Mechanism-based protein design: Attempted "nucleation-condensation" approach to a possible minimal helix-bundle protein

In an intended mechanism‐based de novo approach, a 22‐mer peptide was so designed as to make it both a stereochemically nucleatable and hydrophobically condensable minimal globular protein. Framework‐like nucleation of a triple‐helix bundle was targeted by employing as folding nucleators composite β‐turns that could both nucleate helices and place them in close juxtaposition for possible interhelical interaction. To promote the targeted triple‐helix bundle to condense as a globular protein, an amphipathic sequence pattern was adopted for possible hydrophobic interhelical interaction. A predominantly helicogenic 22‐mer amphipathic peptide was thus designed, punctuating it with composite type II′–III and type II–Asx type β‐turns as the helix nucleators cum chain reversal elements. The peptide made by solid‐phase synthesis was shown by NMR and CD to be a nascent and distorted triple‐helix bundle in a trifluoroethanol (TFE)–water mixture, but more or less a random coil in water. A fold nucleation effect is evident in the TFE–water mixture, but apparently the hydrophobic effect cannot sustain the peptide conformational order in water. A lack of synergy between folding nucleation and hydrophobic condensation of the peptide is possible. Indeed, a mismatch between the sequential H,P pattern of the peptide and its nascent‐type globular fold in a TFE–water mixture is evident based on a simulated annealing study guided by NMR. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 355–363, 2003