1
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Emerging Link between Tsc1 and FNIP Co-Chaperones of Hsp90 and Cancer. Biomolecules 2022; 12:biom12070928. [PMID: 35883484 PMCID: PMC9312812 DOI: 10.3390/biom12070928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Heat shock protein-90 (Hsp90) is an ATP-dependent molecular chaperone that is tightly regulated by a group of proteins termed co-chaperones. This chaperone system is essential for the stabilization and activation of many key signaling proteins. Recent identification of the co-chaperones FNIP1, FNIP2, and Tsc1 has broadened the spectrum of Hsp90 regulators. These new co-chaperones mediate the stability of critical tumor suppressors FLCN and Tsc2 as well as the various classes of Hsp90 kinase and non-kinase clients. Many early observations of the roles of FNIP1, FNIP2, and Tsc1 suggested functions independent of FLCN and Tsc2 but have not been fully delineated. Given the broad cellular impact of Hsp90-dependent signaling, it is possible to explain the cellular activities of these new co-chaperones by their influence on Hsp90 function. Here, we review the literature on FNIP1, FNIP2, and Tsc1 as co-chaperones and discuss the potential downstream impact of this regulation on normal cellular function and in human diseases.
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2
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Xu H. Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones. Biomolecules 2022; 12:832. [PMID: 35740957 PMCID: PMC9221429 DOI: 10.3390/biom12060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each break a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen's hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermodynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways.
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Affiliation(s)
- Huafeng Xu
- Roivant Sciences, New York, NY 10036, USA
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3
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Biebl MM, Delhommel F, Faust O, Zak KM, Agam G, Guo X, Mühlhofer M, Dahiya V, Hillebrand D, Popowicz GM, Kampmann M, Lamb DC, Rosenzweig R, Sattler M, Buchner J. NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems. Mol Cell 2022; 82:555-569.e7. [DOI: 10.1016/j.molcel.2021.12.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/03/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022]
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4
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Kim J, Ahn D, Park CJ. Biophysical investigation of the dual binding surfaces of human transcription factors FOXO4 and p53. FEBS J 2021; 289:3163-3182. [PMID: 34954873 DOI: 10.1111/febs.16333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/21/2021] [Accepted: 12/23/2021] [Indexed: 01/20/2023]
Abstract
Cellular senescence is protective against external oncogenic stress, but its accumulation causes aging-related diseases. Forkhead box O4 (FOXO4) and p53 are human transcription factors known to promote senescence by interacting with each other and activating p21 transcription. Inhibition of the interaction is a strategy for inducing apoptosis of senescent cells, but the binding surfaces that mediate the FOXO4-p53 interaction remain elusive. Here, we investigated two binding sites involved in the interaction between FOXO4 and p53 by NMR spectroscopy. NMR chemical shift perturbation analysis showed that the binding between FOXO4's forkhead domain (FHD) and p53's transactivation domain (TAD), and between FOXO4's C-terminal transactivation domain (CR3) and p53's DNA-binding domain (DBD), mediate the FOXO4-p53 interaction. Isothermal titration calorimetry data showed that both interactions have micromolar Kd values, and FOXO4 FHD-p53 TAD interaction has a higher binding affinity. We also showed that the intramolecular CR3-binding surface of FOXO4 FHD interacts with p53 TAD2, and FOXO4 CR3 interacts with the DNA/p53 TAD-binding surface of p53 DBD, suggesting a network of potentially competitive and/or coordinated interactions. Based on these results, we propose that a network of intramolecular and intermolecular interactions contributes to the two transcription factors' proper localisation on the p21 promoter and consequently promotes p21 transcription and cell senescence. This work provides structural information at the molecular level that is key to understanding the interplay of two proteins responsible for cellular senescence.
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Affiliation(s)
- Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Korea
| | - Dabin Ahn
- Department of Chemistry, Gwangju Institute of Science and Technology, Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Korea
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5
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Lopez A, Dahiya V, Delhommel F, Freiburger L, Stehle R, Asami S, Rutz D, Blair L, Buchner J, Sattler M. Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network. SCIENCE ADVANCES 2021; 7:eabl7295. [PMID: 34919431 PMCID: PMC8682993 DOI: 10.1126/sciadv.abl7295] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 05/31/2023]
Abstract
Hsp90 is a molecular chaperone that interacts with a specific set of client proteins and assists their folding. The underlying molecular mechanisms, involving dynamic transitions between open and closed conformations, are still enigmatic. Combining nuclear magnetic resonance, small-angle x-ray scattering, and biochemical experiments, we have identified a key intermediate state of Hsp90 induced by adenosine triphosphate (ATP) binding, in which rotation of the Hsp90 N-terminal domain (NTD) yields a domain arrangement poised for closing. This ATP-stabilized NTD rotation is allosterically communicated across the full Hsp90 dimer, affecting distant client sites. By analyzing the interactions of four distinct clients, i.e., steroid hormone receptors (glucocorticoid receptor and mineralocorticoid receptor), p53, and Tau, we show that client-specific interactions with Hsp90 select and enhance the NTD-rotated state and promote closing of the full-length Hsp90 dimer. The p23 co-chaperone shifts the population of Hsp90 toward the closed state, thereby enhancing client interaction and processing.
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Affiliation(s)
- Abraham Lopez
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Vinay Dahiya
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Lee Freiburger
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ralf Stehle
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Sam Asami
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Daniel Rutz
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Laura Blair
- USF Health Byrd Institute, Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Johannes Buchner
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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6
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Jin Y, Kotler JLM, Wang S, Huang B, Halpin JC, Street TO. The ER Chaperones BiP and Grp94 Regulate the Formation of Insulin-Like Growth Factor 2 (IGF2) Oligomers. J Mol Biol 2021; 433:166963. [PMID: 33811917 DOI: 10.1016/j.jmb.2021.166963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023]
Abstract
While cytosolic Hsp90 chaperones have been extensively studied, less is known about how the ER Hsp90 paralog Grp94 recognizes clients and influences client folding. Here, we examine how Grp94 and the ER Hsp70 paralog, BiP, influence the folding of insulin-like growth factor 2 (IGF2), an established client protein of Grp94. ProIGF2 is composed of a disulfide-bonded insulin-like hormone and a C-terminal E-peptide that has sequence characteristics of an intrinsically disordered region. BiP and Grp94 have a minimal influence on folding whereby both chaperones slow proIGF2 folding and do not substantially alter the disulfide-bonded folding intermediates, suggesting that BiP and Grp94 may have an additional influence unrelated to proIGF2 folding. Indeed, we made the unexpected discovery that the E-peptide region allows proIGF2 to form dynamic oligomers. ProIGF2 oligomers can transition from a dynamic state that is capable of exchanging monomers to an irreversibly aggregated state, providing a plausible role for BiP and Grp94 in regulating proIGF2 oligomerization. In contrast to the modest influence on folding, BiP and Grp94 have a stronger influence on proIGF2 oligomerization and these chaperones exert counteracting effects. BiP suppresses proIGF2 oligomerization while Grp94 can enhance proIGF2 oligomerization in a nucleotide-dependent manner. We propose that BiP and Grp94 regulate the assembly and dynamic behavior of proIGF2 oligomers, although the biological role of proIGF2 oligomerization is not yet known.
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Affiliation(s)
- Yi Jin
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Judy L M Kotler
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Shiyu Wang
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Bin Huang
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Jackson C Halpin
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Timothy O Street
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
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7
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Grindle MP, Carter B, Alao JP, Connors K, Tehver R, Kravats AN. Structural Communication between the E. coli Chaperones DnaK and Hsp90. Int J Mol Sci 2021; 22:ijms22042200. [PMID: 33672263 PMCID: PMC7926864 DOI: 10.3390/ijms22042200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 01/03/2023] Open
Abstract
The 70 kDa and 90 kDa heat shock proteins Hsp70 and Hsp90 are two abundant and highly conserved ATP-dependent molecular chaperones that participate in the maintenance of cellular homeostasis. In Escherichia coli, Hsp90 (Hsp90Ec) and Hsp70 (DnaK) directly interact and collaborate in protein remodeling. Previous work has produced a model of the direct interaction of both chaperones. The locations of the residues involved have been confirmed and the model has been validated. In this study, we investigate the allosteric communication between Hsp90Ec and DnaK and how the chaperones couple their conformational cycles. Using elastic network models (ENM), normal mode analysis (NMA), and a structural perturbation method (SPM) of asymmetric and symmetric DnaK-Hsp90Ec, we extract biologically relevant vibrations and identify residues involved in allosteric signaling. When one DnaK is bound, the dominant normal modes favor biological motions that orient a substrate protein bound to DnaK within the substrate/client binding site of Hsp90Ec and release the substrate from the DnaK substrate binding domain. The presence of one DnaK molecule stabilizes the entire Hsp90Ec protomer to which it is bound. Conversely, the symmetric model of DnaK binding results in steric clashes of DnaK molecules and suggests that the Hsp90Ec and DnaK chaperone cycles operate independently. Together, this data supports an asymmetric binding of DnaK to Hsp90Ec.
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Affiliation(s)
- Matthew P. Grindle
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH 45056, USA; (M.P.G.); (J.P.A.); (K.C.)
| | - Ben Carter
- Department of Physics, Denison University, Granville, OH 43023, USA; (B.C.); (R.T.)
| | - John Paul Alao
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH 45056, USA; (M.P.G.); (J.P.A.); (K.C.)
| | - Katherine Connors
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH 45056, USA; (M.P.G.); (J.P.A.); (K.C.)
| | - Riina Tehver
- Department of Physics, Denison University, Granville, OH 43023, USA; (B.C.); (R.T.)
| | - Andrea N. Kravats
- Department of Chemistry & Biochemistry, Miami University, Oxford, OH 45056, USA; (M.P.G.); (J.P.A.); (K.C.)
- Correspondence:
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8
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Xu H. ATP-Driven Nonequilibrium Activation of Kinase Clients by the Molecular Chaperone Hsp90. Biophys J 2020; 119:1538-1549. [PMID: 33038305 DOI: 10.1016/j.bpj.2020.08.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/12/2020] [Accepted: 08/24/2020] [Indexed: 11/15/2022] Open
Abstract
The molecular chaperone 90-kDa heat-shock protein (Hsp90) assists the late-stage folding and activation of diverse types of protein substrates (called clients), including many kinases. Previous studies have established that the Hsp90 homodimer undergoes an ATP-driven cycle through open and closed conformations. Here, I propose a model of client activation by Hsp90 that predicts that this cycle enables Hsp90 to use ATP energy to drive a client out of thermodynamic equilibrium toward its active conformation. My model assumes that an Hsp90-bound client can transition between a deactivating conformation and an activating conformation. It suggests that the cochaperone Cdc37 aids Hsp90 to activate kinase clients by differentiating between these two intermediate conformations. My model makes experimentally testable predictions, including how modulating the stepwise kinetics of the Hsp90 cycle-for example, by various cochaperones-affects the activation of different clients. My model may inform client-specific and cell-type-specific therapeutic intervention of Hsp90-mediated protein activation.
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Affiliation(s)
- Huafeng Xu
- Silicon Therapeutics, Boston, Massachusetts.
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9
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Korulu S, Yildiz A. p60-katanin: a novel interacting partner for p53. Mol Biol Rep 2020; 47:4295-4301. [PMID: 32462563 DOI: 10.1007/s11033-020-05557-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/23/2020] [Indexed: 11/29/2022]
Abstract
Katanin, one of the best-characterized microtubule (MT) severing proteins, is composed of two subunits: catalytic p60-katanin, and regulatory p80-katanin. p60-katanin triggers MT reorganization by severing them. MT reorganization is essential for both mitotic cells and post-mitotic neurons in numerous vital processes such as intracellular transport, mitosis, cellular differentiation and apoptosis. Due to the deleterious effect of continuous severing for cells, p60-katanin requires a strategic regulation. However, there are only a few known regulators of p60-katanin. p53 functions in similar cellular processes as katanin such as cell cycle, differentiation, and apoptosis depending on its interacting partners. Considering this similarity, in this study we investigated p53 as a potential regulatory candidate of p60-katanin, and examined their interaction. Co-immunoprecipitation analyses revealed that p60-katanin interacts with p53. We were able to locate a potential interaction site for the two proteins by deleting different candidate regions We showed for the first time that p53 and p60-katanin interact. This interaction appears to occur via p53's DNA binding domain and p60-katanin's C-terminal. This study will pave the way for future studies regarding the functional outcomes of this interaction which is vital for understanding the regulation of cellular events such as cell cycle, differentiation, and apoptosis in disease and in health.
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Affiliation(s)
- Sirin Korulu
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Istanbul Arel University, 34537, Istanbul, Turkey. .,Institute of Natural and Health Sciences, Tallinn University, 10120, Tallinn, Estonia.
| | - Aysegul Yildiz
- Department of Molecular Biology and Genetics, Faculty of Science, Mugla Sitki Kocman University, Mugla, 48000, Turkey
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10
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Wu H, Dyson HJ. Aggregation of zinc-free p53 is inhibited by Hsp90 but not other chaperones. Protein Sci 2019; 28:2020-2023. [PMID: 31503385 DOI: 10.1002/pro.3726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/04/2019] [Accepted: 09/07/2019] [Indexed: 11/09/2022]
Abstract
The structured DNA-binding domain (DBD) of p53 is a well-known client protein of the chaperone Hsp90. The p53 DBD contains a single zinc ion, coordinated by the side chains of Cys176, His179, Cys238, and Cys242; zinc coordination plays a structural role to stabilize the DBD and is required for its DNA binding. The ambiguous nature of the p53-Hsp90 interaction, together with the stabilizing role of the zinc in the structure of the DBD, prompted us to examine the interaction of Hsp90 with zinc-free p53 DBD. NMR spectroscopy and native gel electrophoresis did not show any apparent preference for the interaction of the destabilized zinc-free form of p53 DBD with Hsp90. Intriguingly, however, at lower protein concentrations, closer to physiological concentrations, the addition of Hsp90, but not other chaperones such as Hsp70, Hsp40, p23, and HOP, appears to slow or prevent the aggregation of zinc-free p53 DBD. This result suggests that part of the function of the Hsp90-p53 interaction in the cell may be to stabilize the apoprotein in the absence of zinc.
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Affiliation(s)
- Huiwen Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California
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11
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Biebl MM, Buchner J. Structure, Function, and Regulation of the Hsp90 Machinery. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a034017. [PMID: 30745292 DOI: 10.1101/cshperspect.a034017] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone involved in the maturation of a plethora of substrates ("clients"), including protein kinases, transcription factors, and E3 ubiquitin ligases, positioning Hsp90 as a central regulator of cellular proteostasis. Hsp90 undergoes large conformational changes during its ATPase cycle. The processing of clients by cytosolic Hsp90 is assisted by a cohort of cochaperones that affect client recruitment, Hsp90 ATPase function or conformational rearrangements in Hsp90. Because of the importance of Hsp90 in regulating central cellular pathways, strategies for the pharmacological inhibition of the Hsp90 machinery in diseases such as cancer and neurodegeneration are being developed. In this review, we summarize recent structural and mechanistic progress in defining the function of organelle-specific and cytosolic Hsp90, including the impact of individual cochaperones on the maturation of specific clients and complexes with clients as well as ways of exploiting Hsp90 as a drug target.
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Affiliation(s)
- Maximilian M Biebl
- Center for Integrated Protein Science, Department of Chemistry, Technische Universität München, D-85748 Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science, Department of Chemistry, Technische Universität München, D-85748 Garching, Germany
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12
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Hsp70- and Hsp90-Mediated Regulation of the Conformation of p53 DNA Binding Domain and p53 Cancer Variants. Mol Cell 2019; 74:831-843.e4. [DOI: 10.1016/j.molcel.2019.03.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/06/2019] [Accepted: 03/25/2019] [Indexed: 01/06/2023]
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13
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Dahiya V, Agam G, Lawatscheck J, Rutz DA, Lamb DC, Buchner J. Coordinated Conformational Processing of the Tumor Suppressor Protein p53 by the Hsp70 and Hsp90 Chaperone Machineries. Mol Cell 2019; 74:816-830.e7. [PMID: 31027879 DOI: 10.1016/j.molcel.2019.03.026] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/17/2018] [Accepted: 03/22/2019] [Indexed: 12/21/2022]
Abstract
p53, the guardian of the genome, requires chaperoning by Hsp70 and Hsp90. However, how the two chaperone machineries affect p53 conformation and regulate its function remains elusive. We found that Hsp70, together with Hsp40, unfolds p53 in an ATP-dependent reaction. This unfolded state of p53 is susceptible to aggregation after release induced by the nucleotide exchange factor Bag-1. However, when Hsp90 and the adaptor protein Hop are present, p53 is transferred from Hsp70 to Hsp90, allowing restoration of the native state upon ATP hydrolysis. Our results suggest that the p53 conformation is constantly remodeled by the two major chaperone machineries. This connects p53 activity to stress, and the levels of free molecular chaperones are important factors regulating p53 activity. Together, our findings reveal an intricate interplay and cooperation of Hsp70 and Hsp90 in regulating the conformation of a client.
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Affiliation(s)
- Vinay Dahiya
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Ganesh Agam
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig Maximilians University Munich, Munich, Germany
| | - Jannis Lawatscheck
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Daniel Andreas Rutz
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience, Nanosystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CiPSM), Ludwig Maximilians University Munich, Munich, Germany.
| | - Johannes Buchner
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany.
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14
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Sun M, Kotler JLM, Liu S, Street TO. The endoplasmic reticulum (ER) chaperones BiP and Grp94 selectively associate when BiP is in the ADP conformation. J Biol Chem 2019; 294:6387-6396. [PMID: 30787103 DOI: 10.1074/jbc.ra118.007050] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/09/2019] [Indexed: 11/06/2022] Open
Abstract
Hsp70 and Hsp90 chaperones are critical for protein quality control in the cytosol, whereas organelle-specific Hsp70/Hsp90 paralogs provide similar protection for mitochondria and the endoplasmic reticulum (ER). Cytosolic Hsp70/Hsp90 can operate sequentially with Hsp90 selectively associating with Hsp70 after Hsp70 is bound to a client protein. This observation has long suggested that Hsp90 could have a preference for interacting with clients at their later stages of folding. However, recent work has shown that cytosolic Hsp70/Hsp90 can directly interact even in the absence of a client, which opens up an alternative possibility that the ordered interactions of Hsp70/Hsp90 with clients could be a consequence of regulated changes in the direct interactions between Hsp70 and Hsp90. However, it is unknown how such regulation could occur mechanistically. Here, we find that the ER Hsp70/Hsp90 (BiP/Grp94) can form a direct complex in the absence of a client. Importantly, the direct interaction between BiP and Grp94 is nucleotide-specific, with BiP and Grp94 having higher affinity under ADP conditions and lower affinity under ATP conditions. We show that this nucleotide-specific association between BiP and Grp94 is largely due to the conformation of BiP. When BiP is in the ATP conformation its substrate-binding domain blocks Grp94; in contrast, Grp94 can readily associate with the ADP conformation of BiP, which represents the client-bound state of BiP. Our observations provide a mechanism for the sequential involvement of BiP and Grp94 in client folding where the conformation of BiP provides the signal for the subsequent recruitment of Grp94.
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Affiliation(s)
- Ming Sun
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453
| | - Judy L M Kotler
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453
| | - Shanshan Liu
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453
| | - Timothy O Street
- From the Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453
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15
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Dahiya V, Buchner J. Functional principles and regulation of molecular chaperones. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:1-60. [PMID: 30635079 DOI: 10.1016/bs.apcsb.2018.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To be able to perform their biological function, a protein needs to be correctly folded into its three dimensional structure. The protein folding process is spontaneous and does not require the input of energy. However, in the crowded cellular environment where there is high risk of inter-molecular interactions that may lead to protein molecules sticking to each other, hence forming aggregates, protein folding is assisted. Cells have evolved robust machinery called molecular chaperones to deal with the protein folding problem and to maintain proteins in their functional state. Molecular chaperones promote efficient folding of newly synthesized proteins, prevent their aggregation and ensure protein homeostasis in cells. There are different classes of molecular chaperones functioning in a complex interplay. In this review, we discuss the principal characteristics of different classes of molecular chaperones, their structure-function relationships, their mode of regulation and their involvement in human disorders.
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Affiliation(s)
- Vinay Dahiya
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany.
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16
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Nichols PJ, Born A, Henen MA, Strotz D, Celestine CN, Güntert P, Vögeli B. Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA. Chembiochem 2018; 19:1695-1701. [PMID: 29883016 DOI: 10.1002/cbic.201800237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/24/2023]
Abstract
Distance-dependent nuclear Overhauser enhancements (NOEs) are one of the most popular and important experimental restraints for calculating NMR structures. Despite this, they are mostly employed as semiquantitative upper distance bounds, and this discards the wealth of information that is encoded in the cross-relaxation rate constant. Information that is lost includes exact distances between protons and dynamics that occur on the sub-millisecond timescale. Our recently introduced exact measurement of the NOE (eNOE) requires little additional experimental effort relative to other NMR observables. So far, we have used eNOEs to calculate multistate ensembles of proteins up to approximately 150 residues. Here, we briefly revisit eNOE methodology and present two new directions for the use of eNOEs: applications to large proteins and RNA.
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Affiliation(s)
- Parker J Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Alexandra Born
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
| | - Morkos A Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dean Strotz
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Chi N Celestine
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, 75123, Uppsala, Sweden
| | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
- Institute of Biophysical Chemistry, Goethe Universität Frankfurt, Max-von-Laue-Strasse 9, 60438, Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 East 17th Avenue, Aurora, CO, 80045, USA
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Hiller S, Burmann BM. Chaperone-client complexes: A dynamic liaison. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 289:142-155. [PMID: 29544626 DOI: 10.1016/j.jmr.2017.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/08/2017] [Accepted: 12/10/2017] [Indexed: 06/08/2023]
Abstract
Living cells contain molecular chaperones that are organized in intricate networks to surveil protein homeostasis by avoiding polypeptide misfolding, aggregation, and the generation of toxic species. In addition, cellular chaperones also fulfill a multitude of alternative functionalities: transport of clients towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver clients towards proteolysis machineries. Until recently, the only available source of atomic resolution information for virtually all chaperones were crystal structures of their client-free, apo-forms. These structures were unable to explain details of the functional mechanisms underlying chaperone-client interactions. The difficulties to crystallize chaperones in complexes with clients arise from their highly dynamic nature, making solution NMR spectroscopy the method of choice for their study. With the advent of advanced solution NMR techniques, in the past few years a substantial number of structural and functional studies on chaperone-client complexes have been resolved, allowing unique insight into the chaperone-client interaction. This review summarizes the recent insights provided by advanced high-resolution NMR-spectroscopy to understand chaperone-client interaction mechanisms at the atomic scale.
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Affiliation(s)
- Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, Wallenberg Centre for Molecular and Translational Medicine, University for Gothenburg, 405 30 Göteborg, Sweden.
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18
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Wu H, Hyun J, Martinez-Yamout MA, Park SJ, Dyson HJ. Characterization of an Hsp90-Independent Interaction between Co-Chaperone p23 and Transcription Factor p53. Biochemistry 2018; 57:935-944. [PMID: 29334217 DOI: 10.1021/acs.biochem.7b01076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cancer-suppressing transcription factor p53 is regulated by a wide variety of cellular factors, including many chaperones. The DNA-binding domain (DBD) of p53 is known to interact with the chaperone Hsp90, but the role of other members of the chaperone network, including co-chaperones such as p23, is unknown. Using a combination of nuclear magnetic resonance (NMR) titration, isothermal titration calorimetry, fluorescence anisotropy, and native agarose gel electrophoresis, we have identified a direct interaction between the p53 DBD and Hsp90 co-chaperone p23 that occurs in the absence of Hsp90. The affinity is relatively weak and largely determined by electrostatic interactions between the acidic C-terminal disordered tail of p23 and the two DNA-binding regions of the p53 DBD. We show by NMR and native agarose gel electrophoresis that a p53-specific double-stranded DNA sequence competes successfully with p23 for binding to the p53 DBD. The Hsp90 independence of the interaction between p23 and p53 DBD, together with the competition of p23 versus DNA for p53, raises the intriguing possibility that p23, like other small charged proteins, may affect p53 in hitherto unknown ways.
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Affiliation(s)
- Huiwen Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jashil Hyun
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University , 191 Hambakmoero, Yeonsu-gu, Incheon 406-799, Korea
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sung Jean Park
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University , 191 Hambakmoero, Yeonsu-gu, Incheon 406-799, Korea
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions. Int J Mol Sci 2017; 18:ijms18122761. [PMID: 29257115 PMCID: PMC5751360 DOI: 10.3390/ijms18122761] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/13/2017] [Accepted: 12/15/2017] [Indexed: 12/15/2022] Open
Abstract
Some of the intrinsically disordered proteins and protein regions are promiscuous interactors that are involved in one-to-many and many-to-one binding. Several studies have analyzed enrichment of intrinsic disorder among the promiscuous hub proteins. We extended these works by providing a detailed functional characterization of the disorder-enriched hub protein-protein interactions (PPIs), including both hubs and their interactors, and by analyzing their enrichment among disease-associated proteins. We focused on the human interactome, given its high degree of completeness and relevance to the analysis of the disease-linked proteins. We quantified and investigated numerous functional and structural characteristics of the disorder-enriched hub PPIs, including protein binding, structural stability, evolutionary conservation, several categories of functional sites, and presence of over twenty types of posttranslational modifications (PTMs). We showed that the disorder-enriched hub PPIs have a significantly enlarged number of disordered protein binding regions and long intrinsically disordered regions. They also include high numbers of targeting, catalytic, and many types of PTM sites. We empirically demonstrated that these hub PPIs are significantly enriched among 11 out of 18 considered classes of human diseases that are associated with at least 100 human proteins. Finally, we also illustrated how over a dozen specific human hubs utilize intrinsic disorder for their promiscuous PPIs.
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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21
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Li Y, Kang C. Solution NMR Spectroscopy in Target-Based Drug Discovery. Molecules 2017; 22:E1399. [PMID: 28832542 PMCID: PMC6151424 DOI: 10.3390/molecules22091399] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 12/14/2022] Open
Abstract
Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
| | - Congbao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, #03-01, Singapore 138669, Singapore.
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22
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Uversky VN. Intrinsic Disorder, Protein-Protein Interactions, and Disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 110:85-121. [PMID: 29413001 DOI: 10.1016/bs.apcsb.2017.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
It is recognized now that biologically active proteins without stable tertiary structure (known as intrinsically disordered proteins, IDPs) and hybrid proteins containing ordered domains and intrinsically disordered protein regions (IDPRs) are important players found in any given proteome. These IDPs/IDPRs possess functions that complement functional repertoire of their ordered counterparts, being commonly related to recognition, as well as control and regulation of various signaling pathways. They are interaction masters, being able to utilize a wide spectrum of interaction mechanisms, ranging from induced folding to formation of fuzzy complexes where significant levels of disorder are preserved, to polyvalent stochastic interactions playing crucial roles in the liquid-liquid phase transitions leading to the formation of proteinaceous membrane-less organelles. IDPs/IDPRs are tightly controlled themselves via various means, including alternative splicing, precisely controlled expression and degradation, binding to specific partners, and posttranslational modifications. Distortions in the regulation and control of IDPs/IDPRs, as well as their aberrant interactivity are commonly associated with various human diseases. This review presents some aspects of the intrinsic disorder-based functionality and dysfunctionality, paying special attention to the normal and pathological protein-protein interactions.
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Affiliation(s)
- Vladimir N Uversky
- USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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Abstract
The molecular chaperone Hsp90 is an essential member of the cellular proteostasis system. It plays an important role in the stabilisation and activation of a large number of client proteins and is involved in fatal disease processes, e.g. Alzheimer disease, cancer and cystic fibrosis. This makes Hsp90 a crucial protein to study. Mechanistic studies require large amounts of protein but the production and purification of recombinant human Hsp90 in Escherichia coli is challenging and laborious. Here we identified conditions that influence Hsp90 production, and optimised a fast and efficient purification protocol. We found that the nutrient value of the culturing medium and the length of induction had significant effect on Hsp90 production in Escherichia coli. Our fast, single-day purification protocol resulted in a stable, well-folded and pure sample that was resistant to degradation in a reproducible manner. We anticipate that our results provide a useful tool to produce higher amount of pure, well-folded and stable recombinant human Hsp90β in Escherichia coli in an efficient way.
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Affiliation(s)
- Martina Radli
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
- Science for Life, Utrecht University, CH Utrecht, The Netherlands
| | - Dmitry B. Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Stefan G. D. Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
- Science for Life, Utrecht University, CH Utrecht, The Netherlands
- * E-mail:
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24
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Abstract
The heat shock protein 90 (HSP90) chaperone machinery is a key regulator of proteostasis under both physiological and stress conditions in eukaryotic cells. As HSP90 has several hundred protein substrates (or 'clients'), it is involved in many cellular processes beyond protein folding, which include DNA repair, development, the immune response and neurodegenerative disease. A large number of co-chaperones interact with HSP90 and regulate the ATPase-associated conformational changes of the HSP90 dimer that occur during the processing of clients. Recent progress has allowed the interactions of clients with HSP90 and its co-chaperones to be defined. Owing to the importance of HSP90 in the regulation of many cellular proteins, it has become a promising drug target for the treatment of several diseases, which include cancer and diseases associated with protein misfolding.
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Affiliation(s)
- Florian H Schopf
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
| | - Maximilian M Biebl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Garching, Germany
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25
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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Vandermarliere E, Stes E, Gevaert K, Martens L. Resolution of protein structure by mass spectrometry. MASS SPECTROMETRY REVIEWS 2016; 35:653-665. [PMID: 25536908 DOI: 10.1002/mas.21450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Typically, mass spectrometry is used to identify the peptides present in a complex peptide mixture and subsequently the precursor proteins. As such, mass spectrometry focuses mainly on the primary structure, the (modified) amino acid sequence of peptides and proteins. In contrast, the three-dimensional structure of a protein is typically determined with protein X-ray crystallography or NMR. Despite the close relationship between these two aspects of protein studies (sequence and structure), mass spectrometry and structure determination are not frequently combined. Nevertheless, this combination of approaches, dubbed conformational proteomics, can offer insight into the function, working mechanism, and conformational status of a protein. In this review, we will discuss the developments at the intersection of mass spectrometry-based proteomics and protein structure determination and start from a brief overview of the classic approaches to identify protein structure along with their advantages and disadvantages. We will subsequently discuss the ability of mass spectrometry to overcome some of the hurdles of these classic methods. Finally, we will provide an outlook on the interplay of mass spectrometry and protein structure determination, and highlight several recent experiments in which mass spectrometry was successfully used to either aid or complement structure elucidation. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:653-665, 2016.
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Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Elisabeth Stes
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium
| | - Lennart Martens
- Department of Medical Protein Research, VIB, B-9000, Ghent, Belgium.
- Department of Biochemistry, Ghent University, B- 9000, Ghent, Belgium.
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27
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Verma S, Goyal S, Jamal S, Singh A, Grover A. Hsp90: Friends, clients and natural foes. Biochimie 2016; 127:227-40. [DOI: 10.1016/j.biochi.2016.05.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/29/2016] [Indexed: 12/13/2022]
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28
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Axin cancer mutants form nanoaggregates to rewire the Wnt signaling network. Nat Struct Mol Biol 2016; 23:324-32. [DOI: 10.1038/nsmb.3191] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/12/2016] [Indexed: 12/20/2022]
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29
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Miletta MC, Eblé A, Janner M, Parween S, Pandey AV, Flück CE, Mullis PE. IGHD II: A Novel GH-1 Gene Mutation (GH-L76P) Severely Affects GH Folding, Stability, and Secretion. J Clin Endocrinol Metab 2015; 100:E1575-83. [PMID: 26485222 DOI: 10.1210/jc.2015-3265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
CONTEXT The autosomal dominant form of GH deficiency (IGHD II) is characterized by markedly reduced GH secretion combined with low concentrations of IGF-1 leading to short stature. OBJECTIVE Structure-function analysis of a missense mutation in the GH-1 gene converting codon 76 from leucine (L) to proline (P) yielding a mutant GH-L76P peptide. DESIGN, SETTINGS, AND PATIENTS Heterozygosity for GH-L76P/wt-GH was identified in a nonconsanguineous Spanish family. The index patients, two siblings, a boy and a girl, were referred for assessment of their short stature (-3.2 and -3.8 SD). Their grandmother, father, and aunt were also carrying the same mutation and showed severe short stature; therefore, IGHD II was diagnosed. INTERVENTIONS AND RESULTS AtT-20 cells coexpressing both wt-GH and GH-L76P showed a reduced GH secretion (P < .001) after forskolin stimulation when compared with the cells expressing only wt-GH. In silico mutagenesis and molecular dynamics simulations presented alterations of correct folding and mutant stability compared with wt-GH. Therefore, further structural analysis of the GH-L76P mutant was performed using expressed and purified proteins in Escherichia coli by thermofluor assay and fast degradation proteolysis assay. Both assays revealed that the GH-L76P mutant is unstable and misfolded compared to wt-GH confirming the bioinformatic model prediction. CONCLUSIONS This is the first report of a family suffering from short stature caused by IGHD II, which severely affects intracellular GH folding and stability as well as secretion, highlighting the necessity of functional analysis of any GH variant for defining new mechanisms as a cause for IGHD II.
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Affiliation(s)
- Maria Consolata Miletta
- University Children's Hospital, Department of Pediatric Endocrinology, Diabetology and Metabolism, Inselspital, and Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Andrée Eblé
- University Children's Hospital, Department of Pediatric Endocrinology, Diabetology and Metabolism, Inselspital, and Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Marco Janner
- University Children's Hospital, Department of Pediatric Endocrinology, Diabetology and Metabolism, Inselspital, and Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Shaheena Parween
- University Children's Hospital, Department of Pediatric Endocrinology, Diabetology and Metabolism, Inselspital, and Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Amit V Pandey
- University Children's Hospital, Department of Pediatric Endocrinology, Diabetology and Metabolism, Inselspital, and Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Christa E Flück
- University Children's Hospital, Department of Pediatric Endocrinology, Diabetology and Metabolism, Inselspital, and Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
| | - Primus-E Mullis
- University Children's Hospital, Department of Pediatric Endocrinology, Diabetology and Metabolism, Inselspital, and Department of Clinical Research, University of Bern, 3010 Bern, Switzerland
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The Inhibition of Heat Shock Protein 90 Facilitates the Degradation of Poly-Alanine Expanded Poly (A) Binding Protein Nuclear 1 via the Carboxyl Terminus of Heat Shock Protein 70-Interacting Protein. PLoS One 2015; 10:e0138936. [PMID: 26414348 PMCID: PMC4587574 DOI: 10.1371/journal.pone.0138936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 09/06/2015] [Indexed: 01/24/2023] Open
Abstract
Background Since the identification of poly-alanine expanded poly(A) binding protein nuclear 1 (PABPN1) as the genetic cause of oculopharyngeal muscular dystrophy (OPMD), considerable progress has been made in our understanding of the pathogenesis of the disease. However, the molecular mechanisms that regulate the onset and progression of the disease remain unclear. Results In this study, we show that PABPN1 interacts with and is stabilized by heat shock protein 90 (HSP90). Treatment with the HSP90 inhibitor 17-AAG disrupted the interaction of mutant PABPN1 with HSP90 and reduced the formation of intranuclear inclusions (INIs). Furthermore, mutant PABPN1 was preferentially degraded in the presence of 17-AAG compared with wild-type PABPN1 in vitro and in vivo. The effect of 17-AAG was mediated through an increase in the interaction of PABPN1 with the carboxyl terminus of heat shock protein 70-interacting protein (CHIP). The overexpression of CHIP suppressed the aggregation of mutant PABPN1 in transfected cells. Conclusions Our results demonstrate that the HSP90 molecular chaperone system plays a crucial role in the selective elimination of abnormal PABPN1 proteins and also suggest a potential therapeutic application of the HSP90 inhibitor 17-AAG for the treatment of OPMD.
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Abstract
Hsp90 chaperones receive much attention due to their role in cancer and other pathological conditions, and a tremendous effort of many laboratories has contributed in the past decades to considerable progress in the understanding of their functions. Hsp90 chaperones exist as dimers and, with the help of cochaperones, promote the folding of numerous client proteins. Although the original view of these interactions suggested that these dimeric complexes were symmetrical, it is now clear that many features are asymmetrical. In this review we discuss several recent advances that highlight how asymmetric interactions with cochaperones as well as asymmetric posttranslational modifications provide mechanisms to regulate client interactions and the progression through Hsp90's chaperone cycle.
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Affiliation(s)
- Matthias P Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Laura Le Breton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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32
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A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif. Int J Genomics 2015; 2015:391293. [PMID: 26098630 PMCID: PMC4451777 DOI: 10.1155/2015/391293] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/12/2015] [Accepted: 04/21/2015] [Indexed: 01/03/2023] Open
Abstract
Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD) of heat shock 70 kDa protein (PDB: 1HJO) with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD) simulation. Human DNA binding domain of p53 motif (SCMGGMNR) retrieved from UniProt (UniProtKB: P04637) was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were -0.44 Kcal/mol and -9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.
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Burmann BM, Hiller S. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 86-87:41-64. [PMID: 25919198 DOI: 10.1016/j.pnmrs.2015.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/19/2015] [Accepted: 02/19/2015] [Indexed: 05/20/2023]
Abstract
The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.
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Affiliation(s)
- Björn M Burmann
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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34
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Hsp90 interaction with clients. Trends Biochem Sci 2015; 40:117-25. [PMID: 25579468 DOI: 10.1016/j.tibs.2014.12.002] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/02/2014] [Accepted: 12/04/2014] [Indexed: 01/02/2023]
Abstract
The conserved Hsp90 chaperone is an ATP-controlled machine that assists the folding and controls the stability of select proteins. Emerging data explain how Hsp90 achieves client specificity and its role in the cellular chaperone cascade. Interestingly, Hsp90 has an extended substrate binding interface that crosses domain boundaries, exhibiting specificity for proteins with hydrophobic residues spread over a large area regardless of whether they are disordered, partly folded, or even folded. This specificity principle ensures that clients preferentially bind to Hsp70 early on in the folding path, but downstream folding intermediates bind Hsp90. Discussed here, the emerging model is that the Hsp90 ATPase does not modulate client affinity but instead controls substrate influx from Hsp70.
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35
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Park SJ. NMR Study of larger proteins using isotope labeling. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2014. [DOI: 10.6564/jkmrs.2014.18.2.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Uversky VN. Wrecked regulation of intrinsically disordered proteins in diseases: pathogenicity of deregulated regulators. Front Mol Biosci 2014; 1:6. [PMID: 25988147 PMCID: PMC4428494 DOI: 10.3389/fmolb.2014.00006] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/06/2014] [Indexed: 12/14/2022] Open
Abstract
Biologically active proteins without stable tertiary structure are common in all known proteomes. Functions of these intrinsically disordered proteins (IDPs) are typically related to regulation, signaling, and control. Cellular levels of these important regulators are tightly regulated by a variety mechanisms ranging from firmly controlled expression to precisely targeted degradation. Functions of IDPs are controlled by binding to specific partners, alternative splicing, and posttranslational modifications among other means. In the norm, right amounts of precisely activated IDPs have to be present in right time at right places. Wrecked regulation brings havoc to the ordered world of disordered proteins, leading to protein misfolding, misidentification, and missignaling that give rise to numerous human diseases, such as cancer, cardiovascular disease, neurodegenerative diseases, and diabetes. Among factors inducing pathogenic transformations of IDPs are various cellular mechanisms, such as chromosomal translocations, damaged splicing, altered expression, frustrated posttranslational modifications, aberrant proteolytic degradation, and defective trafficking. This review presents some of the aspects of deregulated regulation of IDPs leading to human diseases.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida Tampa, FL, USA ; Biology Department, Faculty of Science, King Abdulaziz University Jeddah, Saudi Arabia ; Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences Moscow, Russia
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37
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Saio T, Guan X, Rossi P, Economou A, Kalodimos CG. Structural basis for protein antiaggregation activity of the trigger factor chaperone. Science 2014; 344:1250494. [PMID: 24812405 DOI: 10.1126/science.1250494] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular chaperones prevent aggregation and misfolding of proteins, but scarcity of structural data has impeded an understanding of the recognition and antiaggregation mechanisms. We report the solution structure, dynamics, and energetics of three trigger factor (TF) chaperone molecules in complex with alkaline phosphatase (PhoA) captured in the unfolded state. Our data show that TF uses multiple sites to bind to several regions of the PhoA substrate protein primarily through hydrophobic contacts. Nuclear magnetic resonance (NMR) relaxation experiments show that TF interacts with PhoA in a highly dynamic fashion, but as the number and length of the PhoA regions engaged by TF increase, a more stable complex gradually emerges. Multivalent binding keeps the substrate protein in an extended, unfolded conformation. The results show how molecular chaperones recognize unfolded polypeptides and, by acting as unfoldases and holdases, prevent the aggregation and premature (mis)folding of unfolded proteins.
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Affiliation(s)
- Tomohide Saio
- Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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38
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Callon M, Burmann BM, Hiller S. Structural Mapping of a Chaperone-Substrate Interaction Surface. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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39
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Mishra P, Bolon DNA. Designed Hsp90 heterodimers reveal an asymmetric ATPase-driven mechanism in vivo. Mol Cell 2014; 53:344-50. [PMID: 24462207 DOI: 10.1016/j.molcel.2013.12.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/19/2013] [Accepted: 12/24/2013] [Indexed: 02/02/2023]
Abstract
Hsp90 is a homodimeric ATPase that is essential in eukaryotes for the maturation of client proteins frequently involved in signal transduction, including many kinases and nuclear steroid hormone receptors. Competitive inhibitors of ATP binding to Hsp90 prevent client maturation and show promise as anticancer agents in clinical trials. However, the role of ATP binding and hydrolysis in each subunit of the Hsp90 dimer has been difficult to investigate because of an inability to assemble and study dimers of defined composition. We used protein engineering to generate functional Hsp90 subunits that preferentially assemble as heterodimers. We analyzed dimers wherein one subunit harbors a disruptive mutation and observed that ATP binding by both subunits is essential for function in yeast, whereas ATP hydrolysis is only required in one subunit. These findings demonstrate important functional contributions from both symmetric and asymmetric Hsp90 dimers and provide valuable reagents for future investigations of Hsp90 mechanism.
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Affiliation(s)
- Parul Mishra
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel N A Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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40
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Callon M, Burmann BM, Hiller S. Structural mapping of a chaperone-substrate interaction surface. Angew Chem Int Ed Engl 2014; 53:5069-72. [PMID: 24700611 DOI: 10.1002/anie.201310963] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/17/2014] [Indexed: 11/07/2022]
Abstract
NMR spectroscopy is used to detect site-specific intermolecular short-range contacts in a membrane-protein-chaperone complex. This is achieved by an "orthogonal" isotope-labeling scheme that permits the unambiguous detection of intermolecular NOEs between the well-folded chaperone and the unfolded substrate ensemble. The residues involved in these contacts are part of the chaperone-substrate contact interface. The approach is demonstrated for the 70 kDa bacterial Skp-tOmpA complex.
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Affiliation(s)
- Morgane Callon
- Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel (Switzerland)
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41
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van Ingen H, Bonvin AMJJ. Information-driven modeling of large macromolecular assemblies using NMR data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:103-114. [PMID: 24656083 DOI: 10.1016/j.jmr.2013.10.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/25/2013] [Indexed: 06/03/2023]
Abstract
Availability of high-resolution atomic structures is one of the prerequisites for a mechanistic understanding of biomolecular function. This atomic information can, however, be difficult to acquire for interesting systems such as high molecular weight and multi-subunit complexes. For these, low-resolution and/or sparse data from a variety of sources including NMR are often available to define the interaction between the subunits. To make best use of all the available information and shed light on these challenging systems, integrative computational tools are required that can judiciously combine and accurately translate the sparse experimental data into structural information. In this Perspective we discuss NMR techniques and data sources available for the modeling of large and multi-subunit complexes. Recent developments are illustrated by particularly challenging application examples taken from the literature. Within this context, we also position our data-driven docking approach, HADDOCK, which can integrate a variety of information sources to drive the modeling of biomolecular complexes. It is the synergy between experimentation and computational modeling that will provides us with detailed views on the machinery of life and lead to a mechanistic understanding of biomolecular function.
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Affiliation(s)
- Hugo van Ingen
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Faculty of Science - Chemistry, Padulaan 8, 3854 CH Utrecht, The Netherlands.
| | - Alexandre M J J Bonvin
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Faculty of Science - Chemistry, Padulaan 8, 3854 CH Utrecht, The Netherlands.
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42
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Modulation of the Hsp90 Chaperone Cycle by a Stringent Client Protein. Mol Cell 2014; 53:941-53. [DOI: 10.1016/j.molcel.2014.02.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 12/19/2013] [Accepted: 01/28/2014] [Indexed: 11/23/2022]
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43
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Blacklock K, Verkhivker GM. Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90–p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein. J Chem Inf Model 2013; 53:2962-78. [DOI: 10.1021/ci400434g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Kristin Blacklock
- School
of Computational Sciences and Crean School of Health and Life Sciences,
Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- School
of Computational Sciences and Crean School of Health and Life Sciences,
Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department
of Pharmacology, University of California San Diego, 9500 Gilman
Drive, La Jolla, California 92093, United States
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44
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Abstract
Hsp90 is a major molecular chaperone that is expressed abundantly and plays a pivotal role in assisting correct folding and functionality of its client proteins in cells. The Hsp90 client proteins include a wide variety of signal transducing molecules such as protein kinases and steroid hormone receptors. Cancer is a complex disease, but most types of human cancer share common hallmarks, including self-sufficiency in growth signals, insensitivity to growth-inhibitory mechanism, evasion of programmed cell death, limitless replicative potential, sustained angiogenesis, and tissue invasion and metastasis. A surprisingly large number of Hsp90-client proteins play crucial roles in establishing cancer cell hallmarks. We start the review by describing the structure and function of Hsp90 since conformational changes during the ATPase cycle of Hsp90 are closely related to its function. Many co-chaperones, including Hop, p23, Cdc37, Aha1, and PP5, work together with Hsp90 by modulating the chaperone machinery. Post-translational modifications of Hsp90 and its cochaperones are vital for their function. Many tumor-related Hsp90-client proteins, including signaling kinases, steroid hormone receptors, p53, and telomerase, are described. Hsp90 and its co-chaperones are required for the function of these tumor-promoting client proteins; therefore, inhibition of Hsp90 by specific inhibitors such as geldanamycin and its derivatives attenuates the tumor progression. Hsp90 inhibitors can be potential and effective cancer chemotherapeutic drugs with a unique profile and have been examined in clinical trials. We describe possible mechanisms why Hsp90 inhibitors show selectivity to cancer cells even though Hsp90 is essential also for normal cells. Finally, we discuss the "Hsp90-addiction" of cancer cells, and suggest a role for Hsp90 in tumor evolution.
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Affiliation(s)
- Yoshihiko Miyata
- Department of Cell & Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
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45
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Miyata Y, Nakamoto H, Neckers L. The therapeutic target Hsp90 and cancer hallmarks. Curr Pharm Des 2013; 19:347-65. [PMID: 22920906 DOI: 10.2174/138161213804143725] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 08/15/2012] [Indexed: 01/22/2023]
Abstract
Hsp90 is a major molecular chaperone that is expressed abundantly and plays a pivotal role in assisting correct folding and functionality of its client proteins in cells. The Hsp90 client proteins include a wide variety of signal transducing molecules such as protein kinases and steroid hormone receptors. Cancer is a complex disease, but most types of human cancer share common hallmarks, including self-sufficiency in growth signals, insensitivity to growth-inhibitory mechanism, evasion of programmed cell death, limitless replicative potential, sustained angiogenesis, and tissue invasion and metastasis. A surprisingly large number of Hsp90-client proteins play crucial roles in establishing cancer cell hallmarks. We start the review by describing the structure and function of Hsp90 since conformational changes during the ATPase cycle of Hsp90 are closely related to its function. Many co-chaperones, including Hop, p23, Cdc37, Aha1, and PP5, work together with Hsp90 by modulating the chaperone machinery. Post-translational modifications of Hsp90 and its cochaperones are vital for their function. Many tumor-related Hsp90-client proteins, including signaling kinases, steroid hormone receptors, p53, and telomerase, are described. Hsp90 and its co-chaperones are required for the function of these tumor-promoting client proteins; therefore, inhibition of Hsp90 by specific inhibitors such as geldanamycin and its derivatives attenuates the tumor progression. Hsp90 inhibitors can be potential and effective cancer chemotherapeutic drugs with a unique profile and have been examined in clinical trials. We describe possible mechanisms why Hsp90 inhibitors show selectivity to cancer cells even though Hsp90 is essential also for normal cells. Finally, we discuss the "Hsp90-addiction" of cancer cells, and suggest a role for Hsp90 in tumor evolution.
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Affiliation(s)
- Yoshihiko Miyata
- Department of Cell & Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
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46
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Nin DS, Ali AB, Okumura K, Asou N, Chen CS, Chng WJ, Khan M. Akt-induced phosphorylation of N-CoR at serine 1450 contributes to its misfolded conformational dependent loss (MCDL) in acute myeloid leukemia of the M5 subtype. PLoS One 2013; 8:e70891. [PMID: 23940660 PMCID: PMC3733915 DOI: 10.1371/journal.pone.0070891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 06/25/2013] [Indexed: 11/18/2022] Open
Abstract
The nuclear receptor co-repressor (N-CoR) is a key component of the generic co-repressor complex that plays an important role in the control of cellular growth and differentiation. As shown by us recently, the growth suppressive function of N-CoR largely relies on its capacity to repress Flt3, a key regulator of cellular gorwth during normal and malignant hematopoesis. We further demonstrated how de-repression of Flt3 due to the misfolded conformation dependent loss (MCDL) of N-CoR contributed to malignant growth in acute myeloid leukemia (AML). However, the molecular mechanism underlying the MCDL of N-CoR and its implication in AML pathogenesis is not fully understood. Here, we report that Akt-induced phosphorylation of N-CoR at the consensus Akt motif is crucial for its misfolding and subsequent loss in AML (AML-M5). N-CoR displayed significantly higher level of serine specific phosphorylation in almost all AML-M5 derived cells and was subjected to processing by AML-M5 specific aberrant protease activity. To identify the kinase linked to N-CoR phosphorylation, a library of activated kinases was screened with the extracts of AML cells; leading to the identification of Akt as the putative kinase linked to N-CoR phosphorylation. Consistent with this finding, a constitutively active Akt consistently phosphorylated N-CoR leading to its misfolding; while the therapeutic and genetic ablation of Akt largely abrogated the MCDL of N-CoR in AML-M5 cells. Site directed mutagenic analysis of N-CoR identified serine 1450 as the crucial residue whose phosphorylation by Akt was essential for the misfolding and loss of N-CoR protein. Moreover, Akt-induced phosphorylation of N-CoR contributed to the de-repression of Flt3, suggesting a cross talk between Akt signaling and N-CoR misfolding pathway in the pathogenesis of AML-M5. The N-CoR misfolding pathway could be the common downstream thread of pleiotropic Akt signaling activated by various oncogenic insults in some subtypes of leukemia and solid tumors.
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Affiliation(s)
- Dawn Sijin Nin
- Cancer Science Institute of Singapore, Yong Loo Lin School
of Medicine, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine,
National University of Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of
Medicine, National University of Singapore, Singapore
| | - Azhar Bin Ali
- Cancer Science Institute of Singapore, Yong Loo Lin School
of Medicine, National University of Singapore, Singapore
| | - Koichi Okumura
- Cancer Science Institute of Singapore, Yong Loo Lin School
of Medicine, National University of Singapore, Singapore
| | - Norio Asou
- Department of Haematology, Kumamoto University, Kumamoto, Japan
| | - Chien-Shing Chen
- Division of Hematologyand Oncology, School of Medicine, Loma Linda University, Loma Linda, California, United States of America
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, Yong Loo Lin School
of Medicine, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine,
National University of Singapore, Singapore
- Department of Haematology-Oncology, National Cancer
Institute of Singapore, National University Health System,
Singapore
| | - Matiullah Khan
- Cancer Science Institute of Singapore, Yong Loo Lin School
of Medicine, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine,
National University of Singapore, Singapore
- School of Medicine, Asian Institute of Medicine, Science and Technology (AIMST), Bedong, Malaysia
- * E-mail: ,
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47
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Mainz A, Religa TL, Sprangers R, Linser R, Kay LE, Reif B. NMR-Spektroskopie an löslichen Proteinkomplexen mit Molekulargewicht im Mega-Dalton-Bereich. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Mainz A, Religa TL, Sprangers R, Linser R, Kay LE, Reif B. NMR spectroscopy of soluble protein complexes at one mega-dalton and beyond. Angew Chem Int Ed Engl 2013; 52:8746-51. [PMID: 23873792 DOI: 10.1002/anie.201301215] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/30/2013] [Indexed: 01/07/2023]
Affiliation(s)
- Andi Mainz
- Munich Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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49
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Minde DP, Maurice MM, Rüdiger SGD. Determining biophysical protein stability in lysates by a fast proteolysis assay, FASTpp. PLoS One 2012; 7:e46147. [PMID: 23056252 PMCID: PMC3463568 DOI: 10.1371/journal.pone.0046147] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 08/27/2012] [Indexed: 11/26/2022] Open
Abstract
The biophysical stability is an important parameter for protein activity both in vivo and in vitro. Here we propose a method to analyse thermal melting of protein domains in lysates: Fast parallel proteolysis (FASTpp). Combining unfolding by a temperature gradient in a thermal cycler with simultaneous proteolytic cleavage of the unfolded state, we probed stability of single domains in lysates. We validated FASTpp on proteins from 10 kDa to 240 kDa and monitored stabilisation and coupled folding and binding upon interaction with small-molecule ligands. Within a total reaction time of approximately 1 min, we probed subtle stability differences of point mutations with high sensitivity and in agreement with data obtained by intrinsic protein fluorescence. We anticipate a wide range of applications of FASTpp in biomedicine and protein engineering as it requires only standard laboratory equipment.
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Affiliation(s)
- David P. Minde
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Madelon M. Maurice
- Department of Cell Biology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- * E-mail: (SGDR); (MMM)
| | - Stefan G. D. Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
- * E-mail: (SGDR); (MMM)
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50
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Abstract
Hsp90 is a highly abundant and ubiquitous molecular chaperone which plays an essential role in many cellular processes including cell cycle control, cell survival, hormone and other signalling pathways. It is important for the cell's response to stress and is a key player in maintaining cellular homeostasis. In the last ten years, it has become a major therapeutic target for cancer, and there has also been increasing interest in it as a therapeutic target in neurodegenerative disorders, and in the development of anti-virals and anti-protozoan infections. The focus of this review is the structural and mechanistic studies which have been performed in order to understand how this important chaperone acts on a wide variety of different proteins (its client proteins) and cellular processes. As with many of the other classes of molecular chaperone, Hsp90 has a critical ATPase activity, and ATP binding and hydrolysis known to modulate the conformational dynamics of the protein. It also uses a host of cochaperones which not only regulate the ATPase activity and conformational dynamics but which also mediate interactions with Hsp90 client proteins. The system is also regulated by post-translational modifications including phosphorylation and acetylation. This review discusses all these aspects of Hsp90 structure and function.
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