Pancreatic trypsin inhibitor, structure

M. H. Hao, M. R. Pincus, S. Rackovsky, and H. A. Scheraga. Unfolding and refolding of the native structure of bovine pancreatic trypsin inhibitor studied by computer simulations. Biochemistry, 32 9614-9631, 1993. 

Wlodawer, A., Deisenhofer, J., Huber, R. Comparison of two highly refined structures of bovine pancreatic trypsin inhibitor. /. Mol. Biol. 193 145-156, 1987. 

FIGURE 6.25 The three-dimensional structure of bovine pancreatic trypsin inhibitor. 

A few other helical conformations occur occasionally in globular protein structures. The polyproline helix, of the same sort as one strand out of a collagen structure, has been found in pancreatic trypsin inhibitor (Huber et al., 1971) and in cytochrome c551 (Almassy and Dickerson, 1978). An extended e helix has been described as occurring in chymotrypsin (Srinivasan et al., 1976). In view of the usual variability and irregularity seen in local protein conformation it is unclear that either of these last two helix types is reliably distinguishable from simply an isolated extended strand however, the presence of prolines can justify the designation of polyproline helix. 

Fig. 53. The main chain hydrogen bonds of basic pancreatic trypsin inhibitor, plus two of the side chains whose hydrogen bonds stabilize the ends of pieces of secondary structure Ser-47 at the beginning of an a-helix and Asn-43 at the end of a fi strand.

Fig. 103. Basic pancreatic trypsin inhibitor as an example of a small disulfide-rich structure, (a) a-Carbon stereo (b) backbone schematic, viewed as in a, with disulfides shown as zig-zags. Figure 2 shows an all-atom stereo of this protein with side chains.

Several proteins from different sources have been shown to maintain stability at high temperatures and NMR studies have been carried out in order to reveal their structures and/or to understand their activity. The most relevant references of a miscellany of thermostable proteins are reported in Table 3. Some of them such as bovine pancreatic trypsin inhibitor (BPTI), thermolysin and lysozyme have been widely studied as model systems in protein science. 

Several inhibitor-protease complexes have been crystallized and details of their interactions are known. For example, the pancreatic trypsin inhibitor binds at the active site of trypsin with K( >1013 M-1 at neutral pH 496 Tire two molecules fit snugly together,490 497 the inhibitor being bound as if it were a peptide substrate with one edge of the inhibitor molecule forming an antiparallel (1 structure with a peptide chain in the enzyme. Lysine 15, which forms part of this P structure, enters the specific Pj binding site for a basic amino acid in a substrate. Thus, the protease inhibitor is a modified substrate which may actually undergo attack at the active site. However, the fit between the two... 

On the other hand, the ratio obtained for pancreatic trypsin inhibitor calculated per mole of monomer unit is near 0.5, suggesting that the cooperative unit of this protein is a dimer. Thus, we see that it is not possible to generalize completely about the size of a cooperative unit from a knowledge of the protein structure, but that the comparison of these two enthalpy measurements provides insights into the presence of discrete units within the protein domain. 

Kim BC, T Young, E Harder, RA Friesner, BJ Berne (2005) Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water A comparative study of the effects of solvent and protein polarizability. J. Phys. Chem. B 109 (34) 16529-16538... 

Because of the ease with which molecular mechanics calculations may be obtained, there was early recognition that inclusion of solvation effects, particularly for biological molecules associated with water, was essential to describe experimentally observed structures and phenomena [32]. The solvent, usually an aqueous phase, has a fundamental influence on the structure, thermodynamics, and dynamics of proteins at both a global and local level [3/]. Inclusion of solvent effects in a simulation of bovine pancreatic trypsin inhibitor produced a time-averaged structure much more like that observed in high-resolution X-ray studies with smaller atomic amplitudes of vibration and a fewer number of incorrect hydrogen bonds [33], High-resolution proton NMR studies of protein hydration in aqueous... 

Examples of studies of local conformational dynamics include the films made by Richard Feldmann, in collaboration with M. Levitt and with M. Karplus, which show the dynamics of pancreatic trypsin inhibitor and its interaction with solvent, and the study by Case and Karplus of the pathway by which an oxygen molecule can enter and leave the binding pocket of myoglobin (31). (In the static structure, there is no stereochemically feasible path for binding oxygen — the process requires a distortion of the protein structure.)... 

G. Wagner, W. Braun, T. F. Havel, T. Schaumann, N. Go, and K. Wiithrich, /. Mol. Biol., 196, 611 (1987). Protein Structures in Solution by Nuclear Magnetic Resonance and Distance Geometry The Polypeptide Fold of the Basic Pancreatic Trypsin Inhibitor Determined Using Two Different Algorithms. DISGEO and DISMAN. 

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