Polyalanines

Fig. 5.17 Histogram of the normal modes calculated for a polyalanine polypeptide in an a-helical conformation. The height of each bar indicates the number of normal modes in each 50cm section.

This method has been applied to derive a multitude of paths for the coil-to-helix transition in polyalanine using a continuum solvation model [36]. 

An elegant NMR experiment by the group of Lynn Jelinski at Cornell University has established that at least part of the microcrystals is built up from the polyalanine repeats in the protein chains. These experiments, which were made on C-enriched proteins produced by feeding the spiders C-labeled alanine, showed that there were two populations of alanine side chains, one ordered and oriented perpendicular to the fiber axis and a second less ordered. Jelinski s interpretation is that parts of the polyalanine sequences are incorporated as p strands in the microcrystals with an orientation parallel to the fiber axis. Whether or not the Gly-Gly-X repeats also form P strands in the microcrystals remains an open question. 

Sfi.F-Test 19.4B Write the formula for (a) the monomer of poly(methyl methacrylate), used in contact lenses (17) (b) two repeating units of polyalanine, the polymer of the amino acid alanine, CH,CH(NH2)COOH. 

Levy, Y, Jortner, J., and Becker, O. M. (2001). Solvent effects on the energy landscapes and folding kinetics of polyalanine. Proc. Natl. Acad. Sci. USA 98, 2188-2193. 

Endredi, G., C.-M. Liegener, M. A. McAllister, A. Perczel, J. Ladik, and I. G. Csizmadia. 1994. Peptide Models 8. The Use of a Modified Romberg Formalism for the Extrapolation of Molecular Properties from Oligomers to Polymers. Polyalanine Diamide in Its Extended Like or (f3, or (C5)n Conformation. J. Mol. Struct. (Theochem) 306, 1-7. 

Fig. 4.3. Polyalanine. The order parameter is the distance between the first and last a carbon...

Fig. 4. The molecular structure, determined by solution NMR (James et al., 1997), of Syrian hamster 90-231 (SHa90-231) prion with ball-and-stick representation of the HI domain (SHal09-122 MKHMAGAAAAGAW). Note that two short /(-chains (SI, S2) nearly stack in the hydrogen-bonding direction. If the palindromic polyalanine region was also in a /(-conformation, there would be a three-stranded /(-sheet. The structural difference between PrPc and PrPSc is in the 90-145 domain. [Model drawn using MOLSCRIPT (Kraulis, 1991)].

The wide-angle (201) reflection is strong, whereas the (200) reflection at 4.7 A Bragg spacing is much weaker or nonexistent for A8A and lyophilized HI, or is nearly as strong as the (201) reflection for SHal06-122 and solubilized/dried HI. Because the intersheet distance of polyalanine is —5 A, the unit cell should contain two //sheets. 

In HI the intrachain turn creates two antiparallel /1-strands, one consists of larger residues at the N-terminus and the other is the polyalanine... 

Polyalanine PABPN1 Quarter-staggered /1-sheet Shinchuk et al. (2005)... 

We thank our colleagues for their valuable contribution to this research fiber diffraction— Jeremy Bond, Sean Deverin, Dr. Leonid Shinchuk, and Dr. Deepak Sharma prions—Drs. Jack Nguyen, Michael Baldwin, Haydn Ball, Robert Fletterick, Fred Cohen, Stanley Prusiner, and Mario Salmona polyalanine—Drs. Sylvie Blondelle and Natalia Reixach and polyglutamine— Dr. Ron Wetzel. We also thank Dr. Andrew Bohm (Department of Biochemistry, Tufts University) for graciously granting us access to their X-ray diffraction facility. 

Fig. 10.16. Properties of the inner cavity. Half cut presentations of molecule A (left side view, center and right top views) with cut regions shown in dark gray. (Left) Surface representation of the internal tunnel illustrating its molecular-sieve character. Access is restricted to single secondary structure elements as shown by the modeled polyalanine helix, which is colored yellow. (Center) Top view on the...

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