers unable to synthesize pelargonidin type anthocyanins, because their particular DFR enzymes cannot accept dihydrokaempferol as a substrate (Anderson and Markham 2006). 

Provided that equilibrium is maintained between the aqueous and micellar pseudophases (designated by subscripts W and M) the overall reaction rate will be the sum of rates in water and the micelles and will therefore depend upon the distribution of reactants between each pseudophase and the appropriate rate constants in the two pseudophases. Early studies of reactivity in aqueous micelles showed the importance of substrate hydropho-bicity in determining the extent of substrate binding to micelles for example, reactions of a very hydrophilic substrate could be essentially unaffected by added surfactant, whereas large effects were observed with chemically similar, but hydrophobic substrates (Menger and Portnoy, 1967 Cordes and Gitler, 1973 Fendler and Fendler, 1975). 

Fig. 17. Catalytic cycle for PLQ,. After substrate binding, hydrolysis occurs in the rate-determining step, followed by the sequential release of phosphorylcholine and diacylglycerol. Amino acids known to be involved in substrate binding are shown, and zinc ions appear as filled circles...

Concept A new approach to the rational design of enzyme inhibitors has emerged in the last ten to fifteen years that incorporates a substrate (or transition state) analog "core" molecule with additional binding determinants spanning beyond the immediate... 

Aleshin and coworkers (49) have reported the X-ray crystal structure at 2.2-A resolution of a G2-type variant produced by Aspergillus awamori. Meanwhile, an attempt was made to determine the amino acid residues that participate in the substrate binding and catalysis provided by G2 of A. niger (52). The results of the chemical approach indicated that the Asp-176, Glu-179, and Glu-180 form an acidic cluster crucial to the functioning of the enzyme. This conclusion was then tested by site-specific mutagenesis of these amino acid residues, which were replaced, one at a time, with Asn, Gin, and Gin, respectively (53). The substitution at Glu-179 provided an inactive protein. The other two substitutions affected the kinetic parameters but were not of crucial importance to the maintenance of activity. The crystal structure (49) supports the conclusion that Glu-179 functions as the catalytic acid but Asp-17 6 does not appear to be a good candidate for provision of catalytic base. Thus, there still exists considerable uncertainty as to how the disaccharide is accepted into the combining site for hydrolysis. Nevertheless, the kind of scheme presented by Svensson and coworkers (52) almost surely prevails. 

The quantity of any given solute being presented to the reabsorptive mechanisms is determined by the product of the GFR and the solute concentration in plasma. One of the features of any carrier-mediated process is its limited capacity. Binding of a substance to its transport protein follows the same principles as substrate binding to an enzyme or hormone binding to its receptor so we may appropriately liken the dynamics to Michaelis-Menten kinetics. 

In a very real sense, the structure of the closely bound water molecules around a protein are a part of the protein structure they determine conformation of the exposed side chains, stabilize the ends of secondary structures, and occupy positions at active sites where they influence substrate binding and sometimes catalysis. The properties of the bulk water are critical in stabilizing the folded native form of proteins (e.g., Kuntz and Kauzmann, 1974), but it is only the bound water that we will consider to be an actual part of, rather than an influence on, the protein structure. 

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