β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-β-sheet proteins from first principles lags far behind the design of all-α or mixed-αβ domains owing to their non-local nature and the tendency of exposed β-strand edges to aggregate. Through study of loops connecting unpaired β-strands (β-arches), we have identified a series of structural relationships between loop geometry, side chain directionality and β-strand length that arise from hydrogen bonding and packing constraints on regular β-sheet structures. We use these rules to de novo design jellyroll structures with double-stranded β-helices formed by eight antiparallel β-strands. The nuclear magnetic resonance structure of a hyperthermostable design closely matched the computational model, demonstrating accurate control over the β-sheet structure and loop geometry. Our results open the door to the design of a broad range of non-local β-sheet protein structures.

CEITEC Central European Institute of Technology Masaryk University Brno Czech Republic

Department of Biochemistry University of Washington Seattle WA USA Institute for Protein Design University of Washington Seattle WA USA

Department of Biochemistry University of Washington Seattle WA USA Institute for Protein Design University of Washington Seattle WA USA Amazon Seattle WA USA

Department of Biochemistry University of Washington Seattle WA USA Institute for Protein Design University of Washington Seattle WA USA Cyrus Biotechnology Seattle WA USA

Department of Biochemistry University of Washington Seattle WA USA Institute for Protein Design University of Washington Seattle WA USA Institute for Research in Biomedicine Barcelona Institute of Science and Technology Barcelona Spain

Department of Biochemistry University of Washington Seattle WA USA Institute for Protein Design University of Washington Seattle WA USA Institute of Biochemistry Graz University of Technology Graz Austria

Department of Chemistry and Biochemistry University of California Santa Cruz Santa Cruz CA USA

Department of Chemistry and Biochemistry University of California Santa Cruz Santa Cruz CA USA Department of Computer Science University of California Santa Cruz Santa Cruz CA USA

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