Precise assembly of complex beta sheet topologies from de novo designed building blocks
Indigo Chris King,
James Gleixner,
Lindsey Doyle,
Alexandre Kuzin,
John F Hunt,
Rong Xiao,
Gaetano T Montelione,
Barry L Stoddard,
Frank DiMaio,
David Baker
Affiliations
Indigo Chris King
Institute for Protein Design, University of Washington, Seattle, United States
James Gleixner
Institute for Protein Design, University of Washington, Seattle, United States
Lindsey Doyle
Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
Alexandre Kuzin
Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, United States
John F Hunt
Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, United States
Rong Xiao
Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, United States
Gaetano T Montelione
Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, United States
Barry L Stoddard
Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
Frank DiMaio
Institute for Protein Design, University of Washington, Seattle, United States
David Baker
Institute for Protein Design, University of Washington, Seattle, United States
Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we demonstrate that protein topologies with six and seven-stranded beta sheets can be designed by insertion of one de novo designed beta sheet containing protein into another such that the two beta sheets are merged to form a single extended sheet, followed by amino acid sequence optimization at the newly formed strand-strand, strand-helix, and helix-helix interfaces. Crystal structures of two such designs closely match the computational design models. Searches for similar structures in the SCOP protein domain database yield only weak matches with different beta sheet connectivities. A similar beta sheet fusion mechanism may have contributed to the emergence of complex beta sheets during natural protein evolution.
