title: High thermodynamic stability of parametrically designed helical bundles.
abstract: We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.|Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
authors.forename: Po-Ssu
authors.initials: PS
authors.lastname: Huang
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.|Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.|Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria.
authors.forename: Gustav
authors.initials: G
authors.lastname: Oberdorfer
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.|Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
authors.forename: Chunfu
authors.initials: C
authors.lastname: Xu
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
authors.forename: Xue Y
authors.initials: XY
authors.lastname: Pei
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
authors.forename: Brent L
authors.initials: BL
authors.lastname: Nannenga
authors.affiliation: Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Rogers
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.|Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
authors.forename: Frank
authors.initials: F
authors.lastname: DiMaio
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
authors.forename: Tamir
authors.initials: T
authors.lastname: Gonen
authors.affiliation: Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Luisi
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.|Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.|Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D020650:Combinatorial Chemistry Techniques; D018360:Crystallography, X-Ray; D011489:Protein Denaturation; D015202:Protein Engineering / Q000379:methods*; D017433:Protein Structure, Secondary; D013816:Thermodynamics