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Shaw AL, Parson MAH, Truebestein L, Jenkins ML, Leonard TA, Burke JE. ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1. Structure 2023; 31:343-354.e3. [PMID: 36758543 DOI: 10.1016/j.str.2023.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023]
Abstract
Akt is a master regulator of pro-growth signaling in the cell. Akt is activated by phosphoinositides that disrupt the autoinhibitory interface between the kinase and pleckstrin homology (PH) domains and then is phosphorylated at T308 and S473. Akt hyperactivation is oncogenic, which has spurred development of potent and selective inhibitors as therapeutics. Using hydrogen deuterium exchange mass spectrometry (HDX-MS), we interrogated the conformational changes upon binding Akt ATP-competitive and allosteric inhibitors. We compared inhibitors against three different states of Akt1. The allosteric inhibitor caused substantive conformational changes and restricts membrane binding. ATP-competitive inhibitors caused extensive allosteric conformational changes, altering the autoinhibitory interface and leading to increased membrane binding, suggesting that the PH domain is more accessible for membrane binding. This work provides unique insight into the autoinhibitory conformation of the PH and kinase domain and conformational changes induced by Akt inhibitors and has important implications for the design of Akt targeted therapeutics.
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Affiliation(s)
- Alexandria L Shaw
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria; Department of Medical Biochemistry, Medical University of Vienna, 1090 Vienna, Austria
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, the University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
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Reinhardt R, Truebestein L, Schmidt HA, Leonard TA. It Takes Two to Tango: Activation of Protein Kinase D by Dimerization. Bioessays 2020; 42:e1900222. [PMID: 31997382 DOI: 10.1002/bies.201900222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/10/2020] [Indexed: 12/23/2022]
Abstract
The recent discovery and structure determination of a novel ubiquitin-like dimerization domain in protein kinase D (PKD) has significant implications for its activation. PKD is a serine/threonine kinase activated by the lipid second messenger diacylglycerol (DAG). It is an essential and highly conserved protein that is implicated in plasma membrane directed trafficking processes from the trans-Golgi network. However, many open questions surround its mechanism of activation, its localization, and its role in the biogenesis of cargo transport carriers. In reviewing this field, the focus is primarily on the mechanisms that control the activation of PKD at precise locations in the cell. In light of the new structural findings, the understanding of the mechanisms underlying PKD activation is critically evaluated, with particular emphasis on the role of dimerization in PKD autophosphorylation, and the provenance and recognition of the DAG that activates PKD.
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Affiliation(s)
- Ronja Reinhardt
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter, 1030, Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, 1030, Vienna, Austria
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter, 1030, Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, 1030, Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna Biocenter, 1030, Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter, 1030, Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, 1030, Vienna, Austria
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Lučić I, Rathinaswamy MK, Truebestein L, Hamelin DJ, Burke JE, Leonard TA. Conformational sampling of membranes by Akt controls its activation and inactivation. Proc Natl Acad Sci U S A 2018; 115:E3940-E3949. [PMID: 29632185 PMCID: PMC5924885 DOI: 10.1073/pnas.1716109115] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The protein kinase Akt controls myriad signaling processes in cells, ranging from growth and proliferation to differentiation and metabolism. Akt is activated by a combination of binding to the lipid second messenger PI(3,4,5)P3 and its subsequent phosphorylation by phosphoinositide-dependent kinase 1 and mechanistic target of rapamycin complex 2. The relative contributions of these mechanisms to Akt activity and signaling have hitherto not been understood. Here, we show that phosphorylation and activation by membrane binding are mutually interdependent. Moreover, the converse is also true: Akt is more rapidly dephosphorylated in the absence of PIP3, an autoinhibitory process driven by the interaction of its PH and kinase domains. We present biophysical evidence for the conformational changes in Akt that accompany its activation on membranes, show that Akt is robustly autoinhibited in the absence of PIP3 irrespective of its phosphorylation, and map the autoinhibitory PH-kinase interface. Finally, we present a model for the activation and inactivation of Akt by an ordered series of membrane binding, phosphorylation, dissociation, and dephosphorylation events.
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Affiliation(s)
- Iva Lučić
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - Manoj K Rathinaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - Linda Truebestein
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
| | - David J Hamelin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 2Y2
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, 1030 Vienna, Austria;
- Center for Medical Biochemistry, Medical University of Vienna, 1030 Vienna, Austria
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Abstract
Coiled‐coils are found in proteins throughout all three kingdoms of life. Coiled‐coil domains of some proteins are almost invariant in sequence and length, betraying a structural and functional role for amino acids along the entire length of the coiled‐coil. Other coiled‐coils are divergent in sequence, but conserved in length, thereby functioning as molecular spacers. In this capacity, coiled‐coil proteins influence the architecture of organelles such as centrioles and the Golgi, as well as permit the tethering of transport vesicles. Specialized coiled‐coils, such as those found in motor proteins, are capable of propagating conformational changes along their length that regulate cargo binding and motor processivity. Coiled‐coil domains have also been identified in enzymes, where they function as molecular rulers, positioning catalytic activities at fixed distances. Finally, while coiled‐coils have been extensively discussed for their potential to nucleate and scaffold large macromolecular complexes, structural evidence to substantiate this claim is relatively scarce.
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Affiliation(s)
- Linda Truebestein
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
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Abstract
The Rho-associated coiled-coil containing kinases (ROCK) were first identified as effectors of the small GTPase RhoA, hence their nomenclature. Since their discovery, two decades ago, scientists have sought to unravel the structure, regulation, and function of these essential kinases. During that time, a consensus model has formed, in which ROCK activity is regulated via both Rho-dependent and independent mechanisms. However, recent findings have raised significant questions regarding this model. In their recent publication in Nature Communications, Truebestein and colleagues present the structure of a full-length Rho kinase for the first time. In contrast to previous reports, the authors could find no evidence for autoinhibition, RhoA binding, or regulation of kinase activity by phosphorylation. Instead, they propose that ROCK functions as a molecular ruler, in which the central coiled-coil bridges the membrane-binding regulatory domains to the kinase domains at a fixed distance from the plasma membrane. Here, we explore the consequences of the new findings, re-examine old data in the context of this model, and emphasize outstanding questions in the field.
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Affiliation(s)
- Linda Truebestein
- a Department of Structural and Computational Biology , Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC) , Vienna , Austria
| | - Daniel J Elsner
- a Department of Structural and Computational Biology , Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC) , Vienna , Austria
| | - Thomas A Leonard
- a Department of Structural and Computational Biology , Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC) , Vienna , Austria.,b Department of Medical Biochemistry , Medical University of Vienna , Vienna , Austria
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6
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Tennstaedt A, Pöpsel S, Truebestein L, Hauske P, Brockmann A, Schmidt N, Irle I, Sacca B, Niemeyer CM, Brandt R, Ksiezak-Reding H, Tirniceriu AL, Egensperger R, Baldi A, Dehmelt L, Kaiser M, Huber R, Clausen T, Ehrmann M. Human high temperature requirement serine protease A1 (HTRA1) degrades tau protein aggregates. J Biol Chem 2012; 287:20931-41. [PMID: 22535953 PMCID: PMC3375517 DOI: 10.1074/jbc.m111.316232] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/24/2012] [Indexed: 11/06/2022] Open
Abstract
Protective proteases are key elements of protein quality control pathways that are up-regulated, for example, under various protein folding stresses. These proteases are employed to prevent the accumulation and aggregation of misfolded proteins that can impose severe damage to cells. The high temperature requirement A (HtrA) family of serine proteases has evolved to perform important aspects of ATP-independent protein quality control. So far, however, no HtrA protease is known that degrades protein aggregates. We show here that human HTRA1 degrades aggregated and fibrillar tau, a protein that is critically involved in various neurological disorders. Neuronal cells and patient brains accumulate less tau, neurofibrillary tangles, and neuritic plaques, respectively, when HTRA1 is expressed at elevated levels. Furthermore, HTRA1 mRNA and HTRA1 activity are up-regulated in response to elevated tau concentrations. These data suggest that HTRA1 is performing regulated proteolysis during protein quality control, the implications of which are discussed.
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Affiliation(s)
- Annette Tennstaedt
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Simon Pöpsel
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Linda Truebestein
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Patrick Hauske
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Anke Brockmann
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Nina Schmidt
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Inga Irle
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Barbara Sacca
- the Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Christof M. Niemeyer
- the Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Roland Brandt
- the Fachbereich Biologie/Chemie, University Osnabrueck, D-49076 Osnabrueck, Germany
| | - Hanna Ksiezak-Reding
- the Department of Neurology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029
| | - Anca Laura Tirniceriu
- the Center for Neuropathology and Prion Research, Ludwig Maximilians University of Munich, Feodor-Lynen-Strasse 23, 81377 Munich, Germany
| | - Rupert Egensperger
- the Center for Neuropathology and Prion Research, Ludwig Maximilians University of Munich, Feodor-Lynen-Strasse 23, 81377 Munich, Germany
| | - Alfonso Baldi
- the Department of Biochemistry and Biophysics, Section of Pathology, the Second University of Naples, 80100 Naples, Italy
| | - Leif Dehmelt
- the Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Markus Kaiser
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
| | - Robert Huber
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
- the Department for Chemical Biology, Technische Universität Dortmund University, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- the Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, 82152 Martinsried, Germany
- the School of Biosciences, Cardiff University, Cardiff CF10 3US, United Kingdom, and
| | - Tim Clausen
- the Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria
| | - Michael Ehrmann
- From the Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitaetsstrasse, 45141 Essen, Germany
- the School of Biosciences, Cardiff University, Cardiff CF10 3US, United Kingdom, and
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Truebestein L, Tennstaedt A, Mönig T, Krojer T, Canellas F, Kaiser M, Clausen T, Ehrmann M. Substrate-induced remodeling of the active site regulates human HTRA1 activity. Nat Struct Mol Biol 2011; 18:386-8. [PMID: 21297635 DOI: 10.1038/nsmb.2013] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 11/22/2010] [Indexed: 11/09/2022]
Abstract
Crystal structures of active and inactive conformations of the human serine protease HTRA1 reveal that substrate binding to the active site is sufficient to stimulate proteolytic activity. HTRA1 attaches to liposomes, digests misfolded proteins into defined fragments and undergoes substrate-mediated oligomer conversion. In contrast to those of other serine proteases, the PDZ domain of HTRA1 is dispensable for activation or lipid attachment, indicative of different underlying mechanistic features.
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Affiliation(s)
- Linda Truebestein
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
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