Energy minimization studies on alpha-turns.
Using a grid search technique, the entire conformational space of a system of four linked peptide units (tetrapeptide) was scanned to pick out geometrically possible 5-->1 type hydrogen-bonded conformations defined as an alpha-turn. The energy minimization of these conformations led to 23 distinct minimum energy conformations (MECs) falling in 13 different classes. The presence of beta and gamma turn type hydrogen bonds along with 5-->1 type hydrogen bond gave conformational variability in a given class. The occurrence of bifurcated hydrogen bonding network was a characteristic feature of most of the MECs. In many prototype MECs non-glycyl residues such as Ala and Pro could be accommodated. Comparison of MECs with the alpha-turn examples that are observed in proteins showed that the conformationally worked out MECs occurred in isolation in proteins, with the alpha-helical alpha-turn being distinctly the most predominant.
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
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Ramakrishnan
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Nataraj
D004734:Energy Metabolism; D005998:Glycine / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D010363:Pattern Recognition, Automated; D011392:Proline / Q000737:chemistry; D017433:Protein Structure, Secondary
D009842:Oligopeptides; D011392:Proline; D005998:Glycine