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

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 alpha beta -proteins with four or fewer beta -strands. The principles relate local backbone structures to supersecondary-structure packing arrangements of alpha -helices and beta -strands. Here, we test the generality of the principles by employing them to design larger proteins with five- and six- stranded beta -sheets flanked by alpha -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 beta -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. The authors show that consideration of global backbone strain enables successful de novo design of larger alpha beta -proteins with five- and six- stranded beta -sheets flanked by alpha -helices.

Automated summary

The study successfully applied the principles of designing ideal proteins with consistent local and non-local interactions to design larger proteins with five- and six-stranded beta-sheets flanked by alpha-helices. Investigation revealed that the global structures of the design models were more strained than the NMR structures. By incorporating explicit consideration of global backbone strain, proteins with the intended unswapped strand arrangements were successfully designed, highlighting the importance of global tertiary interactions in determining protein topology.