De novo design of proteins with two isoenergetic but structurally divergent ground states

Abstract

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 A height) and the other long (~100 A 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.