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Protein Science (2007), 16:2770-2774. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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FOR THE RECORD

A de novo designed protein–protein interface

Po-Ssu Huang1,2,3, John J. Love3, and Stephen L. Mayo1,2

1 Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
2 Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
3 Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182, USA

(RECEIVED July 16, 2007; FINAL REVISION September 21, 2007; ACCEPTED September 21, 2007)

As an approach to both explore the physical/chemical parameters that drive molecular self-assembly and to generate novel protein oligomers, we have developed a procedure to generate protein dimers from monomeric proteins using computational protein docking and amino acid sequence design. A fast Fourier transform-based docking algorithm was used to generate a model for a dimeric version of the 56-amino-acid beta1 domain of streptococcal protein G. Computational amino acid sequence design of 24 residues at the dimer interface resulted in a heterodimer comprised of 12-fold and eightfold variants of the wild-type protein. The designed proteins were expressed, purified, and characterized using analytical ultracentrifugation and heteronuclear NMR techniques. Although the measured dissociation constant was modest (~300 µM), 2D-[1H,15N]-HSQC NMR spectra of one of the designed proteins in the absence and presence of its binding partner showed clear evidence of specific dimer formation.

Keywords: de novo protein–protein interface; computational protein design; geometric recognition algorithm; protein G; heterodimer; NMR; docking


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Copyright © 2007 by The Protein Society.