The goal of this project is to mimic the helix-turn-helix (HTH) motif of the POU Oct-1 homeodomain and the 434 Cro repressor by constraining the native conformation of this small portion of the protein. The helix-turn-helix motif is found in several DNA-binding proteins that have known 3-dimensional structures. Such chimeric molecules can serve a two-fold health-related purpose. First, the design and biochemical evaluation of the chimeric molecules will explore fundamental aspects of protein folding and protein-DNA interactions. Second, each of the mimics described could serve as biochemical probes of developmental processes. POU homeodomains are transcription factors for human growth hormone, histones, snRNAs, immunoglobulin, herpes simplex virus and other medically important genes. The PI proposes to constrain the conformation of peptides corresponding to the HTH motif via covalent bonds between buried hydrophobic side-chains. Two approaches to this unusual type of side-chain linkage will be taken: 1) aryl linkage and 2) alkyl linkage. The templates are designed to stabilize the conformation of the flexible turn. The designs feature stable organic side-chains which will favor protein folding by burial of the additional hydrophobic moiety. Each template will be synthesized stereospecifically from amino acid starting materials and incorporated by solid-phase synthesis into a peptide corresponding to the sequence of the structurally well-characterized Cro repressor and POU Oct-1 homeodomain. Peptide engineering of the alpha-helices will introduce salt bridges and residues with high helix propensities to improve the helicity of attached peptides. A helix-to-helix crosslink will be introduced to improve the tertiary structure stability. The HTH mimics will be characterized chemically (HPLC, MS, NMR), structurally (CD, NMR and/or x-ray crystallography) and functionally (DNA-binding affinity) to ascertain the success of the mimics.
| Foulds, G J; Etzkorn, F A (1999) DNA-binding affinities of MyoD and E47 homo- and hetero-dimers by capillary electrophoresis mobility shift assay. J Chromatogr A 862:231-6 |
| Foulds, G J; Etzkorn, F A (1998) A capillary electrophoresis mobility shift assay for protein-DNA binding affinities free in solution. Nucleic Acids Res 26:4304-5 |
