Serine proteinase protein inhibitors follow the standard mechanism of inhibition (Laskowski M Jr, Kato I, 1980, Annu Rev Biochem 49:593-626), whereby an enzyme-catalyzed equilibrium between intact (I) and reactive-site hydrolyzed inhibitor (I*) is reached. The hydrolysis constant, K-hyd, is defined as [I*]/[I]. Here, we explore the role of internal dynamics in the resynthesis of the scissile bond by comparing the internal mobility data of intact and cleaved inhibitors belonging to two different families. The inhibitors studied are recombinant Cucurbita maxima trypsin inhibitor III (rCMTI-III; M-r 3 kDa) of the squash family and rCMTI-V (M-r similar to 7 kDa) of the potato I family. These two inhibitors have different binding loop-scaffold interactions and different K-hyd values-2.4 (CMTI-III) and 9 (CMTI-V)-at 25 degrees C. The reactive-site peptide bond (P-1-P-1') is that between Arg(5) and Ile(6) in CMTI-III, and that between Lys(44) and Asp(45) in CMTI-V. The order parameters (S-2) of backbone NHs of uniformly N-15-labeled rCMTI-III and rCMTI-III* were determined from measurements of N-15 spin-lattice and spin-spin relaxation rates, and {H-1}-N-15 steady-state heteronuclear Overhauser effects, using the model-free formalism, and compared with the data reported previously for rCMTI-V and rCMTI-V*. The backbones of rCMTI-III ([S-2] = 0.71) and rCMTI-III* ([S-2] = 0.63) are more flexible than those of rCMTI-V ([S-2] = 0.83) and rCMTI-V* ([S-2] = 0.85). The binding loop residues, P-4-P-1, in the two proteins show the following average order parameters: 0.57 (rCMTI-III) and 0.44 (rCMTI-III*); 0.70 (rCMTI-V) and 0.40 (rCMTI-V*). The P-1'-P-4' residues, on the other hand, are associated with [S-2] values of 0.56 (rCMTI-III) and 0.47 (rCMTI-III*); and 0.73 (rCMTI-V) and 0.83 (rCMTI-V*). The newly formed C-terminal (P-n residues) gains a smaller magnitude of flexibility in rCMTI-III* due to the Cys(3)-Cys(20) crosslink. In contrast, the newly formed N-terminal (P-n' residues) becomes more flexible only in rCMTI-III*, most likely due to lack of an interaction between the P-1' residue and the scaffold in rCMTI-III. Thus, diminished flexibility gain of the P-n residues and, surprisingly, increased flexibility of the P-n' residues seem to facilitate the resynthesis of the P-1-P-1' bond, leading to a lower K-hyd value.
