Systems-level effects of allosteric perturbations to a model molecular switch

• DOI: 10.1038/s41586-021-03982-6
• Publication Date: 2021-10-13T19:03:58Z
• Authors: Tina Perica; Christopher J. P....; Jiewei Xu; Gwendolyn Μ. Jang; Yang Zhang; Robyn Kaake; Noah Ollikainen; Hannes Braberg; Danielle L. Swaney; David G. Lambright; Mark J. S. Kelly; Nevan J. Krogan; Tanja Kortemme
• Keywords: Saccharomyces cerevisiae Proteins; General Science & Technology; 1.1 Normal biological development and functioning; Bioinformatics and Computational Biology; Proteomic analysis; 610 Medicine & health; Bioengineering; Saccharomyces cerevisiae; 03 medical and health sciences; Allosteric Regulation; Underpinning research; Catalytic Domain; 10019 Department of Biochemistry; Genetics; 2.1 Biological and endogenous factors; Guanine Nucleotide Exchange Factors; Point Mutation; GTP-binding protein regulators; Aetiology; Monomeric GTP-Binding Proteins; 1000 Multidisciplinary; 0303 health sciences; Binding Sites; GTPase-Activating Proteins; Nuclear Proteins; Biological Sciences; Molecular conformation; Regulatory networks; Networks and systems biology; Kinetics; 570 Life sciences; biology; HIV/AIDS; Biochemistry and Cell Biology; Generic health relevance; Guanosine Triphosphate; Protein Binding

Molecular switch proteins whose cycling between states is controlled by opposing regulators1,2 are central to biological signal transduction. As switch proteins function within highly connected interaction networks3, the fundamental question arises of how functional specificity is achieved when different processes share common regulators. Here we show that functional specificity of the small GTPase switch protein Gsp1 in Saccharomyces cerevisiae (the homologue of the human protein RAN)4 is linked to differential sensitivity of biological processes to different kinetics of the Gsp1 (RAN) switch cycle. We make 55 targeted point mutations to individual protein interaction interfaces of Gsp1 (RAN) and show through quantitative genetic5 and physical interaction mapping that Gsp1 (RAN) interface perturbations have widespread cellular consequences. Contrary to expectation, the cellular effects of the interface mutations group by their biophysical effects on kinetic parameters of the GTPase switch cycle and not by the targeted interfaces. Instead, we show that interface mutations allosterically tune the GTPase cycle kinetics. These results suggest a model in which protein partner binding, or post-translational modifications at distal sites, could act as allosteric regulators of GTPase switching. Similar mechanisms may underlie regulation by other GTPases, and other biological switches. Furthermore, our integrative platform to determine the quantitative consequences of molecular perturbations may help to explain the effects of disease mutations that target central molecular switches.