Predicted conformation of poly(dehydroalanine): a preference for turns.
Repetitive conformations of poly(dehydroalanine) were studied using molecular mechanics. An exhaustive search of the conformational space was carried out on a delta Ala octapeptide model, using the AMBER force field and the delta Ala parameters of Alagona et al [26], under three dielectric conditions, epsilon = 1 (vacuum), epsilon = r and epsilon = 4r (solvent). In all cases, two major groups of low-energy conformers were found, one corresponding to a regular 3/10 helix or type III turn, the other to an irregular conformation, phi = -157 to -170 degrees, psi = -1 to 15 degrees which however can be found in the i + 2 position of gamma-turns. The data confirm that delta Ala may induce turn-like structures in peptides and also indicate that it may confer flexibility to the peptide chain.
Fábián
P
P
International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.
Chauhan
V S
VS
Pongor
S
S
D006860:Hydrogen Bonding; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D010455:Peptides; C019529:polyalanine