1
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Devlin T, Fleming KG. A team of chaperones play to win in the bacterial periplasm. Trends Biochem Sci 2024; 49:667-680. [PMID: 38677921 DOI: 10.1016/j.tibs.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/29/2024]
Abstract
The survival and virulence of Gram-negative bacteria require proper biogenesis and maintenance of the outer membrane (OM), which is densely packed with β-barrel OM proteins (OMPs). Before reaching the OM, precursor unfolded OMPs (uOMPs) must cross the whole cell envelope. A network of periplasmic chaperones and proteases maintains unfolded but folding-competent conformations of these membrane proteins in the aqueous periplasm while simultaneously preventing off-pathway aggregation. These periplasmic proteins utilize different strategies, including conformational heterogeneity, oligomerization, multivalency, and kinetic partitioning, to perform and regulate their functions. Redundant and unique characteristics of the individual periplasmic players synergize to create a protein quality control team capable responding to changing environmental stresses.
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Affiliation(s)
- Taylor Devlin
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
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2
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Wang S, Sass MI, Kwon Y, Ludlam WG, Smith TM, Carter EJ, Gladden NE, Riggi M, Iwasa JH, Willardson BM, Shen PS. Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller. Mol Cell 2023; 83:3852-3868.e6. [PMID: 37852256 PMCID: PMC10841713 DOI: 10.1016/j.molcel.2023.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/20/2023]
Abstract
The Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β-propeller domains. Here, we determine the structures of human CCT in complex with its accessory co-chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ5, a component of Regulator of G protein Signaling (RGS) complexes. Cryoelectron microscopy (cryo-EM) and image processing reveal an ensemble of distinct snapshots that represent the folding trajectory of Gβ5 from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ5 folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT orchestrates folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
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Affiliation(s)
- Shuxin Wang
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA
| | - Mikaila I Sass
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Yujin Kwon
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - W Grant Ludlam
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Theresa M Smith
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Ethan J Carter
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Nathan E Gladden
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA
| | - Margot Riggi
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA
| | - Janet H Iwasa
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA
| | - Barry M Willardson
- Department of Chemistry and Biochemistry, Brigham Young University, C100 BNSN, Provo, UT 84602, USA.
| | - Peter S Shen
- Department of Biochemistry, School of Medicine, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA.
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3
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Wang S, Sass MI, Kwon Y, Ludlam WG, Smith TM, Carter EJ, Gladden NE, Riggi M, Iwasa JH, Willardson BM, Shen PS. Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539424. [PMID: 37205387 PMCID: PMC10187262 DOI: 10.1101/2023.05.04.539424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The cytosolic Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β-propeller domains. Here, we determined structures of CCT in complex with its accessory co-chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ5, a component of Regulator of G protein Signaling (RGS) complexes. Cryo-EM and image processing revealed an ensemble of distinct snapshots that represent the folding trajectory of Gβ5 from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ5 folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β-sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT directs folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
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Affiliation(s)
- Shuxin Wang
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
| | - Mikaila I. Sass
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Yujin Kwon
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - W. Grant Ludlam
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Theresa M. Smith
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Ethan J. Carter
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Nathan E. Gladden
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Margot Riggi
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
| | - Janet H. Iwasa
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
| | - Barry M. Willardson
- Department of Chemistry and Biochemistry, C100 BNSN, Brigham Young University, Provo, UT, 84602, USA
| | - Peter S. Shen
- Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA
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4
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Doukov T, Herschlag D, Yabukarski F. Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures. Acta Crystallogr D Struct Biol 2023; 79:212-223. [PMID: 36876431 PMCID: PMC9986799 DOI: 10.1107/s205979832300089x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
X-ray crystallography has been invaluable in delivering structural information about proteins. Previously, an approach has been developed that allows high-quality X-ray diffraction data to be obtained from protein crystals at and above room temperature. Here, this previous work is built on and extended by showing that high-quality anomalous signal can be obtained from single protein crystals using diffraction data collected at 220 K up to physiological temperatures. The anomalous signal can be used to directly determine the structure of a protein, i.e. to phase the data, as is routinely performed under cryoconditions. This ability is demonstrated by obtaining diffraction data from model lysozyme, thaumatin and proteinase K crystals, the anomalous signal from which allowed their structures to be solved experimentally at 7.1 keV X-ray energy and at room temperature with relatively low data redundancy. It is also demonstrated that the anomalous signal from diffraction data obtained at 310 K (37°C) can be used to solve the structure of proteinase K and to identify ordered ions. The method provides useful anomalous signal at temperatures down to 220 K, resulting in an extended crystal lifetime and increased data redundancy. Finally, we show that useful anomalous signal can be obtained at room temperature using X-rays of 12 keV energy as typically used for routine data collection, allowing this type of experiment to be carried out at widely accessible synchrotron beamline energies and enabling the simultaneous extraction of high-resolution data and anomalous signal. With the recent emphasis on obtaining conformational ensemble information for proteins, the high resolution of the data allows such ensembles to be built, while the anomalous signal allows the structure to be experimentally solved, ions to be identified, and water molecules and ions to be differentiated. Because bound metal-, phosphorus- and sulfur-containing ions all have anomalous signal, obtaining anomalous signal across temperatures and up to physiological temperatures will provide a more complete description of protein conformational ensembles, function and energetics.
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Affiliation(s)
- Tzanko Doukov
- SMB, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Filip Yabukarski
- Deparment of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Bristol-Myers Squibb, San Diego, CA 92121, USA
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5
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Bardwell JCA. A glimpse into TriC's magic chamber of secrets. Cell 2022; 185:4679-4681. [PMID: 36493750 DOI: 10.1016/j.cell.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
Abstract
Chaperones are important for protein folding, but visualizing this process has proven to be exceptionally difficult. In this issue of Cell, Frydman and colleagues have succeeded in watching tubulin being folded by its chaperonin TRiC at near-atomic resolution.
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Affiliation(s)
- James C A Bardwell
- Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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6
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He W, Li X, Xue H, Yang Y, Mencius J, Bai L, Zhang J, Xu J, Wu B, Xue Y, Quan S. Insights into the client protein release mechanism of the ATP-independent chaperone Spy. Nat Commun 2022; 13:2818. [PMID: 35595811 PMCID: PMC9122904 DOI: 10.1038/s41467-022-30499-x] [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: 11/02/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Molecular chaperones play a central role in regulating protein homeostasis, and their active forms often contain intrinsically disordered regions (IDRs). However, how IDRs impact chaperone action remains poorly understood. Here, we discover that the disordered N terminus of the prototype chaperone Spy facilitates client release. With NMR spectroscopy and molecular dynamics simulations, we find that the N terminus can bind transiently to the client-binding cavity of Spy primarily through electrostatic interactions mediated by the N-terminal D26 residue. This intramolecular interaction results in a dynamic competition of the N terminus with the client for binding to Spy, which promotes client discharge. Our results reveal the mechanism by which Spy releases clients independent of energy input, thus enriching the current knowledge on how ATP-independent chaperones release their clients and highlighting the importance of synergy between IDRs and structural domains in regulating protein function.
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Affiliation(s)
- Wei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Xinming Li
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yuanyuan Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Ling Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jiayin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jianhe Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Yi Xue
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China.
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China. .,Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
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7
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Abstract
The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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8
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Structural and Kinetic Views of Molecular Chaperones in Multidomain Protein Folding. Int J Mol Sci 2022; 23:ijms23052485. [PMID: 35269628 PMCID: PMC8910466 DOI: 10.3390/ijms23052485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/10/2022] Open
Abstract
Despite recent developments in protein structure prediction, the process of the structure formation, folding, remains poorly understood. Notably, folding of multidomain proteins, which involves multiple steps of segmental folding, is one of the biggest questions in protein science. Multidomain protein folding often requires the assistance of molecular chaperones. Molecular chaperones promote or delay the folding of the client protein, but the detailed mechanisms are still unclear. This review summarizes the findings of biophysical and structural studies on the mechanism of multidomain protein folding mediated by molecular chaperones and explains how molecular chaperones recognize the client proteins and alter their folding properties. Furthermore, we introduce several recent studies that describe the concept of kinetics-activity relationships to explain the mechanism of functional diversity of molecular chaperones.
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9
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Wang Y, Yang M, Qin J, Wa W. Interactions between puerarin/daidzein and micellar casein. J Food Biochem 2022; 46:e14048. [PMID: 34981538 DOI: 10.1111/jfbc.14048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 11/27/2022]
Abstract
Puerarin (PUE) and daidzein (DAI) are polyphenols with extensive biological activities. In the present study, the interactions between PUE/DAI and micellar casein (MC) were investigated, and the physicochemical properties of their complexes were analyzed. The results of fluorescence spectrum analysis and molecular docking revealed that the main interactions between DAI and MC were hydrophobic forces, while that between PUE and MC was hydrogen bonding. The FTIR and XRD analyses confirmed the formation of complexes between MC and PUE/DAI. After binding to PUE/DAI, the size of MC increased. The weight loss rate of MC decreased after complexing with PUE/DAI, but its morphology was not extensively modified. The DPPH radical scavenging capacities of PUE-MC and DAI-MC complexes were higher than those of free PUE/DAI in both water and ethanol. In vitro release experiments showed that the release rate of PUE/DAI was inhibited by MC under simulated intestinal conditions. PRACTICAL APPLICATIONS: The low water solubility and poor bioavailability of PUE and DAI limit their application. Micellar casein has high affinity for PUE and DAI. After encapsulated by micellar casein, the release rates of PUE and DAI were prolonged during simulated intestinal digestion. The results would provide useful information for improving the solubility and bioavailability of PUE and DAI, and broadening the use of them in the food and pharmaceutical industry.
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Affiliation(s)
- Yucheng Wang
- College of Science, Gansu Agricultural University, Lanzhou, China
| | - Min Yang
- College of Science, Gansu Agricultural University, Lanzhou, China
| | - Juanjuan Qin
- College of Science, Gansu Agricultural University, Lanzhou, China
| | - Wenqiang Wa
- College of Science, Gansu Agricultural University, Lanzhou, China
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10
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Sučec I, Bersch B, Schanda P. How do Chaperones Bind (Partly) Unfolded Client Proteins? Front Mol Biosci 2021; 8:762005. [PMID: 34760928 PMCID: PMC8573040 DOI: 10.3389/fmolb.2021.762005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/06/2021] [Indexed: 01/03/2023] Open
Abstract
Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.
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Affiliation(s)
- Iva Sučec
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Beate Bersch
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France
| | - Paul Schanda
- CEA, CNRS, Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, Grenoble, France.,Institute of Science and Technology Austria, Klosterneuburg, Austria
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11
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Arhar T, Shkedi A, Nadel CM, Gestwicki JE. The interactions of molecular chaperones with client proteins: why are they so weak? J Biol Chem 2021; 297:101282. [PMID: 34624315 PMCID: PMC8567204 DOI: 10.1016/j.jbc.2021.101282] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/30/2022] Open
Abstract
The major classes of molecular chaperones have highly variable sequences, sizes, and shapes, yet they all bind to unfolded proteins, limit their aggregation, and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK, and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and intermolecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.
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Affiliation(s)
- Taylor Arhar
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Arielle Shkedi
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Cory M Nadel
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry and the Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco California, USA.
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12
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Abstract
Gram-negative bacteria have a multicomponent and constitutively active periplasmic chaperone system to ensure the quality control of their outer membrane proteins (OMPs). Recently, OMPs have been identified as a new class of vulnerable targets for antibiotic development, and therefore a comprehensive understanding of OMP quality control network components will be critical for discovering antimicrobials. Here, we demonstrate that the periplasmic chaperone Spy protects certain OMPs against protein-unfolding stress and can functionally compensate for other periplasmic chaperones, namely Skp and FkpA, in the Escherichia coli K-12 MG1655 strain. After extensive in vivo genetic experiments for functional characterization of Spy, we use nuclear magnetic resonance and circular dichroism spectroscopy to elucidate the mechanism by which Spy binds and folds two different OMPs. Along with holding OMP substrates in a dynamic conformational ensemble, Spy binding enables OmpX to form a partially folded β-strand secondary structure. The bound OMP experiences temperature-dependent conformational exchange within the chaperone, pointing to a multitude of local dynamics. Our findings thus deepen the understanding of functional compensation among periplasmic chaperones during OMP biogenesis and will promote the development of innovative antimicrobials against pathogenic Gram-negative bacteria.
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13
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Macošek J, Mas G, Hiller S. Redefining Molecular Chaperones as Chaotropes. Front Mol Biosci 2021; 8:683132. [PMID: 34195228 PMCID: PMC8237284 DOI: 10.3389/fmolb.2021.683132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023] Open
Abstract
Molecular chaperones are the key instruments of bacterial protein homeostasis. Chaperones not only facilitate folding of client proteins, but also transport them, prevent their aggregation, dissolve aggregates and resolve misfolded states. Despite this seemingly large variety, single chaperones can perform several of these functions even on multiple different clients, thus suggesting a single biophysical mechanism underlying. Numerous recently elucidated structures of bacterial chaperone–client complexes show that dynamic interactions between chaperones and their client proteins stabilize conformationally flexible non-native client states, which results in client protein denaturation. Based on these findings, we propose chaotropicity as a suitable biophysical concept to rationalize the generic activity of chaperones. We discuss the consequences of applying this concept in the context of ATP-dependent and -independent chaperones and their functional regulation.
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14
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Kim H, Wu K, Lee C. Stress-Responsive Periplasmic Chaperones in Bacteria. Front Mol Biosci 2021; 8:678697. [PMID: 34046432 PMCID: PMC8144458 DOI: 10.3389/fmolb.2021.678697] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/19/2021] [Indexed: 01/14/2023] Open
Abstract
Periplasmic proteins are involved in a wide range of bacterial functions, including motility, biofilm formation, sensing environmental cues, and small-molecule transport. In addition, a wide range of outer membrane proteins and proteins that are secreted into the media must travel through the periplasm to reach their final destinations. Since the porous outer membrane allows for the free diffusion of small molecules, periplasmic proteins and those that travel through this compartment are more vulnerable to external environmental changes, including those that result in protein unfolding, than cytoplasmic proteins are. To enable bacterial survival under various stress conditions, a robust protein quality control system is required in the periplasm. In this review, we focus on several periplasmic chaperones that are stress responsive, including Spy, which responds to envelope-stress, DegP, which responds to temperature to modulate chaperone/protease activity, HdeA and HdeB, which respond to acid stress, and UgpB, which functions as a bile-responsive chaperone.
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Affiliation(s)
- Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, South Korea
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
| | - Kevin Wu
- Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
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15
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Mitra R, Gadkari VV, Meinen BA, van Mierlo CPM, Ruotolo BT, Bardwell JCA. Mechanism of the small ATP-independent chaperone Spy is substrate specific. Nat Commun 2021; 12:851. [PMID: 33558474 PMCID: PMC7870927 DOI: 10.1038/s41467-021-21120-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/08/2021] [Indexed: 11/17/2022] Open
Abstract
ATP-independent chaperones are usually considered to be holdases that rapidly bind to non-native states of substrate proteins and prevent their aggregation. These chaperones are thought to release their substrate proteins prior to their folding. Spy is an ATP-independent chaperone that acts as an aggregation inhibiting holdase but does so by allowing its substrate proteins to fold while they remain continuously chaperone bound, thus acting as a foldase as well. The attributes that allow such dual chaperoning behavior are unclear. Here, we used the topologically complex protein apoflavodoxin to show that the outcome of Spy's action is substrate specific and depends on its relative affinity for different folding states. Tighter binding of Spy to partially unfolded states of apoflavodoxin limits the possibility of folding while bound, converting Spy to a holdase chaperone. Our results highlight the central role of the substrate in determining the mechanism of chaperone action.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ben A Meinen
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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16
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Gong S, Yang C, Zhang J, Yu Y, Gu X, Li W, Wang Z. Study on the interaction mechanism of purple potato anthocyanins with casein and whey protein. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106223] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Begeman A, Son A, Litberg TJ, Wroblewski TH, Gehring T, Huizar Cabral V, Bourne J, Xuan Z, Horowitz S. G-Quadruplexes act as sequence-dependent protein chaperones. EMBO Rep 2020; 21:e49735. [PMID: 32945124 PMCID: PMC7534610 DOI: 10.15252/embr.201949735] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 01/06/2023] Open
Abstract
Maintaining proteome health is important for cell survival. Nucleic acids possess the ability to prevent protein aggregation more efficiently than traditional chaperone proteins. In this study, we explore the sequence specificity of the chaperone activity of nucleic acids. Evaluating over 500 nucleic acid sequences' effects on protein aggregation, we show that the holdase chaperone effect of nucleic acids is sequence-dependent. G-Quadruplexes prevent protein aggregation via quadruplex:protein oligomerization. They also increase the folded protein level of a biosensor in E. coli. These observations contextualize recent reports of quadruplexes playing important roles in aggregation-related diseases, such as fragile X and amyotrophic lateral sclerosis (ALS), and provide evidence that nucleic acids have the ability to modulate the folding environment of E. coli.
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Affiliation(s)
- Adam Begeman
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Theodore J Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Tadeusz H Wroblewski
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Thane Gehring
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Veronica Huizar Cabral
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Jennifer Bourne
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
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18
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Hu Y, Li C, He L, Jin C, Liu M. Mechanisms of Chaperones as Active Assistant/Protector for Proteins: Insights from NMR Studies. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.201900441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Lichun He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, Peking University Beijing 100871 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for OptoelectronicsNational Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences (CAS) Wuhan Hubei 430071 China
- University of Chinese Academy of Sciences Beijing 100049 China
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19
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Rocchio S, Duman R, El Omari K, Mykhaylyk V, Orr C, Yan Z, Salmon L, Wagner A, Bardwell JCA, Horowitz S. Identifying dynamic, partially occupied residues using anomalous scattering. Acta Crystallogr D Struct Biol 2019; 75:1084-1095. [PMID: 31793902 PMCID: PMC6889914 DOI: 10.1107/s2059798319014475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/22/2019] [Indexed: 11/24/2022] Open
Abstract
Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as ∼12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.
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Affiliation(s)
- Serena Rocchio
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biochemical Sciences ‘A. Rossi Fanelli’, Sapienza University of Roma, 00185 Rome, Italy
| | - Ramona Duman
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Kamel El Omari
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Vitaliy Mykhaylyk
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Christian Orr
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - Zhen Yan
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 69100 Villeurbanne, France
| | - Armin Wagner
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
| | - James C. A. Bardwell
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Horowitz
- Department of Chemistry and Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, Denver, CO 80208, USA
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20
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Makepeace KAT, Brodie NI, Popov KI, Gudavicius G, Nelson CJ, Petrotchenko EV, Dokholyan NV, Borchers CH. Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations. J Proteomics 2019; 211:103544. [PMID: 31683063 DOI: 10.1016/j.jprot.2019.103544] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/07/2019] [Accepted: 10/07/2019] [Indexed: 01/19/2023]
Abstract
For disordered proteins, ligand binding can be a critical event that changes their structural dynamics. The ability to characterize such changes would facilitate the development of drugs designed to stabilize disordered proteins, whose mis-folding is important for a number of pathologies, including neurodegenerative diseases such as Parkinson's and Alzheimer's diseases. In this study, we used hydrogen/deuterium exchange, differential crosslinking, differential surface modification, and molecular dynamics (MD) simulations to characterize the structural changes in disordered proteins that result from ligand binding. We show here that both an ATP-independent protein chaperone, Spy L32P, and the FK506 binding domain of a prolyl isomerase, FKBP-25 F145A/I223P, are disordered, yet exhibit structures that are distinct from chemically denatured unfolded states in solution, and that they undergo transitions to a more structured state upon ligand binding. These systems may serve as models for the characterization of ligand-induced disorder-to-order transitions in proteins using structural proteomics approaches. SIGNIFICANCE: In this study, we used hydrogen/deuterium exchange, differential crosslinking, differential surface modification, and molecular-dynamics simulations to characterize the structural changes in disordered proteins that result from ligand binding. The protein-ligand systems studied here (the ATP-independent protein chaperone, Spy L32P, and the FK506 binding domain of a prolyl isomerase, FKBP-25 F145A/I223P) may serve as models for understanding ligand-induced disorder-to-order transitions in proteins. Additionally, the structural proteomic techniques demonstrated here are shown to be effective tools for the characterization of disorder-to-order transitions and can be used to facilitate study of other systems in which this class of structural transition can be used for modulating major pathological features of disease, such as the abnormal protein aggregation that occurs with Parkinson's disease and Alzheimer's disease.
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Affiliation(s)
- Karl A T Makepeace
- University of Victoria -Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Nicholas I Brodie
- University of Victoria -Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Konstantin I Popov
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Geoff Gudavicius
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building, Room 270d, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada
| | - Christopher J Nelson
- Department of Biochemistry and Microbiology, University of Victoria, Petch Building, Room 270d, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada
| | - Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, PA 17033, USA
| | - Christoph H Borchers
- University of Victoria -Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada; Department of Biochemistry and Microbiology, University of Victoria, Petch Building, Room 270d, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada.
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21
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Wu K, Stull F, Lee C, Bardwell JCA. Protein folding while chaperone bound is dependent on weak interactions. Nat Commun 2019; 10:4833. [PMID: 31645566 PMCID: PMC6811625 DOI: 10.1038/s41467-019-12774-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/23/2019] [Indexed: 12/31/2022] Open
Abstract
It is generally assumed that protein clients fold following their release from chaperones instead of folding while remaining chaperone-bound, in part because binding is assumed to constrain the mobility of bound clients. Previously, we made the surprising observation that the ATP-independent chaperone Spy allows its client protein Im7 to fold into the native state while continuously bound to the chaperone. Spy apparently permits sufficient client mobility to allow folding to occur while chaperone bound. Here, we show that strengthening the interaction between Spy and a recently discovered client SH3 strongly inhibits the ability of the client to fold while chaperone bound. The more tightly Spy binds to its client, the more it slows the folding rate of the bound client. Efficient chaperone-mediated folding while bound appears to represent an evolutionary balance between interactions of sufficient strength to mediate folding and interactions that are too tight, which tend to inhibit folding. Spy is an ATP independent chaperone that allows folding of its client protein Im7 while continuously bound to Spy. Here the authors employ kinetics measurements to study the folding of another Spy client protein SH3 and find that Spy’s ability to allow a client to fold while bound is inversely related to how strongly it interacts with that client.
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Affiliation(s)
- Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Frederick Stull
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Changhan Lee
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109-1085, USA. .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA.
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22
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Shen K, Gamerdinger M, Chan R, Gense K, Martin EM, Sachs N, Knight PD, Schlömer R, Calabrese AN, Stewart KL, Leiendecker L, Baghel A, Radford SE, Frydman J, Deuerling E. Dual Role of Ribosome-Binding Domain of NAC as a Potent Suppressor of Protein Aggregation and Aging-Related Proteinopathies. Mol Cell 2019; 74:729-741.e7. [PMID: 30982745 PMCID: PMC6527867 DOI: 10.1016/j.molcel.2019.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/22/2019] [Accepted: 03/08/2019] [Indexed: 01/11/2023]
Abstract
The nascent polypeptide-associated complex (NAC) is a conserved ribosome-associated protein biogenesis factor. Whether NAC exerts chaperone activity and whether this function is restricted to de novo protein synthesis is unknown. Here, we demonstrate that NAC directly exerts chaperone activity toward structurally diverse model substrates including polyglutamine (PolyQ) proteins, firefly luciferase, and Aβ40. Strikingly, we identified the positively charged ribosome-binding domain in the N terminus of the βNAC subunit (N-βNAC) as a major chaperone entity of NAC. N-βNAC by itself suppressed aggregation of PolyQ-expanded proteins in vitro, and the positive charge of this domain was critical for this activity. Moreover, we found that NAC also exerts a ribosome-independent chaperone function in vivo. Consistently, we found that a substantial fraction of NAC is non-ribosomal bound in higher eukaryotes. In sum, NAC is a potent suppressor of aggregation and proteotoxicity of mutant PolyQ-expanded proteins associated with human diseases like Huntington's disease and spinocerebellar ataxias.
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Affiliation(s)
- Koning Shen
- Department of Biology, Stanford University, Stanford, CA 94305-5430, USA
| | | | - Rebecca Chan
- Department of Biology, Stanford University, Stanford, CA 94305-5430, USA
| | - Karina Gense
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Esther M Martin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nadine Sachs
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Patrick D Knight
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Renate Schlömer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Katie L Stewart
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Lukas Leiendecker
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ankit Baghel
- Department of Biology, Stanford University, Stanford, CA 94305-5430, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305-5430, USA.
| | - Elke Deuerling
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
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23
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Abstract
The biogenesis of periplasmic and outer membrane proteins (OMPs) in Escherichia coli is assisted by a variety of processes that help with their folding and transport to their final destination in the cellular envelope. Chaperones are macromolecules, usually proteins, that facilitate the folding of proteins or prevent their aggregation without becoming part of the protein's final structure. Because chaperones often bind to folding intermediates, they often (but not always) act to slow protein folding. Protein folding catalysts, on the other hand, act to accelerate specific steps in the protein folding pathway, including disulfide bond formation and peptidyl prolyl isomerization. This review is primarily concerned with E. coli and Salmonella periplasmic and cellular envelope chaperones; it also discusses periplasmic proline isomerization.
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24
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Competing protein-protein interactions regulate binding of Hsp27 to its client protein tau. Nat Commun 2018; 9:4563. [PMID: 30385828 PMCID: PMC6212398 DOI: 10.1038/s41467-018-07012-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/08/2018] [Indexed: 01/17/2023] Open
Abstract
Small heat shock proteins (sHSPs) are a class of oligomeric molecular chaperones that limit protein aggregation. However, it is often not clear where sHSPs bind on their client proteins or how these protein-protein interactions (PPIs) are regulated. Here, we map the PPIs between human Hsp27 and the microtubule-associated protein tau (MAPT/tau). We find that Hsp27 selectively recognizes two aggregation-prone regions of tau, using the conserved β4-β8 cleft of its alpha-crystallin domain. The β4-β8 region is also the site of Hsp27–Hsp27 interactions, suggesting that competitive PPIs may be an important regulatory paradigm. Indeed, we find that each of the individual PPIs are relatively weak and that competition for shared sites seems to control both client binding and Hsp27 oligomerization. These findings highlight the importance of multiple, competitive PPIs in the function of Hsp27 and suggest that the β4-β8 groove acts as a tunable sensor for clients. Small heat shock proteins (sHSPs) limit the aggregation of proteins, such as tau. Here the authors show that Hsp27 recognizes two aggregation-prone regions of tau and that this interaction competes with Hsp27 oligomerization.
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27
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Cheng C, Wu J, Liu G, Shi S, Chen T. Effects of Non-native Interactions on Frustrated Proteins Folding under Confinement. J Phys Chem B 2018; 122:7654-7667. [DOI: 10.1021/acs.jpcb.8b04147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Chenqian Cheng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Jing Wu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Gaoyuan Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Suqing Shi
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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28
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Lee C, Kim H, Bardwell JCA. Electrostatic interactions are important for chaperone-client interaction in vivo. MICROBIOLOGY-SGM 2018; 164:992-997. [PMID: 29870331 DOI: 10.1099/mic.0.000676] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
It has long been thought that chaperones are primarily attracted to their clients through the hydrophobic effect. However, in in vitro studies on the interaction between the chaperone Spy and its substrate Im7, we recently showed that long-range electrostatic interactions also play a key role. Spy functions in the periplasm of Gram-negative bacteria, which is surrounded by a permeable outer membrane. The ionic conditions in the periplasm therefore closely mimic those in the media, which allowed us to vary the ionic strength of the in vivo folding environment. Using folding biosensors that link protein folding to antibiotic resistance, we were able to monitor Spy chaperone activity in Escherichia coli in vivo as a function of media salt concentration. The chaperone activity of Spy decreased when the ionic strength of the media was increased, strongly suggesting that electrostatic forces play a vital role in the action of Spy in vivo.
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Affiliation(s)
- Changhan Lee
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Hyunhee Kim
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
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29
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Chi H, Xu B, Liu Z, Wei J, Li S, Ren H, Xu Y, Lu X, Wang X, Wang X, Huang F. Combined thermodynamic and kinetic analysis of GroEL interacting with CXCR4 transmembrane peptides. Biochim Biophys Acta Gen Subj 2018; 1862:1576-1583. [PMID: 29627450 DOI: 10.1016/j.bbagen.2018.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 04/03/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
Abstract
GroEL along with ATP and its co-chaperonin GroES has been demonstrated to significantly enhance the folding of newly translated G-protein-coupled receptors (GPCRs). This work extends the previous studies to explore the guest capture and release processes in GroEL-assisted folding of GPCRs, by the reduced approach of employing CXCR4 transmembrane peptides as model substrates. Each of the CXCR4-derived peptides exhibited high affinity for GroEL with a binding stoichiometry near seven. It is found that the peptides interact with the paired α helices in the apical domain of the chaperonin which are similar with the binding sites of SBP (strongly binding peptide: SWMTTPWGFLHP). Complementary binding study with a single-ring version of GroEL indicates that each of the two chaperonin rings is competent for accommodating all the seven CXCR4 peptides bound to GroEL under saturation condition. Meanwhile, the binding kinetics of CXCR4 peptides with GroEL was also examined; ATP alone, or in combination of GroES evidently promoted the release of the peptide substrates from the chaperonin. The results obtained would be beneficial to understand the thermodynamic and kinetic nature of GroEL-GPCRs interaction which is the central molecular event in the assisted folding process.
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Affiliation(s)
- Haixia Chi
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; Qingdao Langoo Oceantec Co., Ltd, Qingdao 266235, PR China
| | - Baomei Xu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Zhenzhen Liu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Junting Wei
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Shixin Li
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Yan Xu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Xinwei Lu
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China; College of Science, China University of Petroleum (East China), Qingdao 266580, PR China.
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, PR China.
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30
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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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31
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Salmon L, Ahlstrom LS, Bardwell JCA, Horowitz S. Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ). Methods Mol Biol 2018; 1764:491-504. [PMID: 29605935 PMCID: PMC6148353 DOI: 10.1007/978-1-4939-7759-8_31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Heterogeneous and dynamic biomolecular complexes play a central role in many cellular processes but are poorly understood due to experimental challenges in characterizing their structural ensembles. To address these difficulties, we developed a hybrid methodology that combines X-ray crystallography with ensemble selections typically used in NMR studies to determine structural ensembles of heterogeneous biomolecular complexes. The method, termed READ, for residual electron and anomalous density, enables the visualization of heterogeneous conformational ensembles of complexes within crystals. Here we present a detailed protocol for performing the ensemble selections to construct READ ensembles. From a diverse pool of binding poses, a selection scheme is used to determine a subset of conformations that maximizes agreement with the X-ray data. Overall, READ is a general approach for obtaining a high-resolution view of dynamic protein-protein complexes.
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Affiliation(s)
- Loïc Salmon
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280, CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, Villeurbanne, France.
| | - Logan S Ahlstrom
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Scott Horowitz
- Department of Chemistry and Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.
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32
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Rutsdottir G, I Rasmussen M, Hojrup P, Bernfur K, Emanuelsson C, Söderberg CAG. Chaperone-client interactions between Hsp21 and client proteins monitored in solution by small angle X-ray scattering and captured by crosslinking mass spectrometry. Proteins 2017; 86:110-123. [PMID: 29082555 DOI: 10.1002/prot.25413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 10/13/2017] [Accepted: 10/27/2017] [Indexed: 11/07/2022]
Abstract
The small heat shock protein (sHsp) chaperones are important for stress survival, yet the molecular details of how they interact with client proteins are not understood. All sHsps share a folded middle domain to which is appended flexible N- and C-terminal regions varying in length and sequence between different sHsps which, in different ways for different sHsps, mediate recognition of client proteins. In plants there is a chloroplast-localized sHsp, Hsp21, and a structural model suggests that Hsp21 has a dodecameric arrangement with six N-terminal arms located on the outside of the dodecamer and six inwardly-facing. Here, we investigated the interactions between Hsp21 and thermosensitive model substrate client proteins in solution, by small-angle X-ray scattering (SAXS) and crosslinking mass spectrometry. The chaperone-client complexes were monitored and the Rg -values were found to increase continuously during 20 min at 45°, which could reflect binding of partially unfolded clients to the flexible N-terminal arms of the Hsp21 dodecamer. No such increase in Rg -values was observed with a mutational variant of Hsp21, which is mainly dimeric and has reduced chaperone activity. Crosslinking data suggest that the chaperone-client interactions involve the N-terminal region in Hsp21 and only certain parts in the client proteins. These parts are peripheral structural elements presumably the first to unfold under destabilizing conditions. We propose that the flexible and hydrophobic N-terminal arms of Hsp21 can trap and refold early-unfolding intermediates with or without dodecamer dissociation.
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Affiliation(s)
- Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Lund University, Sweden
| | - Morten I Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Hojrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Lund University, Sweden
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33
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Clark PL, Elcock AH. Molecular chaperones: providing a safe place to weather a midlife protein-folding crisis. Nat Struct Mol Biol 2017; 23:621-3. [PMID: 27384188 DOI: 10.1038/nsmb.3255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Patricia L Clark
- Department of Chemistry &Biochemistry and the Department of Chemical &Biomolecular Engineering, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA
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34
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Horowitz S, Koldewey P, Stull F, Bardwell JC. Folding while bound to chaperones. Curr Opin Struct Biol 2017; 48:1-5. [PMID: 28734135 DOI: 10.1016/j.sbi.2017.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
Chaperones are important in preventing protein aggregation and aiding protein folding. How chaperones aid protein folding remains a key question in understanding their mechanism. The possibility of proteins folding while bound to chaperones was reintroduced recently with the chaperone Spy, many years after the phenomenon was first reported with the chaperones GroEL and SecB. In this review, we discuss the salient features of folding while bound in the cases for which it has been observed and speculate about its biological importance and possible occurrence in other chaperones.
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Affiliation(s)
- Scott Horowitz
- Department of Chemistry & Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80208, USA.
| | - Philipp Koldewey
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
| | - Frederick Stull
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
| | - James Ca Bardwell
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA.
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35
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Bernfur K, Rutsdottir G, Emanuelsson C. The chloroplast-localized small heat shock protein Hsp21 associates with the thylakoid membranes in heat-stressed plants. Protein Sci 2017; 26:1773-1784. [PMID: 28608391 PMCID: PMC5563132 DOI: 10.1002/pro.3213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022]
Abstract
The small heat shock protein (sHsp) chaperones are crucial for cell survival and can prevent aggregation of client proteins that partially unfold under destabilizing conditions. Most investigations on the chaperone activity of sHsps are based on a limited set of thermosensitive model substrate client proteins since the endogenous targets are often not known. There is a high diversity among sHsps with a single conserved β‐sandwich fold domain defining the family, the α‐crystallin domain, whereas the N‐terminal and C‐terminal regions are highly variable in length and sequence among various sHsps and conserved only within orthologues. The endogenous targets are probably also varying among various sHsps, cellular compartments, cell type and organism. Here we have investigated Hsp21, a non‐metazoan sHsp expressed in the chloroplasts in green plants which experience huge environmental fluctuations not least in temperature. We describe how Hsp21 can also interact with the chloroplast thylakoid membranes, both when isolated thylakoid membranes are incubated with Hsp21 protein and when plants are heat‐stressed. The amount of Hsp21 associated with the thylakoid membranes was precisely determined by quantitative mass spectrometry after metabolic 15N‐isotope labeling of either recombinantly expressed and purified Hsp21 protein or intact Arabidopsis thaliana plants. We found that Hsp21 is among few proteins that become associated with the thylakoid membranes in heat‐stressed plants, and that approximately two thirds of the pool of chloroplast Hsp21 is affected. We conclude that for a complete picture of the role of sHsps in plant stress resistance also their association with the membranes should be considered.
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Affiliation(s)
- Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, Sweden
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36
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Koldewey P, Horowitz S, Bardwell JCA. Chaperone-client interactions: Non-specificity engenders multifunctionality. J Biol Chem 2017; 292:12010-12017. [PMID: 28620048 DOI: 10.1074/jbc.r117.796862] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here, we provide an overview of the different mechanisms whereby three different chaperones, Spy, Hsp70, and Hsp60, interact with folding proteins, and we discuss how these chaperones may guide the folding process. Available evidence suggests that even a single chaperone can use many mechanisms to aid in protein folding, most likely due to the need for most chaperones to bind clients promiscuously. Chaperone mechanism may be better understood by always considering it in the context of the client's folding pathway and biological function.
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Affiliation(s)
- Philipp Koldewey
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Scott Horowitz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109.
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37
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Chaperone–substrate interactions monitored via a robust TEM-1 β-lactamase fragment complementation assay. Biotechnol Lett 2017; 39:1191-1199. [DOI: 10.1007/s10529-017-2347-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/04/2017] [Indexed: 10/19/2022]
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38
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He L, Sharpe T, Mazur A, Hiller S. A molecular mechanism of chaperone-client recognition. SCIENCE ADVANCES 2016; 2:e1601625. [PMID: 28138538 PMCID: PMC5262456 DOI: 10.1126/sciadv.1601625] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/12/2016] [Indexed: 05/13/2023]
Abstract
Molecular chaperones are essential in aiding client proteins to fold into their native structure and in maintaining cellular protein homeostasis. However, mechanistic aspects of chaperone function are still not well understood at the atomic level. We use nuclear magnetic resonance spectroscopy to elucidate the mechanism underlying client recognition by the adenosine triphosphate-independent chaperone Spy at the atomic level and derive a structural model for the chaperone-client complex. Spy interacts with its partially folded client Im7 by selective recognition of flexible, locally frustrated regions in a dynamic fashion. The interaction with Spy destabilizes a partially folded client but spatially compacts an unfolded client conformational ensemble. By increasing client backbone dynamics, the chaperone facilitates the search for the native structure. A comparison of the interaction of Im7 with two other chaperones suggests that the underlying principle of recognizing frustrated segments is of a fundamental nature.
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39
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Salmon L, Ahlstrom LS, Horowitz S, Dickson A, Brooks CL, Bardwell JCA. Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling. J Am Chem Soc 2016; 138:9826-39. [PMID: 27415450 DOI: 10.1021/jacs.6b02382] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Chaperones maintain a healthy proteome by preventing aggregation and by aiding in protein folding. Precisely how chaperones influence the conformational properties of their substrates, however, remains unclear. To achieve a detailed description of dynamic chaperone-substrate interactions, we fused site-specific NMR information with coarse-grained simulations. Our model system is the binding and folding of a chaperone substrate, immunity protein 7 (Im7), with the chaperone Spy. We first used an automated procedure in which NMR chemical shifts inform the construction of system-specific force fields that describe each partner individually. The models of the two binding partners are then combined to perform simulations on the chaperone-substrate complex. The binding simulations show excellent agreement with experimental data from multiple biophysical measurements. Upon binding, Im7 interacts with a mixture of hydrophobic and hydrophilic residues on Spy's surface, causing conformational exchange within Im7 to slow down as Im7 folds. Meanwhile, the motion of Spy's flexible loop region increases, allowing for better interaction with different substrate conformations, and helping offset losses in Im7 conformational dynamics that occur upon binding and folding. Spy then preferentially releases Im7 into a well-folded state. Our strategy has enabled a residue-level description of a dynamic chaperone-substrate interaction, improving our understanding of how chaperones facilitate substrate folding. More broadly, we validate our approach using two other binding partners, showing that this approach provides a general platform from which to investigate other flexible biomolecular complexes through the integration of NMR data with efficient computational models.
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Affiliation(s)
- Loïc Salmon
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Logan S Ahlstrom
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Scott Horowitz
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Alex Dickson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Charles L Brooks
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.,Biophysics Program, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - James C A Bardwell
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan , Ann Arbor, Michigan 48109, United States
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40
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Koldewey P, Stull F, Horowitz S, Martin R, Bardwell JCA. Forces Driving Chaperone Action. Cell 2016; 166:369-379. [PMID: 27293188 DOI: 10.1016/j.cell.2016.05.054] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/02/2016] [Accepted: 05/16/2016] [Indexed: 11/30/2022]
Abstract
It is still unclear what molecular forces drive chaperone-mediated protein folding. Here, we obtain a detailed mechanistic understanding of the forces that dictate the four key steps of chaperone-client interaction: initial binding, complex stabilization, folding, and release. Contrary to the common belief that chaperones recognize unfolding intermediates by their hydrophobic nature, we discover that the model chaperone Spy uses long-range electrostatic interactions to rapidly bind to its unfolded client protein Im7. Short-range hydrophobic interactions follow, which serve to stabilize the complex. Hydrophobic collapse of the client protein then drives its folding. By burying hydrophobic residues in its core, the client's affinity to Spy decreases, which causes client release. By allowing the client to fold itself, Spy circumvents the need for client-specific folding instructions. This mechanism might help explain how chaperones can facilitate the folding of various unrelated proteins.
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Affiliation(s)
- Philipp Koldewey
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Frederick Stull
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott Horowitz
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raoul Martin
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - James C A Bardwell
- Department of Molecular, Cellular and Developmental Biology, and the Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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