New tubular single-stranded helix of poly-L-amino acids suggested by molecular mechanics calculations: I. Homopolypeptides in isolated environments.
A search was made in terms of molecular mechanics calculation for tubular, or pore-forming, single-stranded helices of poly-L-amino acids. Such a helix was found in the vicinity of (phi, psi, omega) = 81 degrees, 98 degrees, 170 degrees) in the conformational space. It was the 6.2(20) helix of right-handedness. The 6.2(20) helix, here named the "mu helix," had a cylindrical pore along its helical axis. The diameter of the pore was 6.6 A on the basis of the atom centers of carbonyl carbons and amino nitrogens. The left-handed mu helix was less stable than the right-handed counterpart. The conformation energy of the mu helix, expressed relative to that of the alpha helix of the same polypeptide, depended to a great extent on amino acid composition. It varied over a range of a few kilocalories per mol per residue above and below the conformation energy of the alpha helix of the same polypeptide. This marked diversity in the relative conformation energy of the mu helix can be ascribed primarily to the difference in the relative position of alpha-carbons between the mu and the alpha helices. The conformational entropy made only a small contribution, if any, to the relative stability of the mu helix. There was a hydrogen-bonded network of side chains in the mu helices of poly-L-glutamine and poly-L-asparagine.
Department of Physiology, Tohoku University School of Medicine, Sendai, Japan.
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D006860:Hydrogen Bonding; D008433:Mathematics; D008958:Models, Molecular; D008962:Models, Theoretical; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012984:Software; D013314:Stress, Mechanical; D013329:Structure-Activity Relationship
D010455:Peptides; C019529:polyalanine; C097188:polyglutamine; C045164:polyasparagine