Substrate-binding interactions

Initial rate enzyme kinetics are useful in defining the order of substrate binding interactions in multisubstrate... 

Hanioka N, Korzekwa K, Gonzalez FJ. Sequence requirements for cytochromes P450ILA1 and P450IIA2 catalytic activity evidence for both specific and non-specific substrate binding interactions through use of chimeric cDNAs and cDNA expression. Protein Eng 1990 3(7) 571-575. 

Sem, D.S. and C.B. Kasper (1993). Enzyme-substrate binding interactions of NADPH-cytochrome P-450 oxidoreductase characterized with pH and alternate substrate/inhibitor studies. Biochemistry 32, 11539-11547. 

Fig. 6. Crystal packing contacts mimic substrate binding interactions. See text for description.

Figure 17.3 3D model of substrate-binding interactions for CSS from Neisseria meningitidis created by alignment of the X-ray protein structure (PDB ent 1 EYR [51]) with the CMP-Neu5Ac ligand from the corresponding mouse enzyme (PDB ent IQW] [52]). 

This concerted model assumes furthermore that the symmetry of the molecule is conserved so that the activity of all its subunits is either equally low or equally high, that is, all structural changes are concerted. Subsequently Daniel Koshland, University of California, Berkeley, postulated a sequential model in which each subunit is allowed independently to change its tertiary structure on substrate binding. In this model tertiary structural changes in the subunit with bound ligand alter the interactions of this... 

Destabilization of the ES complex can involve structural strain, desolvation, or electrostatic effects. Destabilization by strain or distortion is usually just a consequence of the fact (noted previously) that the enzyme is designed to bind the transition state more strongly than the substrate. When the substrate binds, the imperfect nature of the fit results in distortion or strain in the substrate, the enzyme, or both. This means that the amino acid residues that make up the active site are oriented to coordinate the transition-state structure precisely, but will interact with the substrate or product less effectively. 

In contrast to 1, isomeric p-nitrophenyl nicotinate shows almost no catalysis. Thus, it is clear that substrate coordination to the metal ion complex plays the critical role for an enormous rate enhancement. The lipophilic ester (R = C5Hn) also undergoes a large rate enhancement indicating the importance of substrate binding into the micellar phase by hydrophobic interaction. A large rate enhancement can also be seen in lipophilic esters which lack the metal coordination site as given below with the enantioselective micellar reactions (Table 9, 10). 

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