A General Computational Approach for Repeat Protein Design. Issue 2 (30th January 2015)

• Record Type: Journal Article
• Authors: Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey; Xiao, Rong; Park, Keunwan; Caprari, Silvia; Su, Min; Seetharaman, Jayaraman; Mao, Lei; Janjua, Haleema; Montelione, Gaetano T.; Hunt, John; Baker, David
• Is Part Of: Journal of molecular biology. Volume 427:Issue 2(2015:Jan. 15)
• Page Start: 563
• Page End: 575
• Publication Date: 2015-01-30
• Subjects: MSA multiple sequence alignment -- AGF analytical gel filtration -- MALS multi-angle light scattering -- VLR variable lymphocyte receptor -- PEG polyethylene glycol -- TPR tetratrico peptide repeat -- LRR leucine rich repeat -- ank ankyrin -- arm armadillo -- CD circular dichroism; repeat proteins -- computational design -- thermodynamic stability -- idealized proteins -- de novo design; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2014.11.005
• Languages: English
• ISSNs: 0022-2836

Abstract

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 1 Å 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. Graphical abstract: Highlights: Several repeat proteins are potential scaffolds for biomaterials and binders. We developed a general computational method for design of repeat proteins. Forty percent of the tested designs were soluble, monomeric and folded with high stability. Crystal structures confirmed the high accuracy of the models. The method can be used to generate easily modular proteins with desired topologies.