A general computational approach for repeat protein design.

Fabio Parmeggiani, Po-Ssu Huang, Sergey Vorobiev, Rong Xiao, Keunwan Park, Silvia Caprari, Min Su, Jayaraman Seetharaman, Lei Mao, Haleema Janjua, Gaetano T Montelione, John Hunt, David Baker

Journal: Journal of molecular biology 2015;427(2):563-75

PMID: 25451037

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Abstract

Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds.

Address: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.; Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA.; Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry and Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.; 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.

DOI: 10.1016/j.jmb.2014.11.005

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MeSH Terms: Amino Acid Sequence, Ankyrins, Armadillo Domain Proteins, Biocompatible Materials, Computer Simulation, Crystallography, X-Ray, Leucine-Rich Repeat Proteins, Microfilament Proteins, Models, Molecular, Molecular Sequence Data, Molecular Structure, Protein Conformation, Protein Engineering, Proteins, Sequence Alignment, Sequence Analysis, Protein