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Moayed F, Bezrukavnikov S, Naqvi MM, Groitl B, Cremers CM, Kramer G, Ghosh K, Jakob U, Tans SJ. The Anti-Aggregation Holdase Hsp33 Promotes the Formation of Folded Protein Structures. Biophys J 2019; 118:85-95. [PMID: 31757359 DOI: 10.1016/j.bpj.2019.10.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/04/2019] [Accepted: 10/15/2019] [Indexed: 11/26/2022] Open
Abstract
Holdase chaperones are known to be central to suppressing aggregation, but how they affect substrate conformations remains poorly understood. Here, we use optical tweezers to study how the holdase Hsp33 alters folding transitions within single maltose binding proteins and aggregation transitions between maltose binding protein substrates. Surprisingly, we find that Hsp33 not only suppresses aggregation but also guides the folding process. Two modes of action underlie these effects. First, Hsp33 binds unfolded chains, which suppresses aggregation between substrates and folding transitions within substrates. Second, Hsp33 binding promotes substrate states in which most of the chain is folded and modifies their structure, possibly by intercalating its intrinsically disordered regions. A statistical ensemble model shows how Hsp33 function results from the competition between these two contrasting effects. Our findings reveal an unexpectedly comprehensive functional repertoire for Hsp33 that may be more prevalent among holdases and dispels the notion of a strict chaperone hierarchy.
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Affiliation(s)
| | | | | | - Bastian Groitl
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Claudia M Cremers
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Guenter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kingshuk Ghosh
- Department of Physics and Astronomy, University of Denver, Denver, Colorado
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
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Rimon O, Suss O, Goldenberg M, Fassler R, Yogev O, Amartely H, Propper G, Friedler A, Reichmann D. A Role of Metastable Regions and Their Connectivity in the Inactivation of a Redox-Regulated Chaperone and Its Inter-Chaperone Crosstalk. Antioxid Redox Signal 2017; 27:1252-1267. [PMID: 28394178 DOI: 10.1089/ars.2016.6900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS A recently discovered group of conditionally disordered chaperones share a very unique feature; they need to lose structure to become active as chaperones. This activation mechanism makes these chaperones particularly suited to respond to protein-unfolding stress conditions, such as oxidative unfolding. However, the role of this disorder in stress-related activation, chaperone function, and the crosstalk with other chaperone systems is not yet clear. Here, we focus on one of the members of the conditionally disordered chaperones, a thiol-redox switch of the bacterial proteostasis system, Hsp33. RESULTS By modifying the Hsp33's sequence, we reveal that the metastable region has evolved to abolish redox-dependent chaperone activity, rather than enhance binding affinity for client proteins. The intrinsically disordered region of Hsp33 serves as an anchor for the reduced, inactive state of Hsp33, and it dramatically affects the crosstalk with the synergetic chaperone system, DnaK/J. Using mass spectrometry, we describe the role that the metastable region plays in determining client specificity during normal and oxidative stress conditions in the cell. Innovation and Conclusion: We uncover a new role of protein plasticity in Hsp33's inactivation, client specificity, crosstalk with the synergistic chaperone system DnaK/J, and oxidative stress-specific interactions in bacteria. Our results also suggest that Hsp33 might serve as a member of the house-keeping proteostasis machinery, tasked with maintaining a "healthy" proteome during normal conditions, and that this function does not depend on the metastable linker region. Antioxid. Redox Signal. 27, 1252-1267.
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Affiliation(s)
- Oded Rimon
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Ohad Suss
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Mor Goldenberg
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Rosi Fassler
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Ohad Yogev
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Hadar Amartely
- 2 Institute of Chemistry, The Hebrew University of Jerusalem , Safra Campus Givat Ram, Jerusalem, Israel
| | - Guy Propper
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
| | - Assaf Friedler
- 2 Institute of Chemistry, The Hebrew University of Jerusalem , Safra Campus Givat Ram, Jerusalem, Israel
| | - Dana Reichmann
- 1 Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram, The Hebrew University of Jerusalem , Jerusalem, Israel
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Trovato F, Tozzini V. Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules. Biophys J 2014; 107:2579-91. [PMID: 25468337 DOI: 10.1016/j.bpj.2014.09.043] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/09/2014] [Accepted: 09/24/2014] [Indexed: 01/07/2023] Open
Abstract
Recent experiments carried out in the dense cytoplasm of living cells have highlighted the importance of proteome composition and nonspecific intermolecular interactions in regulating macromolecule diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochemical properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromolecules was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid. With stochastic molecular-dynamics simulations of a virtual cytoplasm we are able to track the single biomolecule motion, sizing from 3 to 80 nm, on submillisecond-long trajectories. We demonstrate that the size dependence of diffusion coefficients, anomalous exponents, and the effective viscosity experienced by biomolecules in the cytoplasm is fine-tuned by the intermolecular interactions. Accounting only for excluded volume in these potentials gives a weaker size-dependence than that expected from experimental data. On the contrary, adding nonspecific attraction in the range of 1-10 thermal energy units produces a stronger variation of the transport properties at growing biopolymer sizes. Normal and anomalous diffusive regimes emerge straightforwardly from the combination of high macromolecular concentration, poly-dispersity, stochasticity, and weak nonspecific interactions. As a result, small biopolymers experience a viscous cytoplasm, while the motion of big ones is jammed because the entanglements produced by the network of interactions and the entropic effects caused by poly-dispersity are stronger.
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Affiliation(s)
- Fabio Trovato
- Istituto Nanoscienze del Cnr, NEST-Scuola Normale Superiore, Pisa, Italy; Center for Nanotechnology and Innovation@NEST-Istituto Italiano di Tecnologia, Piazza San Silvestro 12, 56127, Pisa, Italy.
| | - Valentina Tozzini
- Istituto Nanoscienze del Cnr, NEST-Scuola Normale Superiore, Pisa, Italy
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Geer MA, Fitzgerald MC. Energetics-based methods for protein folding and stability measurements. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:209-228. [PMID: 24896313 DOI: 10.1146/annurev-anchem-071213-020024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Over the past 15 years, a series of energetics-based techniques have been developed for the thermodynamic analysis of protein folding and stability. These techniques include Stability of Unpurified Proteins from Rates of amide H/D Exchange (SUPREX), pulse proteolysis, Stability of Proteins from Rates of Oxidation (SPROX), slow histidine H/D exchange, lysine amidination, and quantitative cysteine reactivity (QCR). The above techniques, which are the subject of this review, all utilize chemical or enzymatic modification reactions to probe the chemical denaturant- or temperature-induced equilibrium unfolding properties of proteins and protein-ligand complexes. They employ various mass spectrometry-, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)-, and optical spectroscopy-based readouts that are particularly advantageous for high-throughput and in some cases multiplexed analyses. This has created the opportunity to use protein folding and stability measurements in new applications such as in high-throughput screening projects to identify novel protein ligands and in mode-of-action studies to identify protein targets of a particular ligand.
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Affiliation(s)
- M Ariel Geer
- Department of Chemistry, Duke University, Durham, North Carolina 27708-0346;
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Cammarata M, Lin KY, Pruet J, Liu HW, Brodbelt J. Probing the Unfolding of Myoglobin and Domain C of PARP-1 with Covalent Labeling and Top-Down Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2014; 86:2534-42. [DOI: 10.1021/ac4036235] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Michael Cammarata
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Ke-Yi Lin
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Jeff Pruet
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Hung-wen Liu
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
| | - Jennifer Brodbelt
- Department of Chemistry, University of Texas at Austin, 1 University
Station A5300, Austin, Texas 78212, United States
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Reichmann D, Xu Y, Cremers CM, Ilbert M, Mittelman R, Fitzgerald MC, Jakob U. Order out of disorder: working cycle of an intrinsically unfolded chaperone. Cell 2012; 148:947-57. [PMID: 22385960 DOI: 10.1016/j.cell.2012.01.045] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 10/23/2011] [Accepted: 01/31/2012] [Indexed: 11/15/2022]
Abstract
The redox-regulated chaperone Hsp33 protects organisms against oxidative stress that leads to protein unfolding. Activation of Hsp33 is triggered by the oxidative unfolding of its own redox-sensor domain, making Hsp33 a member of a recently discovered class of chaperones that require partial unfolding for full chaperone activity. Here we address the long-standing question of how chaperones recognize client proteins. We show that Hsp33 uses its own intrinsically disordered regions to discriminate between unfolded and partially structured folding intermediates. Binding to secondary structure elements in client proteins stabilizes Hsp33's intrinsically disordered regions, and this stabilization appears to mediate Hsp33's high affinity for structured folding intermediates. Return to nonstress conditions reduces Hsp33's disulfide bonds, which then significantly destabilizes the bound client proteins and in doing so converts them into less-structured, folding-competent client proteins of ATP-dependent foldases. We propose a model in which energy-independent chaperones use internal order-to-disorder transitions to control substrate binding and release.
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Affiliation(s)
- Dana Reichmann
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Liu J, Konermann L. Protein-protein binding affinities in solution determined by electrospray mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:408-17. [PMID: 21472560 DOI: 10.1007/s13361-010-0052-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 12/10/2010] [Accepted: 12/10/2010] [Indexed: 05/23/2023]
Abstract
Electrospray ionization (ESI) allows the transfer of multi-protein complexes into the gas phase, thereby providing a simple approach for monitoring the stoichiometry of these noncovalent assemblies by mass spectrometry (MS). It remains unclear, however, whether the measured ion abundance ratios of free and bound species are suitable for determining solution-phase binding affinities (K(d) values). Many types of mass spectrometers employ rf-only quadrupoles as ion guides. This work demonstrates that the settings used for these devices are a key factor for ensuring uniform transmission behavior, which is a prerequisite for meaningful affinity measurements. Using bovine β-lactoglobulin and hemoglobin as model systems, it is demonstrated that under carefully adjusted conditions the "direct" ESI-MS approach is capable of providing K(d) values that are in good agreement with previously published solution-phase data. Of the several ion sources tested, a regular ESI emitter operated with pressure-driven flow at 1 μL min(-1) provided the most favorable results. Potential problems in these experiments include conformationally-induced differences in ionization efficiencies, inadvertent collision-induced dissociation, and ESI-induced clustering artifacts. A number of simple tests can be conducted to assess whether or not these factors are prevalent under the conditions used. In addition, the fidelity of the method can be scrutinized by performing measurements over a wide concentration range. Overall, this work supports the viability of the direct ESI-MS approach for determining binding affinities of protein-protein complexes in solution.
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Affiliation(s)
- Jiangjiang Liu
- Department of Chemistry, The University of Western Ontario, N6A 5B7 London, Ontario, Canada
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