title: The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.
abstract: Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features.
authors.affiliation: GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium. Electronic address: maxifigueroa@udec.cl.
authors.forename: Maximiliano
authors.initials: M
authors.lastname: Figueroa
authors.affiliation: Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Mike
authors.initials: M
authors.lastname: Sleutel
authors.affiliation: GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
authors.forename: Marylene
authors.initials: M
authors.lastname: Vandevenne
authors.affiliation: GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
authors.forename: Gregory
authors.initials: G
authors.lastname: Parvizi
authors.affiliation: GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
authors.forename: Sophie
authors.initials: S
authors.lastname: Attout
authors.affiliation: GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
authors.forename: Olivier
authors.initials: O
authors.lastname: Jacquin
authors.affiliation: Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium.
authors.forename: Julie
authors.initials: J
authors.lastname: Vandenameele
authors.affiliation: Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.
authors.forename: Axel W
authors.initials: AW
authors.lastname: Fischer
authors.affiliation: Department of Chemistry, Univeristy of Liège, Belgium.
authors.forename: Christian
authors.initials: C
authors.lastname: Damblon
authors.affiliation: Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Erik
authors.initials: E
authors.lastname: Goormaghtigh
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Valerio-Lepiniec
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France.
authors.forename: Agathe
authors.initials: A
authors.lastname: Urvoas
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Durand
authors.affiliation: Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Els
authors.initials: E
authors.lastname: Pardon
authors.affiliation: Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Steyaert
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Minard
authors.affiliation: Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Dominique
authors.initials: D
authors.lastname: Maes
authors.affiliation: Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.
authors.forename: Jens
authors.initials: J
authors.lastname: Meiler
authors.affiliation: Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium.
authors.forename: André
authors.initials: A
authors.lastname: Matagne
authors.affiliation: GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Martial
authors.affiliation: GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium. Electronic address: c.vandeweerdt@ulg.ac.be.
authors.forename: Cécile
authors.initials: C
authors.lastname: Van de Weerdt
mesh_terms: D003198:Computer Simulation / Q000592:standards*; D018360:Crystallography, X-Ray; D019020:Directed Molecular Evolution / Q000379:methods*; D006801:Humans; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D011994:Recombinant Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins; D011994:Recombinant Proteins; C073399:octarellin
keywords: Artificial proteins; De novo design; Molecular modeling; Protein design