title: Analysis and design of turns in alpha-helical hairpins.
abstract: Although the analysis and design of turns that connect the strands in antiparallel beta-hairpins has reached an advanced state, much less is known concerning turns between antiparallel helices in helical hairpins. We have conducted an analysis of the structures and sequence preferences of two types of interhelical turns, each of which connects the two helices by a two-residue linker in an alphaL-beta conformation. Based on this analysis, it became apparent that the turn introduced into a designed four-helix bundle protein, DF1, did not occur within an optimal structural context. DF1 is a dimeric model for the diiron class of proteins. A longer loop with a beta-alphaR-beta conformation was inserted between two helices in the protein, and a sequence was chosen to stabilize its conformation. X-ray crystallography and NMR analysis of the protein showed the structure to be in excellent agreement with design.
authors.affiliation: Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Lahr
authors.forename: Donald E
authors.initials: DE
authors.lastname: Engel
authors.forename: Steven E
authors.initials: SE
authors.lastname: Stayrook
authors.forename: Ornella
authors.initials: O
authors.lastname: Maglio
authors.forename: Benjamin
authors.initials: B
authors.lastname: North
authors.forename: Silvano
authors.initials: S
authors.lastname: Geremia
authors.forename: Angela
authors.initials: A
authors.lastname: Lombardi
authors.forename: William F
authors.initials: WF
authors.lastname: DeGrado
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D017076:Computer-Aided Design; D018360:Crystallography, X-Ray; D009682:Magnetic Resonance Spectroscopy; D008667:Metalloproteins / Q000737:chemistry*; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid
chemical_list: D008667:Metalloproteins