title: Binding geometry of alpha-helices that recognize DNA.
abstract: Many transcription factors have an alpha-helix that binds to DNA bases in a specific fashion. The DNA-binding geometry of these recognition helices varies substantially. We define a set of parameters to describe the binding geometry of recognition helices and analyze specific stereochemical elements that determine particular geometries. Because the convex surface of the helix must fit into the concave surface of the DNA major groove, the number of degrees of freedom of the recognition helix is reduced from a possible six to a single angle, which we call alpha. The chemically interacting DNA bases and amino acid residues must lie along a common line and have the same spacing along it. This pairing of base positions with residue positions seems to restrict the binding geometry further to a set of discrete values for alpha.
authors: MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
authors: M
authors: M
authors: Suzuki
authors: M
authors: M
authors: Gerstein
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D007256:Information Systems; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017433:Protein Structure, Secondary; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA