1
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Stephenson EH, Higgins JMG. Pharmacological approaches to understanding protein kinase signaling networks. Front Pharmacol 2023; 14:1310135. [PMID: 38164473 PMCID: PMC10757940 DOI: 10.3389/fphar.2023.1310135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024] Open
Abstract
Protein kinases play vital roles in controlling cell behavior, and an array of kinase inhibitors are used successfully for treatment of disease. Typical drug development pipelines involve biological studies to validate a protein kinase target, followed by the identification of small molecules that effectively inhibit this target in cells, animal models, and patients. However, it is clear that protein kinases operate within complex signaling networks. These networks increase the resilience of signaling pathways, which can render cells relatively insensitive to inhibition of a single kinase, and provide the potential for pathway rewiring, which can result in resistance to therapy. It is therefore vital to understand the properties of kinase signaling networks in health and disease so that we can design effective multi-targeted drugs or combinations of drugs. Here, we outline how pharmacological and chemo-genetic approaches can contribute to such knowledge, despite the known low selectivity of many kinase inhibitors. We discuss how detailed profiling of target engagement by kinase inhibitors can underpin these studies; how chemical probes can be used to uncover kinase-substrate relationships, and how these tools can be used to gain insight into the configuration and function of kinase signaling networks.
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Affiliation(s)
| | - Jonathan M. G. Higgins
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle uponTyne, United Kingdom
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2
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Lippert LG, Ma N, Ritt M, Jain A, Vaidehi N, Sivaramakrishnan S. Kinase inhibitors allosterically disrupt a regulatory interaction to enhance PKCα membrane translocation. J Biol Chem 2021; 296:100339. [PMID: 33508318 PMCID: PMC7949123 DOI: 10.1016/j.jbc.2021.100339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/14/2021] [Accepted: 01/22/2021] [Indexed: 10/28/2022] Open
Abstract
The eukaryotic kinase domain has multiple intrinsically disordered regions whose conformation dictates kinase activity. Small molecule kinase inhibitors (SMKIs) rely on disrupting the active conformations of these disordered regions to inactivate the kinase. While SMKIs are selected for their ability to cause this disruption, the allosteric effects of conformational changes in disordered regions is limited by a lack of dynamic information provided by traditional structural techniques. In this study, we integrated multiscale molecular dynamics simulations with FRET sensors to characterize a novel allosteric mechanism that is selectively triggered by SMKI binding to the protein kinase Cα domain. The indole maleimide inhibitors BimI and sotrastaurin were found to displace the Gly-rich loop (G-loop) that normally shields the ATP-binding site. Displacement of the G-loop interferes with a newly identified, structurally conserved binding pocket for the C1a domain on the N lobe of the kinase domain. This binding pocket, in conjunction with the N-terminal regulatory sequence, masks a diacylglycerol (DAG) binding site on the C1a domain. SMKI-mediated displacement of the G-loop released C1a and exposed the DAG binding site, enhancing protein kinase Cα translocation both to synthetic lipid bilayers and to live cell membranes in the presence of DAG. Inhibitor chemotype determined the extent of the observed allosteric effects on the kinase domain and correlated with the extent of membrane recruitment. Our findings demonstrate the allosteric effects of SMKIs beyond the confines of kinase catalytic conformation and provide an integrated computational-experimental paradigm to investigate parallel mechanisms in other kinases.
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Affiliation(s)
- Lisa G Lippert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Michael Ritt
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Abhinandan Jain
- The Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA.
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA.
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3
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Gupte TM, Ritt M, Sivaramakrishnan S. ER/K-link-Leveraging a native protein linker to probe dynamic cellular interactions. Methods Enzymol 2020; 647:173-208. [PMID: 33482988 PMCID: PMC8009693 DOI: 10.1016/bs.mie.2020.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
ER/K α-helices are a subset of single alpha helical domains, which exhibit unusual stability as isolated protein secondary structures. They adopt an elongated structural conformation, while regulating the frequency of interactions between proteins or polypeptides fused to their ends. Here we review recent advances on the structure, stability and function of ER/K α-helices as linkers (ER/K linkers) in native proteins. We describe methodological considerations in the molecular cloning, protein expression and measurement of interaction strengths, using sensors incorporating ER/K linkers. We highlight biological insights obtained over the last decade by leveraging distinct biophysical features of ER/K-linked sensors. We conclude with the outlook for the use of ER/K linkers in the selective modulation of dynamic cellular interactions.
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Affiliation(s)
- Tejas M Gupte
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Michael Ritt
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, United States.
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4
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Waszczak N, DeFlorio R, Ismael A, Cheng N, Stone DE, Metodiev MV. Quantitative proteomics reveals a Gα/MAPK signaling hub that controls pheromone-induced cellular polarization in yeast. J Proteomics 2019; 207:103467. [PMID: 31351147 DOI: 10.1016/j.jprot.2019.103467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/20/2019] [Accepted: 07/23/2019] [Indexed: 12/26/2022]
Abstract
The mating-specific yeast Gα controls pheromone signaling by sequestering Gβγ and by regulating the Fus3 MAP kinase. Disrupting Gα-Fus3 interaction leads to severe defects in chemotropism. Because Gα concentrates at the chemotropic growth site where Fus3 is required for the phosphorylation of two known targets, we screened for additional proteins whose phosphorylation depends on pheromone stimulation and Gα-Fus3 interaction. Using a mutant form of Gα severely defective in Fus3-binding, GαDSD, and quantitative mass spectrometry, fourteen proteins were identified as potential targets of Gα-recruited Fus3, ten of which were previously implicated in cell polarity and morphogenesis. To explore the biological relevance of these findings, we focused on the Spa2 polarisome protein, which was hypophosphorylated on multiple serine residues in pheromone-treated GαDSD cells. Six sites were mutagenized to create the Spa26XSA mutant protein. Spa26XSA exhibited increased affinity for Fus3, consistent with a kinase-substrate interaction, and Spa26XSA cells exhibited dramatic defects in gradient sensing and zygote formation. These results suggest that Gα promotes the phosphorylation of Spa2 by Fus3 at the cortex of pheromone-stimulated cells, and that this mechanism plays a role in chemotropism. How the Gα-Fus3 signaling hub affects the other putative targets identified here has yet to be determined. SIGNIFICANCE: Previously, interaction between the G alpha protein, Gpa1, and the MAPK of the pheromone response pathway, Fus3, was shown to be important for efficient sensing of the pheromone gradient and for the maintenance of cell polarity during mating. Here we show that the underlying molecular mechanisms involve the phosphorylation of specific cortical targets of Gpa1/Fus3. These have been identified by quantitative phosphoproteomics using a mutant of Gpa1, which is defective in interacting with Fus3. One of these targets is the polarisome protein Spa2. Alanine substitution of the Spa2 phosphorylation sites targeted by Gpa1/Fus3 lead to a dramatic defect in pheromone gradient sensing and zygote formation. These results reveal how the G alpha protein and the MAPK control cell polarity in a prototypical model system. Our results have wider significance as similar mechanisms exist in higher eukaryotes and are involved in important biological such as neuron development, immunity, and cancer cell metastasis.
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Affiliation(s)
- Nicholaz Waszczak
- Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Ave, Chicago, USA
| | - Reagan DeFlorio
- Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Ave, Chicago, USA
| | - Amber Ismael
- Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Ave, Chicago, USA
| | - Naiyuan Cheng
- Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Ave, Chicago, USA
| | - David E Stone
- Department of Biological Sciences, University of Illinois at Chicago, 900 South Ashland Ave, Chicago, USA.
| | - Metodi V Metodiev
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, UK.
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5
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Li P, Ma Z, Yu Y, Hu X, Zhou Y, Song H. FER promotes cell migration via regulating JNK activity. Cell Prolif 2019; 52:e12656. [PMID: 31264309 PMCID: PMC6797522 DOI: 10.1111/cpr.12656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/11/2022] Open
Abstract
Objectives Cell migration has a key role in cancer metastasis, which contributes to drug resistance and tumour recurrence. Better understanding of the mechanisms involved in this process will potentially reveal new drug targets for cancer therapy. Fer is a non‐receptor protein tyrosine kinase aberrantly expressed in various human cancers, whereas its role in tumour progression remains elusive. Materials and Methods Transgenic flies and epigenetic analysis were employed to investigate the role of Drosophila Fer (FER) in cell migration and underlying mechanisms. Co‐immunoprecipitation assay was used to monitor the interaction between FER and Drosophila JNK (Bsk). The conservation of Fer in regulating JNK signalling was explored in mammalian cancer and non‐cancer cells. Results Overexpression of FER triggered cell migration and activated JNK signalling in the Drosophila wing disc. Upregulation and downregulation in the basal activity of Bsk exacerbated and eliminated FER‐mediated migration, respectively. In addition, loss of FER blocked signal transduction of the JNK pathway. Specifically, FER interacted with and promoted the activity of Bsk, which required both the kinase domain and the C‐terminal of Bsk. Lastly, Fer regulated JNK activities in mammalian cells. Conclusions Our study reveals FER as a positive regulator of JNK‐mediated cell migration and suggests its potential role as a therapeutic target for cancer metastasis.
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Affiliation(s)
- Ping Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhiwei Ma
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yun Yu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xingjie Hu
- School of Public Health, Guangzhou Medical University, Guangdong, China
| | - Yanfeng Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haiyun Song
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
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6
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Samson SC, Elliott A, Mueller BD, Kim Y, Carney KR, Bergman JP, Blenis J, Mendoza MC. p90 ribosomal S6 kinase (RSK) phosphorylates myosin phosphatase and thereby controls edge dynamics during cell migration. J Biol Chem 2019; 294:10846-10862. [PMID: 31138649 PMCID: PMC6635457 DOI: 10.1074/jbc.ra119.007431] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/08/2019] [Indexed: 12/25/2022] Open
Abstract
Cell migration is essential to embryonic development, wound healing, and cancer cell dissemination. Cells move via leading-edge protrusion, substrate adhesion, and retraction of the cell's rear. The molecular mechanisms by which extracellular cues signal to the actomyosin cytoskeleton to control these motility mechanics are poorly understood. The growth factor-responsive and oncogenically activated protein extracellular signal-regulated kinase (ERK) promotes motility by signaling in actin polymerization-mediated edge protrusion. Using a combination of immunoblotting, co-immunoprecipitation, and myosin-binding experiments and cell migration assays, we show here that ERK also signals to the contractile machinery through its substrate, p90 ribosomal S6 kinase (RSK). We probed the signaling and migration dynamics of multiple mammalian cell lines and found that RSK phosphorylates myosin phosphatase–targeting subunit 1 (MYPT1) at Ser-507, which promotes an interaction of Rho kinase (ROCK) with MYPT1 and inhibits myosin targeting. We find that by inhibiting the myosin phosphatase, ERK and RSK promote myosin II–mediated tension for lamella expansion and optimal edge dynamics for cell migration. These findings suggest that ERK activity can coordinately amplify both protrusive and contractile forces for optimal cell motility.
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Affiliation(s)
- Shiela C Samson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 and
| | - Andrew Elliott
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 and
| | - Brian D Mueller
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 and
| | - Yung Kim
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 and
| | - Keith R Carney
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 and
| | - Jared P Bergman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 and
| | - John Blenis
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Michelle C Mendoza
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 and; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115.
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7
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Ahmed SBM, Amer S, Emad M, Rahmani M, Prigent SA. Studying the ShcD and ERK interaction under acute oxidative stress conditions in melanoma cells. Int J Biochem Cell Biol 2019; 112:123-133. [PMID: 31121283 DOI: 10.1016/j.biocel.2019.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 01/11/2023]
Abstract
The newly identified melanoma-associated adaptor ShcD was found to translocate to the nucleus upon hydrogen peroxide treatment. Therefore, the aim of this study was to identify the ShcD network in melanoma cells under oxidative stress. LC-MS/MS and GFP-trap were performed to study the ShcD phosphorylation status during acute severe oxidative stress. ShcD was found to be phosphorylated at threonine-159 (Thr159) in response to 5 mM H2O2 treatment. The GPS 2.1 phosphorylation prediction program predicted that the Thr159Pro motif, housed in the N-terminus of the ShcD-CH2 domain, is a potential phosphorylation site for MAPKs (ERK, JNK or p38). Co-immunoprecipitation experiments revealed that ShcD mainly interacts with ERK in B16 and MM138 melanoma cells under both hydrogen peroxide-untreated and -treated conditions. Moreover, ShcD interacts with both phosphorylated and un-phosphorylated ERK, although the interaction between ShcD and phospho-ERK was primarily observed after H2O2 treatment. A MEK inhibitor (U0126) enhanced the interaction between ShcD and unphosphorylated ERK under oxidative stress conditions. Furthermore, Thr159 was mutated to either alanine (A) or glutamic acid (E) to study whether the threonine phosphorylation state influences the ShcD/ERK interaction. Introducing the T159E mutation obliterated the ShcD/ERK interaction. To identify the functional impact of the ShcD/ERK interaction on cell survival signalling under oxidative stress conditions, caspase 3/7 assays and 7AAD cell death assays were used. The ShcD/ERK interaction promoted anti-survival signalling upon exposure to hydrogen peroxide, while U0126 treatment reduced death signalling. Our data also showed that the death signalling initiated by the ShcD/ERK interaction was accompanied by p21 phosphorylation. In summary, these data identified ShcD, via its interaction with ERK, as a proapoptotic protein under oxidative stress conditions.
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Affiliation(s)
- Samrein B M Ahmed
- Sharjah Institute for Medical Research, University of Sharjah, United Arab Emirates; College of Medicine, University of Sharjah, United Arab Emirates; Molecular and Cell Biology Department, University of Leicester, UK.
| | - Sara Amer
- College of Medicine, University of Sharjah, United Arab Emirates
| | - Mira Emad
- College of Medicine, University of Sharjah, United Arab Emirates
| | - Mohamed Rahmani
- Sharjah Institute for Medical Research, University of Sharjah, United Arab Emirates; College of Medicine, University of Sharjah, United Arab Emirates
| | - Sally A Prigent
- Molecular and Cell Biology Department, University of Leicester, UK
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8
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Ma N, Lippert LG, Devamani T, Levy B, Lee S, Sandhu M, Vaidehi N, Sivaramakrishnan S. Bitopic Inhibition of ATP and Substrate Binding in Ser/Thr Kinases through a Conserved Allosteric Mechanism. Biochemistry 2018; 57:6387-6390. [PMID: 30339352 DOI: 10.1021/acs.biochem.8b00729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein kinases achieve substrate selective phosphorylation through their conformational flexibility and dynamic interaction with the substrate. Designing substrate selective or kinase selective small molecule inhibitors remains a challenge because of a lack of understanding of the dynamic mechanism by which substrates are selected by the kinase. Using a combination of all-atom molecular dynamics simulations and FRET sensors, we have delineated an allosteric mechanism that results in interaction among the DFG motif, G-loop, and activation loop and structurally links the nucleotide and substrate binding interfaces in protein kinase Cα and three other Ser/Thr kinases. ATP-competitive staurosporine analogues engage this allosteric switch region located just outside the ATP binding site to displace substrate binding to varying degrees. These inhibitors function as bitopic ligands by occupying the ATP binding site and interacting with the allosteric switch region. The conserved mechanism identified in this study can be exploited to select and design bitopic inhibitors for kinases.
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Affiliation(s)
- Ning Ma
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Lisa G Lippert
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Titu Devamani
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
| | - Benjamin Levy
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sangbae Lee
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Manbir Sandhu
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine , Beckman Research Institute of the City of Hope , Duarte , California 91010 , United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development , University of Minnesota , Minneapolis , Minnesota 55455 , United States
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9
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Göktuna Sİ. IKBKE inhibits TSC1 to activate the mTOR/S6K pathway for oncogenic transformation. Turk J Biol 2018; 42:268-278. [PMID: 30814890 DOI: 10.3906/biy-1801-57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
IKBKE (IKKε) has emerged as a key modulator of multiple substrates, controlling oncogenic pathways in various malignancies. mTOR signaling, required for cellular growth, proliferation, and vascular angiogenesis in cancer, is potentially one of the pathways regulated by IKKε. Upon activation by various stimuli, PI3K/AKT or similar effectors can relieve the inhibitory effect of the TSC1/TSC2 complex through their phosphorylation to favor mTOR/S6K activation in the downstream. Therefore, any activity that interferes with PI3K/AKT or their downstream targets, such as TSC1/2 or GSK3α/β, may activate the mTOR/S6K pathway for oncogenic transformation in normal cells. Previous studies have shown that PI3K/AKT can be directly phosphoregulated by IKKε. Here, we propose a new regulatory function for IKKε in the mTOR/S6K pathway through its direct interaction with TSC1, leading to TSC1 phosphorylation, which is vital to suppress its inhibitory role in mTOR activation. Experimentally, upon IKKε deficiency in colorectal cancer cells, we observed that S6K activity was diminished while TSC1 levels were found to be stabilized. We hypothesized that these observations may result from direct interaction between IKKε and TSC1. Indeed, the interaction of these two proteins involves the phosphoregulation of TSC1 in various cell lines. Therefore, we propose a mechanism where IKKε, through regulating TSC1 stability in cancer cells, may create an alternative regulatory loop for the activation of mTOR signaling. These results can potentially be important for the development of novel therapeutic strategies targeting mTOR signaling.
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Affiliation(s)
- Serkan İsmail Göktuna
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University , Ankara , Turkey.,Laboratory of Medical Chemistry, Interdisciplinary Genomics and Genoproteomics Research Center (GIGA), University of Liege , Liege , Belgium.,National Nanotechnology Research Center (UNAM), Bilkent University , Ankara , Turkey
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10
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Lee S, Devamani T, Song HD, Sandhu M, Larsen A, Sommese R, Jain A, Vaidehi N, Sivaramakrishnan S. Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα. J Biol Chem 2017; 292:16300-16309. [PMID: 28821615 PMCID: PMC5625059 DOI: 10.1074/jbc.m117.804781] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/04/2017] [Indexed: 11/06/2022] Open
Abstract
Protein kinase Cα (PKCα) belongs to the family of AGC kinases that phosphorylate multiple peptide substrates. Although the consensus sequence motif has been identified and used to explain substrate specificity for PKCα, it does not inform the structural basis of substrate-binding and kinase activity for diverse substrates phosphorylated by this kinase. The transient, dynamic, and unstructured nature of this protein-protein interaction has limited structural mapping of kinase-substrate interfaces. Here, using multiscale MD simulation-based predictions and FRET sensor-based experiments, we investigated the conformational dynamics of the kinase-substrate interface. We found that the binding strength of the kinase-substrate interaction is primarily determined by long-range columbic interactions between basic (Arg/Lys) residues located N-terminally to the phosphorylated Ser/Thr residues in the substrate and by an acidic patch in the kinase catalytic domain. Kinase activity stemmed from conformational flexibility in the region C-terminal to the phosphorylated Ser/Thr residues. Flexibility of the substrate-kinase interaction enabled an Arg/Lys two to three amino acids C-terminal to the phosphorylated Ser/Thr to prime a catalytically active conformation, facilitating phosphoryl transfer to the substrate. The structural mechanisms determining substrate binding and catalytic activity formed the basis of diverse binding affinities and kinase activities of PKCα for 14 substrates with varying degrees of sequence conservation. Our findings provide insight into the dynamic properties of the kinase-substrate interaction that govern substrate binding and turnover. Moreover, this study establishes a modeling and experimental method to elucidate the structural dynamics underlying substrate selectivity among eukaryotic kinases.
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Affiliation(s)
- Sangbae Lee
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Titu Devamani
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, and
| | - Hyun Deok Song
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Manbir Sandhu
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Adrien Larsen
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Ruth Sommese
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, and
| | - Abhinandan Jain
- the Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109
| | - Nagarajan Vaidehi
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010,
| | - Sivaraj Sivaramakrishnan
- the Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455, and
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11
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Sommese RF, Ritt M, Swanson CJ, Sivaramakrishnan S. The Role of Regulatory Domains in Maintaining Autoinhibition in the Multidomain Kinase PKCα. J Biol Chem 2017; 292:2873-2880. [PMID: 28049730 DOI: 10.1074/jbc.m116.768457] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/30/2016] [Indexed: 11/06/2022] Open
Abstract
Resolving the conformational dynamics of large multidomain proteins has proven to be a significant challenge. Here we use a variety of techniques to dissect the roles of individual protein kinase Cα (PKCα) regulatory domains in maintaining catalytic autoinhibition. We find that whereas the pseudosubstrate domain is necessary for autoinhibition it is not sufficient. Instead, each regulatory domain (C1a, C1b, and C2) appears to strengthen the pseudosubstrate-catalytic domain interaction in a nucleotide-dependent manner. The pseudosubstrate and C1a domains, however, are minimally essential for maintaining the inactivated state. Furthermore, disrupting known interactions between the C1a and other regulatory domains releases the autoinhibited interaction and increases basal activity. Modulating this interaction between the catalytic and regulatory domains reveals a direct correlation between autoinhibition and membrane translocation following PKC activation.
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Affiliation(s)
- Ruth F Sommese
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 and
| | - Michael Ritt
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 and
| | - Carter J Swanson
- the Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Sivaraj Sivaramakrishnan
- From the Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 and
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