Improving Protein Expression, Stability, and Function with ProteinMPNN.

Natural proteins are highly optimized for function but are often difficult to produce at a scale suitable for biotechnological applications due to poor expression in heterologous systems, limited solubility, and sensitivity to temperature. Thus, a general method that improves the physical properties of native proteins while maintaining function could have wide utility for protein-based technologies. Here, we show that the deep neural network ProteinMPNN, together with evolutionary and structural information, provides a route to increasing protein expression, stability, and function. For both myoglobin and tobacco etch virus (TEV) protease, we generated designs with improved expression, elevated melting temperatures, and improved function. For TEV protease, we identified multiple designs with improved catalytic activity as compared to the parent sequence and previously reported TEV variants. Our approach should be broadly useful for improving the expression, stability, and function of biotechnologically important proteins.

The Axin scaffold protects the kinase GSK3ß from cross-pathway inhibition.

Multiple signaling pathways regulate the kinase GSK3ß by inhibitory phosphorylation at Ser9, which then occupies the GSK3ß priming pocket and blocks substrate binding. Since this mechanism should affect GSK3ß activity toward all primed substrates, it is unclear why Ser9 phosphorylation does not affect other GSK3ß-dependent pathways, such as Wnt signaling. We used biochemical reconstitution and cell culture assays to evaluate how Wnt-associated GSK3ß is insulated from cross-activation by other signals. We found that the Wnt-specific scaffold protein Axin allosterically protects GSK3ß from phosphorylation at Ser9 by upstream kinases, which prevents accumulation of pS9-GSK3ß in the Axin•GSK3ß complex. Scaffold proteins that protect bound proteins from alternative pathway reactions could provide a general mechanism to insulate signaling pathways from improper crosstalk.

A kinetic mechanism for systems-level behavior in GTPase signaling.

GTPase switches are hubs for multiple distinct cell signaling inputs and outputs. In a new study combining genetic and biochemical methods, Perica, Mathy et al. identify an unexpected connection between the kinetics of a GTPase switch cycle and functional specificity.