1
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Wang Y, Zhou Y, Qi L, Wang Y, Sun L, Cai M, Fan Q, Zhang L. Visualizing Single-Molecule Protein Conformational Transitions and Free Energy Landscape. Anal Chem 2024; 96:12006-12011. [PMID: 38993005 DOI: 10.1021/acs.analchem.4c01970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Monitoring the conformational dynamics of individual proteins is essential to understand the relationship between structure and function in molecular regulatory mechanisms. However, the fast dynamics of single proteins remain poorly understood. Here, we construct a single-molecule sensing platform by introducing plasmonic imaging of single nanoparticles to sense and report the protein conformational changes at the single-molecule level. Tracking the fluctuations of individual nanoparticles with high resolution, we detect and characterize distinct conformational states of molecular chaperone heat shock protein 90 (Hsp90). We also explore the conformational changes of Hsp90 in situ under different nucleotide conditions. Analysis of the conformational fluctuations between the open and closed states of single Hsp90 provides important information on free energy profiles, effective spring constants, and multiphase behaviors. This method offers a strategy to visualize the conformational changes of single proteins in real-time and provides insights into the underlying molecular mechanisms.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Yang Zhou
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Liting Qi
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Yamin Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Le Sun
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Miaomiao Cai
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Quli Fan
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Lei Zhang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
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2
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Hao C, Xu Z, Xu C, Yao R. Anti-herpes simplex virus activities and mechanisms of marine derived compounds. Front Cell Infect Microbiol 2024; 13:1302096. [PMID: 38259968 PMCID: PMC10800978 DOI: 10.3389/fcimb.2023.1302096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Herpes simplex virus (HSV) is the most widely prevalent herpes virus worldwide, and the herpetic encephalitis and genital herpes caused by HSV infection have caused serious harm to human health all over the world. Although many anti-HSV drugs such as nucleoside analogues have been ap-proved for clinical use during the past few decades, important issues, such as drug resistance, toxicity, and high cost of drugs, remain unresolved. Recently, the studies on the anti-HSV activities of marine natural products, such as marine polysaccharides, marine peptides and microbial secondary metabolites are attracting more and more attention all over the world. This review discusses the recent progress in research on the anti-HSV activities of these natural compounds obtained from marine organisms, relating to their structural features and the structure-activity relationships. In addition, the recent findings on the different anti-HSV mechanisms and molecular targets of marine compounds and their potential for therapeutic application will also be summarized in detail.
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Affiliation(s)
- Cui Hao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhongqiu Xu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
- Key Laboratory of Marine Drugs of Ministry of Education, Ocean University of China, Qingdao, China
| | - Can Xu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
- Key Laboratory of Marine Drugs of Ministry of Education, Ocean University of China, Qingdao, China
| | - Ruyong Yao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
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3
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Castelli M, Magni A, Bonollo G, Pavoni S, Frigerio F, Oliveira ASF, Cinquini F, Serapian SA, Colombo G. Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations. Protein Sci 2023; 33:e4880. [PMID: 38145386 PMCID: PMC10895457 DOI: 10.1002/pro.4880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 12/26/2023]
Abstract
Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co-chaperone Hop client-loading and the GR:Hsp90:co-chaperone p23 client-maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide-encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross-talk emerges between the chaperone dynamics states and remodeling of client-interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle.
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Affiliation(s)
| | - Andrea Magni
- Dipartimento di Chimica, Università di Pavia, Pavia, Italy
| | | | - Silvia Pavoni
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - Francesco Frigerio
- Department of Physical Chemistry, R&D Eni SpA, San Donato Milanese, Italy
| | - A Sofia F Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Fabrizio Cinquini
- Upstream & Technical Services - TECS/STES - Eni Spa, San Donato Milanese, Italy
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4
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Yang S, Nie T, She H, Tao K, Lu F, Hu Y, Huang L, Zhu L, Feng D, He D, Qi J, Kukar T, Ma L, Mao Z, Yang Q. Regulation of TFEB nuclear localization by HSP90AA1 promotes autophagy and longevity. Autophagy 2023; 19:822-838. [PMID: 35941759 PMCID: PMC9980472 DOI: 10.1080/15548627.2022.2105561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/02/2022] Open
Abstract
TFEB (transcription factor EB) regulates multiple genes involved in the process of macroautophagy/autophagy and plays a critical role in lifespan determination. However, the detailed mechanisms that regulate TFEB activity are not fully clear. In this study, we identified a role for HSP90AA1 in modulating TFEB. HSP90AA1 was phosphorylated by CDK5 at Ser 595 under basal condition. This phosphorylation inhibited HSP90AA1, disrupted its binding to TFEB, and impeded TFEB's nuclear localization and subsequent autophagy induction. Pro-autophagy signaling attenuated CDK5 activity and enhanced TFEB function in an HSP90AA1-dependent manner. Inhibition of HSP90AA1 function or decrease in its expression significantly attenuated TFEB's nuclear localization and transcriptional function following autophagy induction. HSP90AA1-mediated regulation of a TFEB ortholog was involved in the extended lifespan of Caenorhabditis elegans in the absence of its food source bacteria. Collectively, these findings reveal that this regulatory process plays an important role in modulation of TFEB, autophagy, and longevity.Abbreviations : AL: autolysosome; AP: autophagosome; ATG: autophagy related; BafA1: bafilomycin A1; CDK5: cyclin-dependent kinase 5; CDK5R1: cyclin dependent kinase 5 regulatory subunit 1; CR: calorie restriction; FUDR: 5-fluorodeoxyuridine; HSP90AA1: heat shock protein 90 alpha family class A member 1; MAP1LC3: microtubule associated protein 1 light chain 3; NB: novobiocin sodium; SQSTM1: sequestosome 1; TFEB: transcription factor EB; WT: wild type.
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Affiliation(s)
- Shaosong Yang
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Hua She
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Kai Tao
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Fangfang Lu
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yiman Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Huang
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Lin Zhu
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Dayun Feng
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Dan He
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jing Qi
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Long Ma
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zixu Mao
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Qian Yang
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
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5
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Verkhivker GM. Conformational Dynamics and Mechanisms of Client Protein Integration into the Hsp90 Chaperone Controlled by Allosteric Interactions of Regulatory Switches: Perturbation-Based Network Approach for Mutational Profiling of the Hsp90 Binding and Allostery. J Phys Chem B 2022; 126:5421-5442. [PMID: 35853093 DOI: 10.1021/acs.jpcb.2c03464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the allosteric mechanisms of the Hsp90 chaperone interactions with cochaperones and client protein clientele is fundamental to dissect activation and regulation of many proteins. In this work, atomistic simulations are combined with perturbation-based approaches and dynamic network modeling for a comparative mutational profiling of the Hsp90 binding and allosteric interaction networks in the three Hsp90 maturation complexes with FKBP51 and P23 cochaperones and the glucocorticoid receptor (GR) client. The conformational dynamics signatures of the Hsp90 complexes and dynamics fluctuation analysis revealed how the intrinsic plasticity of the Hsp90 dimer can be modulated by cochaperones and client proteins to stabilize the closed dimer state required at the maturation stage of the ATPase cycle. In silico deep mutational scanning of the protein residues characterized the hot spots of protein stability and binding affinity in the Hsp90 complexes, showing that binding hot spots may often coincide with the regulatory centers that modulate dynamic allostery in the Hsp90 dimer. We introduce a perturbation-based network approach for mutational scanning of allosteric residue potentials and characterize allosteric switch clusters that control mechanism of cochaperone-dependent client recognition and remodeling by the Hsp90 chaperone. The results revealed a conserved network of allosteric switches in the Hsp90 complexes that allow cochaperones and GR protein to become integrated into the Hsp90 system by anchoring to the conformational switch points in the functional Hsp90 regions. This study suggests that the Hsp90 binding and allostery may operate under a regulatory mechanism in which activation or repression of the Hsp90 activity can be pre-encoded in the allosterically regulated Hsp90 dimer motions. By binding directly to the conformational switch centers on the Hsp90, cochaperones and interacting proteins can efficiently modulate the allosteric interactions and long-range communications required for client remodeling and activation.
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Affiliation(s)
- Gennady M Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, California 92866, United States
- Depatment of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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6
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Jussupow A, Lopez A, Baumgart M, Mader SL, Sattler M, Kaila VRI. Extended conformational states dominate the Hsp90 chaperone dynamics. J Biol Chem 2022; 298:102101. [PMID: 35667441 PMCID: PMC9251789 DOI: 10.1016/j.jbc.2022.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
The heat shock protein 90 (Hsp90) is a molecular chaperone central to client protein folding and maturation in eukaryotic cells. During its chaperone cycle, Hsp90 undergoes ATPase-coupled large-scale conformational changes between open and closed states, where the N-terminal and middle domains of the protein form a compact dimerized conformation. However, the molecular principles of the switching motion between the open and closed states remain poorly understood. Here we show by integrating atomistic and coarse-grained molecular simulations with small-angle X-ray scattering experiments and NMR spectroscopy data that Hsp90 exhibits rich conformational dynamics modulated by the charged linker, which connects the N-terminal with the middle domain of the protein. We show that the dissociation of these domains is crucial for the conformational flexibility of the open state, with the separation distance controlled by a β-sheet motif next to the linker region. Taken together, our results suggest that the conformational ensemble of Hsp90 comprises highly extended states, which could be functionally crucial for client processing.
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Affiliation(s)
- Alexander Jussupow
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Abraham Lopez
- Center of Integrated Protein Science, Department Chemie, Technische Universität München Lichtenbergstr. 4, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
| | - Mona Baumgart
- Center of Integrated Protein Science, Department Chemie, Technische Universität München Lichtenbergstr. 4, 85747 Garching (Germany)
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Michael Sattler
- Center of Integrated Protein Science, Department Chemie, Technische Universität München Lichtenbergstr. 4, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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7
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Exploring Mechanisms of Allosteric Regulation and Communication Switching in the Multiprotein Regulatory Complexes of the Hsp90 Chaperone with Cochaperones and Client Proteins : Atomistic Insights from Integrative Biophysical Modeling and Network Analysis of Conformational Landscapes. J Mol Biol 2022; 434:167506. [DOI: 10.1016/j.jmb.2022.167506] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/16/2022]
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8
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Astl L, Stetz G, Verkhivker GM. Dissecting Molecular Principles of the Hsp90 Chaperone Regulation by Allosteric Modulators Using a Hierarchical Simulation Approach and Network Modeling of Allosteric Interactions: Conformational Selection Dictates the Diversity of Protein Responses and Ligand-Specific Functional Mechanisms. J Chem Theory Comput 2020; 16:6656-6677. [PMID: 32941034 DOI: 10.1021/acs.jctc.0c00503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Conformational plasticity of the Hsp90 molecular chaperones underlies the diversity of functional mechanisms that these versatile molecular machines employ to coordinate their vast protein clientele in the cellular environment. Despite a steady progress in studies of the Hsp90 machinery, a great deal remains unknown about molecular principles and ligand-specific functional mechanisms of the Hsp90 regulation by allosteric modulators that attracted significant attention because of their therapeutic potential. Due to structural complexity and dynamic nature of the Hsp90 responses to allosteric modulators, the atomistic details about the mode of action of these small molecules continue to be fairly scarce and controversial. In this work, we employ an integrative strategy that encompassed atomistic simulations of the Hsp90 proteins and hierarchical modeling of Hsp90-ligand binding with network analysis to explore functional mechanisms of the Hsp90 regulation by a panel of allosteric modulators (novobiocin, KU-135, KU-174, and KU-32) with different models of action. The results show that functional mechanisms of allosteric modulation in the Hsp90 proteins may be driven by conformational selection principles in which ligands elicit pre-existing states of the unbound chaperone to drive ligand-specific protein responses and distinct scenarios of Hsp90 regulation. We found that novobiocin can selectively sequester an ensemble of open chaperone conformations and inhibit the progression of the functional cycle through a cascade of cumulative dynamic changes. In contrast, KU-32 displayed unique preferences toward partially closed dynamic states, inducing robust allosteric signaling and stimulation of the ATPase cycle. The proposed model of the Hsp90 regulation by allosteric modulators reconciled diverse experimental data and showed that allosteric modulators may operate via targeted exploitation of dynamic landscapes eliciting vastly different protein responses and diverse mechanisms of action.
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Affiliation(s)
- Lindy Astl
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gabrielle Stetz
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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9
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Hu L, Zhao R, Liu Q, Li Q. New Insights Into Heat Shock Protein 90 in the Pathogenesis of Pulmonary Arterial Hypertension. Front Physiol 2020; 11:1081. [PMID: 33041844 PMCID: PMC7522509 DOI: 10.3389/fphys.2020.01081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/05/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Liqing Hu
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Rui Zhao
- The First Clinical School, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Qianbin Li
- Department of Medicinal Chemistry, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- *Correspondence: Qianbin Li,
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10
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Stetz G, Astl L, Verkhivker GM. Exploring Mechanisms of Communication Switching in the Hsp90-Cdc37 Regulatory Complexes with Client Kinases through Allosteric Coupling of Phosphorylation Sites: Perturbation-Based Modeling and Hierarchical Community Analysis of Residue Interaction Networks. J Chem Theory Comput 2020; 16:4706-4725. [PMID: 32492340 DOI: 10.1021/acs.jctc.0c00280] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding molecular principles underlying chaperone-based modulation of kinase client activity is critically important to dissect functions and activation mechanisms of many oncogenic proteins. The recent experimental studies have suggested that phosphorylation sites in the Hsp90 and Cdc37 proteins can serve as conformational communication switches of chaperone regulation and kinase interactions. However, a mechanism of allosteric coupling between phosphorylation sites in the Hsp90 and Cdc37 during client binding is poorly understood, and the molecular signatures underpinning specific roles of phosphorylation sites in the Hsp90 regulation remain unknown. In this work, we employed a combination of evolutionary analysis, coarse-grained molecular simulations together with perturbation-based network modeling and scanning of the unbound and bound Hsp90 and Cdc37 structures to quantify allosteric effects of phosphorylation sites and identify unique signatures that are characteristic for communication switches of kinase-specific client binding. By using network-based metrics of the dynamic intercommunity bridgeness and community centrality, we characterize specific signatures of phosphorylation switches involved in allosteric regulation. Through perturbation-based analysis of the dynamic residue interaction networks, we show that mutations of kinase-specific phosphorylation switches can induce long-range effects and lead to a global rewiring of the allosteric network and signal transmission in the Hsp90-Cdc37-kinase complex. We determine a specific group of phosphorylation sites in the Hsp90 where mutations may have a strong detrimental effect on allosteric interaction network, providing insight into the mechanism of phosphorylation-induced communication switching. The results demonstrate that kinase-specific phosphorylation switches of communications in the Hsp90 may be partly predisposed for their regulatory role based on preexisting allosteric propensities.
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Affiliation(s)
- Gabrielle Stetz
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Lindy Astl
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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11
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Astl L, Stetz G, Verkhivker GM. Allosteric Mechanism of the Hsp90 Chaperone Interactions with Cochaperones and Client Proteins by Modulating Communication Spines of Coupled Regulatory Switches: Integrative Atomistic Modeling of Hsp90 Signaling in Dynamic Interaction Networks. J Chem Inf Model 2020; 60:3616-3631. [DOI: 10.1021/acs.jcim.0c00380] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Lindy Astl
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gabrielle Stetz
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California92618, United States
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12
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Synthesis of paramagnetic ligands that target the C-terminal binding site of Hsp90. Bioorg Med Chem Lett 2020; 30:127303. [PMID: 32631523 DOI: 10.1016/j.bmcl.2020.127303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 11/22/2022]
Abstract
Identification of a ligand binding site represents the starting point for a structure-based drug development program. Lack of a binding site hampers the development of improved ligands that modulate the protein of interest. In this letter, we describe the development of chemical tools that will allow for elucidation of the Hsp90 C-terminal ligand binding site. Our strategy is based on the preparation of paramagnetic analogs of KU-596, an investigational new drug that is currently undergoing clinical trials for the treatment of neuropathy and interacts with the Hsp90 C-terminal domain. In particular, we report the design and synthesis of three novel paramagnetic analogs of KU-596, which will be used to obtain long range distances for NMR structural studies of Hsp90 in complex with C-terminal ligands.
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13
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Two closed ATP- and ADP-dependent conformations in yeast Hsp90 chaperone detected by Mn(II) EPR spectroscopic techniques. Proc Natl Acad Sci U S A 2019; 117:395-404. [PMID: 31862713 DOI: 10.1073/pnas.1916030116] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hsp90 plays a central role in cell homeostasis by assisting folding and maturation of a large variety of clients. It is a homo-dimer, which functions via hydrolysis of ATP-coupled to conformational changes. Hsp90's conformational cycle in the absence of cochaperones is currently postulated as apo-Hsp90 being an ensemble of "open"/"closed" conformations. Upon ATP binding, Hsp90 adopts an active ATP-bound closed conformation where the N-terminal domains, which comprise the ATP binding site, are in close contact. However, there is no consensus regarding the conformation of the ADP-bound Hsp90, which is considered important for client release. In this work, we tracked the conformational states of yeast Hsp90 at various stages of ATP hydrolysis in frozen solutions employing electron paramagnetic resonance (EPR) techniques, particularly double electron-electron resonance (DEER) distance measurements. Using rigid Gd(III) spin labels, we found the C domains to be dimerized with same distance distribution at all hydrolysis states. Then, we substituted the ATPase Mg(II) cofactor with paramagnetic Mn(II) and followed the hydrolysis state using hyperfine spectroscopy and measured the inter-N-domain distance distributions via Mn(II)-Mn(II) DEER. The point character of the Mn(II) spin label allowed us resolve 2 different closed states: The ATP-bound (prehydrolysis) characterized by a distance distribution having a maximum of 4.3 nm, which broadened and shortened, shifting the mean to 3.8 nm at the ADP-bound state (posthydrolysis). This provides experimental evidence to a second closed conformational state of Hsp90 in solution, referred to as "compact." Finally, the so-called high-energy state, trapped by addition of vanadate, was found structurally similar to the posthydrolysis state.
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14
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Bickel D, Gohlke H. C-terminal modulators of heat shock protein of 90 kDa (HSP90): State of development and modes of action. Bioorg Med Chem 2019; 27:115080. [DOI: 10.1016/j.bmc.2019.115080] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/29/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022]
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15
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Huang B, Friedman LJ, Sun M, Gelles J, Street TO. Conformational Cycling within the Closed State of Grp94, an Hsp90-Family Chaperone. J Mol Biol 2019; 431:3312-3323. [PMID: 31202885 DOI: 10.1016/j.jmb.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 11/29/2022]
Abstract
The Hsp90 family of chaperones requires ATP-driven cycling to perform their function. The presence of two bound ATP molecules is known to favor a closed conformation of the Hsp90 dimer. However, the structural and mechanistic consequences of subsequent ATP hydrolysis are poorly understood. Using single-molecule FRET, we discover novel dynamic behavior in the closed state of Grp94, the Hsp90 family member resident in the endoplasmic reticulum. Under ATP turnover conditions, Grp94 populates two distinct closed states, a relatively static ATP/ATP closed state that adopts one conformation, and a dynamic ATP/ADP closed state that can adopt two conformations. We constructed a Grp94 heterodimer with one arm that is catalytically dead, to extend the lifetime of the ATP/ADP state by preventing hydrolysis of the second ATP. This construct shows prolonged periods of cycling between two closed conformations. Our results enable a quantitative description of how ATP hydrolysis influences Grp94, where sequential ATP hydrolysis steps allow Grp94 to transition between closed states with different dynamic and structural properties. This stepwise transitioning of Grp94's dynamic properties may provide a mechanism to propagate structural changes to a bound client protein.
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Affiliation(s)
- Bin Huang
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Ming Sun
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Jeff Gelles
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Timothy O Street
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
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16
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Li F, Song X, Su G, Wang Y, Wang Z, Qing S, Jia J, Wang Y, Huang L, Zheng K, Wang Y. AT-533, a Hsp90 inhibitor, attenuates HSV-1-induced inflammation. Biochem Pharmacol 2019; 166:82-92. [PMID: 31071330 DOI: 10.1016/j.bcp.2019.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022]
Abstract
Inflammatory events are tightly associated with the death caused by Herpes simplex virus 1 (HSV-1) infection of the brain. Heat shock protein 90 (Hsp90) is a molecular chaperone that is stimulated in response to many stressful conditions (e.g., inflammation and hypoxia) and Hsp90 inhibitors are suggested to be potent inhibitors of the inflammatory response. The aim of this study was to investigate the effect of Hsp90 inhibitor AT-533 on HSV-1-induced inflammation. AT-533 at a non-antiviral concentration was found to show a prominent inhibitory effect on the production of cytokines induced by HSV-1 infection, such as tumor necrosis factor α (TNF-α), interleukin 6 (IL-6) and interleukin 1β (IL-1β). Mechanically, HSV-1 early infection induced inflammation through NF-κB signaling and NLRP3 inflammasome activation, as illustrated by the nuclear translocation of NF-κB and the enhanced cleavage of caspase-1. Besides, HSV-1 enhanced the interaction between NLRP3 and Hsp90. Moreover, AT-533 reduced the nuclear translocation of NF-κB and inflammasome activation via inhibiting the chaperone function of Hsp90. Furthermore, AT-533 inhibited the cleavage of pro-IL-1β to mature IL-1β in a NLRP3-independent manner. In summary, AT-533 may be a promising therapeutic strategy in HSV-1-infected inflammation management.
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Affiliation(s)
- Feng Li
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaowei Song
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Guifeng Su
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yiliang Wang
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhaoyang Wang
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Shurong Qing
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiaoyan Jia
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yuan Wang
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lianzhou Huang
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Kai Zheng
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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17
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Lee BL, Rashid S, Wajda B, Wolmarans A, LaPointe P, Spyracopoulos L. The Hsp90 Chaperone: 1H and 19F Dynamic Nuclear Magnetic Resonance Spectroscopy Reveals a Perfect Enzyme. Biochemistry 2019; 58:1869-1877. [PMID: 30869872 DOI: 10.1021/acs.biochem.9b00144] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hsp90 is a crucial chaperone whose ATPase activity is fundamental for stabilizing and activating a diverse array of client proteins. Binding and hydrolysis of ATP by dimeric Hsp90 drive a conformational cycle characterized by fluctuations between a compact, N- and C-terminally dimerized catalytically competent closed state and a less compact open state that is largely C-terminally dimerized. We used 19F and 1H dynamic nuclear magnetic resonance (NMR) spectroscopy to study the opening and closing kinetics of Hsp90 and to determine the kcat for ATP hydrolysis. We derived a set of coupled ordinary differential equations describing the rate laws for the Hsp90 kinetic cycle and used these to analyze the NMR data. We found that the kinetics of closing and opening for the chaperone are slow and that the lower limit for kcat of ATP hydrolysis is ∼1 s-1. Our results show that the chemical step is optimized and that Hsp90 is indeed a "perfect" enzyme.
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Affiliation(s)
- Brian L Lee
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Suad Rashid
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Benjamin Wajda
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Annemarie Wolmarans
- Department of Cell Biology , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Paul LaPointe
- Department of Cell Biology , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
| | - Leo Spyracopoulos
- Department of Biochemistry , University of Alberta , Edmonton , Alberta T6G 2H7 , Canada
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18
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Galigniana MD. HSP90-Based Heterocomplex as Essential Regulator for Cancer Disease. HEAT SHOCK PROTEINS 2019:19-45. [DOI: 10.1007/978-3-030-23158-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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19
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Lepvrier E, Thomas D, Garnier C. Hsp90 Quaternary Structures and the Chaperone Cycle: Highly Flexible Dimeric and Oligomeric Structures and Their Regulation by Co-Chaperones. CURR PROTEOMICS 2018. [DOI: 10.2174/1570164615666180522095147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Proposed models of the function of Hsp90 are characterised by high flexibility of the dimeric
state and conformational changes regulated by both nucleotide binding and hydrolysis, and by
co-chaperone interactions. In addition to its dimeric state, Hsp90 self-associates upon particular stimuli.
The Hsp90 dimer is the building block up to the hexamer that we named “cosy nest”, and the dodecamer
results from the association of two hexamers. Oligomers exhibit chaperone activity, but their
exact mechanism of action has not yet been determined. One of the best ways to elucidate how oligomers
might operate is to study their interactions with co-chaperone proteins known to regulate the
Hsp90 chaperone cycle, such as p23 and Aha1. In this review, we summarise recent results and conclude
that Hsp90 oligomers are key players in the chaperone cycle. Crucible-shaped quaternary structures
likely provide an ideal environment for client protein accommodation and folding, as is the case
for other Hsp families. Confirmation of the involvement of Hsp90 oligomers in the chaperone cycle
and a better understanding of their functionality will allow us to address some of the more enigmatic
aspects of Hsp90 activity. Utilising this knowledge, future work will highlight how Hsp90 oligomers
and co-chaperones cooperate to build the structures required to fold or refold numerous different client
proteins.
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Affiliation(s)
- Eléonore Lepvrier
- Structure et Dynamique des Macromolecules, UMR-CNRS 6026, Interactions Cellulaires et Moleculaires, Universite de Rennes 1, Campus Beaulieu, 35042 Rennes Cedex, France
| | - Daniel Thomas
- Structure et Dynamique des Macromolecules, UMR-CNRS 6026, Interactions Cellulaires et Moleculaires, Universite de Rennes 1, Campus Beaulieu, 35042 Rennes Cedex, France
| | - Cyrille Garnier
- Universite de Rennes 1, Campus de Beaulieu, F-35042 Rennes Cedex, France
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20
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Hellenkamp B, Thurn J, Stadlmeier M, Hugel T. Kinetics of Transient Protein Complexes Determined via Diffusion-Independent Microfluidic Mixing and Fluorescence Stoichiometry. J Phys Chem B 2018; 122:11554-11560. [PMID: 30351113 DOI: 10.1021/acs.jpcb.8b07437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Low-affinity protein complexes and their transient states are difficult to measure in single-molecule experiments because of their low population at low concentrations. A prominent solution to this problem is the use of microfluidic mixing devices, which rely on diffusion-based mixing. This is not ideal for multiprotein complexes, as the single-molecule fluorescence signal is dominated by the already dissociated species. Here, we designed a microfluidic device with mixing structures for fast and homogeneous mixing of components with varying diffusion coefficients and for fluorescence measurements at a defined single-molecule concentration. This enables direct measurement of dissociation rates at a broad range of timescales from a few milliseconds to several minutes. This further allows us to measure structural properties and stoichiometries of protein complexes with large equilibrium dissociation constants ( KD's) of 5 μM and above. We used the platform to measure structural properties and dissociation rates of heat shock protein 90 (Hsp90) dimers and found at least two dissociation rates which depend on the nucleotide state. Finally, we demonstrate the capability for measuring also equilibrium dissociation constants, resulting in the determination of both the kinetics and thermodynamics of the system under investigation.
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Affiliation(s)
- Björn Hellenkamp
- Columbia University , Engineering and Applied Science , New York , New York , United States
| | - Johann Thurn
- Institute of Physical Chemistry , University of Freiburg , Albertstr. 23a , 79104 Freiburg , Germany
| | - Martina Stadlmeier
- Bildungsakademie Inn-Salzach, InfraServ GmbH & Co. Gendorf KG, Alte-Haupttor-Straße 2 , 84508 Burgkirchen a.d. Alz , Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry , University of Freiburg , Albertstr. 23a , 79104 Freiburg , Germany
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21
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Ye W, Götz M, Celiksoy S, Tüting L, Ratzke C, Prasad J, Ricken J, Wegner SV, Ahijado-Guzmán R, Hugel T, Sönnichsen C. Conformational Dynamics of a Single Protein Monitored for 24 h at Video Rate. NANO LETTERS 2018; 18:6633-6637. [PMID: 30251862 PMCID: PMC6187522 DOI: 10.1021/acs.nanolett.8b03342] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We use plasmon rulers to follow the conformational dynamics of a single protein for up to 24 h at a video rate. The plasmon ruler consists of two gold nanospheres connected by a single protein linker. In our experiment, we follow the dynamics of the molecular chaperone heat shock protein 90 (Hsp90), which is known to show "open" and "closed" conformations. Our measurements confirm the previously known conformational dynamics with transition times in the second to minute time scale and reveals new dynamics on the time scale of minutes to hours. Plasmon rulers thus extend the observation bandwidth 3-4 orders of magnitude with respect to single-molecule fluorescence resonance energy transfer and enable the study of molecular dynamics with unprecedented precision.
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Affiliation(s)
- Weixiang Ye
- Institute
of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
- Graduate
School of Excellence Materials Science in Mainz (MAINZ), Staudinger Weg 9, D-55128 Mainz, Germany
| | - Markus Götz
- Institute of Physical Chemistry and BIOSS Centre for
Biological Signaling Studies, University
of Freiburg, Albertstraße
23a, D-79104 Freiburg, Germany
| | - Sirin Celiksoy
- Institute
of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Laura Tüting
- Institute
of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
- Graduate
School of Excellence Materials Science in Mainz (MAINZ), Staudinger Weg 9, D-55128 Mainz, Germany
| | - Christoph Ratzke
- Institute of Physical Chemistry and BIOSS Centre for
Biological Signaling Studies, University
of Freiburg, Albertstraße
23a, D-79104 Freiburg, Germany
| | - Janak Prasad
- Institute
of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
- Graduate
School of Excellence Materials Science in Mainz (MAINZ), Staudinger Weg 9, D-55128 Mainz, Germany
| | - Julia Ricken
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Seraphine V. Wegner
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Rubén Ahijado-Guzmán
- Institute
of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Thorsten Hugel
- Institute of Physical Chemistry and BIOSS Centre for
Biological Signaling Studies, University
of Freiburg, Albertstraße
23a, D-79104 Freiburg, Germany
- E-mail:
| | - Carsten Sönnichsen
- Institute
of Physical Chemistry, University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
- E-mail:
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22
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Tych KM, Jahn M, Gegenfurtner F, Hechtl VK, Buchner J, Hugel T, Rief M. Nucleotide-Dependent Dimer Association and Dissociation of the Chaperone Hsp90. J Phys Chem B 2018; 122:11373-11380. [PMID: 30179494 DOI: 10.1021/acs.jpcb.8b07301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hsp90 is an essential molecular chaperone, which has to be in a dimeric form for its correct function. While the affinity of the dimer has previously been measured, little is known about how it associates and dissociates and the factors that influence this. We perform an in-depth single molecule characterization of the C-terminal association and dissociation of Hsp90. We find more than one dissociation rate, indicating that the dimer has a stable and an unstable state. Furthermore, we find that the stability of the C-terminal association is dependent on the presence of ATP, despite the C-terminal dimerization interface being distal to the catalytic site.
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Affiliation(s)
| | | | | | | | | | - Thorsten Hugel
- Institute of Physical Chemistry , University of Freiburg , Freiburg , Baden-Württemberg 79104 , Germany
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23
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Roy SS, Kapoor M. In silico identification and analysis of the binding site for aminocoumarin type inhibitors in the C-terminal domain of Hsp90. J Mol Graph Model 2018; 84:215-235. [PMID: 30031951 DOI: 10.1016/j.jmgm.2018.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 11/15/2022]
Abstract
Hsp90 contains two Nucleotide Binding Sites (NBS): one each in its N-terminal domain (NTD) and C-terminal domain (CTD), respectively. Previously we used computational techniques to locate a nucleotide-binding site in the CTD. Nucleotide binding at this site stabilized the structurally labile region within this domain, thus providing a rationale for increased resistance to thermal denaturation and proteolysis. A scan for ligand-binding sites in CTD revealed four potential sites with the requisite volume to accommodate aminocoumarins and -derived inhibitors. Only one of these reproducibly formed docked complexes with inhibitors and showed excellent interactions with residues lining the site. Fortuitously, it was identical to the aforementioned nucleotide-binding site thus providing an explanation for the reported direct competition between inhibitors and nucleotides. Further studies with carefully chosen inhibitors and some inactive analogues provided an explanation for the known Structure-Activity Relationships (SAR) of aminocoumarin and -derived inhibitors. We also performed similar studies of the NTD to discern the reason(s) for its inability to bind aminocoumarins, given the family resemblance to prokaryotic Top-IV and Gyr-B. Our studies permitted the identification of the putative inhibitor binding site in the CTD, an explanation for increased resistance to thermal denaturation and proteolysis upon inhibitor binding as well as direct competition with ATP.
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Affiliation(s)
- Samir S Roy
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Manju Kapoor
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
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24
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Johnston CL, Marzano NR, van Oijen AM, Ecroyd H. Using Single-Molecule Approaches to Understand the Molecular Mechanisms of Heat-Shock Protein Chaperone Function. J Mol Biol 2018; 430:4525-4546. [PMID: 29787765 DOI: 10.1016/j.jmb.2018.05.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/11/2018] [Accepted: 05/13/2018] [Indexed: 02/01/2023]
Abstract
The heat-shock proteins (Hsp) are a family of molecular chaperones, which collectively form a network that is critical for the maintenance of protein homeostasis. Traditional ensemble-based measurements have provided a wealth of knowledge on the function of individual Hsps and the Hsp network; however, such techniques are limited in their ability to resolve the heterogeneous, dynamic and transient interactions that molecular chaperones make with their client proteins. Single-molecule techniques have emerged as a powerful tool to study dynamic biological systems, as they enable rare and transient populations to be identified that would usually be masked in ensemble measurements. Thus, single-molecule techniques are particularly amenable for the study of Hsps and have begun to be used to reveal novel mechanistic details of their function. In this review, we discuss the current understanding of the chaperone action of Hsps and how gaps in the field can be addressed using single-molecule methods. Specifically, this review focuses on the ATP-independent small Hsps and the broader Hsp network and describes how these dynamic systems are amenable to single-molecule techniques.
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Affiliation(s)
- Caitlin L Johnston
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Nicholas R Marzano
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia
| | - Antoine M van Oijen
- School of Chemistry, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
| | - Heath Ecroyd
- School of Biological Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia; Illawarra Health and Medical Research Institute, Wollongong, NSW, 2522, Australia.
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25
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Verkhivker GM. Dynamics-based community analysis and perturbation response scanning of allosteric interaction networks in the TRAP1 chaperone structures dissect molecular linkage between conformational asymmetry and sequential ATP hydrolysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:899-912. [PMID: 29684503 DOI: 10.1016/j.bbapap.2018.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 01/29/2023]
Abstract
Allosteric interactions of the Hsp90 chaperones with cochaperones and diverse protein clients can often exhibit distinct asymmetric features that determine regulatory mechanisms and cellular functions in many signaling networks. The recent crystal structures of the mitochondrial Hsp90 isoform TRAP1 in complexes with ATP analogs have provided first evidence of significant asymmetry in the closed dimerized state that triggers independent activity of the chaperone protomers, whereby preferential hydrolysis of the buckled protomer is followed by conformational flipping between protomers and hydrolysis of the second protomer. Despite significant insights in structural characterizations of the TRAP1 chaperone, the atomistic details and mechanics of allosteric interactions that couple sequential ATP hydrolysis with asymmetric conformational switching in the TRAP1 protomers remain largely unknown. In this work, we explored atomistic and coarse-grained simulations of the TRAP1 dimer structures in combination with the ensemble-based network modeling and perturbation response scanning of residue interaction networks to probe salient features underlying allosteric signaling mechanism. This study has revealed that key effector sites that orchestrate allosteric interactions occupy the ATP binding region and N-terminal interface of the buckled protomer, whereas the main sensors of allosteric signals that drive functional conformational changes during ATPase cycle are consolidated near the client binding region of the straight protomer, channeling the energy of ATP hydrolysis for client remodeling. The community decomposition analysis of the interaction networks and reconstruction of allosteric communication pathways in the TRAP1 structures have quantified mechanism of allosteric regulation, revealing control points and interactions that coordinate asymmetric switching during ATP hydrolysis.
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Affiliation(s)
- Gennady M Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, United States; Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States.
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26
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Huard DJE, Crowley VM, Du Y, Cordova RA, Sun Z, Tomlin MO, Dickey CA, Koren J, Blair L, Fu H, Blagg BSJ, Lieberman RL. Trifunctional High-Throughput Screen Identifies Promising Scaffold To Inhibit Grp94 and Treat Myocilin-Associated Glaucoma. ACS Chem Biol 2018; 13:933-941. [PMID: 29402077 PMCID: PMC6195314 DOI: 10.1021/acschembio.7b01083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gain-of-function mutations within the olfactomedin (OLF) domain of myocilin result in its toxic intracellular accumulation and hasten the onset of open-angle glaucoma. The absence of myocilin does not cause disease; therefore, strategies aimed at eliminating myocilin could lead to a successful glaucoma treatment. The endoplasmic reticulum Hsp90 paralog Grp94 accelerates OLF aggregation. Knockdown or pharmacological inhibition of Grp94 in cells facilitates clearance of mutant myocilin via a non-proteasomal pathway. Here, we expanded our support for targeting Grp94 over cytosolic paralogs Hsp90α and Hsp90β. We then developed a high-throughput screening assay to identify new chemical matter capable of disrupting the Grp94/OLF interaction. When applied to a blind, focused library of 17 Hsp90 inhibitors, our miniaturized single-read in vitro thioflavin T -based kinetics aggregation assay exclusively identified compounds that target the chaperone N-terminal nucleotide binding site. In follow up studies, one compound (2) decreased the extent of co-aggregation of Grp94 with OLF in a dose-dependent manner in vitro, and enabled clearance of the aggregation-prone full-length myocilin variant I477N in cells without inducing the heat shock response or causing cytotoxicity. Comparison of the co-crystal structure of compound 2 and another non-selective hit in complex with the N-terminal domain of Grp94 reveals a docking mode tailored to Grp94 and explains its selectivity. A new lead compound has been identified, supporting a targeted chemical biology assay approach to develop a protein degradation-based therapy for myocilin-associated glaucoma by selectively inhibiting Grp94.
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Affiliation(s)
| | - Vincent M. Crowley
- Emory Chemical Biology Discovery Center, Department of Pharmacology, Emory University
| | - Yuhong Du
- Department of Medicinal Chemistry, The University of Kansas
| | - Ricardo A. Cordova
- Byrd Alzheimer Institute, Department of Molecular Medicine, University of South Florida
| | - Zheying Sun
- Byrd Alzheimer Institute, Department of Molecular Medicine, University of South Florida
| | - Moya O. Tomlin
- School of Chemistry & Biochemistry, Georgia Institute of Technology
| | - Chad A. Dickey
- Byrd Alzheimer Institute, Department of Molecular Medicine, University of South Florida
| | - John Koren
- Byrd Alzheimer Institute, Department of Molecular Medicine, University of South Florida
| | - Laura Blair
- Byrd Alzheimer Institute, Department of Molecular Medicine, University of South Florida
| | - Haian Fu
- Department of Medicinal Chemistry, The University of Kansas
| | - Brian S. J. Blagg
- Emory Chemical Biology Discovery Center, Department of Pharmacology, Emory University
- Department of Chemistry and Biochemistry, The University of Notre Dame
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27
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Aviram HY, Pirchi M, Barak Y, Riven I, Haran G. Two states or not two states: Single-molecule folding studies of protein L. J Chem Phys 2018; 148:123303. [DOI: 10.1063/1.4997584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Haim Yuval Aviram
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Menahem Pirchi
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yoav Barak
- Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbal Riven
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Haran
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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28
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Lou F, Yang J, Wu S, Perrett S. A co-expression strategy to achieve labeling of individual subunits within a dimeric protein for single molecule analysis. Chem Commun (Camb) 2018. [PMID: 28650509 DOI: 10.1039/c7cc03032k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A generic co-expression strategy for site-specific incorporation of a single donor-acceptor dye pair into any position in a dimeric protein, allowing single molecule FRET study of proteins previously inaccessible to this technique, such as the intrinsically disordered prion N-domain of Ure2 in the context of its globular dimeric C-domain.
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Affiliation(s)
- Fei Lou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jie Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China. and University of the Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
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Slow domain reconfiguration causes power-law kinetics in a two-state enzyme. Proc Natl Acad Sci U S A 2018; 115:513-518. [PMID: 29298911 DOI: 10.1073/pnas.1714401115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein dynamics are typically captured well by rate equations that predict exponential decays for two-state reactions. Here, we describe a remarkable exception. The electron-transfer enzyme quiescin sulfhydryl oxidase (QSOX), a natural fusion of two functionally distinct domains, switches between open- and closed-domain arrangements with apparent power-law kinetics. Using single-molecule FRET experiments on time scales from nanoseconds to milliseconds, we show that the unusual open-close kinetics results from slow sampling of an ensemble of disordered domain orientations. While substrate accelerates the kinetics, thus suggesting a substrate-induced switch to an alternative free energy landscape of the enzyme, the power-law behavior is also preserved upon electron load. Our results show that the slow sampling of open conformers is caused by a variety of interdomain interactions that imply a rugged free energy landscape, thus providing a generic mechanism for dynamic disorder in multidomain enzymes.
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30
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Molecular Chaperones: Structure-Function Relationship and their Role in Protein Folding. REGULATION OF HEAT SHOCK PROTEIN RESPONSES 2018. [DOI: 10.1007/978-3-319-74715-6_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Czemeres J, Buse K, Verkhivker GM. Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains. PLoS One 2017; 12:e0190267. [PMID: 29267381 PMCID: PMC5739471 DOI: 10.1371/journal.pone.0190267] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic factors underlying allosteric mechanism of the chaperone-kinase cycle and identify regulatory hotspots that control client recognition. Through comprehensive characterization of conformational dynamics and systematic identification of stabilization centers in the unbound and client- bound Hsp90 forms, we have simulated key stages of the allosteric mechanism, in which Hsp90 binding can induce instability and partial unfolding of Cdk4 client. Conformational landscapes of the Hsp90 and Cdk4 structures suggested that client binding can trigger coordinated dynamic changes and induce global rigidification of the Hsp90 inter-domain regions that is coupled with a concomitant increase in conformational flexibility of the kinase client. This process is allosteric in nature and can involve reciprocal dynamic exchanges that exert global effect on stability of the Hsp90 dimer, while promoting client instability. The network-based rigidity analysis and emulation of thermal unfolding of the Cdk4-cyclin D complex and Hsp90-Cdc37-Cdk4 complex revealed weak spots of kinase instability that are present in the native Cdk4 structure and are targeted by the chaperone during client recruitment. Our findings suggested that this mechanism may be exploited by the Hsp90-Cdc37 chaperone to recruit and protect intrinsically dynamic kinase clients from degradation. The results of this investigation are discussed and interpreted in the context of diverse experimental data, offering new insights into mechanisms of chaperone regulation and binding.
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Affiliation(s)
- Josh Czemeres
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Kurt Buse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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32
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Mamipour M, Yousefi M, Hasanzadeh M. An overview on molecular chaperones enhancing solubility of expressed recombinant proteins with correct folding. Int J Biol Macromol 2017; 102:367-375. [PMID: 28412337 PMCID: PMC7185796 DOI: 10.1016/j.ijbiomac.2017.04.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/14/2017] [Accepted: 04/06/2017] [Indexed: 02/07/2023]
Abstract
The majority of research topics declared that most of the recombinant proteins have been expressed by Escherichia coli in basic investigations. But the majority of high expressed proteins formed as inactive recombinant proteins that are called inclusion body. To overcome this problem, several methods have been used including suitable promoter, environmental factors, ladder tag to secretion of proteins into the periplasm, gene protein optimization, chemical chaperones and molecular chaperones sets. Co-expression of the interest protein with molecular chaperones is one of the common methods The chaperones are a group of proteins, which are involved in making correct folding of recombinant proteins. Chaperones are divided two groups including; cytoplasmic and periplasmic chaperones. Moreover, periplasmic chaperones and proteases can be manipulated to increase the yields of secreted proteins. In this article, we attempted to review cytoplasmic chaperones such as Hsp families and periplasmic chaperones including; generic chaperones, specialized chaperones, PPIases, and proteins involved in disulfide bond formation.
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Affiliation(s)
- Mina Mamipour
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammadreza Yousefi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Biotechnology, Higher Education Institute of Rab-Rashid, Tabriz, Iran
| | - Mohammad Hasanzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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33
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Zuehlke AD, Reidy M, Lin C, LaPointe P, Alsomairy S, Lee DJ, Rivera-Marquez GM, Beebe K, Prince T, Lee S, Trepel JB, Xu W, Johnson J, Masison D, Neckers L. An Hsp90 co-chaperone protein in yeast is functionally replaced by site-specific posttranslational modification in humans. Nat Commun 2017; 8:15328. [PMID: 28537252 PMCID: PMC5458067 DOI: 10.1038/ncomms15328] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is an essential eukaryotic molecular chaperone. To properly chaperone its clientele, Hsp90 proceeds through an ATP-dependent conformational cycle influenced by posttranslational modifications (PTMs) and assisted by a number of co-chaperone proteins. Although Hsp90 conformational changes in solution have been well-studied, regulation of these complex dynamics in cells remains unclear. Phosphorylation of human Hsp90α at the highly conserved tyrosine 627 has previously been reported to reduce client interaction and Aha1 binding. Here we report that these effects are due to a long-range conformational impact inhibiting Hsp90α N-domain dimerization and involving a region of the middle domain/carboxy-terminal domain interface previously suggested to be a substrate binding site. Although Y627 is not phosphorylated in yeast, we demonstrate that the non-conserved yeast co-chaperone, Hch1, similarly affects yeast Hsp90 (Hsp82) conformation and function, raising the possibility that appearance of this PTM in higher eukaryotes represents an evolutionary substitution for HCH1.
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Affiliation(s)
- Abbey D Zuehlke
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Michael Reidy
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Room 225, 8 Center Drive, Bethesda, Maryland 20892, USA
| | - Coney Lin
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Room 225, 8 Center Drive, Bethesda, Maryland 20892, USA
| | - Paul LaPointe
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Sarah Alsomairy
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - D Joshua Lee
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Genesis M Rivera-Marquez
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Kristin Beebe
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Thomas Prince
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Sunmin Lee
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Jane B Trepel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Wanping Xu
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
| | - Jill Johnson
- Department of Biological Sciences and the Center for Reproductive Biology, University of Idaho, Moscow, Idaho 83844, USA
| | - Daniel Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Room 225, 8 Center Drive, Bethesda, Maryland 20892, USA
| | - Len Neckers
- Urologic Oncologic Branch, Center for Cancer Research, National Cancer Institute, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
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34
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Ciechanover A, Kwon YT. Protein Quality Control by Molecular Chaperones in Neurodegeneration. Front Neurosci 2017; 11:185. [PMID: 28428740 PMCID: PMC5382173 DOI: 10.3389/fnins.2017.00185] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/20/2017] [Indexed: 12/14/2022] Open
Abstract
Protein homeostasis (proteostasis) requires the timely degradation of misfolded proteins and their aggregates by protein quality control (PQC), of which molecular chaperones are an essential component. Compared with other cell types, PQC in neurons is particularly challenging because they have a unique cellular structure with long extensions. Making it worse, neurons are postmitotic, i.e., cannot dilute toxic substances by division, and, thus, are highly sensitive to misfolded proteins, especially as they age. Failure in PQC is often associated with neurodegenerative diseases, such as Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD), and prion disease. In fact, many neurodegenerative diseases are considered to be protein misfolding disorders. To prevent the accumulation of disease-causing aggregates, neurons utilize a repertoire of chaperones that recognize misfolded proteins through exposed hydrophobic surfaces and assist their refolding. If such an effort fails, chaperones can facilitate the degradation of terminally misfolded proteins through either the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome system (hereafter autophagy). If soluble, the substrates associated with chaperones, such as Hsp70, are ubiquitinated by Ub ligases and degraded through the proteasome complex. Some misfolded proteins carrying the KFERQ motif are recognized by the chaperone Hsc70 and delivered to the lysosomal lumen through a process called, chaperone-mediated autophagy (CMA). Aggregation-prone misfolded proteins that remain unprocessed are directed to macroautophagy in which cargoes are collected by adaptors, such as p62/SQSTM-1/Sequestosome-1, and delivered to the autophagosome for lysosomal degradation. The aggregates that have survived all these refolding/degradative processes can still be directly dissolved, i.e., disaggregated by chaperones. Studies have shown that molecular chaperones alleviate the pathogenic symptoms by neurodegeneration-causing protein aggregates. Chaperone-inducing drugs and anti-aggregation drugs are actively exploited for beneficial effects on symptoms of disease. Here, we discuss how chaperones protect misfolded proteins from aggregation and mediate the degradation of terminally misfolded proteins in collaboration with cellular degradative machinery. The topics also include therapeutic approaches to improve the expression and turnover of molecular chaperones and to develop anti-aggregation drugs.
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Affiliation(s)
- Aaron Ciechanover
- Department of Biomedical Sciences, Protein Metabolism Medical Research Center, College of Medicine, Seoul National UniversitySeoul, South Korea.,Technion Integrated Cancer Center, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Yong Tae Kwon
- Department of Biomedical Sciences, Protein Metabolism Medical Research Center, College of Medicine, Seoul National UniversitySeoul, South Korea.,Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National UniversitySeoul, South Korea
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35
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Interaction of E. coli Hsp90 with DnaK Involves the DnaJ Binding Region of DnaK. J Mol Biol 2016; 429:858-872. [PMID: 28013030 DOI: 10.1016/j.jmb.2016.12.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 01/05/2023]
Abstract
The 90-kDa heat shock protein (Hsp90) is a widely conserved and ubiquitous molecular chaperone that participates in ATP-dependent protein remodeling in both eukaryotes and prokaryotes. It functions in conjunction with Hsp70 and the Hsp70 cochaperones, an Hsp40 (J-protein) and a nucleotide exchange factor. In Escherichia coli, the functional collaboration between Hsp90Ec and Hsp70, DnaK, requires that the two chaperones directly interact. We used molecular docking to model the interaction of Hsp90Ec and DnaK. The top-ranked docked model predicted that a region in the nucleotide-binding domain (NBD) of DnaK interacted with a region in the middle domain of Hsp90Ec. We then made substitution mutants in DnaK residues suggested by the model to interact with Hsp90Ec. Of the 12 mutants tested, 11 were defective or partially defective in their ability to interact with Hsp90Ecin vivo in a bacterial two-hybrid assay and in vitro in a bio-layer interferometry assay. These DnaK mutants were also defective in their ability to function collaboratively in protein remodeling with Hsp90Ec but retained the ability to act with DnaK cochaperones. Taken together, these results suggest that a specific region in the NBD of DnaK is involved in the interaction with Hsp90Ec, and this interaction is functionally important. Moreover, the region of DnaK that we found to be necessary for Hsp90Ec binding includes residues that are also involved in J-protein binding, suggesting a functional interplay among DnaK, DnaK cochaperones, and Hsp90Ec.
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36
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Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr Opin Struct Biol 2016; 40:163-185. [PMID: 27939973 DOI: 10.1016/j.sbi.2016.11.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 01/11/2023]
Abstract
Förster Resonance Energy Transfer (FRET) combined with single-molecule spectroscopy probes macromolecular structure and dynamics and identifies coexisting conformational states. We review recent methodological developments in integrative structural modeling by satisfying spatial restraints on networks of FRET pairs (hybrid-FRET). We discuss procedures to incorporate prior structural knowledge and to obtain optimal distance networks. Finally, a workflow for hybrid-FRET is presented that automates integrative structural modeling and experiment planning to put hybrid-FRET on rails. To test this workflow, we simulate realistic single-molecule experiments and resolve three protein conformers, exchanging at 30μs and 10ms, with accuracies of 1-3Å RMSD versus the target structure. Incorporation of data from other spectroscopies and imaging is also discussed.
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Affiliation(s)
- Mykola Dimura
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany; Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas O Peulen
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Christian A Hanke
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Aiswaria Prakash
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Claus Am Seidel
- Chair for Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
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37
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Roy SS, Kapoor M. In silico identification and computational analysis of the nucleotide binding site in the C-terminal domain of Hsp90. J Mol Graph Model 2016; 70:253-274. [PMID: 27771574 DOI: 10.1016/j.jmgm.2016.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/02/2016] [Indexed: 12/28/2022]
Abstract
Hsp90 contains two distinct Nucleotide Binding Sites (NBS), in its N-terminal domain (NTD) and C-terminal domain (CTD), respectively. The NTD site belongs to the GHKL super-family of ATPases and has been the subject of extensive characterization. However, a structure of the nucleotide-bound form of CTD is still unavailable. In this study molecular modeling was employed to incorporate experimental data using partial constructs of the CTD, from work published by many research groups, onto existing structural models of its apo- form. Our attempts to locate potential nucleotide ligand-binding sites or cavities yielded one major candidate-a structurally unconventional site-exhibiting the requisite shape and volume for accommodation of tri-phosphate nucleotides. Its structure was refined by molecular dynamics (MD)-based techniques. We reproducibly docked the Mg2+ complexed form of ATP, GTP, CTP, TTP and UTP to this putative NBS. These docking simulations and calculated ligand-binding scores are in general agreement with published data about experimentally measured binding to the CTD. The overall pattern of interactions between residues lining the site and docked nucleotides is conserved and broadly similar to that of other nucleotide-binding sites. Our docking simulations suggest that nucleotide binding stabilizes the only structurally labile region, thereby providing a rationale for the increased resistance to thermal denaturation and proteolysis. The docked nucleotides do not intrude onto the surface of residues involved in dimerization or chaperoning. Our molecular modeling permitted recognition of larger structural changes in the nucleotide-bound CTD dimer, including stabilization of helix-2 in both chains and intra- and inter- chain interactions between three residues (I613, Q617, R620).
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Affiliation(s)
- Samir S Roy
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada
| | - Manju Kapoor
- Department of Biological Sciences, The University of Calgary, 2500 University Drive NW, Calgary, AB, T2N 1N4, Canada.
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38
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Abstract
The chaperome constitutes a broad family of molecular chaperones and co-chaperones that facilitate the folding, refolding, and degradation of the proteome. Heat shock protein 90 (Hsp90) promotes the folding of numerous oncoproteins to aid survival of malignant phenotypes, and small molecule inhibitors of the Hsp90 chaperone complex offer a viable approach to treat certain cancers. One therapeutic attribute of this approach is the selectivity of these molecules to target high affinity oncogenic Hsp90 complexes present in tumor cells, which are absent in nontransformed cells. This selectivity has given rise to the idea that disease may contribute to forming a stress chaperome that is functionally distinct in its ability to interact with small molecule Hsp90 modulators. Consistent with this premise, modulating Hsp90 improves clinically relevant endpoints of diabetic peripheral neuropathy but has little impact in nondiabetic nerve. The concept of targeting the "diabetic chaperome" to treat diabetes and its complications is discussed.
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Affiliation(s)
- Rick T Dobrowsky
- Department of Pharmacology and Toxicology, The University of Kansas, 5064 Malott Hall 1251 Wescoe Hall Dr., Lawrence, KS, 66045, USA.
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39
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Hofmann H. Chaperones: Speedy motion for function. Nat Chem Biol 2016; 12:576-7. [PMID: 27434765 DOI: 10.1038/nchembio.2130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hagen Hofmann
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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40
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Bopp B, Ciglia E, Ouald-Chaib A, Groth G, Gohlke H, Jose J. Design and biological testing of peptidic dimerization inhibitors of human Hsp90 that target the C-terminal domain. Biochim Biophys Acta Gen Subj 2016; 1860:1043-55. [DOI: 10.1016/j.bbagen.2016.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 11/16/2022]
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41
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Vettoretti G, Moroni E, Sattin S, Tao J, Agard DA, Bernardi A, Colombo G. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands. Sci Rep 2016; 6:23830. [PMID: 27032695 PMCID: PMC4817115 DOI: 10.1038/srep23830] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/15/2016] [Indexed: 12/31/2022] Open
Abstract
Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone's active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.
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Affiliation(s)
- Gerolamo Vettoretti
- Istituto di Chimica del Riconoscimento Molecolare, CNR (ICRM-CNR), via Mario Bianco, 9, 20131, Milan, Italy
| | - Elisabetta Moroni
- Istituto di Chimica del Riconoscimento Molecolare, CNR (ICRM-CNR), via Mario Bianco, 9, 20131, Milan, Italy
| | - Sara Sattin
- Università degli Studi di Milano, Dipartimento di Chimica, via Golgi, 19, 20133, Milan, Italy
| | - Jiahui Tao
- Howard Hughes Medical Institute and Dept. of Biochemistry & Biophysics, University of California, San Francisco, 94158 USA
| | - David A. Agard
- Howard Hughes Medical Institute and Dept. of Biochemistry & Biophysics, University of California, San Francisco, 94158 USA
| | - Anna Bernardi
- Università degli Studi di Milano, Dipartimento di Chimica, via Golgi, 19, 20133, Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR (ICRM-CNR), via Mario Bianco, 9, 20131, Milan, Italy
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42
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Genest O, Hoskins JR, Kravats AN, Doyle SM, Wickner S. Hsp70 and Hsp90 of E. coli Directly Interact for Collaboration in Protein Remodeling. J Mol Biol 2015; 427:3877-89. [PMID: 26482100 DOI: 10.1016/j.jmb.2015.10.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/30/2015] [Accepted: 10/09/2015] [Indexed: 10/22/2022]
Abstract
Hsp90 is a highly conserved molecular chaperone that remodels hundreds of client proteins, many involved in the progression of cancer and other diseases. It functions with the Hsp70 chaperone and numerous cochaperones. The bacterial Hsp90 functions with an Hsp70 chaperone, DnaK, but is independent of Hsp90 cochaperones. We explored the collaboration between Escherichia coli Hsp90 and DnaK and found that the two chaperones form a complex that is stabilized by client protein binding. A J-domain protein, CbpA, facilitates assembly of the Hsp90Ec-DnaK-client complex. We identified E. coli Hsp90 mutants defective in DnaK interaction in vivo and show that the purified mutant proteins are defective in physical and functional interaction with DnaK. Understanding how Hsp90 and Hsp70 collaborate in protein remodeling will provide the groundwork for the development of new therapeutic strategies targeting multiple chaperones and cochaperones.
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Affiliation(s)
- Olivier Genest
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joel R Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea N Kravats
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shannon M Doyle
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Kim HS, Hong M, Lee SC, Lee HY, Suh YG, Oh DC, Seo JH, Choi H, Kim JY, Kim KW, Kim JH, Kim J, Kim YM, Park SJ, Park HJ, Lee J. Ring-truncated deguelin derivatives as potent Hypoxia Inducible Factor-1α (HIF-1α) inhibitors. Eur J Med Chem 2015; 104:157-64. [PMID: 26457742 DOI: 10.1016/j.ejmech.2015.09.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/24/2015] [Accepted: 09/25/2015] [Indexed: 11/17/2022]
Abstract
A series of fluorophenyl and pyridine analogues of 1 and 2 were synthesized as ring-truncated deguelin surrogates and evaluated for their HIF-1α inhibition. Their structure-activity relationship was systematically investigated based on the variation of the linker B-region moiety. Among the inhibitors, compound 25 exhibited potent HIF-1α inhibition in a dose-dependent manner and significant antitumor activity in H1299 with less toxicity than deguelin. It also inhibited in vitro hypoxia-mediated angiogenic processes in HRMECs. The docking study indicates that 25 occupied the C-terminal ATP-binding pocket of HSP90 in a similar mode as 1, which implies that the anticancer and antiangiogenic activities of 25 are derived from HIF-1α destabilization by binding to the C-terminal ATP-binding site of hHSP90.
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Affiliation(s)
- Ho Shin Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Mannkyu Hong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Su-Chan Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Ho-Young Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Young-Ger Suh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Ji Hae Seo
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Hoon Choi
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Jun Yong Kim
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea
| | - Kyu-Won Kim
- SNU-Harvard NeuroVascular Protection Research Center, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea; Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, 151-742, South Korea
| | - Jeong Hun Kim
- College of Medicine, Seoul National University, Seoul, 151-742, South Korea
| | - Joohwan Kim
- School of Medicine, Kangwon National University, Kangwon-do, 200-701, South Korea
| | - Young-Myeong Kim
- School of Medicine, Kangwon National University, Kangwon-do, 200-701, South Korea
| | - So-Jung Park
- School of Pharmacy, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Hyun-Ju Park
- School of Pharmacy, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Jeewoo Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, South Korea.
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44
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Lepvrier E, Moullintraffort L, Nigen M, Goude R, Allegro D, Barbier P, Peyrot V, Thomas D, Nazabal A, Garnier C. Hsp90 Oligomers Interacting with the Aha1 Cochaperone: An Outlook for the Hsp90 Chaperone Machineries. Anal Chem 2015; 87:7043-51. [PMID: 26076190 DOI: 10.1021/acs.analchem.5b00051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The 90-kDa heat shock protein (Hsp90) is a highly flexible dimer able to self-associate in the presence of divalent cations or under heat shock. This study investigated the relationship between Hsp90 oligomers and the Hsp90 cochaperone Aha1 (activator of Hsp90 ATPase). The interactions of Aha1 with Hsp90 dimers and oligomers were evaluated by ultracentrifugation, size-exclusion chromatography coupled to multiangle laser light scattering and high-mass matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Hsp90 dimer was able to bind up to four Aha1 molecules, and Hsp90 oligomers are also able to interact with Aha1. The binding of Aha1 did not interfere with the Hsp90 oligomerization process. Except for Hsp90 dimer, the stoichiometry of the interaction remained constant, at 2 Aha1 molecules per Hsp90 dimer, regardless of the degree of Hsp90 oligomerization. Moreover, Aha1 predominantly bound to Hsp90 oligomers. Thus, the ability of Hsp90 oligomers to bind the Aha1 ATPase activator reinforces their role within the Hsp90 chaperone machineries.
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Affiliation(s)
- Eléonore Lepvrier
- †Translation and Folding, UMR-CNRS 6290, Université de Rennes 1, Campus Beaulieu, 263 Avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Laura Moullintraffort
- †Translation and Folding, UMR-CNRS 6290, Université de Rennes 1, Campus Beaulieu, 263 Avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | - Michaël Nigen
- ‡UMR1208 Ingénierie des Agropolymères et Technologies Emergentes INRA-Montpellier SupAgro-CIRAD, Université Montpellier, 2 Place Pierre Viala, F-34060 Montpellier, France
| | - Renan Goude
- §Microbiologie risques infectieux, EA 1254, Université de Rennes 1, Campus Beaulieu, 35042 Rennes, Cedex, France
| | - Diane Allegro
- ∥Aix-Marseille Université, INSERM UMR 911, Centre de Recherche en Oncologie biologique et Onco-pharmacologie, 13385 Marseille, Cedex 5, France
| | - Pascale Barbier
- ∥Aix-Marseille Université, INSERM UMR 911, Centre de Recherche en Oncologie biologique et Onco-pharmacologie, 13385 Marseille, Cedex 5, France
| | - Vincent Peyrot
- ∥Aix-Marseille Université, INSERM UMR 911, Centre de Recherche en Oncologie biologique et Onco-pharmacologie, 13385 Marseille, Cedex 5, France
| | - Daniel Thomas
- †Translation and Folding, UMR-CNRS 6290, Université de Rennes 1, Campus Beaulieu, 263 Avenue du Général Leclerc, 35042 Rennes, Cedex, France
| | | | - Cyrille Garnier
- †Translation and Folding, UMR-CNRS 6290, Université de Rennes 1, Campus Beaulieu, 263 Avenue du Général Leclerc, 35042 Rennes, Cedex, France
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45
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Alternative approaches to Hsp90 modulation for the treatment of cancer. Future Med Chem 2015; 6:1587-605. [PMID: 25367392 DOI: 10.4155/fmc.14.89] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hsp90 is responsible for the conformational maturation of newly synthesized polypeptides (client proteins) and the re-maturation of denatured proteins via the Hsp90 chaperone cycle. Inhibition of the Hsp90 N-terminus has emerged as a clinically relevant strategy for anticancer chemotherapeutics due to the involvement of clients in a variety of oncogenic pathways. Several immunophilins, co-chaperones and partner proteins are also necessary for Hsp90 chaperoning activity. Alternative strategies to inhibit Hsp90 function include disruption of the C-terminal dimerization domain and the Hsp90 heteroprotein complex. C-terminal inhibitors and Hsp90 co-chaperone disruptors prevent cancer cell proliferation similar to N-terminal inhibitors and destabilize client proteins without induction of heat shock proteins. Herein, current Hsp90 inhibitors, the chaperone cycle, and regulation of this cycle will be discussed.
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46
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Abstract
Hsp90 chaperones receive much attention due to their role in cancer and other pathological conditions, and a tremendous effort of many laboratories has contributed in the past decades to considerable progress in the understanding of their functions. Hsp90 chaperones exist as dimers and, with the help of cochaperones, promote the folding of numerous client proteins. Although the original view of these interactions suggested that these dimeric complexes were symmetrical, it is now clear that many features are asymmetrical. In this review we discuss several recent advances that highlight how asymmetric interactions with cochaperones as well as asymmetric posttranslational modifications provide mechanisms to regulate client interactions and the progression through Hsp90's chaperone cycle.
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Affiliation(s)
- Matthias P Mayer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Laura Le Breton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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47
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Lee SC, Min HY, Choi H, Kim HS, Kim KC, Park SJ, Seong MA, Seo JH, Park HJ, Suh YG, Kim KW, Hong HS, Kim H, Lee MY, Lee J, Lee HY. Synthesis and Evaluation of a Novel Deguelin Derivative, L80, which Disrupts ATP Binding to the C-terminal Domain of Heat Shock Protein 90. Mol Pharmacol 2015; 88:245-55. [PMID: 25976766 DOI: 10.1124/mol.114.096883] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 05/05/2015] [Indexed: 01/14/2023] Open
Abstract
The clinical benefit of current anticancer regimens for lung cancer therapy is still limited due to moderate efficacy, drug resistance, and recurrence. Therefore, the development of effective anticancer drugs for first-line therapy and for optimal second-line treatment is necessary. Because the 90-kDa molecular chaperone heat shock protein (Hsp90) contributes to the maturation of numerous mutated or overexpressed oncogenic proteins, targeting Hsp90 may offer an effective anticancer therapy. Here, we investigated antitumor activities and toxicity of a novel deguelin-derived C-terminal Hsp90 inhibitor, designated L80. L80 displayed significant inhibitory effects on the viability, colony formation, angiogenesis-stimulating activity, migration, and invasion of a panel of non-small cell lung cancer cell lines and their sublines with acquired resistance to paclitaxel with minimal toxicity to normal lung epithelial cells, hippocampal cells, vascular endothelial cells, and ocular cells. Biochemical analyses and molecular docking simulation revealed that L80 disrupted Hsp90 function by binding to the C-terminal ATP-binding pocket of Hsp90, leading to the disruption of the interaction between hypoxia-inducible factor (HIF)-1α and Hsp90, downregulation of HIF-1α and its target genes, including vascular endothelial growth factor (VEGF) and insulin-like growth factor 2 (IGF2), and decreased the expression of various Hsp90 client proteins. Consistent with these in vitro findings, L80 exhibited significant antitumor and antiangiogenic activities in H1299 xenograft tumors. These results suggest that L80 represents a novel C-terminal Hsp90 inhibitor with effective anticancer activities with minimal toxicities.
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Affiliation(s)
- Su-Chan Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Hye-Young Min
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Hoon Choi
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Ho Shin Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Kyong-Cheol Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - So-Jung Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Myeong A Seong
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Ji Hae Seo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Hyun-Ju Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Young-Ger Suh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Kyu-Won Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Hyun-Seok Hong
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Hee Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Min-Young Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Jeewoo Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
| | - Ho-Young Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea (S.-C.L., H.-Y.M., H.C., H.S.K., K.-C.K., M.A.S., J.H.S., Y.-G.S., K.-W.K., J.L., H.-Y.L.); School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea (S.-J.P., H.-J.P.); and Medifron-DBT, Ansan, Republic of Korea (H.-S.H., H.K., M.-Y.L.)
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48
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Chehab M, Caza T, Skotnicki K, Landas S, Bratslavsky G, Mollapour M, Bourboulia D. Targeting Hsp90 in urothelial carcinoma. Oncotarget 2015; 6:8454-73. [PMID: 25909217 PMCID: PMC4496161 DOI: 10.18632/oncotarget.3502] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/09/2015] [Indexed: 02/06/2023] Open
Abstract
Urothelial carcinoma, or transitional cell carcinoma, is the most common urologic malignancy that carries significant morbidity, mortality, recurrence risk and associated health care costs. Despite use of current chemotherapies and immunotherapies, long-term remission in patients with muscle-invasive or metastatic disease remains low, and disease recurrence is common. The molecular chaperone Heat Shock Protein-90 (Hsp90) may offer an ideal treatment target, as it is a critical signaling hub in urothelial carcinoma pathogenesis and potentiates chemoradiation. Preclinical testing with Hsp90 inhibitors has demonstrated reduced proliferation, enhanced apoptosis and synergism with chemotherapies and radiation. Despite promising preclinical data, clinical trials utilizing Hsp90 inhibitors for other malignancies had modest efficacy. Therefore, we propose that Hsp90 inhibition would best serve as an adjuvant treatment in advanced muscle-invasive or metastatic bladder cancers to potentiate other therapies. An overview of bladder cancer biology, current treatments, molecular targeted therapies, and the role for Hsp90 inhibitors in the treatment of urothelial carcinoma is the focus of this review.
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MESH Headings
- Angiogenesis Inhibitors/therapeutic use
- Antineoplastic Agents/therapeutic use
- Apoptosis
- BCG Vaccine/therapeutic use
- Carcinoma, Transitional Cell/epidemiology
- Carcinoma, Transitional Cell/metabolism
- Carcinoma, Transitional Cell/pathology
- Carcinoma, Transitional Cell/therapy
- Cell Cycle/drug effects
- Cell Division
- Cell Transformation, Neoplastic
- Chemoradiotherapy
- Chemotherapy, Adjuvant
- Clinical Trials as Topic
- Combined Modality Therapy
- Cystectomy
- Drug Resistance, Neoplasm
- Drugs, Investigational/therapeutic use
- HSP90 Heat-Shock Proteins/antagonists & inhibitors
- HSP90 Heat-Shock Proteins/chemistry
- HSP90 Heat-Shock Proteins/physiology
- Histone Code/drug effects
- Humans
- Models, Biological
- Molecular Targeted Therapy
- Muscle, Smooth/pathology
- Neoplasm Invasiveness
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/physiology
- Protein Kinase Inhibitors/therapeutic use
- Signal Transduction/drug effects
- Transcription, Genetic/drug effects
- Urologic Neoplasms/epidemiology
- Urologic Neoplasms/metabolism
- Urologic Neoplasms/pathology
- Urologic Neoplasms/therapy
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Affiliation(s)
- Mahmoud Chehab
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Tiffany Caza
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Kamil Skotnicki
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Steve Landas
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Research Institute, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Research Institute, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Research Institute, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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49
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Guzman I, Ghaemi Z, Baranger A, Luthey-Schulten Z, Gruebele M. Native Conformational Dynamics of the Spliceosomal U1A Protein. J Phys Chem B 2015; 119:3651-61. [DOI: 10.1021/jp511760m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
| | | | - Anne Baranger
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
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50
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Synoradzki K, Bieganowski P. Middle domain of human Hsp90 isoforms differentially binds Aha1 in human cells and alters Hsp90 activity in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:445-52. [PMID: 25486457 DOI: 10.1016/j.bbamcr.2014.11.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 11/23/2014] [Accepted: 11/24/2014] [Indexed: 11/28/2022]
Abstract
Hsp90 is an essential chaperone for more than 200 client proteins in eukaryotic cells. The human genome encodes two highly similar cytosolic Hsp90 proteins called Hsp90α and Hsp90β. Most of the client proteins can interact with either Hsp90 protein; however, only a handful client proteins and one co-chaperone that interact specifically with one of the Hsp90 isoforms were identified. Structural differences underlying these isoform-specific interactions were not studied. Here we report for the first time that the Hsp90 co-chaperone Aha1 interacts preferentially with Hsp90α. The distinction depends on the middle domain of Hsp90. The middle domain of Hsp90α is also responsible for the slow growth phenotype of yeasts that express this isoform as a sole source of Hsp90. These results suggest that differences in the middle domain of Hsp90α and Hsp90β may be responsible for the isoform-specific interactions with selected proteins. Also shown here within, we determine that preferential chaperoning of cIAP1 by Hsp90β is mediated by the N-terminal domain of this isoform.
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Affiliation(s)
- Kamil Synoradzki
- Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., Warsaw 02-106, Poland
| | - Pawel Bieganowski
- Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., Warsaw 02-106, Poland.
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