title: Protein design on computers. Five new proteins: Shpilka, Grendel, Fingerclasp, Leather, and Aida.
abstract: What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded beta-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Finger-clasp, a dimer of interdigitating beta-beta-alpha units, the simplest variant of the "handshake" structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather--a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.
authors.affiliation: European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany.
authors.forename: C
authors.initials: C
authors.lastname: Sander
authors.forename: G
authors.initials: G
authors.lastname: Vriend
authors.forename: F
authors.initials: F
authors.lastname: Bazan
authors.forename: A
authors.initials: A
authors.lastname: Horovitz
authors.forename: H
authors.initials: H
authors.lastname: Nakamura
authors.forename: L
authors.initials: L
authors.lastname: Ribas
authors.forename: A V
authors.initials: AV
authors.lastname: Finkelstein
authors.forename: A
authors.initials: A
authors.lastname: Lockhart
authors.forename: R
authors.initials: R
authors.lastname: Merkl
authors.forename: L J
authors.initials: LJ
authors.lastname: Perry
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D003201:Computers; D005418:Flavodoxin / Q000378:metabolism; D008969:Molecular Sequence Data; D009243:NAD / Q000378:metabolism; D011487:Protein Conformation; D015202:Protein Engineering; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D011994:Recombinant Proteins
chemical_list: D002352:Carrier Proteins; D005418:Flavodoxin; D011506:Proteins; D011994:Recombinant Proteins; D009243:NAD; C075079:Grendel protein, recombinant; C075081:Fingerclasp protein, recombinant; C075083:Aida protein, synthetic; C075084:Leather protein, synthetic; C075078:Shpilka protein, synthetic