title: Miniature homeodomains: high specificity without an N-terminal arm.
abstract: Recently, we described a strategy for the design of miniature proteins that bind DNA and protein surfaces with high affinity and selectivity. This strategy involves identifying the functional epitope required for macromolecular recognition by a natural protein and presenting it on a small, stable protein scaffold. In previous work, high-affinity DNA recognition was achieved only when the miniature protein contained the complete functional epitope. Here we report a miniature homeodomain that recognizes its 6-bp target site in the nanomolar concentration range at 25 degrees C, despite the absence of DNA contact residues located along the homeodomain N-terminal arm. We conclude that miniature proteins can achieve high affinity and selectivity for DNA by design even when the functional epitope is incomplete by using pre-organization to effectively compensate for lost protein-DNA contacts. In this case it has been possible to miniaturize both the recognition surface and the structural framework of a globular protein fold.
authors.affiliation: Department of Chemistry, Yale University, P.O. Box 208217, New Haven, Connecticut 06520-8107, USA.
authors.forename: Jin Kim
authors.initials: JK
authors.lastname: Montclare
authors.forename: Alanna
authors.initials: A
authors.lastname: Schepartz
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D010191:Pancreatic Polypeptide / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D013379:Substrate Specificity
chemical_list: D018398:Homeodomain Proteins; C009725:pancreatic polypeptide, avian; D010191:Pancreatic Polypeptide; D004247:DNA