Conformational preferences of oligopeptides rich in alpha-aminoisobutyric acid. II. A model for the 3(10)/alpha-helix transition with composition and sequence sensitivity.
The analysis of the factors that control the helical folding of Aib-rich peptides is extended to include sensitivity to sequence patterns, and in particular the presence of contiguous non-Aib alpha-mono-alkylated residues. The distinct hydrogen-bonding network of the 3(10)-helix, as contrasted with that of the competing alpha-helical structure, is explicitly incorporated into a theoretical model for the 3(10)-helix/alpha-helix equilibrium constant for a given peptide. Finite length effects and the "extra" intrahelical hydrogen bond of the 3(10) form are expressed naturally as a result of this loop analysis. This semiempirical model captures all the established features of existing empirical rules for helical conformational transitions in Aib-rich sequences, as well as the recently detected helical transition induced solely by sequence permutation.
Basu
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G
Cornell University, Department of Chemistry, Baker Laboratory, Ithaca, New York 14853.
Kuki
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A
D000595:Amino Acid Sequence; D000621:Aminoisobutyric Acids / Q000737:chemistry*; D006860:Hydrogen Bonding; D008433:Mathematics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation
D000621:Aminoisobutyric Acids; D009842:Oligopeptides; C100049:2-aminoisobutyric acid