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 beta-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 beta-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.
Department of Chemistry, Indian Institute of Technology, Bombay, Mumbai-400 076, India.
K
K
Mohanraja
M
M
Dhanasekaran
B
B
Kundu
S
S
Durani
D000595:Amino Acid Sequence; D002942:Circular Dichroism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D010455:Peptides