Bovine pancreatic trypsin inhibitor BPTI

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]. 

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. 

Bovine Pancreatic Trypsin Inhibitor (BPTI) Simulations... 

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. 

Bovine pancreatic trypsin inhibitor (BPTI) Bos taurus 84 333-339... 

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. 

Figure 4 shows a TOCSY spectrum with C(wi)-half-filter recorded with the small globular protein bovine pancreatic trypsin inhibitor (BPTI) using the pulse sequence of fig. 3. Although proton multiplets are usually difficult... 

P16.3 The protein, bovine pancreatic trypsin inhibitor (BPTI), contains a disulfide bond between cystine amino acids located at positions 30 and 51. This bond is buried deep within the hydrophobic core of the protein. Using spectroscopy and calorimetry, Breslauer et al.i9 have studied the effects on the stability of this protein when the disulfide bond is eliminated through the substitution of different amino acids at these two positions. Some of their results are summarized below ... 

Several such hydration models have been evaluated in terms of their abilities to discriminate among various folded forms of bovine pancreatic trypsin inhibitor (BPTI)97-99. In this approach, the free energy of hydration, V, is added to the conformational energy of the oligopeptide in the absence of solvent, U, of Eq. [1], to obtain the total conformational energy, G ... 

Another globular protein, bovine pancreatic trypsin inhibitor (BPTI), has also been treated by the build-up procedure however, because of a limitation on computer time when the calculation on this protein was carried out, a limited set of simulated NMR distance constraints (taken from the known X-ray structure225) was used226-227 to reduce the number of conformations... 

The stress-70 proteins interact with a broad spectrum of polypeptide substrates, but they have some degree of specificity in their interactions. In several instances, it has been shown that a stress-70 protein can bind to proteins [e.g., bovine pancreatic trypsin inhibitor (BPTI), a-lactalbumin] that have been stabilized in a nonnative, or denatured, form by reduction and carboxymethylation of the cysteines that would normally form disulfides at the same time, they will not bind to the native forms of the same proteins (Liberek et al., 1991b Palleros et ai, 1991, 1992). This suggests that the peptide-binding activity of the stress-70 proteins discriminates in favor of polypeptides in a denatured, and possibly extended, conformation over those in a compact secondary and tertiary structure. NMR experiments demonstrating that the E. coli dnaK... 

As shown in Scheme 28, 1 peptide fragments as building blocks (based on the minimum protection strategy) for the synthesis of bovine pancreatic trypsin inhibitor (BPTI) were prepared by solid-phase methods. ... 

Verification of the structural and dynamic behavior of proteins predicted by simulations has been possible by comparison with experiment. Approximate agreement between the average structure obtained in the first simulation of a protein (McCammon et al. 1977), that of bovine pancreatic trypsin inhibitor (BPTI), and the... 

Electrostatic complementarity between the enzyme and its ligand is illustrated on the example of the binding of the Lys-15 side chain of bovine pancreatic trypsin inhibitor (BPTI) to the specificity pocket of trypsin (Figure 4.). The MEP of BPTI which is displayed on the van der Waals envelope of the Lys side chain is complementary to that displayed on the same surface but emerging from the enzyme... 

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