A CD STUDY OF THE ALPHA-HELIX NUCLEATION HYPOTHESIS

One of the dilemmas in predicting the secondary structure of proteins from their amino acid propensity for a given conformation is the prese nce of all amino acids in all types of secondary structure, regardless of their propensity for that specific structure. One explanation is t he nucleation hypothesis that only a few residues with a strong propen sity for the secondary structure, such as the alpha-helix structure, i nitiates its formation and propagates the structure through indifferen t sequences until strong breakers terminate the growth on both ends. E ight 15-mer peptides were studied to examine the alpha-helix nucleatio n hypothesis. The nucleation sequence of VAEAK, with high helix propen sity, was mixed with an indifferent sequence of TSDSR in all possible permutations. From the percent alpha-helix structure derived from the CD at 222 nm, it appears that helicity does not propagate through the indifferent sequence. (C) 1994 John Wiley & Sons, Inc.