Pancreatic polypeptide, conformation

I. Glover, I. Haneef, J. Pitts, S. Wood, D. Moss, 1. Tickle, and T. Blundell, Biopolymers, 22, 293 (1983). Conformational Flexibility in a Small Globular Hormone X-ray Analysis of Avian Pancreatic Polypeptide at 0.98-A Resolution. 

In a controversial study, Sun [34] was able to use a GA to achieve surprisingly good predictions for very small proteins, like melittin, with 26 residues, and for avian pancreatic polypeptide inhibitor, with 36 residues. The algorithm involved a very complicated scheme and was able to achieve accuracy of less than 2 A versus the native conformation. However, careful analysis of this report suggests that the algorithm took advantage of the fact that the predicted proteins were actually included, in an indirect way, in the training phase that was used to parameterize the fitness function, and in a sense the GA procedure retrieved the known structure rather than predicted it. 

Glover, I., Haneef, I., Pitts, J., Wood, S., Moss, D., Tickle, I., and Blundell, T. Conformational flexibility in a small globular hormone X-ray analysis of avian pancreatic polypeptide at 0.98-A resolution. Biopolymers 22, 293-304 (1983). 

Tonan, K., Kawata, Y Hamaguchi, K. (1990) Conformation of isolated fragments of pancreatic polypeptide. Biochemistry 29, 4424 4429. 

The protein model on which the method is tested uses a three-atom per residue backbone and a one-atom side chain. " Optimization was carried out on melittin (26 residues), avian pancreatic polypeptide inhibitor (APPI) (36 residues), and apamin (18 residues). The fitness function used a molecular mechanics penalty as well as a penalty on the radius of gyration, which is a relatively straightforward value to obtain experimentally. In all three proteins, the GA found conformations of lower energy than that of the native structure, which was a problem with the force field, rather than with the optimization method. A standard SA method was also applied to this problem. It still found low-energy conformations, but took 100-200 times more function evaluations. 

Figure 11. The backbone conformation of avian pancreatic polypeptide. Circles represent the a-carbon positions of each amino acid residue.

Fig. 2. Temperature dependence of the partial specific heat capacity for pancreatic ribonuclease A (RNase), hen egg-white lysozyme (Lys), sperm whale myoglobin (Mb), and catalase from Thermus thermophilus (CTT). The flattened curves are for RNase and Lys with disrupted disulfide cross-links and for apomyoglobin, when polypeptide chains have a random coil conformation without noticeable residual structure (Privalov et al., 1988).

On the Multiple-Minima Problem in the Conformational Analysis of Polypeptides. V. Application of the Self-consistent Electrostatic Field and the Electrostatically Driven Monte Carlo Methods to Bovine Pancreatic Trypsin Inhibitor. 

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... 

Studies by Anfinsen of the reversible denaturation of the pancreatic enzyme ribonuclease prompted the hypothesis that secondary and tertiary structures are derived inclusively from the primary structure of a protein (Figures 4-11 and 4-12). RNase A, which consists of a single polypeptide chain of 124 amino acid residues, has four disulfide bonds. Treatment of the enzyme with 8 M urea, which disrupts noncovalent bonds, and j8-mercaptoethanol, which reduces disulfide linkages to cysteinyl residues, yields a random coil conformation. 

The anomalous activity characteristics have been attributed to conformational changes of the solubilized enzyme [49], but more recent spectroscopic studies seem to indicate that this is not the main cause. Solubilization of an enzyme into microemulsion droplets does not normally lead to major conformational alterations, as indicated, e.g., by fluorescence and phosphorescence spectral investigations [28,50]. The situation is complex, however, and it has been shown by circular dichroism (CD) measurements that the influence of the oil/water interface on enzyme conformation may vary even between enzymes belonging to the same class [51]. In the case of human pancreatic lipase, the conformation of the polypeptide chain is hardly altered after the enzyme is transferred from a bulk aqueous solution to the microenvironment of reverse micelles. Conversely, the CD spectra of the lipases from... 

Protein folding the folding of a random coil polypeptide into its native structure, i.e. its 3-dimensional, biologically functional structure, also known as the native conformation. Loss of this native structure is known as denaturation, and the re-establishment of native structure is known as renaturation. (For the reductive denaturation and oxidative renaturation of pancreatic ribonuclease, see Protein). 

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