Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design

Abstract

The de novo design of globular β-sheet proteins remains largely an unsolved problem. It is unclear if most designs are failing because the designed sequences do not have favorable energies in the target conformations or if more emphasis should be placed on negative design, i.e. explicitly identifying sequences that have poor energies when adopting undesired conformations. We tested if we could redesign the sequence of a naturally occurring β-sheet protein, tenascin, with a design algorithm that does not include explicit negative design. Denaturation experiments indicate that the designs are significantly more stable than the wild type protein and the crystal structure of one design closely matches the design model. These results suggest that extensive negative design is not required to create well-folded β-sandwich proteins. However, it is important to note that negative design elements may be encoded in the conformation of the protein backbone which was preserved from the wild type protein