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In paper [5] a simplified model for the hydrophobic binding sites of trypsin was proposed, showing where 1-amino-n-alkanes and α,ω-diamino-n-alkanes are bound while they competitively inhibit the catalyzed hydrolysis of a substrate ester. In the model, the enzyme bas two hydrophobic binding sites separated by an aqueous region which presumably contains the catalytic important residues. The first site binds up to 4 methylene groups of the aliphatic side chain adjacent to the ω-amino group: additional—CH2 groups in t, he chain extend into the aqueous region. If the chain is larger than 7 carbon atoms, the additional methylene or methyl groups are bound to the second hydrophobic site. This site is found to bind less strongly than the first site. This paper presents a thermodynamic investigation of the binding properties of trypsin in the formation of complexes with cationic esters and amids which bear an ammonium group on either the end of the acid side chain or the end of the alcohol or amine component. Free energy and in addition enthalpy and entropy of binding were measured as a function of the length of the inhibitor molecule and as a function of the position of the ester or amide carbonyl group. It was found that thc stability of a complex increases linearly with length of the molecule, and that the magnitude of increase depends on the position of the carbonyl group. Amides always exhibit a smaller increase than esters. Inhibitors with the ammonium group on the alcohol component, were bound with about, the same stability than the corresponding ω-aminoacidesters. The results are consistent, with the model. Positioning of the carbonyl group within the first or second binding site reduces stability due to restricted interaction of the hydrophobic residues on enzyme and inhibitor. Only when the carbonyl group falls into the aqueous region, the free energy for an inhibitor containing the ester group is similar to that for a 1-amino-n-alkane with identical chain length. Enthalpy and entropy as functions of the position of the carbonyl group show minima for the position within the aqueous region. This observation is correlated with the jump of enthalpy and entropy of complex formation of trypsin in the series of 1-amino-n-alkanes reported earlier. It is shown that the magnitude of free energy of complex formation with specific substrates is well estimated on basis of the model. As a consequence, the alternative binding of either the 2-N-acyl group or the alcohol or amine component, to the second hydrophobic site may imply a mode of less productive binding. It is emphasized that unproductive binding should be reflected in the Michaelis Menten constants for substrate amides whereas thc Michaelis Menten constant, for a substrate ester is normally not perturbed. [ABSTRACT FROM AUTHOR]