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Journal of the American Chemical Society, Vol.118, No.13, 3073-3081, 1996
Economy in Protein Design - Evolution of a Metal-Independent Beta-Beta-Alpha Motif Based on the Zinc-Finger Domains
An iterative design process involving the synthesis and structural analyses of five polypeptides patterned after the zinc finger domains is described. This process has led to the development of a metal-independent folded beta beta alpha motif, BBA1. In contrast to the zinc fingers and other naturally occurring peptides of similar size, this small monomeric structure folds without the assistance of metal cation ligation or disulfide bridges. To probe the effect of metal binding on the secondary and tertiary structure of peptides throughout the design process, a non-standard amino acid 3-(1,10-phenanthrol-2-yl)-L-alanine (Fen) was incorporated and its unique chromophore utilized for circular dichroism (CD) analysis. Advanced designs were analyzed by both CD and 2D NMR. The solution structure of BBA1 was determined using NOE restrained simulated annealing. The average RMSD for the backbone atoms of residues 1-22 is 0.9 +/- 0.3 Angstrom. Analysis of the resulting structure reveals that the alpha-helix and beta-hairpin are associated via a well-defined hydrophobic core including several key hydrophobic residues. A key design feature of BBA1 is the utilization of a type II’ reverse turn to promote beta-hairpin formation; a control peptide, in which the beta-turn of three-dimensional structure of this motif are dramatic. BBA1, a 23-residue mixed alpha/beta motif, defines a new lower limit for the size of an independently folded polypeptide with native structure.
Keywords:DEPENDENT STRUCTURE;PEPTIDE-FRAGMENTS;CRYSTAL-STRUCTURE;4-HELIX BUNDLE;BINDING;WATER;SPECTROSCOPY;INITIATION;PHASE;FORM