We re port our prog ress in un der stand ing the struc ture-function re la tion ship of the interaction between protein inhibitors and several serine proteases. Recently, we have de ter mined high res o lu tion so lu tion struc tures of two in hib i tors Apis mellifera chymotrypsin in hib i tor-1 (AMCI-I) and Linum usitatissimumtrypsin in hib i tor (LUTI) in the free state and an ul tra high res o lu tion X-ray struc ture of BPTI. All three in hib i tors, de spite to tally dif fer ent scaf folds, con tain a sol vent ex posed loop of sim i lar con- for ma tion which is highly com ple men tary to the en zyme ac tive site. Iso ther mal calorim e try data show that the in ter ac tion be tween wild type BPTI and chymotrypsin is entropy driven and that the enthalpy com po nent op poses com plex for ma tion. Our research is fo cused on ex ten sive mu ta gen e sis of the four po si tions from the pro te ase bind ing loop of BPTI: P1, P1', P3, and P4. We mu tated these res i dues to dif fer ent amino ac ids and the vari ants were char ac ter ized by de ter mi na tion of the as so ci a tion con stants, sta bil ity pa ram e ters and crys tal struc tures of pro te ase–in hib i tor complexes. Ac com mo da tion of the P1 res i due in the S1 pocket of four pro teas es: chymotrypsin, trypsin, neutrophil elastase and cathepsin G was probed with 18 P1 vari ants. High res o lu tion X-ray struc tures of ten com plexes be tween bo vine trypsin and P1 vari ants of BPTI have been de ter mined and com pared with the cog nate P1 Lysside chain. Mu ta tions of the wild type Ala16 (P1') to larger side chains al ways caused a drop of the as so ci a tion con stant. Ac cord ing to the crys tal struc ture of the Leu16 BPTI–trypsin com plex, in tro duc tion of the larger res i due at the P1' po si tion leads to steric con flicts in the vi cin ity of the mu ta tion. Finally, mu ta tions at the P4 site al lowed an im prove ment of the as so ci a tion with sev eral serine pro teas es in volved in blood clot ting. Con versely, in tro duc tion of Ser, Val, and Phe in place of Gly12 (P4) had invariably a destabilizing ef fect on the com plex with these pro teas es.
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