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Schiapparelli P, Pirman NL, Mohler K, Miranda-Herrera PA, Zarco N, Kilic O, Miller C, Shah SR, Rogulina S, Hungerford W, Abriola L, Hoyer D, Turk BE, Guerrero-Cázares H, Isaacs FJ, Quiñones-Hinojosa A, Levchenko A, Rinehart J. Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function. Cell Rep 2021; 36:109416. [PMID: 34289367 PMCID: PMC8379681 DOI: 10.1016/j.celrep.2021.109416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/23/2020] [Accepted: 06/28/2021] [Indexed: 12/15/2022] Open
Abstract
Advances in genetic code expansion have enabled the production of proteins containing site-specific, authentic post-translational modifications. Here, we use a recoded bacterial strain with an expanded genetic code to encode phosphoserine into a human kinase protein. We directly encode phosphoserine into WNK1 (with-no-lysine [K] 1) or WNK4 kinases at multiple, distinct sites, which produced activated, phosphorylated WNK that phosphorylated and activated SPAK/OSR kinases, thereby synthetically activating this human kinase network in recoded bacteria. We used this approach to identify biochemical properties of WNK kinases, a motif for SPAK substrates, and small-molecule kinase inhibitors for phosphorylated SPAK. We show that the kinase inhibitors modulate SPAK substrates in cells, alter cell volume, and reduce migration of glioblastoma cells. Our work establishes a protein-engineering platform technology that demonstrates that synthetically active WNK kinase networks can accurately model cellular systems and can be used more broadly to target networks of phosphorylated proteins for research and discovery.
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Affiliation(s)
| | - Natasha L Pirman
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kyle Mohler
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | | | - Natanael Zarco
- Department of Neurologic Surgery, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Onur Kilic
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chad Miller
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sagar R Shah
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Svetlana Rogulina
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - William Hungerford
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | | | - Farren J Isaacs
- Systems Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | | | - Andre Levchenko
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA.
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Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE. Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output. PLoS Biol 2019; 17:e2006540. [PMID: 30897078 PMCID: PMC6445471 DOI: 10.1371/journal.pbio.2006540] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 04/02/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022] Open
Abstract
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates. While the impact of localization and recruitment on kinase-substrate targeting can be readily assessed, evaluating the relative importance of direct phosphorylation site interactions remains challenging. In this study, we examine the STE20 family of protein serine-threonine kinases to investigate basic mechanisms of substrate targeting. We used peptide arrays to define the phosphorylation site specificity for the majority of STE20 kinases and categorized them into four distinct groups. Using structure-guided mutagenesis, we identified key specificity-determining residues within the kinase catalytic cleft, including an unappreciated role for the kinase β3-αC loop region in controlling specificity. Exchanging key residues between the STE20 kinases p21-activated kinase 4 (PAK4) and Mammalian sterile 20 kinase 4 (MST4) largely interconverted their phosphorylation site preferences. In cells, a reprogrammed PAK4 mutant, engineered to recognize MST substrates, failed to phosphorylate PAK4 substrates or to mediate remodeling of the actin cytoskeleton. In contrast, this mutant could rescue signaling through the Hippo pathway in cells lacking multiple MST kinases. These observations formally demonstrate the importance of catalytic site specificity for directing protein kinase signal transduction pathways. Our findings further suggest that phosphorylation site specificity is both necessary and sufficient to mediate distinct signaling outputs of STE20 kinases and imply broad applicability to other kinase signaling systems.
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Affiliation(s)
- Chad J. Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Hua Jane Lou
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Craig Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bert van de Kooij
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Byung Hak Ha
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oriana S. Fisher
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Natasha L. Pirman
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Titus J. Boggon
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology and Systems Biology Institute, Yale University, New Haven, Connecticut, United States of America
| | - Michael B. Yaffe
- Departments of Biological Engineering and Biology, MIT Center for Precision Cancer Medicine and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin E. Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut, United States of America
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Casey TM, Liu Z, Esquiaqui JM, Pirman NL, Milshteyn E, Fanucci GE. Continuous wave W- and D-band EPR spectroscopy offer "sweet-spots" for characterizing conformational changes and dynamics in intrinsically disordered proteins. Biochem Biophys Res Commun 2014; 450:723-8. [PMID: 24950408 DOI: 10.1016/j.bbrc.2014.06.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 06/10/2014] [Indexed: 11/28/2022]
Abstract
Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for characterizing conformational sampling and dynamics in biological macromolecules. Here we demonstrate that nitroxide spectra collected at frequencies higher than X-band (∼9.5 GHz) have sensitivity to the timescale of motion sampled by highly dynamic intrinsically disordered proteins (IDPs). The 68 amino acid protein IA3, was spin-labeled at two distinct sites and a comparison of X-band, Q-band (35 GHz) and W-band (95 GHz) spectra are shown for this protein as it undergoes the helical transition chemically induced by tri-fluoroethanol. Experimental spectra at W-band showed pronounced line shape dispersion corresponding to a change in correlation time from ∼0.3 ns (unstructured) to ∼0.6 ns (α-helical) as indicated by comparison with simulations. Experimental and simulated spectra at X- and Q-bands showed minimal dispersion over this range, illustrating the utility of SDSL EPR at higher frequencies for characterizing structural transitions and dynamics in IDPs.
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Affiliation(s)
- Thomas M Casey
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Natasha L Pirman
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Eugene Milshteyn
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA.
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Pirman NL, Milshteyn E, Galiano L, Hewlett JC, Fanucci GE. Characterization of the disordered-to-α-helical transition of IA₃ by SDSL-EPR spectroscopy. Protein Sci 2011; 20:150-9. [PMID: 21080428 DOI: 10.1002/pro.547] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy coupled with site-directed spin labeling (SDSL) is a valuable tool for characterizing the mobility and conformational changes of proteins but has seldom been applied to intrinsically disordered proteins (IDPs). Here, IA₃ is used as a model system demonstrating SDSL-EPR characterization of conformational changes in small IDP systems. IA₃ has 68 amino acids, is unstructured in solution, and becomes α-helical upon addition of the secondary structural stabilizer 2,2,2-trifluoroethanol (TFE). Two single cysteine substitutions, one in the N-terminus (S14C) and one in the C-terminus (N58C), were generated and labeled with three different nitroxide spin labels. The resultant EPR line shapes of each of the labels were compared and each reported changes in mobility upon addition of TFE. Specifically, the spectral line shape parameters h((+1))/h(₀), the local tumbling volume (V(L)), and the percent change of the h(₋₁) intensity were utilized to quantitatively monitor TFE-induced conformational changes. The values of h((+1)/)h(₀) as a function of TFE titration varied in a sigmoidal manner and were fit to a two-state Boltzmann model that provided values for the midpoint of the transition, thus, reporting on the global conformational change of IA₃. The other parameters provide site-specific information and show that S14C-SL undergoes a conformational change resulting in more restricted motion than N58C-SL, which is consistent with previously published results obtained by studies using NMR and circular dichroism spectroscopy indicating a higher degree of α-helical propensity of the N-terminal segment of IA₃. Overall, the results provide a framework for data analyzes that can be used to study induced unstructured-to-helical conformations in IDPs by SDSL.
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Affiliation(s)
- Natasha L Pirman
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
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