Abstract
The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. For example, class I viral fusion proteins undergo large scale conformational changes from a pre-fusion to a post-fusion structure critical for the virus to enter cells(Ivanovic et al., 2013; Podbilewicz, 2014; Skehel and Wiley, 2000). While computational methods have been used to de novo design proteins in single deep free energy minima(Huang et al., 2016), designing sequences with two well-separated free energy minima corresponding to well-defined, but divergent structures is substantially more challenging, and has not yet been achieved. Here, we design sequences which can adopt two very different homotrimeric helical bundle conformations -- one short (~66 Å height) and the other long (~100 Å height) -- reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization of a set of closely related sequences show that both the short and long structures fold as designed, and suggest that the two states are nearly isoenergetic as small sequence changes and/or changes in measurement conditions switch the observed state.
