Ionizable groups

Use of the finite-difference PB (FDPB) method to calculate the self- and interaction-energies of the ionizable groups in the protein and solvent. 

Gilson, M. K. Multiple-site titration and molecular modeling Two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins Struct. Punct. Genet. 15 (1993) 266-282. 

While the previous receptors are typically used in organic solvents, except for the cyclodextrins, there are special cases of cyclophane receptors supphed with peripheral charges (ammonium units) (107—12) or ionizable groups (carboxylate functions) (113,114) (Fig. 17) to allow substrate recognition, as in nature, in an aqueous medium, profiting from the solvophobic effects of water (115). 

Despite the intrinsically nonspecific nature of ion-exchange and reversed-phase/hydrophobic interactions, it is often found that chromatographic techniques based on these interactions can exhibit remarkable resolution this is attributed to the dynamics of multisite interactions being different for proteins having differing surface distributions of hydrophobic and/or ionizable groups. 

ST Russell, A Warshel. Calculations of electrostatic energies m proteins The energetics of ionized groups m bovine pancreatic trypsin inhibitor. J Mol Biol 185 389-404, 1985. 

A less obvious scheme that can lead to a bell-shaped curve has been recognized by Zemer and Bender. The substrate is a weak acid or base, but possesses only one ionizable group, and no other ionizable reactant is involved (other than water). The second inflection in the curve is ascribed to an ionizable group created in an intermediate. An example has been discovered in the hydrolysis of o-carboxy-phthalimide ... 

A bell-shaped pH-rate profile can also be produced in a two-step reaction involving a single ionizable group if the rate-determining step changes when the pH is altered. An example, the oximation of acetone, is shown in Fig. 5-12. 

From a chemical point of view, the common amino acids are all weak polyprotic acids. The ionizable groups are not strongly dissociating ones, and the degree of dissociation thus depends on the pH of the medium. All the amino acids contain at least two dissociable hydrogens. 

FIGURE 14.11 The pH activity profiles of four different enzymes. Trypsin, an intestinal protease, has a slightly alkaline pH optimnm, whereas pepsin, a gastric protease, acts in the acidic confines of the stomach and has a pH optimmn near 2. Papain, a protease found in papaya, is relatively insensitive to pHs between 4 and 8. Cholinesterase activity is pH-sensitive below pH 7 but not between pH 7 and 10. The cholinesterase pH activity profile suggests that an ionizable group with a pK near 6 is essential to its activity. Might it be a histidine residue within the active site ... 

The first hint that two active-site carboxyl groups—one proto-nated and one ionized—might be involved in the catalytic activity of the aspartic proteases came from studies of the pH dependence of enzymatic activity. If an ionizable group in an enzyme active site is essential for activity, a plot of enzyme activity versus pH may look like one of the plots at right. 

The bell-shaped curve in part (c) of the figure combines both of these behaviors, so that activity first increases, then decreases, as pH is increased. This is consistent with the involvement of two ionizable groups—one with a low pA that acts as a base above its pK, and a second group with a higher pK that acts as an acid below its pK. ... 

The pH dependence of HIV-1 protease has been assessed by measuring the apparent inhibition constant for a synthetic substrate analog (b). The data are consistent with the catalytic involvement of ionizable groups with pK values of 3.3 and 5.3. Maximal enzymatic activity occurs in the pH range between these two values. On the basis of the accumulated kinetic and structural data on HIV-1 protease, these pK values have been ascribed to the... 

Bell-shaped activity versus pH profiles arise from two separate active-site ionizations, (a) Enzyme activity increases upon deprotonation of (b) Enzyme activity decreases upon deprotonation of A-H. (c) Enzyme activity is maximal in the pH range where one ionizable group is deprotonated (as B ) and the odier group is protonated (as A-H). 

Molecules that contain an equal number of ionizable groups of opposite charge and that therefore bear no net charge are termed zwitterions. Amino acids in blood and most tissues thus should be represented as in A, below. 

Table 3-2. Typical range of pK values for ionizable groups in proteins.

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