One-shot design elevates functional expression levels of a voltage-gated potassium channel

Abstract

Membrane proteins play critical physiological roles as receptors, channels, pumps, and transporters. Despite their importance, however, low expression levels often hamper the experimental characterization of membrane proteins. We present an automated and web-accessible design algorithm called mPROSS (https://mPROSS.weizmann.ac.il), which uses phylogenetic analysis and an atomistic potential, including an empirical lipophilicity scale, to improve native-state energy. As a stringent test, we apply mPROSS to the Kv1.2-Kv2.1 paddle chimera voltage-gated potassium channel. Four designs, encoding 9-26 mutations relative to the parental channel, were functional and maintained potassium-selective permeation and voltage dependence in Xenopus oocytes with up to 14-fold increase in whole-cell current densities. Additionally, single-channel recordings reveal no significant change in the channel-opening probability nor in unitary conductance, indicating that functional expression levels increase without impacting the activity profile of individual channels. Our results suggest that the expression levels of other dynamical channels and receptors may be enhanced through one-shot design calculations. Significance statementHeterologous expression levels of membrane proteins are often low, limiting research and applications. We combine homologous-sequence analysis with Rosetta atomistic calculations to enable one-shot design of dozens of mutations that improve native-state energy. Applied to a voltage-gated potassium channel, designs exhibited up to 14-fold improved functional expression levels in oocytes with almost no change in the single-channel activity profile. This design approach may accelerate research of many challenging membrane proteins, including receptors, channels, and transporters.