1
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Magni A, Sciva C, Castelli M, Digwal CS, Rodina A, Sharma S, Ochiana S, Patel HJ, Shah S, Chiosis G, Moroni E, Colombo G. N-Glycosylation-Induced Pathologic Protein Conformations as a Tool to Guide the Selection of Biologically Active Small Molecules. Chemistry 2024; 30:e202401957. [PMID: 39042517 DOI: 10.1002/chem.202401957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/11/2024] [Accepted: 07/23/2024] [Indexed: 07/25/2024]
Abstract
Post-translational modifications such as protein N-glycosylation, significantly influence cellular processes. Dysregulated N-glycosylation, exemplified in Grp94, a member of the Hsp90 family, leads to structural changes and the formation of epichaperomes, contributing to pathologies. Targeting N-glycosylation-induced conformations offers opportunities for developing selective chemical tools and drugs for these pathologic forms of chaperones. We here demonstrate how a specific Grp94 conformation induced by N-glycosylation, identified previously via molecular dynamics simulations, rationalizes the distinct behavior of similar ligands. Integrating dynamic ligand unbinding information with SAR development, we differentiate ligands productively engaging the pathologic Grp94 conformers from those that are not. Additionally, analyzing binding site stereoelectronic properties and QSAR models using cytotoxicity data unveils relationships between chemical, conformational properties, and biological activities. These findings facilitate the design of ligands targeting specific Grp94 conformations induced by abnormal glycosylation, selectively disrupting pathogenic protein networks while sparing normal mechanisms.
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Affiliation(s)
- Andrea Magni
- Department of Chemistry, University of Pavia, 27100, Pavia, Italy
| | - Cristiano Sciva
- Department of Chemistry, University of Pavia, 27100, Pavia, Italy
- Institute of Chemical Sciences and Technologies (SCITEC), Italian National Research Council (CNR), 20131, Milano, Italy
| | - Matteo Castelli
- Department of Chemistry, University of Pavia, 27100, Pavia, Italy
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sahil Sharma
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Stefan Ochiana
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hardik J Patel
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Smit Shah
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Elisabetta Moroni
- Institute of Chemical Sciences and Technologies (SCITEC), Italian National Research Council (CNR), 20131, Milano, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, 27100, Pavia, Italy
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2
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Guarra F, Sciva C, Bonollo G, Pasala C, Chiosis G, Moroni E, Colombo G. Cracking the chaperone code through the computational microscope. Cell Stress Chaperones 2024; 29:626-640. [PMID: 39142378 PMCID: PMC11399801 DOI: 10.1016/j.cstres.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/09/2024] [Indexed: 08/16/2024] Open
Abstract
The heat shock protein 90 kDa (Hsp90) chaperone machinery plays a crucial role in maintaining cellular homeostasis. Beyond its traditional role in protein folding, Hsp90 is integral to key pathways influencing cellular function in health and disease. Hsp90 operates through the modular assembly of large multiprotein complexes, with their composition, stability, and localization adapting to the cell's needs. Its functional dynamics are finely tuned by ligand binding and post-translational modifications (PTMs). Here, we discuss how to disentangle the intricacies of the complex code that governs the crosstalk between dynamics, binding, PTMs, and the functions of the Hsp90 machinery using computer-based approaches. Specifically, we outline the contributions of computational and theoretical methods to the understanding of Hsp90 functions, ranging from providing atomic-level insights into its dynamics to clarifying the mechanisms of interactions with protein clients, cochaperones, and ligands. The knowledge generated in this framework can be actionable for the design and development of chemical tools and drugs targeting Hsp90 in specific disease-associated cellular contexts. Finally, we provide our perspective on how computation can be integrated into the study of the fine-tuning of functions in the highly complex Hsp90 landscape, complementing experimental methods for a comprehensive understanding of this important chaperone system.
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Affiliation(s)
| | | | | | - Chiranjeevi Pasala
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Elisabetta Moroni
- Institute of Chemical Sciences and Technologies (SCITEC) - Italian National Research Council (CNR), Milano, Italy.
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3
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Noureddine J, Mu B, Hamidzada H, Mok WL, Bonea D, Nambara E, Zhao R. Knockout of endoplasmic reticulum-localized molecular chaperone HSP90.7 impairs seedling development and cellular auxin homeostasis in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:218-236. [PMID: 38565312 DOI: 10.1111/tpj.16754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
The Arabidopsis endoplasmic reticulum-localized heat shock protein HSP90.7 modulates tissue differentiation and stress responses; however, complete knockout lines have not been previously reported. In this study, we identified and analyzed a mutant allele, hsp90.7-1, which was unable to accumulate the HSP90.7 full-length protein and showed seedling lethality. Microscopic analyses revealed its essential role in male and female fertility, trichomes and root hair development, proper chloroplast function, and apical meristem maintenance and differentiation. Comparative transcriptome and proteome analyses also revealed the role of the protein in a multitude of cellular processes. Particularly, the auxin-responsive pathway was specifically downregulated in the hsp90.7-1 mutant seedlings. We measured a much-reduced auxin content in both root and shoot tissues. Through comprehensive histological and molecular analyses, we confirmed PIN1 and PIN5 accumulations were dependent on the HSP90 function, and the TAA-YUCCA primary auxin biosynthesis pathway was also downregulated in the mutant seedlings. This study therefore not only fulfilled a gap in understanding the essential role of HSP90 paralogs in eukaryotes but also provided a mechanistic insight on the ER-localized chaperone in regulating plant growth and development via modulating cellular auxin homeostasis.
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Affiliation(s)
- Jenan Noureddine
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Bona Mu
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Homaira Hamidzada
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Wai Lam Mok
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Diana Bonea
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eiji Nambara
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Rongmin Zhao
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Cell & Systems Biology, University of Toronto, Toronto, Ontario, Canada
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4
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Wickramaratne AC, Wickner S, Kravats AN. Hsp90, a team player in protein quality control and the stress response in bacteria. Microbiol Mol Biol Rev 2024; 88:e0017622. [PMID: 38534118 PMCID: PMC11332350 DOI: 10.1128/mmbr.00176-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
SUMMARYHeat shock protein 90 (Hsp90) participates in proteostasis by facilitating protein folding, activation, disaggregation, prevention of aggregation, degradation, and protection against degradation of various cellular proteins. It is highly conserved from bacteria to humans. In bacteria, protein remodeling by Hsp90 involves collaboration with the Hsp70 molecular chaperone and Hsp70 cochaperones. In eukaryotes, protein folding by Hsp90 is more complex and involves collaboration with many Hsp90 cochaperones as well as Hsp70 and Hsp70 cochaperones. This review focuses primarily on bacterial Hsp90 and highlights similarities and differences between bacterial and eukaryotic Hsp90. Seminal research findings that elucidate the structure and the mechanisms of protein folding, disaggregation, and reactivation promoted by Hsp90 are discussed. Understanding the mechanisms of bacterial Hsp90 will provide fundamental insight into the more complex eukaryotic chaperone systems.
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Affiliation(s)
- Anushka C. Wickramaratne
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrea N. Kravats
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
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5
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Zhang M, Bi X. Heat Shock Proteins and Breast Cancer. Int J Mol Sci 2024; 25:876. [PMID: 38255948 PMCID: PMC10815085 DOI: 10.3390/ijms25020876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Heat shock proteins (Hsps) are a group of stress-induced proteins involved in protein folding and maturation. Based on their molecular weight, Hsps can be divided into six families: small Hsps, Hsp40, Hsp60, Hsp70, Hsp90, and large Hsps. In the process of breast cancer tumorigenesis, Hsps play a central role in regulating cell reactions and functions including proliferation, metastasis, and apoptosis. Moreover, some of the critical Hsps also regulate the fine balance between the protective and destructive immunological responses within the tumor microenvironment. In this review, we systematically summarize the roles of major Hsps in breast cancer biology and point out the potential uses of these proteins in breast cancer diagnosis and therapy. Understanding the roles of different families of Hsps in breast cancer pathogenesis will help in the development of more effective prevention and treatment measures for breast cancer.
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Affiliation(s)
- Miao Zhang
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China;
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Xiaowen Bi
- Department of Medical Genetics and Cell Biology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China;
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6
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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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7
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Xiang Y, Liu X, Sun Q, Liao K, Liu X, Zhao Z, Feng L, Liu Y, Wang B. The development of cancers research based on mitochondrial heat shock protein 90. Front Oncol 2023; 13:1296456. [PMID: 38098505 PMCID: PMC10720920 DOI: 10.3389/fonc.2023.1296456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
Mitochondrial heat shock protein 90 (mtHsp90), including Tumor necrosis factor receptor-associated protein 1 (TRAP1) and Hsp90 translocated from cytoplasm, modulating cellular metabolism and signaling pathways by altering the conformation, activity, and stability of numerous client proteins, and is highly expressed in tumors. mtHsp90 inhibition results in the destabilization and eventual degradation of its client proteins, leading to interference with various tumor-related pathways and efficient control of cancer cell development. Among these compounds, gamitrinib, a specific mtHsp90 inhibitor, has demonstrated its safety and efficacy in several preclinical investigations and is currently undergoing evaluation in clinical trials. This review aims to provide a comprehensive overview of the present knowledge pertaining to mtHsp90, encompassing its structure and function. Moreover, our main emphasis is on the development of mtHsp90 inhibitors for various cancer therapies, to present a thorough overview of the recent pre-clinical and clinical advancements in this field.
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Affiliation(s)
- Yuchu Xiang
- West China Hospital of Sichuan University, Sichuan University, Chengdu, China
| | - Xudong Liu
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Qi Sun
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, Centre for Safe Medication Practice and Research, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Kuo Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaohan Liu
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Zihui Zhao
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lishuang Feng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yan Liu
- Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Bo Wang
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
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8
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Castelli M, Yan P, Rodina A, Digwal CS, Panchal P, Chiosis G, Moroni E, Colombo G. How aberrant N-glycosylation can alter protein functionality and ligand binding: An atomistic view. Structure 2023; 31:987-1004.e8. [PMID: 37343552 PMCID: PMC10526633 DOI: 10.1016/j.str.2023.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/21/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Protein-assembly defects due to an enrichment of aberrant conformational protein variants are emerging as a new frontier in therapeutics design. Understanding the structural elements that rewire the conformational dynamics of proteins and pathologically perturb functionally oriented ensembles is important for inhibitor development. Chaperones are hub proteins for the assembly of multiprotein complexes and an enrichment of aberrant conformers can affect the cellular proteome, and in turn, phenotypes. Here, we integrate computational and experimental tools to investigte how N-glycosylation of specific residues in glucose-regulated protein 94 (GRP94) modulates internal dynamics and alters the conformational fitness of regions fundamental for the interaction with ATP and synthetic ligands and impacts substructures important for the recognition of interacting proteins. N-glycosylation plays an active role in modulating the energy landscape of GRP94, and we provide support for leveraging the knowledge on distinct glycosylation variants to design molecules targeting GRP94 disease-associated conformational states and assemblies.
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Affiliation(s)
- Matteo Castelli
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Pengrong Yan
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna Rodina
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chander S Digwal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Palak Panchal
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriela Chiosis
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | | | - Giorgio Colombo
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy.
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9
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Alao JP, Obaseki I, Amankwah YS, Nguyen Q, Sugoor M, Unruh E, Popoola HO, Tehver R, Kravats AN. Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics. J Phys Chem B 2023; 127:5389-5409. [PMID: 37294929 PMCID: PMC10292203 DOI: 10.1021/acs.jpcb.3c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/17/2023] [Indexed: 06/11/2023]
Abstract
Grp94, an ER-localized molecular chaperone, is required for the folding and activation of many membrane and secretory proteins. Client activation by Grp94 is mediated by nucleotide and conformational changes. In this work, we aim to understand how microscopic changes from nucleotide hydrolysis can potentiate large-scale conformational changes of Grp94. We performed all-atom molecular dynamics simulations on the ATP-hydrolysis competent state of the Grp94 dimer in four different nucleotide bound states. We found that Grp94 was the most rigid when ATP was bound. ATP hydrolysis or nucleotide removal enhanced mobility of the N-terminal domain and ATP lid, resulting in suppression of interdomain communication. In an asymmetric conformation with one hydrolyzed nucleotide, we identified a more compact state, similar to experimental observations. We also identified a potential regulatory role of the flexible linker, as it formed electrostatic interactions with the Grp94 M-domain helix near the region where BiP is known to bind. These studies were complemented with normal-mode analysis of an elastic network model to investigate Grp94's large-scale conformational changes. SPM analysis identified residues that are important in signaling conformational change, many of which have known functional relevance in ATP coordination and catalysis, client binding, and BiP binding. Our findings suggest that ATP hydrolysis in Grp94 alters allosteric wiring and facilitates conformational changes.
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Affiliation(s)
- John Paul Alao
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Ikponwmosa Obaseki
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yaa Sarfowah Amankwah
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Quinn Nguyen
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
| | - Meghana Sugoor
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Erin Unruh
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell,
Molecular, and Structural Biology Program, Department of Chemistry
& Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | | | - Riina Tehver
- Department
of Physics, Denison University, Granville, Ohio 43023, United States
| | - Andrea N. Kravats
- Department
of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
- Cell,
Molecular, and Structural Biology Program, Department of Chemistry
& Biochemistry, Miami University, Oxford, Ohio 45056, United States
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10
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Kang S, Kang BH. Structure, Function, and Inhibitors of the Mitochondrial Chaperone TRAP1. J Med Chem 2022; 65:16155-16172. [PMID: 36507721 DOI: 10.1021/acs.jmedchem.2c01633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tumor necrosis factor receptor-associated protein 1 (TRAP1) is a mitochondrial molecular chaperone modulating cellular metabolism and signaling pathways by altering the conformation, activity, and stability of numerous substrate proteins called clients. It exerts its chaperone function as an adaptive response to counter cellular stresses instead of maintaining housekeeping protein homeostasis. However, the stress-adaptive machinery becomes dysregulated to support the progression and maintenance of human diseases, such as cancers; therefore, TRAP1 has been proposed as a promising target protein for anticancer drug development. In this review, by collating recent reports on high-resolution TRAP1 structures and structure-activity relationships of inhibitors, we aimed to provide better insights into the chaperoning mechanism of the emerging drug target and to suggest an efficient strategy for the development of potent TRAP1 inhibitors.
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Affiliation(s)
- Soosung Kang
- College of Pharmacy, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Byoung Heon Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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11
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Cannino G, Urbani A, Gaspari M, Varano M, Negro A, Filippi A, Ciscato F, Masgras I, Gerle C, Tibaldi E, Brunati AM, Colombo G, Lippe G, Bernardi P, Rasola A. The mitochondrial chaperone TRAP1 regulates F-ATP synthase channel formation. Cell Death Differ 2022; 29:2335-2346. [PMID: 35614131 PMCID: PMC9751095 DOI: 10.1038/s41418-022-01020-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 01/31/2023] Open
Abstract
Binding of the mitochondrial chaperone TRAP1 to client proteins shapes bioenergetic and proteostatic adaptations of cells, but the panel of TRAP1 clients is only partially defined. Here we show that TRAP1 interacts with F-ATP synthase, the protein complex that provides most cellular ATP. TRAP1 competes with the peptidyl-prolyl cis-trans isomerase cyclophilin D (CyPD) for binding to the oligomycin sensitivity-conferring protein (OSCP) subunit of F-ATP synthase, increasing its catalytic activity and counteracting the inhibitory effect of CyPD. Electrophysiological measurements indicate that TRAP1 directly inhibits a channel activity of purified F-ATP synthase endowed with the features of the permeability transition pore (PTP) and that it reverses PTP induction by CyPD, antagonizing PTP-dependent mitochondrial depolarization and cell death. Conversely, CyPD outcompetes the TRAP1 inhibitory effect on the channel. Our data identify TRAP1 as an F-ATP synthase regulator that can influence cell bioenergetics and survival and can be targeted in pathological conditions where these processes are dysregulated, such as cancer.
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Affiliation(s)
- Giuseppe Cannino
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Andrea Urbani
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, viale Europa, 88100, Catanzaro, Italy
| | - Mariaconcetta Varano
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, viale Europa, 88100, Catanzaro, Italy
| | - Alessandro Negro
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Antonio Filippi
- Department of Medicine, University of Udine, via Colugna 50, 33100, Udine, Italy
| | - Francesco Ciscato
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
| | - Ionica Masgras
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
- Institute of Neuroscience, National Research Council, Viale G. Colombo 3, 35131, Padova, Italy
| | - Christoph Gerle
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Elena Tibaldi
- Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121, Padova, Italy
| | - Anna Maria Brunati
- Department of Molecular Medicine, University of Padova, via Gabelli 63, 35121, Padova, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100, Pavia, Italy
- Institute of Chemical and Technological Sciences "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131, Milano, Italy
| | - Giovanna Lippe
- Department of Medicine, University of Udine, via Colugna 50, 33100, Udine, Italy
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy
- Institute of Neuroscience, National Research Council, Viale G. Colombo 3, 35131, Padova, Italy
| | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131, Padova, Italy.
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12
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Kim S, Backe SJ, Wengert LA, Johnson AE, Isakov RV, Bratslavsky MS, Woodford MR. O-GlcNAcylation suppresses TRAP1 activity and promotes mitochondrial respiration. Cell Stress Chaperones 2022; 27:573-585. [PMID: 35976490 PMCID: PMC9485411 DOI: 10.1007/s12192-022-01293-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/03/2022] Open
Abstract
The molecular chaperone TNF-receptor-associated protein-1 (TRAP1) controls mitochondrial respiration through regulation of Krebs cycle and electron transport chain activity. Post-translational modification (PTM) of TRAP1 regulates its activity, thereby controlling global metabolic flux. O-GlcNAcylation is one PTM that is known to impact mitochondrial metabolism, however the major effectors of this regulatory PTM remain inadequately resolved. Here we demonstrate that TRAP1-O-GlcNAcylation decreases TRAP1 ATPase activity, leading to increased mitochondrial metabolism. O-GlcNAcylation of TRAP1 occurs following mitochondrial import and provides critical regulatory feedback, as the impact of O-GlcNAcylation on mitochondrial metabolism shows TRAP1-dependence. Mechanistically, loss of TRAP1-O-GlcNAcylation decreased TRAP1 binding to ATP, and interaction with its client protein succinate dehydrogenase (SDHB). Taken together, TRAP1-O-GlcNAcylation serves to regulate mitochondrial metabolism by the reversible attenuation of TRAP1 chaperone activity.
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Affiliation(s)
- Seungchan Kim
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Laura A Wengert
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Anna E Johnson
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Roman V Isakov
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Michael S Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
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13
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Faienza F, Rasola A, Filomeni G. Nitric oxide-based regulation of metabolism: Hints from TRAP1 and SIRT3 crosstalk. Front Mol Biosci 2022; 9:942729. [PMID: 35959462 PMCID: PMC9360569 DOI: 10.3389/fmolb.2022.942729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fiorella Faienza
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Giuseppe Filomeni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Redox Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
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14
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Joshi A, Ito T, Picard D, Neckers L. The Mitochondrial HSP90 Paralog TRAP1: Structural Dynamics, Interactome, Role in Metabolic Regulation, and Inhibitors. Biomolecules 2022; 12:biom12070880. [PMID: 35883436 PMCID: PMC9312948 DOI: 10.3390/biom12070880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
The HSP90 paralog TRAP1 was discovered more than 20 years ago; yet, a detailed understanding of the function of this mitochondrial molecular chaperone remains elusive. The dispensable nature of TRAP1 in vitro and in vivo further complicates an understanding of its role in mitochondrial biology. TRAP1 is more homologous to the bacterial HSP90, HtpG, than to eukaryotic HSP90. Lacking co-chaperones, the unique structural features of TRAP1 likely regulate its temperature-sensitive ATPase activity and shed light on the alternative mechanisms driving the chaperone’s nucleotide-dependent cycle in a defined environment whose physiological temperature approaches 50 °C. TRAP1 appears to be an important bioregulator of mitochondrial respiration, mediating the balance between oxidative phosphorylation and glycolysis, while at the same time promoting mitochondrial homeostasis and displaying cytoprotective activity. Inactivation/loss of TRAP1 has been observed in several neurodegenerative diseases while TRAP1 expression is reported to be elevated in multiple cancers and, as with HSP90, evidence of addiction to TRAP1 has been observed. In this review, we summarize what is currently known about this unique HSP90 paralog and why a better understanding of TRAP1 structure, function, and regulation is likely to enhance our understanding of the mechanistic basis of mitochondrial homeostasis.
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Affiliation(s)
- Abhinav Joshi
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892, USA; (A.J.); (T.I.)
| | - Takeshi Ito
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892, USA; (A.J.); (T.I.)
| | - Didier Picard
- Department of Molecular and Cellular Biology, Université de Genève, Sciences III, 30 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland;
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), Bethesda, MD 20892, USA; (A.J.); (T.I.)
- Correspondence: ; Tel.: +1-240-858-3918
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15
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Xu H. Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones. Biomolecules 2022; 12:832. [PMID: 35740957 PMCID: PMC9221429 DOI: 10.3390/biom12060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/14/2022] Open
Abstract
Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each break a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen's hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermodynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways.
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Affiliation(s)
- Huafeng Xu
- Roivant Sciences, New York, NY 10036, USA
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16
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Wengert LA, Backe SJ, Bourboulia D, Mollapour M, Woodford MR. TRAP1 Chaperones the Metabolic Switch in Cancer. Biomolecules 2022; 12:biom12060786. [PMID: 35740911 PMCID: PMC9221471 DOI: 10.3390/biom12060786] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/02/2022] [Accepted: 06/02/2022] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial function is dependent on molecular chaperones, primarily due to their necessity in the formation of respiratory complexes and clearance of misfolded proteins. Heat shock proteins (Hsps) are a subset of molecular chaperones that function in all subcellular compartments, both constitutively and in response to stress. The Hsp90 chaperone TNF-receptor-associated protein-1 (TRAP1) is primarily localized to the mitochondria and controls both cellular metabolic reprogramming and mitochondrial apoptosis. TRAP1 upregulation facilitates the growth and progression of many cancers by promoting glycolytic metabolism and antagonizing the mitochondrial permeability transition that precedes multiple cell death pathways. TRAP1 attenuation induces apoptosis in cellular models of cancer, identifying TRAP1 as a potential therapeutic target in cancer. Similar to cytosolic Hsp90 proteins, TRAP1 is also subject to post-translational modifications (PTM) that regulate its function and mediate its impact on downstream effectors, or ‘clients’. However, few effectors have been identified to date. Here, we will discuss the consequence of TRAP1 deregulation in cancer and the impact of post-translational modification on the known functions of TRAP1.
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Affiliation(s)
- Laura A. Wengert
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (L.A.W.); (S.J.B.); (D.B.); (M.M.)
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sarah J. Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (L.A.W.); (S.J.B.); (D.B.); (M.M.)
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (L.A.W.); (S.J.B.); (D.B.); (M.M.)
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (L.A.W.); (S.J.B.); (D.B.); (M.M.)
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mark R. Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (L.A.W.); (S.J.B.); (D.B.); (M.M.)
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Correspondence:
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17
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Advances towards Understanding the Mechanism of Action of the Hsp90 Complex. Biomolecules 2022; 12:biom12050600. [PMID: 35625528 PMCID: PMC9138868 DOI: 10.3390/biom12050600] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 12/24/2022] Open
Abstract
Hsp90 (Heat Shock Protein 90) is an ATP (Adenosine triphosphate) molecular chaperone responsible for the activation and maturation of client proteins. The mechanism by which Hsp90 achieves such activation, involving structurally diverse client proteins, has remained enigmatic. However, recent advances using structural techniques, together with advances in biochemical studies, have not only defined the chaperone cycle but have shed light on its mechanism of action. Hsp90 hydrolysis of ATP by each protomer may not be simultaneous and may be dependent on the specific client protein and co-chaperone complex involved. Surprisingly, Hsp90 appears to remodel client proteins, acting as a means by which the structure of the client protein is modified to allow its subsequent refolding to an active state, in the case of kinases, or by making the client protein competent for hormone binding, as in the case of the GR (glucocorticoid receptor). This review looks at selected examples of client proteins, such as CDK4 (cyclin-dependent kinase 4) and GR, which are activated according to the so-called ‘remodelling hypothesis’ for their activation. A detailed description of these activation mechanisms is paramount to understanding how Hsp90-associated diseases develop.
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18
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Triveri A, Sanchez-Martin C, Torielli L, Serapian SA, Marchetti F, D'Acerno G, Pirota V, Castelli M, Moroni E, Ferraro M, Quadrelli P, Rasola A, Colombo G. Protein allostery and ligand design: Computational design meets experiments to discover novel chemical probes. J Mol Biol 2022; 434:167468. [DOI: 10.1016/j.jmb.2022.167468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 10/19/2022]
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19
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Yoon NG, Lee H, Kim SY, Hu S, Kim D, Yang S, Hong KB, Lee JH, Kang S, Kim BG, Myung K, Lee C, Kang BH. Mitoquinone Inactivates Mitochondrial Chaperone TRAP1 by Blocking the Client Binding Site. J Am Chem Soc 2021; 143:19684-19696. [PMID: 34758612 DOI: 10.1021/jacs.1c07099] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Heat shock protein 90 (Hsp90) family proteins are molecular chaperones that modulate the functions of various substrate proteins (clients) implicated in pro-tumorigenic pathways. In this study, the mitochondria-targeted antioxidant mitoquinone (MitoQ) was identified as a potent inhibitor of mitochondrial Hsp90, known as a tumor necrosis factor receptor-associated protein 1 (TRAP1). Structural analyses revealed an asymmetric bipartite interaction between MitoQ and the previously unrecognized drug binding sites located in the middle domain of TRAP1, believed to be a client binding region. MitoQ effectively competed with TRAP1 clients, and MitoQ treatment facilitated the identification of 103 TRAP1-interacting mitochondrial proteins in cancer cells. MitoQ and its redox-crippled SB-U014/SB-U015 exhibited more potent anticancer activity in vitro and in vivo than previously reported mitochondria-targeted TRAP1 inhibitors. The findings indicate that targeting the client binding site of Hsp90 family proteins offers a novel strategy for the development of potent anticancer drugs.
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Affiliation(s)
- Nam Gu Yoon
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Hakbong Lee
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - So-Yeon Kim
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Sung Hu
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Darong Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Sujae Yang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, South Korea
| | - Ki Bum Hong
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Ji Hoon Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, South Korea
| | - Soosung Kang
- College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, South Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Changwook Lee
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, South Korea
| | - Byoung Heon Kang
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, South Korea
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20
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TRAP1 in Oxidative Stress and Neurodegeneration. Antioxidants (Basel) 2021; 10:antiox10111829. [PMID: 34829705 PMCID: PMC8614808 DOI: 10.3390/antiox10111829] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/13/2021] [Accepted: 11/15/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor necrosis factor receptor-associated protein 1 (TRAP1), also known as heat shock protein 75 (HSP75), is a member of the heat shock protein 90 (HSP90) chaperone family that resides mainly in the mitochondria. As a mitochondrial molecular chaperone, TRAP1 supports protein folding and contributes to the maintenance of mitochondrial integrity even under cellular stress. TRAP1 is a cellular regulator of mitochondrial bioenergetics, redox homeostasis, oxidative stress-induced cell death, apoptosis, and unfolded protein response (UPR) in the endoplasmic reticulum (ER). TRAP1 has attracted increasing interest as a therapeutical target, with a special focus on the design of TRAP1 specific inhibitors. Although TRAP1 was extensively studied in the oncology field, its role in central nervous system cells, under physiological and pathological conditions, remains largely unknown. In this review, we will start by summarizing the biology of TRAP1, including its structure and related pathways. Thereafter, we will continue by debating the role of TRAP1 in the maintenance of redox homeostasis and protection against oxidative stress and apoptosis. The role of TRAP1 in neurodegenerative disorders will also be discussed. Finally, we will review the potential of TRAP1 inhibitors as neuroprotective drugs.
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21
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Stofberg ML, Caillet C, de Villiers M, Zininga T. Inhibitors of the Plasmodium falciparum Hsp90 towards Selective Antimalarial Drug Design: The Past, Present and Future. Cells 2021; 10:2849. [PMID: 34831072 PMCID: PMC8616389 DOI: 10.3390/cells10112849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022] Open
Abstract
Malaria is still one of the major killer parasitic diseases in tropical settings, posing a public health threat. The development of antimalarial drug resistance is reversing the gains made in attempts to control the disease. The parasite leads a complex life cycle that has adapted to outwit almost all known antimalarial drugs to date, including the first line of treatment, artesunate. There is a high unmet need to develop new strategies and identify novel therapeutics to reverse antimalarial drug resistance development. Among the strategies, here we focus and discuss the merits of the development of antimalarials targeting the Heat shock protein 90 (Hsp90) due to the central role it plays in protein quality control.
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Affiliation(s)
| | | | | | - Tawanda Zininga
- Department of Biochemistry, Stellenbosch University, Stellenbosch 7600, South Africa; (M.L.S.); (C.C.); (M.d.V.)
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22
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Hajredini F, Ghose R. An ATPase with a twist: A unique mechanism underlies the activity of the bacterial tyrosine kinase, Wzc. SCIENCE ADVANCES 2021; 7:eabj5836. [PMID: 34550748 PMCID: PMC8457666 DOI: 10.1126/sciadv.abj5836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BY-kinases constitute a protein tyrosine kinase family that encodes unique catalytic domains that deviate from those of eukaryotic kinases resembling P-loop nucleotide triphosphatases (NTPases) instead. We have used computational and supporting biochemical approaches using the catalytic domain of the Escherichia coli BY-kinase, Wzc, to illustrate mechanistic divergences between BY-kinases and NTPases despite their deployment of similar catalytic motifs. In NTPases, the “arginine finger” drives the reactive conformation of ATP while also displacing its solvation shell, thereby making favorable enthalpic and entropic contributions toward βγ-bond cleavage. In BY-kinases, the reactive state of ATP is enabled by ATP·Mg2+-induced global conformational transitions coupled to the conformation of the Walker-A lysine. While the BY-kinase arginine finger does promote the desolvation of ATP, it does so indirectly by generating an ordered active site in combination with other structural elements. Bacteria, using these mechanistic variations, have thus repurposed an ancient fold to phosphorylate on tyrosine.
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Affiliation(s)
- Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
- PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA
- PhD Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA
- Corresponding author.
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23
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Wickner S, Nguyen TLL, Genest O. The Bacterial Hsp90 Chaperone: Cellular Functions and Mechanism of Action. Annu Rev Microbiol 2021; 75:719-739. [PMID: 34375543 DOI: 10.1146/annurev-micro-032421-035644] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone that folds and remodels proteins, thereby regulating the activity of numerous substrate proteins. Hsp90 is widely conserved across species and is essential in all eukaryotes and in some bacteria under stress conditions. To facilitate protein remodeling, bacterial Hsp90 collaborates with the Hsp70 molecular chaperone and its cochaperones. In contrast, the mechanism of protein remodeling performed by eukaryotic Hsp90 is more complex, involving more than 20 Hsp90 cochaperones in addition to Hsp70 and its cochaperones. In this review, we focus on recent progress toward understanding the basic mechanisms of bacterial Hsp90-mediated protein remodeling and the collaboration between Hsp90 and Hsp70. We describe the universally conserved structure and conformational dynamics of these chaperones and their interactions with one another and with client proteins. The physiological roles of Hsp90 in Escherichia coli and other bacteria are also discussed. We anticipate that the information gained from exploring the mechanism of the bacterial chaperone system will provide a framework for understanding the more complex eukaryotic Hsp90 system. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Thu-Lan Lily Nguyen
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Olivier Genest
- Aix-Marseille Université, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, 13009 Marseille, France;
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24
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Masgras I, Laquatra C, Cannino G, Serapian SA, Colombo G, Rasola A. The molecular chaperone TRAP1 in cancer: From the basics of biology to pharmacological targeting. Semin Cancer Biol 2021; 76:45-53. [PMID: 34242740 DOI: 10.1016/j.semcancer.2021.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 12/22/2022]
Abstract
TRAP1, the mitochondrial component of the Hsp90 family of molecular chaperones, displays important bioenergetic and proteostatic functions. In tumor cells, TRAP1 contributes to shape metabolism, dynamically tuning it with the changing environmental conditions, and to shield from noxious insults. Hence, TRAP1 activity has profound effects on the capability of neoplastic cells to evolve towards more malignant phenotypes. Here, we discuss our knowledge on the biochemical functions of TRAP1 in the context of a growing tumor mass, and we analyze the possibility of targeting its chaperone functions for developing novel anti-neoplastic approaches.
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Affiliation(s)
- Ionica Masgras
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy; Istituto di Neuroscienze, Consiglio Nazionale Delle Ricerche (CNR), Padova, Italy
| | - Claudio Laquatra
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy
| | - Giuseppe Cannino
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy
| | | | | | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy.
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25
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Serapian SA, Moroni E, Ferraro M, Colombo G. Atomistic Simulations of the Mechanisms of the Poorly Catalytic Mitochondrial Chaperone Trap1: Insights into the Effects of Structural Asymmetry on Reactivity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Stefano A. Serapian
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100 Pavia, Italy
| | - Elisabetta Moroni
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
| | - Mariarosaria Ferraro
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Torquato Taramelli 12, 27100 Pavia, Italy
- ″Giulio Natta” Institute of Chemical and Technological Sciences (SCITEC), Via Mario Bianco 9, 20131 Milan, Italy
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26
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Dekker FA, Rüdiger SGD. The Mitochondrial Hsp90 TRAP1 and Alzheimer's Disease. Front Mol Biosci 2021; 8:697913. [PMID: 34222342 PMCID: PMC8249562 DOI: 10.3389/fmolb.2021.697913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/02/2021] [Indexed: 12/31/2022] Open
Abstract
Alzheimer’s Disease (AD) is the most common form of dementia, characterised by intra- and extracellular protein aggregation. In AD, the cellular protein quality control (PQC) system is derailed and fails to prevent the formation of these aggregates. Especially the mitochondrial paralogue of the conserved Hsp90 chaperone class, tumour necrosis factor receptor-associated protein 1 (TRAP1), is strongly downregulated in AD, more than other major PQC factors. Here, we review molecular mechanism and cellular function of TRAP1 and subsequently discuss possible links to AD. TRAP1 is an interesting paradigm for the Hsp90 family, as it chaperones proteins with vital cellular function, despite not being regulated by any of the co-chaperones that drive its cytosolic paralogues. TRAP1 encloses late folding intermediates in a non-active state. Thereby, it is involved in the assembly of the electron transport chain, and it favours the switch from oxidative phosphorylation to glycolysis. Another key function is that it ensures mitochondrial integrity by regulating the mitochondrial pore opening through Cyclophilin D. While it is still unclear whether TRAP1 itself is a driver or a passenger in AD, it might be a guide to identify key factors initiating neurodegeneration.
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Affiliation(s)
- Françoise A Dekker
- Medicinal Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, Netherlands.,Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.,Science for Life, Utrecht University, Utrecht, Netherlands
| | - Stefan G D Rüdiger
- Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands.,Science for Life, Utrecht University, Utrecht, Netherlands
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27
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Nemchinova M, Melcr J, Wassenaar TA, Marrink SJ, Guskov A. Asymmetric CorA Gating Mechanism as Observed by Molecular Dynamics Simulations. J Chem Inf Model 2021; 61:2407-2417. [PMID: 33886304 PMCID: PMC8154316 DOI: 10.1021/acs.jcim.1c00261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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The CorA family of
proteins plays a housekeeping role in the homeostasis
of divalent metal ions in many bacteria and archaea as well as in
mitochondria of eukaryotes, rendering it an important target to study
the mechanisms of divalent transport and regulation across different
life domains. Despite numerous studies, the mechanistic details of
the channel gating and the transport of the metal ions are still not
entirely understood. Here, we use all-atom and coarse-grained molecular
dynamics simulations combined with in vitro experiments
to investigate the influence of divalent cations on the function of
CorA. Simulations reveal pronounced asymmetric movements of monomers
that enable the rotation of the α7 helix and the cytoplasmic
subdomain with the subsequent formation of new interactions and the
opening of the channel. These computational results are functionally
validated using site-directed mutagenesis of the intracellular cytoplasmic
domain residues and biochemical assays. The obtained results infer
a complex network of interactions altering the structure of CorA to
allow gating. Furthermore, we attempt to reconcile the existing gating
hypotheses for CorA to conclude the mechanism of transport of divalent
cations via these proteins.
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Affiliation(s)
- Mariia Nemchinova
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Josef Melcr
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Tsjerk A Wassenaar
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
| | - Albert Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG Groningen, The Netherlands
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28
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Sanchez-Martin C, Menon D, Moroni E, Ferraro M, Masgras I, Elsey J, Arbiser JL, Colombo G, Rasola A. Honokiol Bis-Dichloroacetate Is a Selective Allosteric Inhibitor of the Mitochondrial Chaperone TRAP1. Antioxid Redox Signal 2021; 34:505-516. [PMID: 32438819 PMCID: PMC8020504 DOI: 10.1089/ars.2019.7972] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aims: TNF receptor-associated protein 1 (TRAP1), the mitochondrial paralog of the heat shock protein 90 (Hsp90) family of molecular chaperones, is required for neoplastic growth in several tumor cell models, where it inhibits succinate dehydrogenase (SDH) activity, thus favoring bioenergetic rewiring, maintenance of redox homeostasis, and orchestration of a hypoxia-inducible factor 1-alpha (HIF1α)-mediated pseudohypoxic program. Development of selective TRAP1 inhibitors is instrumental for targeted development of antineoplastic drugs, but it has been hampered up to now by the high degree of homology among catalytic pockets of Hsp90 family members. The vegetal derivative honokiol and its lipophilic bis-dichloroacetate ester, honokiol DCA (HDCA), are small-molecule compounds with antineoplastic activity. HDCA leads to oxidative stress and apoptosis in in vivo tumor models and displays an action that is functionally opposed to that of TRAP1, as it induces both SDH and the mitochondrial deacetylase sirtuin-3 (SIRT3), which further enhances SDH activity. We investigated whether HDCA could interact with TRAP1, inhibiting its chaperone function, and the effects of HDCA on tumor cells harboring TRAP1. Results: An allosteric binding site in TRAP1 is able to host HDCA, which inhibits TRAP1 but not Hsp90 ATPase activity. In neoplastic cells, HDCA reverts TRAP1-dependent downregulation of SDH, decreases proliferation rate, increases mitochondrial superoxide levels, and abolishes tumorigenic growth. Innovation: HDCA is a potential lead compound for the generation of antineoplastic approaches based on the allosteric inhibition of TRAP1 chaperone activity. Conclusions: We have identified a selective TRAP1 inhibitor that can be used to better dissect TRAP1 biochemical functions and to tailor novel tumor-targeting strategies.
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Affiliation(s)
| | - Daniela Menon
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy
| | - Elisabetta Moroni
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
| | | | - Ionica Masgras
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy.,Istituto di Neuroscienze, CNR, Padova, Italy
| | - Justin Elsey
- Atlanta Veterans Administration Medical Center, Decatur, Georgia, USA.,Department of Dermatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jack L Arbiser
- Atlanta Veterans Administration Medical Center, Decatur, Georgia, USA.,Department of Dermatology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy.,Dipartimento di Chimica, Università di Pavia, Pavia, Italy
| | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, Padova, Italy
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29
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Serapian SA, Triveri A, Marchetti F, Castelli M, Colombo G. Exploiting Folding and Degradation Machineries To Target Undruggable Proteins: What Can a Computational Approach Tell Us? ChemMedChem 2021; 16:1593-1599. [PMID: 33443306 DOI: 10.1002/cmdc.202000960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Indexed: 01/03/2023]
Abstract
Advances in genomics and proteomics have unveiled an ever-growing number of key proteins and provided mechanistic insights into the genesis of pathologies. This wealth of data showed that changes in expression levels of specific proteins, mutations, and post-translational modifications can result in (often subtle) perturbations of functional protein-protein interaction networks, which ultimately determine disease phenotypes. Although many such validated pathogenic proteins have emerged as ideal drug targets, there are also several that escape traditional pharmacological regulation; these proteins have thus been labeled "undruggable". The challenges posed by undruggable targets call for new sorts of molecular intervention. One fascinating solution is to perturb a pathogenic protein's expression levels, rather than blocking its activities. In this Concept paper, we shall discuss chemical interventions aimed at recruiting undruggable proteins to the ubiquitin proteasome system, or aimed at disrupting protein-protein interactions in the chaperone-mediated cellular folding machinery: both kinds of intervention lead to a decrease in the amount of active pathogenic protein expressed. Specifically, we shall discuss the role of computational strategies in understanding the molecular determinants characterizing the function of synthetic molecules typically designed for either type of intervention. Finally, we shall provide our perspectives and views on the current limitations and possibilities to expand the scope of rational approaches to the design of chemical regulators of protein levels.
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Affiliation(s)
- Stefano A Serapian
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Alice Triveri
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Filippo Marchetti
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Matteo Castelli
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italy
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30
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Edkins AL, Boshoff A. General Structural and Functional Features of Molecular Chaperones. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1340:11-73. [PMID: 34569020 DOI: 10.1007/978-3-030-78397-6_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular chaperones are a group of structurally diverse and highly conserved ubiquitous proteins. They play crucial roles in facilitating the correct folding of proteins in vivo by preventing protein aggregation or facilitating the appropriate folding and assembly of proteins. Heat shock proteins form the major class of molecular chaperones that are responsible for protein folding events in the cell. This is achieved by ATP-dependent (folding machines) or ATP-independent mechanisms (holders). Heat shock proteins are induced by a variety of stresses, besides heat shock. The large and varied heat shock protein class is categorised into several subfamilies based on their sizes in kDa namely, small Hsps (HSPB), J domain proteins (Hsp40/DNAJ), Hsp60 (HSPD/E; Chaperonins), Hsp70 (HSPA), Hsp90 (HSPC), and Hsp100. Heat shock proteins are localised to different compartments in the cell to carry out tasks specific to their environment. Most heat shock proteins form large oligomeric structures, and their functions are usually regulated by a variety of cochaperones and cofactors. Heat shock proteins do not function in isolation but are rather part of the chaperone network in the cell. The general structural and functional features of the major heat shock protein families are discussed, including their roles in human disease. Their function is particularly important in disease due to increased stress in the cell. Vector-borne parasites affecting human health encounter stress during transmission between invertebrate vectors and mammalian hosts. Members of the main classes of heat shock proteins are all represented in Plasmodium falciparum, the causative agent of cerebral malaria, and they play specific functions in differentiation, cytoprotection, signal transduction, and virulence.
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Affiliation(s)
- Adrienne Lesley Edkins
- Biomedical Biotechnology Research Unit (BioBRU), Department of Biochemistry and Microbiology, Rhodes University, Makhanda/Grahamstown, South Africa.
- Rhodes University, Makhanda/Grahamstown, South Africa.
| | - Aileen Boshoff
- Rhodes University, Makhanda/Grahamstown, South Africa.
- Biotechnology Innovation Centre, Rhodes University, Makhanda/Grahamstown, South Africa.
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31
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Ferraro M, Moroni E, Ippoliti E, Rinaldi S, Sanchez-Martin C, Rasola A, Pavarino LF, Colombo G. Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1. J Phys Chem B 2020; 125:101-114. [PMID: 33369425 PMCID: PMC8016192 DOI: 10.1021/acs.jpcb.0c09742] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Allosteric
molecules provide a powerful means to modulate protein
function. However, the effect of such ligands on distal orthosteric
sites cannot be easily described by classical docking methods. Here,
we applied machine learning (ML) approaches to expose the links between
local dynamic patterns and different degrees of allosteric inhibition
of the ATPase function in the molecular chaperone TRAP1. We focused
on 11 novel allosteric modulators with similar affinities to the target
but with inhibitory efficacy between the 26.3 and 76%. Using a set
of experimentally related local descriptors, ML enabled us to connect
the molecular dynamics (MD) accessible to ligand-bound (perturbed)
and unbound (unperturbed) systems to the degree of ATPase allosteric
inhibition. The ML analysis of the comparative perturbed ensembles
revealed a redistribution of dynamic states in the inhibitor-bound
versus inhibitor-free systems following allosteric binding. Linear
regression models were built to quantify the percentage of experimental
variance explained by the predicted inhibitor-bound TRAP1 states.
Our strategy provides a comparative MD–ML framework to infer
allosteric ligand functionality. Alleviating the time scale issues
which prevent the routine use of MD, a combination of MD and ML represents
a promising strategy to support in silico mechanistic
studies and drug design.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Elisabetta Moroni
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Emiliano Ippoliti
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.,JARA-HPC, Forschungszentrum Jülich, D-54245 Jülich, Germany
| | - Silvia Rinaldi
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy
| | - Carlos Sanchez-Martin
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, viale G. Colombo 3, 35131 Padova, Italy
| | - Luca F Pavarino
- Dipartimento di Matematica "F. Casorati", Università di Pavia, Via Ferrata 5, 27100 Pavia Italy
| | - Giorgio Colombo
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta"- SCITEC, Via Mario Bianco 9, 20131 Milano, Italy.,Dipartimento di Chimica, Università di Pavia, via Taramelli 12, 27100 Pavia, Italy
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32
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Visualizing the Dynamics of a Protein Folding Machinery: The Mechanism of Asymmetric ATP Processing in Hsp90 and its Implications for Client Remodelling. J Mol Biol 2020; 433:166728. [PMID: 33275968 DOI: 10.1016/j.jmb.2020.166728] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 01/22/2023]
Abstract
The Hsp90 chaperone system interacts with a wide spectrum of client proteins, forming variable and dynamic multiprotein complexes that involve the intervention of cochaperone partners. Recent results suggest that the role of Hsp90 complexes is to establish interactions that suppress unwanted client activities, allow clients to be protected from degradation and respond to biochemical signals. Cryo-electron microscopy (cryoEM) provided the first key molecular picture of Hsp90 in complex with a kinase, Cdk4, and a cochaperone, Cdc37. Here, we use a combination of molecular dynamics (MD) simulations and advanced comparative analysis methods to elucidate key aspects of the functional dynamics of the complex, with different nucleotides bound at the N-terminal Domain of Hsp90. The results reveal that nucleotide-dependent structural modulations reverberate in a striking asymmetry of the dynamics of Hsp90 and identify specific patterns of long-range coordination between the nucleotide binding site, the client binding pocket, the cochaperone and the client. Our model establishes a direct atomic-resolution cross-talk between the ATP-binding site, the client region that is to be remodeled and the surfaces of the Cdc37-cochaperone.
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33
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Xu H. ATP-Driven Nonequilibrium Activation of Kinase Clients by the Molecular Chaperone Hsp90. Biophys J 2020; 119:1538-1549. [PMID: 33038305 DOI: 10.1016/j.bpj.2020.08.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/12/2020] [Accepted: 08/24/2020] [Indexed: 11/15/2022] Open
Abstract
The molecular chaperone 90-kDa heat-shock protein (Hsp90) assists the late-stage folding and activation of diverse types of protein substrates (called clients), including many kinases. Previous studies have established that the Hsp90 homodimer undergoes an ATP-driven cycle through open and closed conformations. Here, I propose a model of client activation by Hsp90 that predicts that this cycle enables Hsp90 to use ATP energy to drive a client out of thermodynamic equilibrium toward its active conformation. My model assumes that an Hsp90-bound client can transition between a deactivating conformation and an activating conformation. It suggests that the cochaperone Cdc37 aids Hsp90 to activate kinase clients by differentiating between these two intermediate conformations. My model makes experimentally testable predictions, including how modulating the stepwise kinetics of the Hsp90 cycle-for example, by various cochaperones-affects the activation of different clients. My model may inform client-specific and cell-type-specific therapeutic intervention of Hsp90-mediated protein activation.
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Affiliation(s)
- Huafeng Xu
- Silicon Therapeutics, Boston, Massachusetts.
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34
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Paladino A, Woodford MR, Backe SJ, Sager RA, Kancherla P, Daneshvar MA, Chen VZ, Bourboulia D, Ahanin EF, Prodromou C, Bergamaschi G, Strada A, Cretich M, Gori A, Veronesi M, Bandiera T, Vanna R, Bratslavsky G, Serapian SA, Mollapour M, Colombo G. Chemical Perturbation of Oncogenic Protein Folding: from the Prediction of Locally Unstable Structures to the Design of Disruptors of Hsp90-Client Interactions. Chemistry 2020; 26:9459-9465. [PMID: 32167602 PMCID: PMC7415569 DOI: 10.1002/chem.202000615] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 12/20/2022]
Abstract
Protein folding quality control in cells requires the activity of a class of proteins known as molecular chaperones. Heat shock protein-90 (Hsp90), a multidomain ATP driven molecular machine, is a prime representative of this family of proteins. Interactions between Hsp90, its co-chaperones, and client proteins have been shown to be important in facilitating the correct folding and activation of clients. Hsp90 levels and functions are elevated in tumor cells. Here, we computationally predict the regions on the native structures of clients c-Abl, c-Src, Cdk4, B-Raf and Glucocorticoid Receptor, that have the highest probability of undergoing local unfolding, despite being ordered in their native structures. Such regions represent potential ideal interaction points with the Hsp90-system. We synthesize mimics spanning these regions and confirm their interaction with partners of the Hsp90 complex (Hsp90, Cdc37 and Aha1) by Nuclear Magnetic Resonance (NMR). Designed mimics selectively disrupt the association of their respective clients with the Hsp90 machinery, leaving unrelated clients unperturbed and causing apoptosis in cancer cells. Overall, selective targeting of Hsp90 protein-protein interactions is achieved without causing indiscriminate degradation of all clients, setting the stage for the development of therapeutics based on specific chaperone:client perturbation.
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Affiliation(s)
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- College of Medicine, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Priyanka Kancherla
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Michael A Daneshvar
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Victor Z Chen
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Elham F Ahanin
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | | | | | | | | | | | - Marina Veronesi
- D3-PharmaChemistry, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Tiziano Bandiera
- D3-PharmaChemistry, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Renzo Vanna
- Institute for Photonics and Nanotechnologies, IFN-CNR, c/o Dept. of Physics, Politecnico di Milano, Piazza L. Da Vinci 32, 20133, Milano, Italy
| | - Gennady Bratslavsky
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Stefano A Serapian
- University of Pavia, Department of Chemistry, Viale Taramelli 10, 27100, Pavia, Italy
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Giorgio Colombo
- SCITEC-CNR, via Mario Bianco 9, 20131, Milano, Italy
- University of Pavia, Department of Chemistry, Viale Taramelli 10, 27100, Pavia, Italy
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35
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Sanchez-Martin C, Serapian SA, Colombo G, Rasola A. Dynamically Shaping Chaperones. Allosteric Modulators of HSP90 Family as Regulatory Tools of Cell Metabolism in Neoplastic Progression. Front Oncol 2020; 10:1177. [PMID: 32766157 PMCID: PMC7378685 DOI: 10.3389/fonc.2020.01177] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/10/2020] [Indexed: 12/31/2022] Open
Abstract
Molecular chaperones have recently emerged as fundamental regulators of salient biological routines, including metabolic adaptations to environmental changes. Yet, many of the molecular mechanisms at the basis of their functions are still unknown or at least uncertain. This is in part due to the lack of chemical tools that can interact with the chaperones to induce measurable functional perturbations. In this context, the use of small molecules as modulators of protein functions has proven relevant for the investigation of a number of biomolecular systems. Herein, we focus on the functions, interactions and signaling pathways of the HSP90 family of molecular chaperones as possible targets for the discovery of new molecular entities aimed at tuning their activity and interactions. HSP90 and its mitochondrial paralog, TRAP1, regulate the activity of crucial metabolic circuitries, making cells capable of efficiently using available energy sources, with relevant implications both in healthy conditions and in a variety of disease states and especially cancer. The design of small-molecules targeting the chaperone cycle of HSP90 and able to inhibit or stimulate the activity of the protein can provide opportunities to finely dissect their biochemical activities and to obtain lead compounds to develop novel, mechanism-based drugs.
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Affiliation(s)
| | | | - Giorgio Colombo
- Dipartimento di Chimica, Università di Pavia, Pavia, Italy.,Istituto di Chimica del Riconoscimento Molecolare, CNR, Milan, Italy
| | - Andrea Rasola
- Dipartimento di Scienze Biomediche, Università di Padova, Padua, Italy
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36
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Abstract
Mitochondria are essential organelles in eukaryotes. Most mitochondrial proteins are encoded by the nuclear genome and translated in the cytosol. Nuclear-encoded mitochondrial proteins need to be imported, processed, folded, and assembled into their functional states. To maintain protein homeostasis (proteostasis), mitochondria are equipped with a distinct set of quality control machineries. Deficiencies in such systems lead to mitochondrial dysfunction, which is a hallmark of aging and many human diseases, such as neurodegenerative diseases, cardiovascular diseases, and cancer. In this review, we discuss the unique challenges and solutions of proteostasis in mitochondria. The import machinery coordinates with mitochondrial proteases and chaperones to maintain the mitochondrial proteome. Moreover, mitochondrial proteostasis depends on cytosolic protein quality control mechanisms during crises. In turn, mitochondria facilitate cytosolic proteostasis. Increasing evidence suggests that enhancing mitochondrial proteostasis may hold therapeutic potential to protect against protein aggregation-associated cellular defects.
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Affiliation(s)
- Linhao Ruan
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yuhao Wang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xi Zhang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Alexis Tomaszewski
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joshua T McNamara
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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37
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New insights into molecular chaperone TRAP1 as a feasible target for future cancer treatments. Life Sci 2020; 254:117737. [PMID: 32376268 DOI: 10.1016/j.lfs.2020.117737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/07/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023]
Abstract
Tumor necrosis factor receptor-associated protein 1 (TRAP1), a molecular chaperone, is a major member of the mitochondrial heat shock protein 90 (Hsp90) family. Studies have shown that TRAP1 can prevent hypoxia-induced damage to cardiomyocytes, maintain cardiomyocytes viability and mitochondrial membrane potential, and protect cardiomyocytes. In addition, it can also protect astrocytes from ischemic damage in vitro. In recent years, there have been many new discoveries in tumors. The abnormal expression of TRAP1 is closely related to the occurrence and development of various tumors. TRAP1 protein seems to be a central regulatory protein, involved in the activation of various oncogenic proteins and signaling pathways, and has a balanced function at tumor transformation and the intersection of different metabolic processes. Targeting its chaperone activity and molecular interactions can destroy the metabolism and survival adaptability of tumor cells, paving the way for the development of highly selective mitochondrial anti-tumor drugs. Moreover, the combination of TRAP1 inhibition and current traditional cancer therapies has shown promising applications. These findings have important implications for the diagnosis and treatment of tumors. Therefore, we reviewed the recently identified functions of the molecular chaperone TRAP1 in cancer development and progression, as well as the discovery and recent advances in selective TRAP1 inhibitors as anticancer drug therapies, opening up new attractive prospects for exploring strategies for targeting TRAP1 as a tumor cell target.
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Sanchez-Martin C, Moroni E, Ferraro M, Laquatra C, Cannino G, Masgras I, Negro A, Quadrelli P, Rasola A, Colombo G. Rational Design of Allosteric and Selective Inhibitors of the Molecular Chaperone TRAP1. Cell Rep 2020; 31:107531. [DOI: 10.1016/j.celrep.2020.107531] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 02/28/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023] Open
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Mader SL, Lopez A, Lawatscheck J, Luo Q, Rutz DA, Gamiz-Hernandez AP, Sattler M, Buchner J, Kaila VRI. Conformational dynamics modulate the catalytic activity of the molecular chaperone Hsp90. Nat Commun 2020; 11:1410. [PMID: 32179743 PMCID: PMC7075974 DOI: 10.1038/s41467-020-15050-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/16/2020] [Indexed: 12/31/2022] Open
Abstract
The heat shock protein 90 (Hsp90) is a molecular chaperone that employs the free energy of ATP hydrolysis to control the folding and activation of several client proteins in the eukaryotic cell. To elucidate how the local ATPase reaction in the active site couples to the global conformational dynamics of Hsp90, we integrate here large-scale molecular simulations with biophysical experiments. We show that the conformational switching of conserved ion pairs between the N-terminal domain, harbouring the active site, and the middle domain strongly modulates the catalytic barrier of the ATP-hydrolysis reaction by electrostatic forces. Our combined findings provide a mechanistic model for the coupling between catalysis and protein dynamics in Hsp90, and show how long-range coupling effects can modulate enzymatic activity. The chaperone Hsp90 uses the free energy from ATP hydrolysis to control the folding of client proteins in eukaryotic cells. Here the authors provide mechanistic insights into how its catalytic activity is coupled to conformational changes by combining large-scale molecular simulations with NMR, FRET and SAXS experiments.
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Affiliation(s)
- Sophie L Mader
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany
| | - Abraham Lopez
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany
| | - Jannis Lawatscheck
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany
| | - Qi Luo
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany.,Soft Matter Research Center and Department of Chemistry, Zhejiang University, Hangzhou, 310027, China
| | - Daniel A Rutz
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany
| | - Ana P Gamiz-Hernandez
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany.,Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden
| | - Michael Sattler
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg, 85764, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany
| | - Ville R I Kaila
- Center for Integrated Protein Science Munich at the Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, D85748, Garching, Germany. .,Department of Biochemistry and Biophysics, Stockholm University, SE-10691, Stockholm, Sweden.
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Faienza F, Lambrughi M, Rizza S, Pecorari C, Giglio P, Salamanca Viloria J, Allega MF, Chiappetta G, Vinh J, Pacello F, Battistoni A, Rasola A, Papaleo E, Filomeni G. S-nitrosylation affects TRAP1 structure and ATPase activity and modulates cell response to apoptotic stimuli. Biochem Pharmacol 2020; 176:113869. [PMID: 32088262 DOI: 10.1016/j.bcp.2020.113869] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/18/2020] [Indexed: 12/21/2022]
Abstract
The mitochondrial chaperone TRAP1 has been involved in several mitochondrial functions, and modulation of its expression/activity has been suggested to play a role in the metabolic reprogramming distinctive of cancer cells. TRAP1 posttranslational modifications, i.e. phosphorylation, can modify its capability to bind to different client proteins and modulate its oncogenic activity. Recently, it has been also demonstrated that TRAP1 is S-nitrosylated at Cys501, a redox modification associated with its degradation via the proteasome. Here we report molecular dynamics simulations of TRAP1, together with analysis of long-range structural communication, providing a model according to which Cys501 S-nitrosylation induces conformational changes to distal sites in the structure of the protein. The modification is also predicted to alter open and closing motions for the chaperone function. By means of colorimetric assays and site directed mutagenesis aimed at generating C501S variant, we also experimentally confirmed that selective S-nitrosylation of Cys501 decreases ATPase activity of recombinant TRAP1. Coherently, C501S mutant was more active and conferred protection to cell death induced by staurosporine. Overall, our results provide the first in silico, in vitro and cellular evidence of the relevance of Cys501 S-nitrosylation in TRAP1 biology.
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Affiliation(s)
- Fiorella Faienza
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Matteo Lambrughi
- Computational Biology Laboratory, Center of Excellence in Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Salvatore Rizza
- Redox Signaling and Oxidative Stress Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Chiara Pecorari
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy; Redox Signaling and Oxidative Stress Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Paola Giglio
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Juan Salamanca Viloria
- Computational Biology Laboratory, Center of Excellence in Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Maria Francesca Allega
- Computational Biology Laboratory, Center of Excellence in Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Redox Signaling and Oxidative Stress Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Giovanni Chiappetta
- Laboratory of Proteomics and Biological Mass Spectrometry, USR, CNRS - ESPCI Paris, PSL University, 3149, 10 rue, Vauquelin, Paris cedex, 05 75231, France
| | - Joëlle Vinh
- Laboratory of Proteomics and Biological Mass Spectrometry, USR, CNRS - ESPCI Paris, PSL University, 3149, 10 rue, Vauquelin, Paris cedex, 05 75231, France
| | - Francesca Pacello
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Andrea Battistoni
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Elena Papaleo
- Computational Biology Laboratory, Center of Excellence in Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Giuseppe Filomeni
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy; Redox Signaling and Oxidative Stress Group, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Center for Healthy Aging, University of Copenhagen, Denmark.
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41
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Hu S, Ferraro M, Thomas AP, Chung JM, Yoon NG, Seol JH, Kim S, Kim HU, An MY, Ok H, Jung HS, Ryu JH, Colombo G, Kang BH. Dual Binding to Orthosteric and Allosteric Sites Enhances the Anticancer Activity of a TRAP1-Targeting Drug. J Med Chem 2020; 63:2930-2940. [DOI: 10.1021/acs.jmedchem.9b01420] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sung Hu
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Mariarosaria Ferraro
- Istituto di Chimica del Riconoscimento Molecolare (ICRM), Consiglio Nazionale delle Ricerche (CNR), Milan 20131, Italy
| | - Ajesh P. Thomas
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jeong Min Chung
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Nam Gu Yoon
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Ji-Hoon Seol
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sangpil Kim
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Han-ul Kim
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Mi Young An
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Haewon Ok
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyun Suk Jung
- Division of Chemistry and Biochemistry, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Giorgio Colombo
- University of Pavia, Department of Chemistry, Pavia 27100, Italy
| | - Byoung Heon Kang
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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Joshi A, Dai L, Liu Y, Lee J, Ghahhari NM, Segala G, Beebe K, Jenkins LM, Lyons GC, Bernasconi L, Tsai FTF, Agard DA, Neckers L, Picard D. The mitochondrial HSP90 paralog TRAP1 forms an OXPHOS-regulated tetramer and is involved in mitochondrial metabolic homeostasis. BMC Biol 2020; 18:10. [PMID: 31987035 PMCID: PMC6986101 DOI: 10.1186/s12915-020-0740-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/16/2020] [Indexed: 01/01/2023] Open
Abstract
Background The molecular chaperone TRAP1, the mitochondrial isoform of cytosolic HSP90, remains poorly understood with respect to its pivotal role in the regulation of mitochondrial metabolism. Most studies have found it to be an inhibitor of mitochondrial oxidative phosphorylation (OXPHOS) and an inducer of the Warburg phenotype of cancer cells. However, others have reported the opposite, and there is no consensus on the relevant TRAP1 interactors. This calls for a more comprehensive analysis of the TRAP1 interactome and of how TRAP1 and mitochondrial metabolism mutually affect each other. Results We show that the disruption of the gene for TRAP1 in a panel of cell lines dysregulates OXPHOS by a metabolic rewiring that induces the anaplerotic utilization of glutamine metabolism to replenish TCA cycle intermediates. Restoration of wild-type levels of OXPHOS requires full-length TRAP1. Whereas the TRAP1 ATPase activity is dispensable for this function, it modulates the interactions of TRAP1 with various mitochondrial proteins. Quantitatively by far, the major interactors of TRAP1 are the mitochondrial chaperones mtHSP70 and HSP60. However, we find that the most stable stoichiometric TRAP1 complex is a TRAP1 tetramer, whose levels change in response to both a decline and an increase in OXPHOS. Conclusions Our work provides a roadmap for further investigations of how TRAP1 and its interactors such as the ATP synthase regulate cellular energy metabolism. Our results highlight that TRAP1 function in metabolism and cancer cannot be understood without a focus on TRAP1 tetramers as potentially the most relevant functional entity.
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Affiliation(s)
- Abhinav Joshi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland.,Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Li Dai
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Yanxin Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA
| | - Jungsoon Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Present address: Department of Pediatrics, Tropical Medicine, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nastaran Mohammadi Ghahhari
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Gregory Segala
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Kristin Beebe
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Gaelyn C Lyons
- Laboratory of Cell Biology, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Lilia Bernasconi
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, 94143, USA
| | - Len Neckers
- Urologic Oncology Branch, Center for Cancer Research, NCI, Bethesda, MD, 20892, USA
| | - Didier Picard
- Département de Biologie Cellulaire, Université de Genève, Sciences III, 30, quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland.
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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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44
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Plasmodium falciparum R2TP complex: driver of parasite Hsp90 function. Biophys Rev 2019; 11:1007-1015. [PMID: 31734827 DOI: 10.1007/s12551-019-00605-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/30/2019] [Indexed: 02/04/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is essential for the development of the main malaria agent, Plasmodium falciparum. Inhibitors that target Hsp90 function are known to not only kill the parasite, but also reverse resistance of the parasite to traditional antimalarials such as chloroquine. For this reason, Hsp90 has been tagged as a promising antimalarial drug target. As a molecular chaperone, Hsp90 facilitates folding of proteins such as steroid hormone receptors and kinases implicated in cell cycle and development. Central to Hsp90 function is its regulation by several co-chaperones. Various co-chaperones interact with Hsp90 to modulate its co-operation with other molecular chaperones such as Hsp70 and to regulate its interaction with substrates. The role of Hsp90 in the development of malaria parasites continues to receive research attention, and several Hsp90 co-chaperones have been mapped out. Recently, focus has shifted to P. falciparum R2TP proteins, which are thought to couple Hsp90 to a diverse set of client proteins. R2TP proteins are generally known to form a complex with Hsp90, and this complex drives multiple cellular processes central to signal transduction and cell division. Given the central role that the R2TP complex may play, the current review highlights the structure-function features of Hsp90 relative to R2TPs of P. falciparum.
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45
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D'Annessa I, Raniolo S, Limongelli V, Di Marino D, Colombo G. Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90. J Chem Theory Comput 2019; 15:6368-6381. [PMID: 31538783 DOI: 10.1021/acs.jctc.9b00319] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The molecular chaperone HSP90 oversees the functional activation of a large number of client proteins. Because of its role in multiple pathways linked to cancer and neurodegeneration, drug discovery targeting HSP90 has been actively pursued. Yet, a number of inhibitors failed to meet expectations due to induced toxicity problems. In this context, allosteric perturbation has emerged as an alternative strategy for the pharmacological modulation of HSP90 functions. Specifically, novel allosteric stimulators showed the interesting capability of accelerating HSP90 closure dynamics and ATPase activities while inducing tumor cell death. Here, we gain atomistic insight into the mechanisms of allosteric ligand recognition and their consequences on the functional dynamics of HSP90, starting from the fully unbound state. We integrate advanced computational sampling methods based on FunnelMetadynamics, with the analysis of internal dynamics of the structural ensembles visited during the simulations. We observe several binding/unbinding events, and from these, we derive an accurate estimation of the absolute binding free energy. Importantly, we show that different binding poses induce different dynamics states. Our work for the first time explicitly correlates HSP90 responses to binding/unbinding of an allosteric ligand to the modulation of functionally oriented protein motions.
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Affiliation(s)
| | - Stefano Raniolo
- Università della Svizzera Italiana (USI) , Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , via G. Buffi 13 , CH-Lugano , Switzerland
| | - Vittorio Limongelli
- Università della Svizzera Italiana (USI) , Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , via G. Buffi 13 , CH-Lugano , Switzerland.,Department of Pharmacy , University of Naples ″Federico II″ , via D. Montesano 49 , I-80131 Naples , Italy
| | - Daniele Di Marino
- Università della Svizzera Italiana (USI) , Faculty of Biomedical Sciences, Institute of Computational Science - Center for Computational Medicine in Cardiology , via G. Buffi 13 , CH-Lugano , Switzerland.,Department of Life and Environmental Sciences - New York-Marche Structural Biology Center (NY-MaSBiC) , Polytechnic University of Marche , Via Brecce Bianche , 60131 Ancona , Italy
| | - Giorgio Colombo
- ICRM-CNR , Via Mario Bianco 9 , 20131 Milano , Italy.,Department of Chemistry , University of Pavia , V.le Taramelli 12 , 27100 Pavia , Italy
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Biebl MM, Buchner J. Structure, Function, and Regulation of the Hsp90 Machinery. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a034017. [PMID: 30745292 DOI: 10.1101/cshperspect.a034017] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone involved in the maturation of a plethora of substrates ("clients"), including protein kinases, transcription factors, and E3 ubiquitin ligases, positioning Hsp90 as a central regulator of cellular proteostasis. Hsp90 undergoes large conformational changes during its ATPase cycle. The processing of clients by cytosolic Hsp90 is assisted by a cohort of cochaperones that affect client recruitment, Hsp90 ATPase function or conformational rearrangements in Hsp90. Because of the importance of Hsp90 in regulating central cellular pathways, strategies for the pharmacological inhibition of the Hsp90 machinery in diseases such as cancer and neurodegeneration are being developed. In this review, we summarize recent structural and mechanistic progress in defining the function of organelle-specific and cytosolic Hsp90, including the impact of individual cochaperones on the maturation of specific clients and complexes with clients as well as ways of exploiting Hsp90 as a drug target.
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Affiliation(s)
- Maximilian M Biebl
- Center for Integrated Protein Science, Department of Chemistry, Technische Universität München, D-85748 Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science, Department of Chemistry, Technische Universität München, D-85748 Garching, Germany
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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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48
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Ming Q, Gonzalez-Perez D, Luca VC. Molecular engineering strategies for visualizing low-affinity protein complexes. Exp Biol Med (Maywood) 2019; 244:1559-1567. [PMID: 31184923 DOI: 10.1177/1535370219855401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The growing availability of complex structures in the Protein Data Bank has provided key insight into the molecular architecture of protein–protein interfaces. The remarkable diversity observed in protein binding modes is paralleled by a tremendous variation in binding affinities, with interaction half-lives ranging from days to milliseconds. Within the protein interactome, low-affinity binding events have been particularly difficult to visualize by traditional structural methods, which has spurred the development of innovative strategies for reconstituting these short-lived yet biologically essential assemblies. An important takeaway from structural studies of low-affinity systems is that there is no universal solution for stabilizing protein complexes, and approaches such as single-chain fusions, biochemical linkages, and affinity-maturation have each been successful in certain contexts. In this article, we review how advances in molecular engineering have been used to capture weakly associated complexes for structure determination, and we provide perspectives on how the continued application of these methods can shed new light on the “hidden world” of low-affinity interactions. Impact statement Low-affinity protein interactions, while biologically essential, have been difficult to visualize by traditional methods in structural biology. In this review, we describe a series of innovative molecular engineering strategies that have been used to stabilize weakly bound protein complexes for structure determination. By highlighting several examples from the literature along with potential advantages and disadvantages of the individual approaches, we hope to provide an introductory resource for structural biologists studying low-affinity systems.
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Affiliation(s)
- Qianqian Ming
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - David Gonzalez-Perez
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Vincent C Luca
- Department of Drug Discovery, Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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Nicolas E, Demidova EV, Iqbal W, Serebriiskii IG, Vlasenkova R, Ghatalia P, Zhou Y, Rainey K, Forman AF, Dunbrack RL, Golemis EA, Hall MJ, Daly MB, Arora S. Interaction of germline variants in a family with a history of early-onset clear cell renal cell carcinoma. Mol Genet Genomic Med 2019; 7:e556. [PMID: 30680959 PMCID: PMC6418363 DOI: 10.1002/mgg3.556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022] Open
Abstract
Background Identification of genetic factors causing predisposition to renal cell carcinoma has helped improve screening, early detection, and patient survival. Methods We report the characterization of a proband with renal and thyroid cancers and a family history of renal and other cancers by whole‐exome sequencing (WES), coupled with WES analysis of germline DNA from additional affected and unaffected family members. Results This work identified multiple predicted protein‐damaging variants relevant to the pattern of inherited cancer risk. Among these, the proband and an affected brother each had a heterozygous Ala45Thr variant in SDHA, a component of the succinate dehydrogenase (SDH) complex. SDH defects are associated with mitochondrial disorders and risk for various cancers; immunochemical analysis indicated loss of SDHB protein expression in the patient’s tumor, compatible with SDH deficiency. Integrated analysis of public databases and structural predictions indicated that the two affected individuals also had additional variants in genes including TGFB2, TRAP1, PARP1, and EGF, each potentially relevant to cancer risk alone or in conjunction with the SDHA variant. In addition, allelic imbalances of PARP1 and TGFB2 were detected in the tumor of the proband. Conclusion Together, these data suggest the possibility of risk associated with interaction of two or more variants.
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Affiliation(s)
- Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Elena V Demidova
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Kazan Federal University, Kazan, Russia
| | - Waleed Iqbal
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ilya G Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Kazan Federal University, Kazan, Russia
| | | | - Pooja Ghatalia
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yan Zhou
- Biostatistics and Bioinformatics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kim Rainey
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Andrea F Forman
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Roland L Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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Genest O, Wickner S, Doyle SM. Hsp90 and Hsp70 chaperones: Collaborators in protein remodeling. J Biol Chem 2018; 294:2109-2120. [PMID: 30401745 DOI: 10.1074/jbc.rev118.002806] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Heat shock proteins 90 (Hsp90) and 70 (Hsp70) are two families of highly conserved ATP-dependent molecular chaperones that fold and remodel proteins. Both are important components of the cellular machinery involved in protein homeostasis and participate in nearly every cellular process. Although Hsp90 and Hsp70 each carry out some chaperone activities independently, they collaborate in other cellular remodeling reactions. In eukaryotes, both Hsp90 and Hsp70 function with numerous Hsp90 and Hsp70 co-chaperones. In contrast, bacterial Hsp90 and Hsp70 are less complex; Hsp90 acts independently of co-chaperones, and Hsp70 uses two co-chaperones. In this review, we focus on recent progress toward understanding the basic mechanisms of Hsp90-mediated protein remodeling and the collaboration between Hsp90 and Hsp70, with an emphasis on bacterial chaperones. We describe the structure and conformational dynamics of these chaperones and their interactions with each other and with client proteins. The physiological roles of Hsp90 in Escherichia coli and other bacteria are also discussed. We anticipate that the information gained from exploring the mechanism of the bacterial chaperone system will provide the groundwork for understanding the more complex eukaryotic Hsp90 system and its modulation by Hsp90 co-chaperones.
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Affiliation(s)
- Olivier Genest
- From the Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, 13402 Marseille, France and
| | - Sue Wickner
- the Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Shannon M Doyle
- the Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892
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