Using evolutionary changes to achieve species-specific inhibition of enzyme action--studies with triosephosphate isomerase.

BACKGROUND: Many studies that attempt to design species-specific drugs focus on differences in the three-dimensional structures of homologous enzymes. The structures of homologous enzymes are generally well conserved especially at the active site, but the amino-acid sequences are often very different. We reasoned that if a non-conserved amino acid is fundamental to the function or stability of an enzyme from one particular species, one should be able to inhibit only the enzyme from that species by using an inhibitor targeted to that residue. We set out to test this hypothesis in a model system. RESULTS: We first identified a non-conserved amino acid (Cys14) whose integrity is important for catalysis in triosephosphate isomerase (TIM) from Trypanosoma brucei. The equivalent residues in rabbit and yeast TIM are Met and Leu, respectively. A Cys14Leu mutant of trypanosomal TIM had a tendency to aggregate, reduced stability and altered kinetics. To model the effects of a molecule targeted to Cys14, we used methyl methanethiosulfonate (MMTS) to derivatize Cys14 to a methyl sulfide. This treatment dramatically inhibited TIMs with a Cys residue at a position equivalent to Cys14, but not rabbit TIM (20% inhibition) or yeast TIM (negligible inhibition), which lack this residue. CONCLUSIONS: Cys14 of trypanosomal TIM is a non-conserved amino acid whose alteration leads to loss of enzyme structure and function. TIMs that have a cysteine residue at position 14 could be selectively inhibited by MMTS. This approach may offer an alternative route to species-specific enzyme inhibition.

Differential inactivation of rabbit and yeast triosephosphate isomerase: effect of oxidations produced by chloramine-T.

Triosephosphate isomerase from rabbit has 5 Cys and 2 Met, while triosephosphate isomerase from yeast has 2 Cys (present in the rabbit enzyme in equivalent positions) and no Met. Since chloramine-T oxidizes Cys and Met, we determined the effect it has on the activity and structure of both enzymes. The activity of triosephosphate isomerase from rabbit was more sensitive to chloramine-T than that of the yeast enzyme (under conditions where the rabbit isomerase was completely inactive, the yeast enzyme exhibited approximately 50% activity). An initial effect of chloramine-T on triosephosphate isomerase was the oxidation of Cys and the formation of catalytically active acidic isoforms. For the yeast isomerase, the two processes were slower. Our data suggest that oxidation of Cys 126, which is conserved in all of the studied species, does not abolish catalysis. Chloramine-T also oxidized the two Met of the rabbit enzyme. At ratios of 50 chloramine-T/monomer, circular dichroism studies showed that the rabbit enzyme, but not that from yeast, underwent extensive alterations of tertiary and secondary structures. This was accompanied by formation of stable dimers, whose cross-linking was not through disulfide bonds. Studies of dimer formation at various enzyme concentrations showed that cross-linking was between monomers of the same dimer. Under conditions that led to cross-linking, rabbit triosephosphate isomerase took up 2.7 mol of 3H from NaB3H4/mol dimer, and the yeast enzyme incorporated only 0.4 mol of 3H. Thus cross-linking was most likely via a Schiff base. The results revealed the points whose modification caused inactivation of the rabbit enzyme.

Stereochemical metrics of lectin-carbohydrate interactions: comparison with protein-protein interfaces.

A global census of stereochemical metrics including interface size, hydropathy, amino acid propensities, packing and hydrogen bonding was carried out on 32 x-ray-elucidated structures of lectin-carbohydrate complexes covering eight different lectin families. It is shown that the interactions at primary binding subsites are more efficient than at other subsites. Another salient behavior found for primary subsites was a marked negative correlation between the interface size and the polar surface content. It is noteworthy that this demographic rule is delineated by lectins with unrelated phylogenetic origin, indicating that independent interface architectures have evolved through common optimization paths. The structural properties of lectin-carbohydrate interfaces were compared with those characterizing a set of 32 protein homodimers. Overall, the analysis shows that the stereochemical bases of lectin-carbohydrate and protein-protein interfaces differ drastically from each other. In comparison with protein-protein complexes, lectin-carbohydrate interfaces have superior packing efficiency, better hydrogen bonding stereochemistry, and higher interaction cooperativity. A similar conclusion holds in the comparison with protein-protein heterocomplexes. We propose that the energetic consequence of this better interaction geometry is a larger decrease in free energy per unit of area buried, feature that enables lectins and carbohydrates to form stable complexes with relatively small interface areas. These observations lend support to the emerging notion that systems differing from each other in their stereochemical metrics may rely on different energetic bases.

Spectroscopic and thermodynamic evidence for a complex denaturation mechanism of bovine beta-lactoglobulin A.

We present a spectroscopic and calorimetric study on the thermal denaturation of bovine beta-lactoglobulin (beta-lg) variant A. Spectroscopic data allowed detection of a stable intermediate emerging from structural modifications restricted to local regions of the native molecule. It is suggested that this kind of intermediate could be a common property of lipocalins. Using the same set of parameters that has successfully related thermodynamics and structural properties of other proteins, it is shown that the thermally denatured state of beta-lg retains a significant amount of buried hydrophobic surface area. Thus, despite being a small protein composed of a single structural domain, beta-lg exhibits a complex unfolding mechanism, comprising at least two other species different from the native and completely unfolded states.

New insights into the molecular basis of lectin-carbohydrate interactions: a calorimetric and structural study of the association of hevein to oligomers of N-acetylglucosamine.

Isothermal titration calorimetry was used to characterize thermodynamically the association of hevein, a lectin from the rubber tree latex, with the dimer and trimer of N-acetylglucosamine (GlcNAc). Considering the changes in polar and apolar accessible surface areas due to complex formation, we found that the experimental binding heat capacities can be reproduced adequately by means of parameters used in protein-unfolding studies. The same conclusion applies to the association of the lectin concanavalin A with methyl-alpha-mannopyranoside. When reduced by the polar area change, binding enthalpy values show a minimal dispersion around 100 degrees C. These findings resemble the convergence observed in protein-folding events; however, the average of reduced enthalpies for lectin-carbohydrate associations is largely higher than that for the folding of proteins. Analysis of hydrogen bonds present at lectin-carbohydrate interfaces revealed geometries closer to ideal values than those observed in protein structures. Thus, the formation of more energetic hydrogen bonds might well explain the high association enthalpies of lectin-carbohydrate systems. We also have calculated the energy associated with the desolvation of the contact zones in the binding molecules and from it the binding enthalpy in vacuum. This latter resulted 20% larger than the interaction energy derived from the use of potential energy functions.