DeepMind presented remarkably accurate predictions at the recent CASP14 protein structure prediction assessment conference. We explored network architectures incorporating related ideas and obtained the best performance with a three-track network in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging X-ray crystallography and cryo-EM structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short circuiting traditional approaches which require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.

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Class I Phosphoinositide 3-kinases (PI3Ks) are master regulators of cellular functions, with the class IB PI3K catalytic subunit (p110g) playing key roles in immune signalling. p110g is a key factor in inflammatory diseases, and has been identified as a therapeutic target for cancers due to its immunomodulatory role. Using a combined biochemical/biophysical approach, we have revealed insight into regulation of kinase activity, specifically defining how immunodeficiency and oncogenic mutations of R1021 in the C-terminus can inactivate or activate enzyme activity. Screening of inhibitors using HDX-MS revealed that activation loop-binding inhibitors induce allosteric conformational changes that mimic those in the R1021C mutant. Structural analysis of advanced PI3K inhibitors in clinical development revealed novel binding pockets that can be exploited for further therapeutic development. Overall this work provides unique insights into regulatory mechanisms that control PI3Kg kinase activity, and shows a framework for the design of PI3K isoform and mutant selective inhibitors.

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Phosphoinositide kinases are central regulators of myriad cellular processes, and their misregulation is causative of multiple human diseases. We are currently focusing on the structural basis for the regulation of phosphoinositide kinases, specifically the Golgi localised phosphatidylinositol 4‐kinase beta (PI4KB). We have identified a previously uncharacterised protein binding partner of PI4KB, the GTPase regulatory protein c10orf76 1, and revealed novel insight into an unexpected PI4K positive feedback loop. Using a combined hydrogen deuterium exchange mass spectrometry (HDX‐MS) and structural biology approach we have defined the molecular basis of regulation by the protein c10orf76, revealing novel insight into the role of these PI4KB in viral replication. This has revealed key insight into unexpected feedback loops with Ras superfamily GTPases. Overall, this approach has provided a novel toolbox of engineered mutations to tease out the molecular basis of regulation of phosphoinositide kinases in both homeostasis and disease, and has revealed novel opportunities for the development of small molecule therapeutics for multiple pathogenic viral infections. Support or Funding Information Research was supported by the Canadian Institute of Health Research (CRN‐142393), and salary award for the CIHR new investigator and MSFHR scholar programs. McPhailEMBO Reports 2018