title: Synthetic beta-solenoid proteins with the fragment-free computational design of a beta-hairpin extension.
abstract: The ability to design and construct structures with atomic level precision is one of the key goals of nanotechnology. Proteins offer an attractive target for atomic design because they can be synthesized chemically or biologically and can self-assemble. However, the generalized protein folding and design problem is unsolved. One approach to simplifying the problem is to use a repetitive protein as a scaffold. Repeat proteins are intrinsically modular, and their folding and structures are better understood than large globular domains. Here, we have developed a class of synthetic repeat proteins based on the pentapeptide repeat family of beta-solenoid proteins. We have constructed length variants of the basic scaffold and computationally designed de novo loops projecting from the scaffold core. The experimentally solved 3.56-Å resolution crystal structure of one designed loop matches closely the designed hairpin structure, showing the computational design of a backbone extension onto a synthetic protein core without the use of backbone fragments from known structures. Two other loop designs were not clearly resolved in the crystal structures, and one loop appeared to be in an incorrect conformation. We have also shown that the repeat unit can accommodate whole-domain insertions by inserting a domain into one of the designed loops.
authors: Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom;
authors: James T
authors: JT
authors: MacDonald
authors: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom;
authors: Burak V
authors: BV
authors: Kabasakal
authors: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom;
authors: David
authors: D
authors: Godding
authors: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; Laboratory of Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.
authors: Sebastian
authors: S
authors: Kraatz
authors: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom;
authors: Louie
authors: L
authors: Henderson
authors: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom;
authors: James
authors: J
authors: Barber
authors: Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, United Kingdom; Department of Medicine, Imperial College London, London SW7 2AZ, United Kingdom;
authors: Paul S
authors: PS
authors: Freemont
authors: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom; j.w.murray@imperial.ac.uk.
authors: James W
authors: JW
authors: Murray
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D018360:Crystallography, X-Ray; D010455:Peptides / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D015202:Protein Engineering; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D020449:Repetitive Sequences, Amino Acid / Q000235:genetics*
chemical_list: D010455:Peptides; D011506:Proteins
keywords: coarse-grained model; computational protein design; de novo backbone design; synthetic repeat proteins