title: Computational design of a self-assembling symmetrical β-propeller protein.
abstract: The modular structure of many protein families, such as β-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical β-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry.
authors.affiliation: Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan; and Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Arnout R D
authors.initials: AR
authors.lastname: Voet
authors.affiliation: Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Noguchi
authors.affiliation: Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Christine
authors.initials: C
authors.lastname: Addy
authors.affiliation: Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan; and.
authors.forename: David
authors.initials: D
authors.lastname: Simoncini
authors.affiliation: Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Daiki
authors.initials: D
authors.lastname: Terada
authors.affiliation: Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Unzai
authors.affiliation: Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Sam-Yong
authors.initials: SY
authors.lastname: Park
authors.affiliation: Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan; and kamzhang@riken.jp jtame@tsurumi.yokohama-cu.ac.jp.
authors.forename: Kam Y J
authors.initials: KY
authors.lastname: Zhang
authors.affiliation: Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan kamzhang@riken.jp jtame@tsurumi.yokohama-cu.ac.jp.
authors.forename: Jeremy R H
authors.initials: JR
authors.lastname: Tame
mesh_terms: D000595:Amino Acid Sequence; D001703:Biophysics; D002942:Circular Dichroism; D018360:Crystallography, X-Ray; D008027:Light; D008958:Models, Molecular; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D036103:Nanotechnology; D015202:Protein Engineering; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012542:Scattering, Radiation; D017386:Sequence Homology, Amino Acid; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization; D014461:Ultracentrifugation
chemical_list: D011506:Proteins
keywords: computational protein design; protein crystallography; protein evolution; self-assembly; β-propeller