51
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Röhm S, Krämer A, Knapp S. Function, Structure and Topology of Protein Kinases. PROTEINKINASE INHIBITORS 2020. [DOI: 10.1007/7355_2020_97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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52
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Bello M, Guadarrama-García C, Rodriguez-Fonseca RA. Dissecting the molecular recognition of dual lapatinib derivatives for EGFR/HER2. J Comput Aided Mol Des 2019; 34:293-303. [DOI: 10.1007/s10822-019-00270-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/06/2019] [Indexed: 01/22/2023]
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53
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Dynamic Protein Allosteric Regulation and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:25-43. [DOI: 10.1007/978-981-13-8719-7_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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54
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Kondo Y, Ognjenović J, Banerjee S, Karandur D, Merk A, Kulhanek K, Wong K, Roose JP, Subramaniam S, Kuriyan J. Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases. Science 2019; 366:109-115. [PMID: 31604311 DOI: 10.1126/science.aay0543] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022]
Abstract
Raf kinases are important cancer drug targets. Paradoxically, many B-Raf inhibitors induce the activation of Raf kinases. Cryo-electron microscopy structural analysis of a phosphorylated B-Raf kinase domain dimer in complex with dimeric 14-3-3, at a resolution of ~3.9 angstroms, shows an asymmetric arrangement in which one kinase is in a canonical "active" conformation. The distal segment of the C-terminal tail of this kinase interacts with, and blocks, the active site of the cognate kinase in this asymmetric arrangement. Deletion of the C-terminal segment reduces Raf activity. The unexpected asymmetric quaternary architecture illustrates how the paradoxical activation of Raf by kinase inhibitors reflects an innate mechanism, with 14-3-3 facilitating inhibition of one kinase while maintaining activity of the other. Conformational modulation of these contacts may provide new opportunities for Raf inhibitor development.
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Affiliation(s)
- Yasushi Kondo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jana Ognjenović
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Saikat Banerjee
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20814, USA
| | - Kayla Kulhanek
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kathryn Wong
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA. .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Divisions of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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55
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Tamirat MZ, Koivu M, Elenius K, Johnson MS. Structural characterization of EGFR exon 19 deletion mutation using molecular dynamics simulation. PLoS One 2019; 14:e0222814. [PMID: 31536605 PMCID: PMC6752865 DOI: 10.1371/journal.pone.0222814] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor important in diverse biological processes including cell proliferation and survival. Upregulation of EGFR activity due to over-expression or mutation is widely implicated in cancer. Activating somatic mutations of the EGFR kinase are postulated to affect the conformation and/or stability of the protein, shifting the EGFR inactive-active state equilibrium towards the activated state. Here, we examined a common EGFR deletion mutation, Δ746ELREA750, which is frequently observed in non-small cell lung cancer patients. By using molecular dynamics simulation, we investigated the structural effects of the mutation that lead to the experimentally reported increases in kinase activity. Simulations of the active form wild-type and ΔELREA EGFRs revealed the deletion stabilizes the αC helix of the kinase domain, which is located adjacent to the deletion site, by rigidifying the flexible β3-αC loop that accommodates the ELREA sequence. Consequently, the αC helix is stabilized in the “αC-in” active conformation that would prolong the time of the activated state. Moreover, in the mutant kinase, a salt bridge between E762 and K745, which is key for EGFR activity, was also stabilized during the simulation. Additionally, the interaction between EGFR and ATP was favored by ΔELREA EGFR over wild-type EGFR, as reflected by the number of hydrogen bonds formed and the free energy of binding. Simulation of inactive EGFR suggested the deletion would promote a shift from the inactive conformation towards active EGFR, which is supported by the inward movement of the αC helix. The MDS results also align with the effects of tyrosine kinase inhibitors on ΔELREA and wild-type EGFR lung cancer cell lines, where more pronounced inhibition was observed against ΔELREA than for wild-type EGFR by inhibitors recognizing the active kinase conformation.
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Affiliation(s)
- Mahlet Z. Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Marika Koivu
- Medicity Research Laboratories and Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Klaus Elenius
- Medicity Research Laboratories and Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- * E-mail:
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56
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Maurice F, Pérébaskine N, Thore S, Fribourg S. In vitro dimerization of human RIO2 kinase. RNA Biol 2019; 16:1633-1642. [PMID: 31390939 DOI: 10.1080/15476286.2019.1653679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
RIO proteins form a conserved family of atypical protein kinases. RIO2 is a serine/threonine protein kinase/ATPase involved in pre-40S ribosomal maturation. Current crystal structures of archaeal and fungal Rio2 proteins report a monomeric form of the protein. Here, we describe three atomic structures of the human RIO2 kinase showing that it forms a homodimer in vitro. Upon self-association, each protomer ATP-binding pocket is partially remodelled and found in an apostate. The homodimerization is mediated by key residues previously shown to be responsible for ATP binding and catalysis. This unusual in vitro protein kinase dimer reveals an intricate mechanism where identical residues are involved in substrate binding and oligomeric state formation. We speculate that such an oligomeric state might be formed also in vivo and might function in maintaining the protein in an inactive state and could be employed during import.
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Affiliation(s)
| | | | - Stéphane Thore
- INSERM U1212, UMR CNRS 5320, Université de Bordeaux , Bordeaux , France
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57
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Black LE, Longo JF, Carroll SL. Mechanisms of Receptor Tyrosine-Protein Kinase ErbB-3 (ERBB3) Action in Human Neoplasia. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1898-1912. [PMID: 31351986 DOI: 10.1016/j.ajpath.2019.06.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/16/2022]
Abstract
It is well established that the epidermal growth factor (EGF) receptor, receptor tyrosine-protein kinase erbB-2 (ERBB2)/human EGF receptor 2 (HER2), and, to a lesser extent, ERBB4/HER4, promote the pathogenesis of many types of human cancers. In contrast, the role that ERBB3/HER3, the fourth member of the ERBB family of receptor tyrosine kinases, plays in these diseases is poorly understood and, until recently, underappreciated. In large part, this was because early structural and functional studies suggested that ERBB3 had little, if any, intrinsic tyrosine kinase activity and, thus, was unlikely to be an important therapeutic target. Since then, however, numerous publications have demonstrated an important role for ERBB3 in carcinogenesis, metastasis, and acquired drug resistance. Furthermore, somatic ERBB3 mutations are frequently encountered in many types of human cancers. Dysregulation of ERBB3 trafficking as well as cooperation with other receptor tyrosine kinases further enhance ERBB3's role in tumorigenesis and drug resistance. As a result of these advances in our understanding of the structure and biochemistry of ERBB3, and a growing focus on the development of precision and combinatorial therapeutic regimens, ERBB3 is increasingly considered to be an important therapeutic target in human cancers. In this review, we discuss the unique structural and functional features of ERBB3 and how this information is being used to develop effective new therapeutic agents that target ERBB3 in human cancers.
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Affiliation(s)
- Laurel E Black
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Jody F Longo
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina.
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58
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PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization. Proc Natl Acad Sci U S A 2019; 116:15495-15504. [PMID: 31311869 DOI: 10.1073/pnas.1906360116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Members of the New Kinase Family 3 (NKF3), PEAK1/SgK269 and Pragmin/SgK223 pseudokinases, have emerged as important regulators of cell motility and cancer progression. Here, we demonstrate that C19orf35 (PEAK3), a newly identified member of the NKF3 family, is a kinase-like protein evolutionarily conserved across mammals and birds and a regulator of cell motility. In contrast to its family members, which promote cell elongation when overexpressed in cells, PEAK3 overexpression does not have an elongating effect on cell shape but instead is associated with loss of actin filaments. Through an unbiased search for PEAK3 binding partners, we identified several regulators of cell motility, including the adaptor protein CrkII. We show that by binding to CrkII, PEAK3 prevents the formation of CrkII-dependent membrane ruffling. This function of PEAK3 is reliant upon its dimerization, which is mediated through a split helical dimerization domain conserved among all NKF3 family members. Disruption of the conserved DFG motif in the PEAK3 pseudokinase domain also interferes with its ability to dimerize and subsequently bind CrkII, suggesting that the conformation of the pseudokinase domain might play an important role in PEAK3 signaling. Hence, our data identify PEAK3 as an NKF3 family member with a unique role in cell motility driven by dimerization of its pseudokinase domain.
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59
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Oashi A, Yasuda H, Kobayashi K, Tani T, Hamamoto J, Masuzawa K, Manabe T, Terai H, Ikemura S, Kawada I, Naoki K, Soejima K. Monomer Preference of EGFR Tyrosine Kinase Inhibitors Influences the Synergistic Efficacy of Combination Therapy with Cetuximab. Mol Cancer Ther 2019; 18:1593-1601. [PMID: 31253648 DOI: 10.1158/1535-7163.mct-18-1036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/15/2019] [Accepted: 06/24/2019] [Indexed: 11/16/2022]
Abstract
EGFR-mutated lung cancer is a significant subgroup of non-small cell lung cancer. To inhibit EGFR-mediated signals, multiple EGFR tyrosine kinase inhibitors (EGFR-TKI) have been developed; however, approximately one third of patients with EGFR-mutated lung cancer do not respond to EGFR-TKIs. More effective inhibition of EGFR-mediated signals is therefore necessary. For cancers expressing mutated EGFR, including EGFR T790M, which confers resistance to first- (gefitinib and erlotinib) and second- (afatinib) generation EGFR-TKIs, the synergistic efficacy of afatinib and cetuximab combination therapy has been reported in preclinical and clinical studies; however, the mechanisms underlying this effect remain elusive. In this study, we evaluated the effects of multiple EGFR-TKIs on the EGFR monomer-dimer equilibrium by inducing dimerization-impairing mutations in cells expressing EGFR Interestingly, we found that afatinib and dacomitinib exhibit a monomer preference: cells expressing dimerization-impaired EGFR mutants exhibited increased sensitivity to afatinib and dacomitinib relative to those with dimerization-competent EGFR mutants. Although EGFR-TKIs themselves induce dimerization of EGFR, the inhibition of dimerization by cetuximab overcame EGFR-TKI-induced dimerization. By shifting the monomer-dimer equilibrium toward monomer dominance using cetuximab, the effectiveness of afatinib and dacomitinib improved significantly. We report a novel and clinically relevant phenomenon, the monomer preference of EGFR-TKIs, which can explain the mechanism underlying the synergism observed in afatinib and cetuximab combination therapy. In addition, we propose the novel concept that monomer-dimer equilibrium is an important factor in determining EGFR-TKI efficacy. These findings provide novel insights into treatment strategies for EGFR-TKI-refractory non-small cell lung cancer.
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Affiliation(s)
- Ayano Oashi
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan.
| | - Keigo Kobayashi
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Tetsuo Tani
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Keita Masuzawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Tadashi Manabe
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Hideki Terai
- Kitasato Institute Hospital, Department of Internal Medicine, Minatoku, Tokyo, Japan
| | - Shinnosuke Ikemura
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan.,Keio Cancer Center, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Katsuhiko Naoki
- Keio Cancer Center, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Shinjuku-ku, Tokyo, Japan
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60
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Mayo CB, Erlandsen H, Mouser DJ, Feinstein AG, Robinson VL, May ER, Cole JL. Structural Basis of Protein Kinase R Autophosphorylation. Biochemistry 2019; 58:2967-2977. [PMID: 31246429 DOI: 10.1021/acs.biochem.9b00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The RNA-activated protein kinase, PKR, is a key mediator of the innate immunity response to viral infection. Viral double-stranded RNAs induce PKR dimerization and autophosphorylation. The PKR kinase domain forms a back-to-back dimer. However, intermolecular ( trans) autophosphorylation is not feasible in this arrangement. We have obtained PKR kinase structures that resolves this dilemma. The kinase protomers interact via the known back-to-back interface as well as a front-to-front interface that is formed by exchange of activation segments. Mutational analysis of the front-to-front interface support a functional role in PKR activation. Molecular dynamics simulations reveal that the activation segment is highly dynamic in the front-to-front dimer and can adopt conformations conducive to phosphoryl transfer. We propose a mechanism where back-to-back dimerization induces a conformational change that activates PKR to phosphorylate a "substrate" kinase docked in a front-to-front geometry. This mechanism may be relevant to related kinases that phosphorylate the eukaryotic initiation factor eIF2α.
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61
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Schwarz D, Merget B, Deane C, Fulle S. Modeling conformational flexibility of kinases in inactive states. Proteins 2019; 87:943-951. [PMID: 31168936 PMCID: PMC6852311 DOI: 10.1002/prot.25756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/26/2019] [Indexed: 02/02/2023]
Abstract
Kinase structures in the inactive "DFG-out" state provide a wealth of druggable binding site variants. The conformational plasticity of this state can be mainly described by different conformations of binding site-forming elements such as DFG motif, A-loop, P-loop, and αC-helix. Compared to DFG-in structures, DFG-out structures are largely underrepresented in the Protein Data Bank (PDB). Thus, structure-based drug design efforts for DFG-out inhibitors may benefit from an efficient approach to generate an ensemble of DFG-out structures. Accordingly, the presented modeling pipeline systematically generates homology models of kinases in several DFG-out conformations based on a sophisticated creation of template structures that represent the major states of the flexible structural elements. Eighteen template classes were initially selected from all available kinase structures in the PDB and subsequently employed for modeling the entire kinome in different DFG-out variants by fusing individual structural elements to multiple chimeric template structures. Molecular dynamics simulations revealed that conformational transitions between the different DFG-out states generally do not occur within trajectories of a few hundred nanoseconds length. This underlines the benefits of the presented homology modeling pipeline to generate relevant conformations of "DFG-out" kinase structures for subsequent in silico screening or binding site analysis studies.
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Affiliation(s)
- Dominik Schwarz
- BioMed X Innovation Center, Heidelberg, Germany.,Department of Statistics, University of Oxford, Oxford, UK
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62
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Diwanji D, Thaker T, Jura N. More than the sum of the parts: Toward full-length receptor tyrosine kinase structures. IUBMB Life 2019; 71:706-720. [PMID: 31046201 DOI: 10.1002/iub.2060] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/20/2019] [Indexed: 01/01/2023]
Abstract
Intercellular communication governs complex physiological processes ranging from growth and development to the maintenance of cellular and organ homeostasis. In nearly all metazoans, receptor tyrosine kinases (RTKs) are central players in these diverse and fundamental signaling processes. Aberrant RTK signaling is at the root of many developmental diseases and cancers and it remains a key focus of targeted therapies, several of which have achieved considerable success in patients. These therapeutic advances in targeting RTKs have been propelled by numerous genetic, biochemical, and structural studies detailing the functions and molecular mechanisms of regulation and activation of RTKs. The latter in particular have proven to be instrumental for the development of new drugs, selective targeting of mutant forms of RTKs found in disease, and counteracting ensuing drug resistance. However, to this day, such studies have not yet yielded high-resolution structures of intact RTKs that encompass the extracellular and intracellular domains and the connecting membrane-spanning transmembrane domain. Technically challenging to obtain, these structures are instrumental to complete our understanding of the mechanisms by which RTKs are activated by extracellular ligands and of the effect of pathological mutations that do not directly reside in the catalytic sites of tyrosine kinase domains. In this review, we focus on the recent progress toward obtaining such structures and the insights already gained by structural studies of the subdomains of the receptors that belong to the epidermal growth factor receptor, insulin receptor, and platelet-derived growth factor receptor RTK families. © 2019 IUBMB Life, 71(6):706-720, 2019.
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Affiliation(s)
- Devan Diwanji
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tarjani Thaker
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.,Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
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63
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Molecular dynamics simulation-guided drug sensitivity prediction for lung cancer with rare EGFR mutations. Proc Natl Acad Sci U S A 2019; 116:10025-10030. [PMID: 31043566 PMCID: PMC6525482 DOI: 10.1073/pnas.1819430116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A variety of rare mutations account for 10–20% of EGFR mutations in nonsmall cell lung cancer. However, due to high diversity, proper medication for patients with such mutations is impossible in daily clinic. To appropriately treat lung cancer patients harboring such rare EGFR mutations, a robust prediction model to predict sensitivities of rare EGFR mutants to existing drugs is strongly needed. Using molecular dynamics simulation-based model, we successfully predicted diverse sensitivities of EGFR exon 20 insertion mutants to existing inhibitors. The findings suggest the usefulness of in silico simulation to overcome mutation diversity at a clinically relevant level. The present in silico model will help in selecting effective drugs for these patients. Next generation sequencing (NGS)-based tumor profiling identified an overwhelming number of uncharacterized somatic mutations, also known as variants of unknown significance (VUS). The therapeutic significance of EGFR mutations outside mutational hotspots, consisting of >50 types, in nonsmall cell lung carcinoma (NSCLC) is largely unknown. In fact, our pan-nation screening of NSCLC without hotspot EGFR mutations (n = 3,779) revealed that the majority (>90%) of cases with rare EGFR mutations, accounting for 5.5% of the cohort subjects, did not receive EGFR-tyrosine kinase inhibitors (TKIs) as a first-line treatment. To tackle this problem, we applied a molecular dynamics simulation-based model to predict the sensitivity of rare EGFR mutants to EGFR-TKIs. The model successfully predicted the diverse in vitro and in vivo sensitivities of exon 20 insertion mutants, including a singleton, to osimertinib, a third-generation EGFR-TKI (R2 = 0.72, P = 0.0037). Additionally, our model showed a higher consistency with experimentally obtained sensitivity data than other prediction approaches, indicating its robustness in analyzing complex cancer mutations. Thus, the in silico prediction model will be a powerful tool in precision medicine for NSCLC patients carrying rare EGFR mutations in the clinical setting. Here, we propose an insight to overcome mutation diversity in lung cancer.
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64
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Martin-Fernandez ML, Clarke DT, Roberts SK, Zanetti-Domingues LC, Gervasio FL. Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer. Cells 2019; 8:E316. [PMID: 30959819 PMCID: PMC6523254 DOI: 10.3390/cells8040316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/25/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is historically the prototypical receptor tyrosine kinase, being the first cloned and the first where the importance of ligand-induced dimer activation was ascertained. However, many years of structure determination has shown that EGFR is not completely understood. One challenge is that the many structure fragments stored at the PDB only provide a partial view because full-length proteins are flexible entities and dynamics play a key role in their functionality. Another challenge is the shortage of high-resolution data on functionally important higher-order complexes. Still, the interest in the structure/function relationships of EGFR remains unabated because of the crucial role played by oncogenic EGFR mutants in driving non-small cell lung cancer (NSCLC). Despite targeted therapies against EGFR setting a milestone in the treatment of this disease, ubiquitous drug resistance inevitably emerges after one year or so of treatment. The magnitude of the challenge has inspired novel strategies. Among these, the combination of multi-disciplinary experiments and molecular dynamic (MD) simulations have been pivotal in revealing the basic nature of EGFR monomers, dimers and multimers, and the structure-function relationships that underpin the mechanisms by which EGFR dysregulation contributes to the onset of NSCLC and resistance to treatment.
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Affiliation(s)
- Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - David T Clarke
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Selene K Roberts
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
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65
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Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput Biol 2019; 15:e1006658. [PMID: 30921324 PMCID: PMC6438456 DOI: 10.1371/journal.pcbi.1006658] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
At the root of the so-called precision medicine or precision oncology, which is our focus here, is the hypothesis that cancer treatment would be considerably better if therapies were guided by a tumor’s genomic alterations. This hypothesis has sparked major initiatives focusing on whole-genome and/or exome sequencing, creation of large databases, and developing tools for their statistical analyses—all aspiring to identify actionable alterations, and thus molecular targets, in a patient. At the center of the massive amount of collected sequence data is their interpretations that largely rest on statistical analysis and phenotypic observations. Statistics is vital, because it guides identification of cancer-driving alterations. However, statistics of mutations do not identify a change in protein conformation; therefore, it may not define sufficiently accurate actionable mutations, neglecting those that are rare. Among the many thematic overviews of precision oncology, this review innovates by further comprehensively including precision pharmacology, and within this framework, articulating its protein structural landscape and consequences to cellular signaling pathways. It provides the underlying physicochemical basis, thereby also opening the door to a broader community.
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66
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Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
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Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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67
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Liu L, Fan S, Li W, Tao W, Shi T, Zhao YL. Theoretical Investigation of the Structural Characteristics in the Active State of Akt1 Kinase. J Chem Inf Model 2019; 59:316-325. [PMID: 30571108 DOI: 10.1021/acs.jcim.8b00506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Akt (known as protein kinase B or PKB) is a serine/threonine kinase that regulates multiple biological processes, including cell growth, survival, and differentiation. Akt plays a critical role in the intracellular signaling network through conformational changes responsive to diverse signal inputs, and dysregulation of Akt activity could give rise to a number of diseases. However, understanding of Akt's dynamic structures and conformational transitions between active and inactive states remains unclear. In this work, classical MD simulations and QM/MM calculations were carried out to unveil the structural characteristics of Akt1, especially in its active state. The doubly protonated H194 was investigated, and both ATP-Akt1 and ADP-Akt1 complexes were constructed to demonstrate the significance of ATP in maintaining the ATP-K179-E198 salt bridge and the corresponding allosteric pathway. Besides, conformational transitions from the inactive state to the active state showed different permeation patterns of water molecules in the ATP pocket. The coordination modes of Mg2+ in the dominant representative conformations ( I and I') are presented. Unlike the water-free conformation I', three water molecules appear around Mg2+ in the water-occupied conformation I, which can finally exert an influence on the catalytic mechanism of Akt1. Furthermore, QM/MM calculations were performed to study the phosphoryl-transfer reaction of Akt1. The transfer of ATP γ-phosphate was achieved through a reversible conformational change from the reactant to a critical prereaction state, with a water molecule moving into the reaction center to coordinate with Mg2+, after which the γ-phosphate group was transferred from ATP to the substrate. Taken together, our results elucidate the structural characteristics of the Akt1 active state and shed new light on the catalytic mechanism of Akt kinases.
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Affiliation(s)
- Lanxuan Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Shuobing Fan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Wenjuan Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
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68
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Astl L, Tse A, Verkhivker GM. Interrogating Regulatory Mechanisms in Signaling Proteins by Allosteric Inhibitors and Activators: A Dynamic View Through the Lens of Residue Interaction Networks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:187-223. [DOI: 10.1007/978-981-13-8719-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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69
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Hasegawa H, Yasuda H, Hamamoto J, Masuzawa K, Tani T, Nukaga S, Hirano T, Kobayashi K, Manabe T, Terai H, Ikemura S, Kawada I, Naoki K, Soejima K. Efficacy of afatinib or osimertinib plus cetuximab combination therapy for non-small-cell lung cancer with EGFR exon 20 insertion mutations. Lung Cancer 2018; 127:146-152. [PMID: 30642543 DOI: 10.1016/j.lungcan.2018.11.039] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Epidermal growth factor receptor (EGFR) mutation-positive lung cancer accounts for a significant subgroup of non-small cell lung cancers (NSCLC). Approximately 4-10% of EGFR mutations in NSCLC are EGFR exon 20 insertion mutations, which are reportedly associated with resistance to EGFR tyrosine kinase inhibitor (EGFR-TKI) treatment. NSCLC patients carrying these mutations are rarely treated with EGFR-TKIs. The purpose of this study was to evaluate the efficacy of afatinib or osimertinib plus cetuximab combination therapy in experimental NSCLC models with EGFR exon 20 insertion mutations. MATERIALS AND METHODS The EGFR mutations examined in this study were A763_Y764insFQEA, Y764_V765insHH, A767_V769dupASV, and D770_N771insNPG. Ba/F3 cells constitutively expressing wild type or mutated EGFR were used to determine the efficacy of afatinib or osimertinib plus cetuximab combination therapy in vitro. To determine the efficacy of the combination therapy in vivo, female BALB/c-nu mice were injected subcutaneously with 1 million Ba/F3 cells carrying EGFR A767_V769dupASV or Y764_V765insHH. RESULTS We observed a mild but significant (P < 0.05) additive effect of the combination therapy against several EGFR exon 20 insertion mutations in vitro. Regarding EGFR A767_V769dupASV and EGFR Y764_V765insHH, cetuximab and afatinib single treatment did not induce significant inhibition of tumor formation; however, afatinib plus cetuximab combination treatment induced significant (P < 0.05) tumor growth inhibition without significant body weight loss or skin rash. CONCLUSION The combination therapy induced a more potent inhibitory effect against several EGFR exon 20 insertion mutations than either therapy alone. Cetuximab can potentially increase the efficacy of afatinib or osimertinib in NSCLC with EGFR exon 20 insertion mutations.
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Affiliation(s)
- Hanako Hasegawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Keita Masuzawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Tetsuo Tani
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Shigenari Nukaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Toshiyuki Hirano
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Keigo Kobayashi
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Tadashi Manabe
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hideki Terai
- Kitasato Institute Hospital, Department of Internal Medicine, 5-9-1 Shirokane, Minatoku, Tokyo, 108-8642, Japan
| | - Shinnosuke Ikemura
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan; Keio Cancer Center, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Katsuhiko Naoki
- Keio Cancer Center, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
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Carlino L, Christodoulou MS, Restelli V, Caporuscio F, Foschi F, Semrau MS, Costanzi E, Tinivella A, Pinzi L, Lo Presti L, Battistutta R, Storici P, Broggini M, Passarella D, Rastelli G. Structure-Activity Relationships of Hexahydrocyclopenta[c
]quinoline Derivatives as Allosteric Inhibitors of CDK2 and EGFR. ChemMedChem 2018; 13:2627-2634. [DOI: 10.1002/cmdc.201800687] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Luca Carlino
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Michael S. Christodoulou
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Valentina Restelli
- IRCSS Istituto di Ricerche Farmacologiche Mario Negri; Via La Masa 19 20156 Milano Italy
| | - Fabiana Caporuscio
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Francesca Foschi
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Marta S. Semrau
- Structural Biology Lab; Elettra Sincrotrone Trieste S.C.p.A.; SS 14 km 163.5, AREA Science Park 34149 Trieste Italy
| | - Elisa Costanzi
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35131 Padova Italy
| | - Annachiara Tinivella
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Luca Pinzi
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
| | - Leonardo Lo Presti
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche; Via Golgi 19 20133 Milano Italy
| | - Roberto Battistutta
- Dipartimento di Scienze Chimiche; Università degli Studi di Padova; Via Marzolo 1 35131 Padova Italy
| | - Paola Storici
- Structural Biology Lab; Elettra Sincrotrone Trieste S.C.p.A.; SS 14 km 163.5, AREA Science Park 34149 Trieste Italy
| | - Massimo Broggini
- IRCSS Istituto di Ricerche Farmacologiche Mario Negri; Via La Masa 19 20156 Milano Italy
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano; Via Golgi 19 20133 Milano Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita; Università degli Studi di Modena e Reggio Emilia; Via Campi 103 41125 Modena Italy
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71
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Barletta GP, Hasenahuer MA, Fornasari MS, Parisi G, Fernandez-Alberti S. Dynamics fingerprints of active conformers of epidermal growth factor receptor kinase. J Comput Chem 2018; 39:2472-2480. [PMID: 30298935 DOI: 10.1002/jcc.25590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/06/2018] [Accepted: 08/19/2018] [Indexed: 12/29/2022]
Abstract
Epidermal growth factor receptor (EGFR) is a prototypical cell-surface receptor that plays a key role in the regulation of cellular signaling, proliferation and differentiation. Mutations of its kinase domain have been associated with the development of a variety of cancers and, therefore, it has been the target of drug design. Single amino acid substitutions (SASs) in this domain have been proven to alter the equilibrium of pre-existing conformer populations. Despite the advances in structural descriptions of its so-called active and inactive conformations, the associated dynamics aspects that characterize them have not been thoroughly studied yet. As the dynamic behaviors and molecular motions of proteins are important for a complete understanding of their structure-function relationships we present a novel procedure, using (or based on) normal mode analysis, to identify the collective dynamics shared among different conformers in EGFR kinase. The method allows the comparison of patterns of low-frequency vibrational modes defining representative directions of motions. Our procedure is able to emphasize the main similarities and differences between the collective dynamics of different conformers. In the case of EGFR kinase, two representative directions of motions have been found as dynamics fingerprints of the active conformers. Protein motion along both directions reveals to have a significant impact on the cavity volume of the main pocket of the active site. Otherwise, the inactive conformers exhibit a more heterogeneous distribution of collective motions. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- German P Barletta
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Marcia Anahi Hasenahuer
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | - Sebastian Fernandez-Alberti
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
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Shah NH, Amacher JF, Nocka LM, Kuriyan J. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Crit Rev Biochem Mol Biol 2018; 53:535-563. [PMID: 30183386 PMCID: PMC6328253 DOI: 10.1080/10409238.2018.1495173] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.
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Affiliation(s)
- Neel H. Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jeanine F. Amacher
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Laura M. Nocka
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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73
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Guo J, Collins S, Miller WT, Rizzo RC. Identification of a Water-Coordinating HER2 Inhibitor by Virtual Screening Using Similarity-Based Scoring. Biochemistry 2018; 57:4934-4951. [PMID: 29975516 PMCID: PMC6110523 DOI: 10.1021/acs.biochem.8b00524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Human
epidermal growth factor receptor 2 (HER2) is a validated
breast cancer drug target for small molecule inhibitors that target
the ATP-binding pocket of the kinase domain. In this work, a large-scale
virtual screen was performed to a novel homology model of HER2, in
a hypothesized “fully active” state, that considered
water-mediated interactions during the prioritization of compounds
for experimental testing. This screen led to the identification of
a new inhibitor with micro molar affinity and potency (Kd = 7.0 μM, IC50 = 4.6 μM). Accompanying
molecular dynamics simulations showed that inhibitor binding likely
involves water coordination through an important water-mediated network
previously identified in our laboratory. The predicted binding geometry
also showed a remarkable overlap with the crystallographic poses for
two previously reported inhibitors of the related Chk1 kinase. Concurrent
with the HER2 studies, we developed formalized computational protocols
that leverage solvated footprints (per-residue interaction maps that
include bridging waters) to identify ligands that can “coordinate”
or “displace” key binding site waters. Proof-of-concept
screens targeting HIVPR and PARP1 demonstrate that molecules with
high footprint overlap can be effectively identified in terms of their
coordination or displacement patterns relative to a known reference.
Overall, the procedures developed as a result of this study should
be useful for researchers targeting HER2 and, more generally, for
any protein in which the identification of compounds that exploit
binding site waters is desirable.
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74
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Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism. Biochem J 2018; 475:2209-2224. [DOI: 10.1042/bcj20180077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022]
Abstract
The type VI secretion system (T6SS) is a versatile and widespread export system found in many Gram-negative bacteria that delivers effector proteins into target cells. The functions of T6SSs are tightly regulated by diverse mechanisms at multiple levels, including post-translational modification through threonine phosphorylation via the Ser/Thr protein kinase (STPK) PpkA. Here, we identified that PpkA is essential for T6SS secretion in Serratia marcescens since its deletion eliminated the secretion of haemolysin co-regulated protein, while the periplasmic and transmembrane portion of PpkA was found to be disposable for T6SS secretion. We further determined the crystal structure of the kinase domain of PpkA (PpkA-294). The structure of PpkA-294 was determined in its apo form to a 1.6 Å resolution as well as in complex with ATP to a 1.41 Å resolution and with an ATP analogue AMP-PCP to a 1.45 Å resolution. The residues in the activation loop of PpkA-294 were fully determined, and the N-terminus of the loop was folded into an unprecedented inhibitory helix, revealing that the PpkA kinase domain was in an auto-inhibitory state. The ternary MgATP–PpkA-294 complex was also inactive with nucleotide ribose and phosphates in unexpected and unproductive conformations. The αC-helix in the inactive PpkA-294 adopted a conformation towards the active site but with the conserved glutamate in the helix rotated away, which we suggest to be a general conformation for all STPK kinases in the inactive form. Structural comparison of PpkA with its eukaryotic homologues reinforced the universal regulation mechanism of protein kinases.
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75
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Okatsu K, Sato Y, Yamano K, Matsuda N, Negishi L, Takahashi A, Yamagata A, Goto-Ito S, Mishima M, Ito Y, Oka T, Tanaka K, Fukai S. Structural insights into ubiquitin phosphorylation by PINK1. Sci Rep 2018; 8:10382. [PMID: 29991771 PMCID: PMC6039469 DOI: 10.1038/s41598-018-28656-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/31/2018] [Indexed: 11/09/2022] Open
Abstract
Mutations of PTEN-induced putative kinase 1 (PINK1) and the E3 ubiquitin (Ub) ligase parkin can cause familial parkinsonism. These two proteins are essential for ubiquitylation of damaged mitochondria and subsequent degradation. PINK1 phosphorylates Ser65 of Ub and the Ub-like (UBL) domain of parkin to allosterically relieve the autoinhibition of parkin. To understand the structural mechanism of the Ub/UBL-specific phosphorylation by PINK1, we determined the crystal structure of Tribolium castaneum PINK1 kinase domain (TcPINK1) in complex with a nonhydrolyzable ATP analogue at 2.5 Å resolution. TcPINK1 consists of the N- and C-terminal lobes with the PINK1-specific extension. The ATP analogue is bound in the cleft between the N- and C-terminal lobes. The adenine ring of the ATP analogue is bound to a hydrophobic pocket, whereas the triphosphate group of the ATP analogue and two coordinated Mg ions interact with the catalytic hydrophilic residues. Comparison with protein kinases A and C (PKA and PKC, respectively) unveils a putative Ub/UBL-binding groove, which is wider than the peptide-binding groove of PKA or PKC to accommodate the globular head of Ub or UBL. Further crosslinking analyses suggested a PINK1-interacting surface of Ub. Structure-guided mutational analyses support the findings from the present structural analysis of PINK1.
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Affiliation(s)
- Kei Okatsu
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Koji Yamano
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Noriyuki Matsuda
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, 332-0012, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Akiko Takahashi
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Masaki Mishima
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Yutaka Ito
- Graduate School of Science & Engineering, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Toshihiko Oka
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Keiji Tanaka
- Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. .,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
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76
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Singh R, Karri D, Shen H, Shao J, Dasgupta S, Huang S, Edwards DP, Ittmann MM, O'Malley BW, Yi P. TRAF4-mediated ubiquitination of NGF receptor TrkA regulates prostate cancer metastasis. J Clin Invest 2018; 128:3129-3143. [PMID: 29715200 DOI: 10.1172/jci96060] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 04/27/2018] [Indexed: 12/29/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are important drivers of cancers. In addition to genomic alterations, aberrant activation of WT RTKs plays an important role in driving cancer progression. However, the mechanisms underlying how RTKs drive prostate cancer remain incompletely characterized. Here we show that non-proteolytic ubiquitination of RTK regulates its kinase activity and contributes to RTK-mediated prostate cancer metastasis. TRAF4, an E3 ubiquitin ligase, is highly expressed in metastatic prostate cancer. We demonstrated here that it is a key player in regulating RTK-mediated prostate cancer metastasis. We further identified TrkA, a neurotrophin RTK, as a TRAF4-targeted ubiquitination substrate that promotes cancer cell invasion and found that inhibition of TrkA activity abolished TRAF4-dependent cell invasion. TRAF4 promoted K27- and K29-linked ubiquitination at the TrkA kinase domain and increased its kinase activity. Mutation of TRAF4-targeted ubiquitination sites abolished TrkA tyrosine autophosphorylation and its interaction with downstream proteins. TRAF4 knockdown also suppressed nerve growth factor (NGF) stimulated TrkA downstream p38 MAPK activation and invasion-associated gene expression. Furthermore, elevated TRAF4 levels significantly correlated with increased NGF-stimulated invasion-associated gene expression in prostate cancer patients, indicating that this signaling axis is significantly activated during oncogenesis. Our results revealed a posttranslational modification mechanism contributing to aberrant non-mutated RTK activation in cancer cells.
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Affiliation(s)
- Ramesh Singh
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Dileep Karri
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Hong Shen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Jiangyong Shao
- Diana Helis Henry Medical Research Foundation, New Orleans, Louisiana, USA
| | - Subhamoy Dasgupta
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.,Dan L. Duncan Comprehensive Cancer Center and
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Michael M Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA.,Michael E. DeBakey Department of Veterans Affairs Medical Center, Houston, Texas, USA
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
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77
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Meng Y, Gao C, Clawson D, Atwell S, Russell M, Vieth M, Roux B. Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models. J Chem Theory Comput 2018; 14:2721-2732. [PMID: 29474075 PMCID: PMC6317529 DOI: 10.1021/acs.jctc.7b01170] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding protein conformational variability remains a challenge in drug discovery. The issue arises in protein kinases, whose multiple conformational states can affect the binding of small-molecule inhibitors. To overcome this challenge, we propose a comprehensive computational framework based on Markov state models (MSMs). Our framework integrates the information from explicit-solvent molecular dynamics simulations to accurately rank-order the accessible conformational variants of a target protein. We tested the methodology using Abl kinase with a reference and blind-test set. Only half of the Abl conformational variants discovered by our approach are present in the disclosed X-ray structures. The approach successfully identified a protein conformational state not previously observed in public structures but evident in a retrospective analysis of Lilly in-house structures: the X-ray structure of Abl with WHI-P154. Using a MSM-derived model, the free energy landscape and kinetic profile of Abl was analyzed in detail highlighting opportunities for targeting the unique metastable states.
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Affiliation(s)
- Yilin Meng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Cen Gao
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - David Clawson
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Shane Atwell
- Applied Molecular Evolution, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA, 92121, USA
| | - Marijane Russell
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA, 92121, USA
| | - Michal Vieth
- Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA, 92121, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
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78
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Zhang H, Zhu Q, Cui J, Wang Y, Chen MJ, Guo X, Tagliabracci VS, Dixon JE, Xiao J. Structure and evolution of the Fam20 kinases. Nat Commun 2018; 9:1218. [PMID: 29572475 PMCID: PMC5865150 DOI: 10.1038/s41467-018-03615-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/28/2018] [Indexed: 01/04/2023] Open
Abstract
The Fam20 proteins are novel kinases that phosphorylate secreted proteins and proteoglycans. Fam20C phosphorylates hundreds of secreted proteins and is activated by the pseudokinase Fam20A. Fam20B phosphorylates a xylose residue to regulate proteoglycan synthesis. Despite these wide-ranging and important functions, the molecular and structural basis for the regulation and substrate specificity of these kinases are unknown. Here we report molecular characterizations of all three Fam20 kinases, and show that Fam20C is activated by the formation of an evolutionarily conserved homodimer or heterodimer with Fam20A. Fam20B has a unique active site for recognizing Galβ1-4Xylβ1, the initiator disaccharide within the tetrasaccharide linker region of proteoglycans. We further show that in animals the monomeric Fam20B preceded the appearance of the dimeric Fam20C, and the dimerization trait of Fam20C emerged concomitantly with a change in substrate specificity. Our results provide comprehensive structural, biochemical, and evolutionary insights into the function of the Fam20 kinases.
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Affiliation(s)
- Hui Zhang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Qinyu Zhu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Jixin Cui
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yuxin Wang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Mark J Chen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38015, USA
| | - Xing Guo
- The Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Vincent S Tagliabracci
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Junyu Xiao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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79
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Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation. J Mol Biol 2018; 430:881-889. [PMID: 29410316 PMCID: PMC6279248 DOI: 10.1016/j.jmb.2018.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 01/11/2023]
Abstract
Tyrosine kinases are enzymes playing a critical role in cellular signaling. Molecular dynamics umbrella sampling potential of mean force computations are used to quantify the impact of activating and inactivating mutations of c-Src kinase. The potential of mean force computations predict that a specific double mutant can stabilize c-Src kinase into an active-like conformation while disabling the binding of ATP in the catalytic active site. The active-like conformational equilibrium of this catalytically dead kinase is affected by a hydrophobic unit that connects to the hydrophobic spine network via the C-helix. The αC-helix plays a crucial role in integrating the hydrophobic residues, making it a hub for allosteric regulation of kinase activity and the active conformation. The computational free-energy landscapes reported here illustrate novel design principles focusing on the important role of the hydrophobic spines. The relative stability of the spines could be exploited in future efforts to artificially engineer active-like but catalytically dead forms of protein kinases.
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Affiliation(s)
- Yilin Meng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lalima G Ahuja
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Alexandr P Kornev
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
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80
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Abstract
Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. PKs propagate biochemical signals by catalyzing phosphorylation of other proteins, including other PKs, which can undergo conformational changes upon phosphorylation and catalyze further phosphorylations. Although PKs have been studied thoroughly across the domains of life, the structures of these proteins are sparsely understood in numerous groups of organisms, including plants. In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. This approach of experimental structural biology coupled with computational biophysics has led to improved understanding of how PKs become catalytically active and why mutations cause pathological PK behavior, at spatial and temporal resolutions inaccessible to current experimental methods alone. In this review, we argue for the value of applying MD simulation to plant PKs. We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. We conclude with a discussion of the future of MD simulations and plant PKs, arguing for the importance of molecular simulation in the future of plant PK research.
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81
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Hirano T, Yasuda H, Hamamoto J, Nukaga S, Masuzawa K, Kawada I, Naoki K, Niimi T, Mimasu S, Sakagami H, Soejima K, Betsuyaku T. Pharmacological and Structural Characterizations of Naquotinib, a Novel Third-Generation EGFR Tyrosine Kinase Inhibitor, in EGFR-Mutated Non-Small Cell Lung Cancer. Mol Cancer Ther 2018; 17:740-750. [PMID: 29467275 DOI: 10.1158/1535-7163.mct-17-1033] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 12/13/2017] [Accepted: 02/05/2018] [Indexed: 11/16/2022]
Abstract
Multiple epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (EGFR-TKI) have been developed to effectively inhibit EGFR-derived signals in non-small cell lung cancer (NSCLC). In this study, we assessed the efficacy of EGFR-TKIs, including a novel third-generation inhibitor naquotinib (ASP8273), in clinically relevant EGFR mutations, including L858R, exon 19 deletion, L858R+T790M, exon 19 deletion+T790M with or without a C797S mutation, and several exon 20 insertion mutations. Using structural analyses, we also elucidated the mechanism of activation and sensitivity/resistance to EGFR-TKIs in EGFR exon 20 insertion mutations. The efficacy of naquotinib in cells with L858R, exon 19 deletion and exon 19 deletion+T790M was comparable with that of osimertinib. Interestingly, naquotinib was more potent than osimertinib for L858R+T790M. Additionally, naquotinib and osimertinib had comparable efficacy and a wide therapeutic window for cells with EGFR exon 20 insertions. Structural modeling partly elucidated the mechanism of activation and sensitivity/resistance to EGFR-TKIs in two EGFR exon 20 insertion mutants, A767_V769dupASV and Y764_V765insHH. In summary, we have characterized the efficacy of EGFR-TKIs for NSCLC using in vitro and structural analyses and suggested the mechanism of activation and resistance to EGFR-TKIs of EGFR exon 20 insertion mutations. Our findings should guide the selection of appropriate EGFR-TKIs for the treatment of NSCLC with EGFR mutations and help clarify the biology of EGFR exon 20 insertion mutations. Mol Cancer Ther; 17(4); 740-50. ©2018 AACR.
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Affiliation(s)
- Toshiyuki Hirano
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan.
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Shigenari Nukaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Keita Masuzawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Katsuhiko Naoki
- Kitasato University School of Medicine, Department of Respiratory Medicine, Kanagawa, Japan
| | - Tatsuya Niimi
- Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc., Tokyo, Japan
| | - Shinya Mimasu
- Medicinal Chemistry Research Labs, Drug Discovery Research, Astellas Pharma Inc., Tokyo, Japan
| | - Hideki Sakagami
- Research Program Management Office, Drug Discovery Research, Astellas Pharma Inc., Tokyo, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
| | - Tomoko Betsuyaku
- Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan
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82
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Moffett AS, Bender KW, Huber SC, Shukla D. Allosteric Control of a Plant Receptor Kinase through S-Glutathionylation. Biophys J 2018; 113:2354-2363. [PMID: 29211989 DOI: 10.1016/j.bpj.2017.08.059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/27/2017] [Accepted: 08/02/2017] [Indexed: 12/01/2022] Open
Abstract
Growing evidence supports the importance of protein S-glutathionylation as a regulatory post-translational modification with functional consequences for proteins. Discoveries of redox-state-dependent protein kinase S-glutathionylation have fueled discussion of redox-sensitive signaling. Following previously published experimental evidence for S-glutathionylation induced deactivation of the Arabidopsis thaliana kinase BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR-LIKE KINASE 1 (BAK1), we investigated the consequences of S-glutathionylation on the equilibrium conformational ensemble of BAK1 using all-atom molecular dynamics simulations. We found that glutathionylation of C408 allosterically destabilizes the active-like state of BAK1 and stabilizes an inactive conformation known to recur in protein kinases. Glutathionylation of C408 also has structural consequences throughout the BAK1 kinase domain, whereas glutathionylation of C353 in the N-lobe and C374 near the ATP-binding site have few notable effects on BAK1 compared with the unmodified protein. Our results suggest an allosteric mechanism for inhibition of BAK1 by C408 S-glutathionylation, and more generally, support the notion of protein kinase S-glutathionylation as a means of redox signaling in plant cells.
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Affiliation(s)
- Alexander S Moffett
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois
| | - Kyle W Bender
- Department of Plant Biology, University of Illinois, Urbana, Illinois
| | - Steven C Huber
- Department of Plant Biology, University of Illinois, Urbana, Illinois; Global Change and Photosynthesis Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, Illinois
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois; Department of Plant Biology, University of Illinois, Urbana, Illinois; Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois.
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83
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Hasenahuer MA, Barletta GP, Fernandez-Alberti S, Parisi G, Fornasari MS. Pockets as structural descriptors of EGFR kinase conformations. PLoS One 2017; 12:e0189147. [PMID: 29228029 PMCID: PMC5724837 DOI: 10.1371/journal.pone.0189147] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/20/2017] [Indexed: 12/19/2022] Open
Abstract
Epidermal Growth Factor Receptor (EGFR), a tyrosine kinase receptor, is one of the main tumor markers in different types of cancers. The kinase native state is mainly composed of two populations of conformers: active and inactive. Several sequence variations in EGFR kinase region promote the differential enrichment of conformers with higher activity. Some structural characteristics have been proposed to differentiate kinase conformations, but these considerations could lead to ambiguous classifications. We present a structural characterisation of EGFR kinase conformers, focused on active site pocket comparisons, and the mapping of known pathological sequence variations. A structural based clustering of this pocket accurately discriminates active from inactive, well-characterised conformations. Furthermore, this main pocket contains, or is in close contact with, ≈65% of cancer-related variation positions. Although the relevance of protein dynamics to explain biological function has been extensively recognised, the usage of the ensemble of conformations in dynamic equilibrium to represent the functional state of proteins and the importance of pockets, cavities and/or tunnels was often neglected in previous studies. These functional structures and the equilibrium between them could be structurally analysed in wild type as well as in sequence variants. Our results indicate that biologically important pockets, as well as their shape and dynamics, are central to understanding protein function in wild-type, polymorphic or disease-related variations.
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Affiliation(s)
- Marcia Anahi Hasenahuer
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - German Patricio Barletta
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
| | - María Silvina Fornasari
- Departamento de Ciencia Y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
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84
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Pfleger C, Minges A, Boehm M, McClendon CL, Torella R, Gohlke H. Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery. J Chem Theory Comput 2017; 13:6343-6357. [PMID: 29112408 DOI: 10.1021/acs.jctc.7b00529] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allostery describes the functional coupling between sites in biomolecules. Recently, the role of changes in protein dynamics for allosteric communication has been highlighted. A quantitative and predictive description of allostery is fundamental for understanding biological processes. Here, we integrate an ensemble-based perturbation approach with the analysis of biomolecular rigidity and flexibility to construct a model of dynamic allostery. Our model, by definition, excludes the possibility of conformational changes, evaluates static, not dynamic, properties of molecular systems, and describes allosteric effects due to ligand binding in terms of a novel free-energy measure. We validated our model on three distinct biomolecular systems: eglin c, protein tyrosine phosphatase 1B, and the lymphocyte function-associated antigen 1 domain. In all cases, it successfully identified key residues for signal transmission in very good agreement with the experiment. It correctly and quantitatively discriminated between positively or negatively cooperative effects for one of the systems. Our model should be a promising tool for the rational discovery of novel allosteric drugs.
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Affiliation(s)
- Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Alexander Minges
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Markus Boehm
- Medicinal Sciences, Pfizer, Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Christopher L McClendon
- Medicinal Sciences, Pfizer, Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Rubben Torella
- Medicinal Sciences, Pfizer, Inc. , 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf , Universitätsstr. 1, 40225 Düsseldorf, Germany
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85
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Martin MP, Endicott JA, Noble MEM. Structure-based discovery of cyclin-dependent protein kinase inhibitors. Essays Biochem 2017; 61:439-452. [PMID: 29118092 PMCID: PMC6248306 DOI: 10.1042/ebc20170040] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 09/24/2017] [Accepted: 09/25/2017] [Indexed: 01/02/2023]
Abstract
The cell fate-determining roles played by members of the cyclin-dependent protein kinase (CDK) family explain why their dysregulation can promote proliferative diseases, and identify them as potential targets for drug discovery in oncology and beyond. After many years of research, the first efficacious CDK inhibitors have now been registered for clinical use in a defined segment of breast cancer. Research is underway to identify inhibitors with appropriate CDK-inhibitory profiles to recapitulate this success in other disease settings. Here, we review the structural data that illustrate the interactions and properties that confer upon inhibitors affinity and/or selectivity toward different CDK family members. We conclude that where CDK inhibitors display selectivity, that selectivity derives from exploiting active site sequence peculiarities and/or from the capacity of the target CDK(s) to access conformations compatible with optimizing inhibitor-target interactions.
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Affiliation(s)
- Mathew P Martin
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Martin E M Noble
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Paul O'Gorman Building, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K.
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86
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Masuzawa K, Yasuda H, Hamamoto J, Nukaga S, Hirano T, Kawada I, Naoki K, Soejima K, Betsuyaku T. Characterization of the efficacies of osimertinib and nazartinib against cells expressing clinically relevant epidermal growth factor receptor mutations. Oncotarget 2017; 8:105479-105491. [PMID: 29285266 PMCID: PMC5739653 DOI: 10.18632/oncotarget.22297] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 08/26/2017] [Indexed: 12/13/2022] Open
Abstract
Third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (EGFR-TKIs) were developed to overcome EGFR T790M-mediated resistance to first- and second-generation EGFR-TKIs. Third-generation EGFR-TKIs, such as osimertinib and nazartinib, are effective for patients with the EGFR T790M mutation. However, there are no direct comparison data to guide the selection of a third-generation EGFR-TKI for patients with different EGFR mutations. We previously established an in vitro model to estimate the therapeutic windows of EGFR-TKIs by comparing their relative efficacies against cells expressing mutant or wild type EGFRs. The present study used this approach to characterize the efficacy of third-generation EGFR-TKIs and compare them with that of other EGFR-TKIs. Treatment efficacy was examined using human lung cancer-derived cell lines and Ba/F3 cells, which were transduced with clinically relevant mutant EGFRs. Interestingly, mutation-related differences in EGFR-TKI sensitivity were observed. For classic EGFR mutations (exon 19 deletion and L858R, with or without T790M), osimertinib showed lower IC50 values and wider therapeutic windows than nazartinib. For less common EGFR mutations (G719S or L861Q), afatinib showed the lowest IC50 values. For G719S+T790M or L861Q+T790M, the IC50 values of osimertinib and nazartinib were around 100 nM, which was 10- to 100-fold higher than those for classic+T790M mutations. On the contrary, osimertinib and nazartinib showed similar efficacies in cells expressing EGFR exon 20 insertions. The findings highlight the diverse mutation-related sensitivity pattern of EGFR-TKIs. These data may help in the selection of EGFR-TKIs for non-small cell lung cancer patients harboring EGFR mutations.
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Affiliation(s)
- Keita Masuzawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shigenari Nukaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toshiyuki Hirano
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Katsuhiko Naoki
- Keio Cancer Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomoko Betsuyaku
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
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87
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Stetz G, Tse A, Verkhivker GM. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PLoS One 2017; 12:e0186089. [PMID: 29095844 PMCID: PMC5667858 DOI: 10.1371/journal.pone.0186089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.
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Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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88
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White KA, Ruiz DG, Szpiech ZA, Strauli NB, Hernandez RD, Jacobson MP, Barber DL. Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins. Sci Signal 2017; 10:10/495/eaam9931. [PMID: 28874603 DOI: 10.1126/scisignal.aam9931] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The intracellular pH (pHi) of most cancers is constitutively higher than that of normal cells and enhances proliferation and cell survival. We found that increased pHi enabled the tumorigenic behaviors caused by somatic arginine-to-histidine mutations, which are frequent in cancer and confer pH sensing not seen with wild-type proteins. Experimentally raising the pHi increased the activity of R776H mutant epidermal growth factor receptor (EGFR-R776H), thereby increasing proliferation and causing transformation in fibroblasts. An Arg-to-Gly mutation did not confer these effects. Molecular dynamics simulations of EGFR suggested that decreased protonation of His776 at high pH causes conformational changes in the αC helix that may stabilize the active form of the kinase. An Arg-to-His, but not Arg-to-Lys, mutation in the transcription factor p53 (p53-R273H) decreased its transcriptional activity and attenuated the DNA damage response in fibroblasts and breast cancer cells with high pHi. Lowering pHi attenuated the tumorigenic effects of both EGFR-R776H and p53-R273H. Our data suggest that some somatic mutations may confer a fitness advantage to the higher pHi of cancer cells.
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Affiliation(s)
- Katharine A White
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zachary A Szpiech
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicolas B Strauli
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.,Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diane L Barber
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
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89
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Phosphorylation of AMPK by upstream kinases is required for activity in mammalian cells. Biochem J 2017; 474:3059-3073. [PMID: 28694351 PMCID: PMC5565919 DOI: 10.1042/bcj20170458] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 06/29/2017] [Accepted: 07/10/2017] [Indexed: 01/01/2023]
Abstract
AMP-activated protein kinase (AMPK) plays a major role in regulating metabolism and has attracted significant attention as a therapeutic target for treating metabolic disorders. AMPK activity is stimulated more than 100-fold by phosphorylation of threonine 172 (Thr172). Binding of AMP to the γ subunit allosterically activates the kinase. Additionally, many small molecules, e.g. 991, have been identified that bind between the kinase domain and the carbohydrate-binding module of the β subunit, stabilising their interaction and leading to activation. It was reported recently that non-phosphorylated Thr172 AMPK is activated by AMP and A769662. We present here the crystal structure of non-phosphorylated Thr172 AMPK in complex with AMP and 991. This structure reveals that the activation loop, as well as the complex overall, is similar to the Thr172 phosphorylated complex. We find that in the presence of AMP and 991 non-phosphorylated Thr172, AMPK is much less active than the Thr172 phosphorylated enzyme. In human cells, the basal level of Thr172 phosphorylation is very low (∼1%), but is increased 10-fold by treatment with 2-deoxyglucose. In cells lacking the major Thr172 kinases, LKB1 and CaMKKβ, Thr172 phosphorylation is almost completely abolished, and AMPK activity is virtually undetectable. Our data show that AMP and 991 binding to non-phosphorylated Thr172 AMPK can induce an ordered, active-like, conformation of the activation loop explaining how AMPK activity can be measured in vitro without Thr172 phosphorylation. However, in a cellular context, phosphorylation of Thr172 is critical for significant activation of AMPK.
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90
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Ito T, Ishida S, Oe S, Fukazawa J, Takahashi Y. Autophosphorylation Affects Substrate-Binding Affinity of Tobacco Ca 2+-Dependent Protein Kinase1. PLANT PHYSIOLOGY 2017; 174:2457-2468. [PMID: 28637832 PMCID: PMC5543960 DOI: 10.1104/pp.17.00515] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/19/2017] [Indexed: 05/22/2023]
Abstract
Protein kinases regulate diverse physiological processes. Because many kinases preserve inherent autophosphorylation capability, autophosphorylation appears to be one of the most important mechanisms for cellular signaling. However, physiological functions of autophosphorylation are still largely unknown, other than the self-activation by phosphorylation of activation loop in the catalytic domain. REPRESSION OF SHOOT GROWTH (RSG) is the transcription factor involved in gibberellin (GA) feedback regulation. The tobacco (Nicotiana tabacum) Ca2+-dependent protein kinase, NtCDPK1, phosphorylates RSG, resulting in the negative regulation of RSG. NtCDPK1 was previously shown to be autophosphorylated in a Ca2+-dependent manner. Here, we investigated the functional importance of autophosphorylation in NtCDPK1. Ser-6 and Thr-21 were identified as autophosphorylation sites of NtCDPK1. Autophosphorylation not only reduced the binding affinity of NtCDPK1 for RSG, but also inhibited the homodimerization of NtCDPK1. Furthermore, autophosphorylation decreased the phosphorylation efficiency of RSG yet increased that of myelin basic protein. Ser-6 and Thr-21 of NtCDPK1 were phosphorylated in response to GAs in plants. The substitution of these autophosphorylation sites with Ala enhanced the NtCDPK1 overexpression-induced sensitization of seeds to a GA biosynthetic inhibitor during germination. These results suggest new functions of autophosphorylation in CDPKs, namely, autophosphorylation can prevent the excessive phosphorylation of substrates and alter the substrate preference of CDPKs.
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Affiliation(s)
- Takeshi Ito
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Sarahmi Ishida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shota Oe
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Jutarou Fukazawa
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Yohsuke Takahashi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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91
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Leroux AE, Schulze JO, Biondi RM. AGC kinases, mechanisms of regulation and innovative drug development. Semin Cancer Biol 2017; 48:1-17. [PMID: 28591657 DOI: 10.1016/j.semcancer.2017.05.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/16/2017] [Accepted: 05/31/2017] [Indexed: 12/22/2022]
Abstract
The group of AGC kinases consists of 63 evolutionarily related serine/threonine protein kinases comprising PDK1, PKB/Akt, SGK, PKC, PRK/PKN, MSK, RSK, S6K, PKA, PKG, DMPK, MRCK, ROCK, NDR, LATS, CRIK, MAST, GRK, Sgk494, and YANK, while two other families, Aurora and PLK, are the most closely related to the group. Eight of these families are physiologically activated downstream of growth factor signalling, while other AGC kinases are downstream effectors of a wide range of signals. The different AGC kinase families share aspects of their mechanisms of inhibition and activation. In the present review, we update the knowledge of the mechanisms of regulation of different AGC kinases. The conformation of the catalytic domain of many AGC kinases is regulated allosterically through the modulation of the conformation of a regulatory site on the small lobe of the kinase domain, the PIF-pocket. The PIF-pocket acts like an ON-OFF switch in AGC kinases with different modes of regulation, i.e. PDK1, PKB/Akt, LATS and Aurora kinases. In this review, we make emphasis on how the knowledge of the molecular mechanisms of regulation can guide the discovery and development of small allosteric modulators. Molecular probes stabilizing the PIF-pocket in the active conformation are activators, while compounds stabilizing the disrupted site are allosteric inhibitors. One challenge for the rational development of allosteric modulators is the lack of complete structural information of the inhibited forms of full-length AGC kinases. On the other hand, we suggest that the available information derived from molecular biology and biochemical studies can already guide screening strategies for the identification of innovative mode of action molecular probes and the development of selective allosteric drugs for the treatment of human diseases.
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Affiliation(s)
- Alejandro E Leroux
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina.
| | - Jörg O Schulze
- Research Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ricardo M Biondi
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires C1425FQD, Argentina; Research Group PhosphoSites, Medizinische Klinik 1, Universitätsklinikum Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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92
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Moffett AS, Bender KW, Huber SC, Shukla D. Molecular dynamics simulations reveal the conformational dynamics of Arabidopsis thaliana BRI1 and BAK1 receptor-like kinases. J Biol Chem 2017; 292:12643-12652. [PMID: 28559283 DOI: 10.1074/jbc.m117.792762] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 05/18/2017] [Indexed: 11/06/2022] Open
Abstract
The structural motifs responsible for activation and regulation of eukaryotic protein kinases in animals have been studied extensively in recent years, and a coherent picture of their activation mechanisms has begun to emerge. In contrast, non-animal eukaryotic protein kinases are not as well understood from a structural perspective, representing a large knowledge gap. To this end, we investigated the conformational dynamics of two key Arabidopsis thaliana receptor-like kinases, brassinosteroid-insensitive 1 (BRI1) and BRI1-associated kinase 1 (BAK1), through extensive molecular dynamics simulations of their fully phosphorylated kinase domains. Molecular dynamics simulations calculate the motion of each atom in a protein based on classical approximations of interatomic forces, giving researchers insight into protein function at unparalleled spatial and temporal resolutions. We found that in an otherwise "active" BAK1 the αC helix is highly disordered, a hallmark of deactivation, whereas the BRI1 αC helix is moderately disordered and displays swinging behavior similar to numerous animal kinases. An analysis of all known sequences in the A. thaliana kinome found that αC helix disorder may be a common feature of plant kinases.
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Affiliation(s)
- Alexander S Moffett
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801
| | - Kyle W Bender
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801
| | - Steven C Huber
- Department of Plant Biology, University of Illinois, Urbana, Illinois 61801; Global Change and Photosynthesis Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, Illinois 61801
| | - Diwakar Shukla
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, Illinois 61801; Department of Plant Biology, University of Illinois, Urbana, Illinois 61801; Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois 61801.
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93
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Pellegrini E, Signor L, Singh S, Boeri Erba E, Cusack S. Structures of the inactive and active states of RIP2 kinase inform on the mechanism of activation. PLoS One 2017; 12:e0177161. [PMID: 28545134 PMCID: PMC5436651 DOI: 10.1371/journal.pone.0177161] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
Innate immune receptors NOD1 and NOD2 are activated by bacterial peptidoglycans leading to recruitment of adaptor kinase RIP2, which, upon phosphorylation and ubiquitination, becomes a scaffold for downstream effectors. The kinase domain (RIP2K) is a pharmaceutical target for inflammatory diseases caused by aberrant NOD2-RIP2 signalling. Although structures of active RIP2K in complex with inhibitors have been reported, the mechanism of RIP2K activation remains to be elucidated. Here we analyse RIP2K activation by combining crystal structures of the active and inactive states with mass spectrometric characterization of their phosphorylation profiles. The active state has Helix αC inwardly displaced and the phosphorylated Activation Segment (AS) disordered, whilst in the inactive state Helix αC is outwardly displaced and packed against the helical, non-phosphorylated AS. Biophysical measurements show that the active state is a stable dimer whilst the inactive kinase is in a monomer-dimer equilibrium, consistent with the observed structural differences at the dimer interface. We conclude that RIP2 kinase auto-phosphorylation is intimately coupled to dimerization, similar to the case of BRAF. Our results will help drug design efforts targeting RIP2 as a potential treatment for NOD2-RIP2 related inflammatory diseases.
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Affiliation(s)
| | - Luca Signor
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Saurabh Singh
- European Molecular Biology Laboratory, Grenoble, France
| | - Elisabetta Boeri Erba
- University Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France
- * E-mail:
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94
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Xie J, Wang CL, Yang W, Wang J, Chen C, Zheng L, Sung KP, Zhou X. Modulation of MMP-2 and MMP-9 through connected pathways and growth factors is critical for extracellular matrix balance of intra-articular ligaments. J Tissue Eng Regen Med 2017; 12:e550-e565. [PMID: 27684403 DOI: 10.1002/term.2325] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 07/29/2016] [Accepted: 09/26/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Jing Xie
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology; Sichuan University; Chengdu Sichuan Province China
| | - Chun-Li Wang
- Key Laboratory of Biorheological Science and Technology, Bioengineering College; Chongqing University; Chongqing China
| | - Wenbin Yang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology; Sichuan University; Chengdu Sichuan Province China
| | - Jue Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology; Sichuan University; Chengdu Sichuan Province China
| | - Cheng Chen
- Centre for Joint Surgery, Southwest Hospital; Third Military Medical University; Chongqing China
| | - Liwei Zheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology; Sichuan University; Chengdu Sichuan Province China
| | - K.L. Paul Sung
- Key Laboratory of Biorheological Science and Technology, Bioengineering College; Chongqing University; Chongqing China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology; Sichuan University; Chengdu Sichuan Province China
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95
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Nukaga S, Yasuda H, Tsuchihara K, Hamamoto J, Masuzawa K, Kawada I, Naoki K, Matsumoto S, Mimaki S, Ikemura S, Goto K, Betsuyaku T, Soejima K. Amplification of EGFR Wild-Type Alleles in Non–Small Cell Lung Cancer Cells Confers Acquired Resistance to Mutation-Selective EGFR Tyrosine Kinase Inhibitors. Cancer Res 2017; 77:2078-2089. [DOI: 10.1158/0008-5472.can-16-2359] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/04/2017] [Accepted: 01/23/2017] [Indexed: 11/16/2022]
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96
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Perdios L, Lowe AR, Saladino G, Bunney TD, Thiyagarajan N, Alexandrov Y, Dunsby C, French PMW, Chin JW, Gervasio FL, Tate EW, Katan M. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET. Sci Rep 2017; 7:39841. [PMID: 28045057 PMCID: PMC5206623 DOI: 10.1038/srep39841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.
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Affiliation(s)
- Louis Perdios
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Alan R. Lowe
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
- London Centre for Nanotechnology, 17-19 Gower St, London, WC1H 0AH, UK
- Division of Biosciences, Birkbeck College, Malet St, London, WC1E 7HX, UK
| | - Giorgio Saladino
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Yuriy Alexandrov
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Christopher Dunsby
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Paul M. W. French
- Department of Physics, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Jason W. Chin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Francesco Luigi Gervasio
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St, London WC1E 6BT, UK
| | - Edward W. Tate
- Department of Chemistry, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
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97
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Verkhivker GM. Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. MOLECULAR BIOSYSTEMS 2017; 13:2235-2253. [DOI: 10.1039/c7mb00355b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Network modeling and percolation analysis of conformational dynamics and energetics of regulatory mechanisms in cyclin-dependent kinases.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Biosciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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98
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Plaza-Menacho I, Barnouin K, Barry R, Borg A, Orme M, Chauhan R, Mouilleron S, Martínez-Torres RJ, Meier P, McDonald NQ. RET Functions as a Dual-Specificity Kinase that Requires Allosteric Inputs from Juxtamembrane Elements. Cell Rep 2016; 17:3319-3332. [PMID: 28009299 PMCID: PMC5199340 DOI: 10.1016/j.celrep.2016.11.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 10/02/2016] [Accepted: 11/20/2016] [Indexed: 12/25/2022] Open
Abstract
Receptor tyrosine kinases exhibit a variety of activation mechanisms despite highly homologous catalytic domains. Such diversity arises through coupling of extracellular ligand-binding portions with highly variable intracellular sequences flanking the tyrosine kinase domain and specific patterns of autophosphorylation sites. Here, we show that the juxtamembrane (JM) segment enhances RET catalytic domain activity through Y687. This phospho-site is also required by the JM region to rescue an otherwise catalytically deficient RET activation-loop mutant lacking tyrosines. Structure-function analyses identified interactions between the JM hinge, αC helix, and an unconventional activation-loop serine phosphorylation site that engages the HRD motif and promotes phospho-tyrosine conformational accessibility and regulatory spine assembly. We demonstrate that this phospho-S909 arises from an intrinsic RET dual-specificity kinase activity and show that an equivalent serine is required for RET signaling in Drosophila. Our findings reveal dual-specificity and allosteric components for the mechanism of RET activation and signaling with direct implications for drug discovery.
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Affiliation(s)
- Iván Plaza-Menacho
- Structural Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Karin Barnouin
- Protein Analysis and Proteomics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rachael Barry
- The Breast Cancer Now Toby Robins Research Centre, Mary-Jean Mitchell Green Building, Institute of Cancer Research, SW3 6JB London, UK
| | - Annabel Borg
- Protein Production Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariam Orme
- The Breast Cancer Now Toby Robins Research Centre, Mary-Jean Mitchell Green Building, Institute of Cancer Research, SW3 6JB London, UK
| | - Rakhee Chauhan
- Structural Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rubén J Martínez-Torres
- Structural Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, Mary-Jean Mitchell Green Building, Institute of Cancer Research, SW3 6JB London, UK
| | - Neil Q McDonald
- Structural Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, WC1E 7HX London, UK.
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99
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Qie S, Diehl JA. Cyclin D1, cancer progression, and opportunities in cancer treatment. J Mol Med (Berl) 2016; 94:1313-1326. [PMID: 27695879 PMCID: PMC5145738 DOI: 10.1007/s00109-016-1475-3] [Citation(s) in RCA: 445] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/06/2016] [Accepted: 09/13/2016] [Indexed: 12/15/2022]
Abstract
Mammalian cells encode three D cyclins (D1, D2, and D3) that coordinately function as allosteric regulators of cyclin-dependent kinase 4 (CDK4) and CDK6 to regulate cell cycle transition from G1 to S phase. Cyclin expression, accumulation, and degradation, as well as assembly and activation of CDK4/CDK6 are governed by growth factor stimulation. Cyclin D1 is more frequently dysregulated than cyclin D2 or D3 in human cancers, and as such, it has been more extensively characterized. Overexpression of cyclin D1 results in dysregulated CDK activity, rapid cell growth under conditions of restricted mitogenic signaling, bypass of key cellular checkpoints, and ultimately, neoplastic growth. This review discusses cyclin D1 transcriptional, translational, and post-translational regulations and its biological function with a particular focus on the mechanisms that result in its dysregulation in human cancers.
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Affiliation(s)
- Shuo Qie
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St, Charleston, SC, 29425, USA
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St, Charleston, SC, 29425, USA.
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100
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Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J. Structure of protein O-mannose kinase reveals a unique active site architecture. eLife 2016; 5. [PMID: 27879205 PMCID: PMC5142810 DOI: 10.7554/elife.22238] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/22/2016] [Indexed: 12/20/2022] Open
Abstract
The ‘pseudokinase’ SgK196 is a protein O-mannose kinase (POMK) that catalyzes an essential phosphorylation step during biosynthesis of the laminin-binding glycan on α-dystroglycan. However, the catalytic mechanism underlying this activity remains elusive. Here we present the crystal structure of Danio rerio POMK in complex with Mg2+ ions, ADP, aluminum fluoride, and the GalNAc-β3-GlcNAc-β4-Man trisaccharide substrate, thereby providing a snapshot of the catalytic transition state of this unusual kinase. The active site of POMK is established by residues located in non-canonical positions and is stabilized by a disulfide bridge. GalNAc-β3-GlcNAc-β4-Man is recognized by a surface groove, and the GalNAc-β3-GlcNAc moiety mediates the majority of interactions with POMK. Expression of various POMK mutants in POMK knockout cells further validated the functional requirements of critical residues. Our results provide important insights into the ability of POMK to function specifically as a glycan kinase, and highlight the structural diversity of the human kinome. DOI:http://dx.doi.org/10.7554/eLife.22238.001
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Affiliation(s)
- Qinyu Zhu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - David Venzke
- Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States.,Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States.,Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
| | - Ameya S Walimbe
- Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States.,Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States.,Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
| | - Mary E Anderson
- Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States.,Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States.,Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
| | - Qiuyu Fu
- National Institute of Biological Sciences, Beijing, China
| | - Lisa N Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Wei Wang
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.,Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Xing Chen
- Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Synthetic and Functional Biomolecules Center, Peking University, Beijing, China.,Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Niu Huang
- National Institute of Biological Sciences, Beijing, China
| | - Liping Yu
- Medical Nuclear Magnetic Resonance Facility, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, United States.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States
| | - Kevin P Campbell
- Department of Molecular Physiology and Biophysics, Howard Hughes Medical Institute, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, United States.,Department of Neurology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States.,Department of Internal Medicine, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa, United States
| | - Junyu Xiao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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