Role of backbone strain in de novo design of complex α/β protein structures

Nobuyasu Koga (), Rie Koga, Gaohua Liu, Javier Castellanos, Gaetano T. Montelione () and David Baker ()
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Nobuyasu Koga: University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle
Rie Koga: University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle
Gaohua Liu: Nexomics Biosciences
Javier Castellanos: University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle
Gaetano T. Montelione: and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy
David Baker: University of Washington, Department of Biochemistry and Howard Hughes Medical Institute, Seattle

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract We previously elucidated principles for designing ideal proteins with completely consistent local and non-local interactions which have enabled the design of a wide range of new αβ-proteins with four or fewer β-strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of α-helices and β-strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded β-sheets flanked by α-helices. The initial designs were monomeric in solution with high thermal stability, and the nuclear magnetic resonance (NMR) structure of one was close to the design model, but for two others the order of strands in the β-sheet was swapped. Investigation into the origins of this strand swapping suggested that the global structures of the design models were more strained than the NMR structures. We incorporated explicit consideration of global backbone strain into the design methodology, and succeeded in designing proteins with the intended unswapped strand arrangements. These results illustrate the value of experimental structure determination in guiding improvement of de novo design, and the importance of consistency between local, supersecondary, and global tertiary interactions in determining protein topology. The augmented set of principles should inform the design of larger functional proteins.

Date: 2021
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DOI: 10.1038/s41467-021-24050-7

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