Pancreatic trypsin inhibitor system

In periodic boimdary conditions, one possible way to avoid truncation of electrostatic interaction is to apply the so-called Particle Mesh Ewald (PME) method, which follows the Ewald summation method of calculating the electrostatic energy for a number of charges [27]. It was first devised by Ewald in 1921 to study the energetics of ionic crystals [28]. PME has been widely used for highly polar or charged systems. York and Darden applied the PME method already in 1994 to simulate a crystal of the bovine pancreatic trypsin inhibitor (BPTI) by molecular dynamics [29]. 

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. 

Grzesiak A, Krokoszynska I, Krowarsch D, Buczek O, Dadlez M, Otlewski J. Inhibition of six serine proteinases of the human coagulation system by mutants of bovine pancreatic trypsin inhibitor. J Biol Chem 2000 275 33346-33352. 

We have made the following approximate calculation to estimate protein-water interactions by a less cumbersome procedure it is assumed that the protein molecule has a unique fixed structure determined by x-ray crystallography and interactions are calculated between the protein and a single water molecule in the absence of other solvent molecules. Using this simple system, one may consider all positions and orientations of the single water molecule relative to the protein in a step-wise manner. We present here the result of this calculation for the crystal of bovine pancreatic trypsin inhibitor (BPTI). The calculated energy, mapped in three dimensions, is a highly informative description of the crystal s solvent space. 

Conversely, there are cases where the lyophilization from co-solvents can produce a less stable system. An example of this occurrence is illustrated by the lyophilization of the protein, bovine pancreatic trypsin inhibitor, from 1% water/dimethyl sulfoxide [43]. The data appear to support the premise that the protein-dissolving dimethyl sulfoxide denatures the protein sufficiently to reduce its enzymatic activity after reconstitution. Additionally, it is important to evaluate the impact of residual organic solvent remaining at the end of primary drying since the combination of the solvent and higher product temperatures during secondary drying may lead to undesirable chemical reactions [31]. 

In this paper an outline of the method will be given. Both technical and chemical aspects of the generation and detection of the polarization effects will be discussed. The CIDNP behaviour of the aromatic amino acids provides the basic Information necessary for applying the method to protein systems. The proteins that will be considered are the bovine pancreatic trypsin Inhibitor (BPTI), HEW lysozyme, and rlbonuclease A and S. These proteins have been extensively studied by nmr and X-ray crystallographic methods and may therefore suitably serve as model systems. Since the active sites of enzymes are necessarily accessible (at least to substrates ) there Is a good chance of observing CIDNP In active site residues. Examples of this will be given In the cases of both rlbonuclease and lysozyme. 

Finishing this section, I want to mention some work on water in bio-molecular systems in solution. Wierzuchowska and Blicharska studied proton relaxation and CPMG relaxation dispersion for water protons in solutions of some proteins. The dependences on the protein concentration were also obtained. Persson and Halle analysed the millisecond all-atom MD trajectory (produced by Shaw et for the protein bovine pancreatic trypsin inhibitor and compared the results with the experimental NMRD data as interpreted using the exchange-mediated orientational randomization model. I shall return to the issue of water dynamics in biological gels in subsection 3.5.4. 

Bovine pancreatic trypsin inhibitor (BPTI) has been a widely used model protein for study. There is a good deal of both experiment and computational study on this system. There are a number of crystal and NMR structures of the native, oxidized form of BPTI. The protein with the disulfide linkage reduced, an presumably unfolded state, has been the subject of a number of experimental studies and previous simulations in our group. ... 

Hirano T, Manabe T. Human urinary trypsin inhibitor, urinastatin, prevents pancreatic injuries induced by pancreaticobiliary duct obstruction with caerulein stimulation and systemic hypotension in the rat. Arch Surg 1993 128 1322-1329. 

One goal in the design of an inhibitor is specificity. Often this is a considerable challenge since physiological systems contain a number of closely related proteases. For example, there are at least four chymo-trypsin-like enzymes in humans. These include pancreatic chymotrypsin, cathepsin G, and two mast cell proteases (the human enzymes have not been characterized yet, but two are found in rats). All of these enzymes... 

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