Thermodynamics of substrates and reversible inhibitors binding to the active site cleft of human alpha-thrombin

Abstract

The study of the temperature effect on the binding to the active site of human alpha-thrombin for ten different ligands, i.e. nine peptide substrates and the tight binding inhibitor N alpha -(naphthalene-sulphonyl-glycyl)-4-amidino-DL-phenyl-alanine-piperidine (alpha-NAPAP), showed that the enthalpy is constant over the temperature range spanning from 10 to 40 degrees C. It was found that the values of the binding enthalpy are linearly correlated to those of entropy, and that this correlation arises from a real phenomenon of chemical compensation. On the other hand, no compensatory chemical effect was found for the process of thrombin acylation. Additional experiments showed that binding to thrombin of two competitive thrombin inhibitors, i.e. proflavin and p-aminobenzamidine, is characterized by a change in the standard heat capacity change (delta Cp), approximately equal to -1 kcal/mol K. By analogy with model compound transfer studies and protein folding investigations, it is proposed that a burial of a large surface area of non-polar residues, roughly equal to 3000 A2, brings about the observed heat capacity change. Altogether, the observed phenomena of the chemical compensation and heat capacity change, although qualitatively different, are interpreted as expressions of the same property of the enzyme, i.e. the capacity to undergo conformational transitions upon ligation of the catalytic domain. These structural transitions are strictly ligand-linked and could play a central role for setting the rules which regulate the specificity of substrates and inhibitors binding to the catalytic groove of human alpha-thrombin.