Trypsin inhibitor pancreatic

As examples of applications, we present the overall accuracy of predicted ionization constants for about 50 groups in 4 proteins, changes in the average charge of bovine pancreatic trypsin inhibitor at pH 7 along a molecular dynamics trajectory, and finally, we discuss some preliminary results obtained for protein kinases and protein phosphatases. 

The presented algorithm was applied to 4 proteins (lysozyme, ribonuclease A, ovomucid and bovine pancreatic trypsin inhibitor) containing 51 titratable residues with experimentally known pKaS [32, 33]. Fig. 2 shows the correlation between the experimental and calculated pKaS. The linear correlation coefficient is r = 0.952 the slope of the line is A = 1.028 and the intercept is B = -0.104. This shows that the overall agreement between the experimental and predicted pKaS is good. 

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. 

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]. 

Brooks B and M Karplus 1983. Harmonic Dynamics of Proteins Normal Modes and Fluctuations in Bovine Pancreatic Trypsin Inhibitor. Proceedings of the National Academy of Sciences USA 80 6571-6575. 

M Vasquez, ElA Scheraga. Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data. J Biomol Struct Dyn 5 705-755, 1988. 

The details of many all-atom unfolding simulation studies have been summarized in several reviews [17,46,47]. These studies include unfolding simulations of a-lactalbumin, lysozyme, bovine pancreatic trypsin inhibitor (BPTI), barnase, apomyoglobin, [3-lacta-mase, and more. The advantage of these simulations is that they provide much more detailed information than is available from experiment. However, it should be stressed that there is still only limited evidence that the pathways and intermediates observed in the nanosecond unfolding simulations correlate with the intermediates observed in the actual experiments. 

ST Russell, A Warshel. Calculations of electrostatic energies m proteins The energetics of ionized groups m bovine pancreatic trypsin inhibitor. J Mol Biol 185 389-404, 1985. 

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

Weissman, J.S., Kim, P.S. Kinetic role of non-native species in the folding of bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA 89 9900-9904, 1992. 

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

Figure 5.37 (a) Conventional phase-sensitive COSY spectrum of basic pancreatic trypsin inhibitor, (b) Double-quantum filtered (DQF) phase-sensitive COSY spectrum of the same trypsin inhibitor, in which singlet resonances and solvent signal are largely suppressed. Notice how clean the spectrum is, especially in the region near the diagonal line. (Reprinted from Biochem. Biophys. Res. Comm. 117, M. Ranee, et al., 479, copyright (1983) with permission from Academic Press, Inc.)... 

Bovine Pancreatic Trypsin Inhibitor (BPTI) Simulations... 

Levitt, M., Sander, C., Stern, R S., Normal-mode dynamics of a protein bovine pancreatic trypsin inhibitor, Int. J. Quant. Chem Quant. Biol. Symp. 1983,10, 181-199... 

Lu, W., Starovasnik, M.A., and Kent, S.B. (1998) Total chemical synthesis of bovine pancreatic trypsin inhibitor by native chemical ligation. FEBS Lett. 429(1), 31-35. 

We extrapolate from two simulations, the 10 ps simulation on bovine pancreatic trypsin inhibitor (BPTI) reported over twenty years ago [61] and the recent 1 gs simulation on the villin headpiece subdomain. [9] Each of these was a state-of-the-art simulation, using the best algorithms and the most powerful hardware available at the time. 

A. Kasprzak and G. Weber, Fluorescence depolarization and rotational modes of tyrosine in bovine pancreatic trypsin inhibitor, Biochemistry 21, 5924-5927 (1982). 

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