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Shahzadi Z, Yousaf Z, Anjum I, Bilal M, Yasin H, Aftab A, Booker A, Ullah R, Bari A. Network pharmacology and molecular docking: combined computational approaches to explore the antihypertensive potential of Fabaceae species. BIORESOUR BIOPROCESS 2024; 11:53. [PMID: 38767701 PMCID: PMC11106056 DOI: 10.1186/s40643-024-00764-6] [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: 01/31/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Hypertension is a major global public health issue, affecting quarter of adults worldwide. Numerous synthetic drugs are available for treating hypertension; however, they often come with a higher risk of side effects and long-term therapy. Modern formulations with active phytoconstituents are gaining popularity, addressing some of these issues. This study aims to discover novel antihypertensive compounds in Cassia fistula, Senna alexandrina, and Cassia occidentalis from family Fabaceae and understand their interaction mechanism with hypertension targeted genes, using network pharmacology and molecular docking. Total 414 compounds were identified; initial screening was conducted based on their pharmacokinetic and ADMET properties, with a particular emphasis on adherence to Lipinski's rules. 6 compounds, namely Germichrysone, Benzeneacetic acid, Flavan-3-ol, 5,7,3',4'-Tetrahydroxy-6, 8-dimethoxyflavon, Dihydrokaempferol, and Epiafzelechin, were identified as effective agents. Most of the compounds found non-toxic against various indicators with greater bioactivity score. 161 common targets were obtained against these compounds and hypertension followed by compound-target network construction and protein-protein interaction, which showed their role in diverse biological system. Top hub genes identified were TLR4, MMP9, MAPK14, AKT1, VEGFA and HSP90AA1 with their respective associates. Higher binding affinities was found with three compounds Dihydrokaempferol, Flavan-3-ol and Germichrysone, -7.1, -9.0 and -8.0 kcal/mol, respectively. The MD simulation results validate the structural flexibility of two complexes Flavan-MMP9 and Germich-TLR4 based on no. of hydrogen bonds, root mean square deviations and interaction energies. This study concluded that C. fistula (Dihydrokaempferol, Flavan-3-ol) and C. occidentalis (Germichrysone) have potential therapeutic active constituents to treat hypertension and in future novel drug formulation.
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Affiliation(s)
- Zainab Shahzadi
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Zubaida Yousaf
- Department of Botany, Lahore College for Women University, Lahore, Pakistan.
| | - Irfan Anjum
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Muhammad Bilal
- Centers for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hamna Yasin
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Arusa Aftab
- Department of Botany, Lahore College for Women University, Lahore, Pakistan
| | - Anthony Booker
- Research Centre for Optimal Health, School of Life Sciences, College of Liberal Arts and Sciences, University of Westminster, 115 New Cavendish Street, London, W1W 6UW, UK.
- Research Group 'Pharmacognosy and Phytotherapy', UCL School of Pharmacy, Univ. London, 29 - 39 Brunswick Sq., London, WC1N 1AX, UK.
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy King, Saud University, Riyadh, Saudi Arabia
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2
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Vassileva V, Georgieva M, Todorov D, Mishev K. Small Sized Yet Powerful: Nuclear Distribution C Proteins in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 13:119. [PMID: 38202427 PMCID: PMC10780334 DOI: 10.3390/plants13010119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024]
Abstract
The family of Nuclear Distribution C (NudC) proteins plays a pivotal and evolutionarily conserved role in all eukaryotes. In animal systems, these proteins influence vital cellular processes like cell division, protein folding, nuclear migration and positioning, intracellular transport, and stress response. This review synthesizes past and current research on NudC family members, focusing on their growing importance in plants and intricate contributions to plant growth, development, and stress tolerance. Leveraging information from available genomic databases, we conducted a thorough characterization of NudC family members, utilizing phylogenetic analysis and assessing gene structure, motif organization, and conserved protein domains. Our spotlight on two Arabidopsis NudC genes, BOB1 and NMig1, underscores their indispensable roles in embryogenesis and postembryonic development, stress responses, and tolerance mechanisms. Emphasizing the chaperone activity of plant NudC family members, crucial for mitigating stress effects and enhancing plant resilience, we highlight their potential as valuable targets for enhancing crop performance. Moreover, the structural and functional conservation of NudC proteins across species suggests their potential applications in medical research, particularly in functions related to cell division, microtubule regulation, and associated pathways. Finally, we outline future research avenues centering on the exploration of under investigated functions of NudC proteins in plants.
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Affiliation(s)
- Valya Vassileva
- Department of Molecular Biology and Genetics, Laboratory of Regulation of Gene Expression, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.G.); (D.T.)
| | | | | | - Kiril Mishev
- Department of Molecular Biology and Genetics, Laboratory of Regulation of Gene Expression, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (M.G.); (D.T.)
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3
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Backe SJ, Mollapour M, Woodford MR. Saccharomyces cerevisiae as a tool for deciphering Hsp90 molecular chaperone function. Essays Biochem 2023; 67:781-795. [PMID: 36912239 PMCID: PMC10497724 DOI: 10.1042/ebc20220224] [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: 12/21/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 03/14/2023]
Abstract
Yeast is a valuable model organism for their ease of genetic manipulation, rapid growth rate, and relative similarity to higher eukaryotes. Historically, Saccharomyces cerevisiae has played a major role in discovering the function of complex proteins and pathways that are important for human health and disease. Heat shock protein 90 (Hsp90) is a molecular chaperone responsible for the stabilization and activation of hundreds of integral members of the cellular signaling network. Much important structural and functional work, including many seminal discoveries in Hsp90 biology are the direct result of work carried out in S. cerevisiae. Here, we have provided a brief overview of the S. cerevisiae model system and described how this eukaryotic model organism has been successfully applied to the study of Hsp90 chaperone function.
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Affiliation(s)
- Sarah J. Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
| | - Mark R. Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
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4
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Jussupow A, Kaila VRI. Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models. J Chem Theory Comput 2023; 19:1965-1975. [PMID: 36961997 PMCID: PMC11181330 DOI: 10.1021/acs.jctc.2c01027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Indexed: 03/26/2023]
Abstract
Recent breakthroughs in neural network-based structure prediction methods, such as AlphaFold2 and RoseTTAFold, have dramatically improved the quality of computational protein structure prediction. These models also provide statistical confidence scores that can estimate uncertainties in the predicted structures, but it remains unclear to what extent these scores are related to the intrinsic conformational dynamics of proteins. Here, we compare AlphaFold2 prediction scores with explicit large-scale molecular dynamics simulations of 28 one- and two-domain proteins with varying degrees of flexibility. We demonstrate a strong correlation between the statistical prediction scores and the explicit motion derived from extensive atomistic molecular dynamics simulations and further derive an elastic network model based on the statistical scores of AlphFold2 (AF-ENM), which we benchmark in combination with coarse-grained molecular dynamics simulations. We show that our AF-ENM method reproduces the global protein dynamics with improved accuracy, providing a powerful way to derive effective molecular dynamics using neural network-based structure prediction models.
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Affiliation(s)
- Alexander Jussupow
- Department of Biochemistry
and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry
and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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5
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p23 and Aha1: Distinct Functions Promote Client Maturation. Subcell Biochem 2023; 101:159-187. [PMID: 36520307 DOI: 10.1007/978-3-031-14740-1_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Hsp90 is a conserved molecular chaperone regulating the folding and activation of a diverse array of several hundreds of client proteins. The function of Hsp90 in client processing is fine-tuned by a cohort of co-chaperones that modulate client activation in a client-specific manner. They affect the Hsp90 ATPase activity and the recruitment of client proteins and can in addition affect chaperoning in an Hsp90-independent way. p23 and Aha1 are central Hsp90 co-chaperones that regulate Hsp90 in opposing ways. While p23 inhibits the Hsp90 ATPase and stabilizes a client-bound Hsp90 state, Aha1 accelerates ATP hydrolysis and competes with client binding to Hsp90. Even though both proteins have been intensively studied for decades, research of the last few years has revealed intriguing new aspects of these co-chaperones that expanded our perception of how they regulate client activation. Here, we review the progress in understanding p23 and Aha1 as promoters of client processing. We highlight the structures of Aha1 and p23, their interaction with Hsp90, and how their association with Hsp90 affects the conformational cycle of Hsp90 in the context of client maturation.
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6
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Henot F, Rioual E, Favier A, Macek P, Crublet E, Josso P, Brutscher B, Frech M, Gans P, Loison C, Boisbouvier J. Visualizing the transiently populated closed-state of human HSP90 ATP binding domain. Nat Commun 2022; 13:7601. [PMID: 36494347 PMCID: PMC9734131 DOI: 10.1038/s41467-022-35399-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
HSP90 are abundant molecular chaperones, assisting the folding of several hundred client proteins, including substrates involved in tumor growth or neurodegenerative diseases. A complex set of large ATP-driven structural changes occurs during HSP90 functional cycle. However, the existence of such structural rearrangements in apo HSP90 has remained unclear. Here, we identify a metastable excited state in the isolated human HSP90α ATP binding domain. We use solution NMR and mutagenesis to characterize structures of both ground and excited states. We demonstrate that in solution the HSP90α ATP binding domain transiently samples a functionally relevant ATP-lid closed state, distant by more than 30 Å from the ground state. NMR relaxation enables to derive information on the kinetics and thermodynamics of this interconversion, while molecular dynamics simulations establish that the ATP-lid in closed conformation is a metastable exited state. The precise description of the dynamics and structures sampled by human HSP90α ATP binding domain provides information for the future design of new therapeutic ligands.
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Affiliation(s)
- Faustine Henot
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Elisa Rioual
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France ,grid.7849.20000 0001 2150 7757Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Adrien Favier
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Pavel Macek
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France ,NMR-Bio, 5 place Robert Schuman, F-38025 Grenoble, France
| | - Elodie Crublet
- NMR-Bio, 5 place Robert Schuman, F-38025 Grenoble, France
| | - Pierre Josso
- grid.7849.20000 0001 2150 7757Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Bernhard Brutscher
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Matthias Frech
- grid.39009.330000 0001 0672 7022Discovery Technologies, Merck KGaA, Frankfurter Straße 250, 64293 Darmstadt, Germany
| | - Pierre Gans
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
| | - Claire Loison
- grid.7849.20000 0001 2150 7757Institut Lumière Matière, University of Lyon, Université Claude Bernard Lyon 1, CNRS, F-69622 Villeurbanne, France
| | - Jerome Boisbouvier
- grid.4444.00000 0001 2112 9282Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71, avenue des martyrs, F-38044 Grenoble, France
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7
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Jamabo M, Bentley SJ, Macucule-Tinga P, Tembo P, Edkins AL, Boshoff A. In silico analysis of the HSP90 chaperone system from the African trypanosome, Trypanosoma brucei. Front Mol Biosci 2022; 9:947078. [PMID: 36213128 PMCID: PMC9538636 DOI: 10.3389/fmolb.2022.947078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
African trypanosomiasis is a neglected tropical disease caused by Trypanosoma brucei (T. brucei) and spread by the tsetse fly in sub-Saharan Africa. The trypanosome relies on heat shock proteins for survival in the insect vector and mammalian host. Heat shock protein 90 (HSP90) plays a crucial role in the stress response at the cellular level. Inhibition of its interactions with chaperones and co-chaperones is being explored as a potential therapeutic target for numerous diseases. This study provides an in silico overview of HSP90 and its co-chaperones in both T. brucei brucei and T. brucei gambiense in relation to human and other trypanosomal species, including non-parasitic Bodo saltans and the insect infecting Crithidia fasciculata. A structural analysis of T. brucei HSP90 revealed differences in the orientation of the linker and C-terminal domain in comparison to human HSP90. Phylogenetic analysis displayed the T. brucei HSP90 proteins clustering into three distinct groups based on subcellular localizations, namely, cytosol, mitochondria, and endoplasmic reticulum. Syntenic analysis of cytosolic HSP90 genes revealed that T. b. brucei encoded for 10 tandem copies, while T. b. gambiense encoded for three tandem copies; Leishmania major (L. major) had the highest gene copy number with 17 tandem copies. The updated information on HSP90 from recently published proteomics on T. brucei was examined for different life cycle stages and subcellular localizations. The results show a difference between T. b. brucei and T. b. gambiense with T. b. brucei encoding a total of twelve putative HSP90 genes, while T. b. gambiense encodes five HSP90 genes. Eighteen putative co-chaperones were identified with one notable absence being cell division cycle 37 (Cdc37). These results provide an updated framework on approaching HSP90 and its interactions as drug targets in the African trypanosome.
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Affiliation(s)
- Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | | | | | - Praise Tembo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | - Adrienne Lesley Edkins
- Department of Biochemistry and Microbiology, Biomedical Biotechnology Research Unit (BioBRU), Rhodes University, Grahamstown, South Africa
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
- *Correspondence: Aileen Boshoff,
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8
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Yoodee S, Peerapen P, Plumworasawat S, Thongboonkerd V. Roles of heat-shock protein 90 and its four domains (N, LR, M and C) in calcium oxalate stone-forming processes. Cell Mol Life Sci 2022; 79:454. [PMID: 35900595 PMCID: PMC9330963 DOI: 10.1007/s00018-022-04483-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/17/2022]
Abstract
Human heat-shock protein 90 (HSP90) has four functional domains, including NH2-terminal (N), charged linker region (LR), middle (M) and COOH-terminal (C) domains. In kidney stone disease (or nephrolithiasis/urolithiasis), HSP90 serves as a receptor for calcium oxalate monohydrate (COM), which is the most common crystal to form kidney stones. Nevertheless, roles of HSP90 and its four domains in kidney stone formation remained unclear and under-investigated. We thus examined and compared their effects on COM crystals during physical (crystallization, growth and aggregation) and biological (crystal–cell adhesion and crystal invasion through extracellular matrix (ECM)) pathogenic processes of kidney stone formation. The analyses revealed that full-length (FL) HSP90 obviously increased COM crystal size and abundance during crystallization and markedly promoted crystal growth, aggregation, adhesion onto renal cells and ECM invasion. Comparing among four individual domains, N and C domains exhibited the strongest promoting effects, whereas LR domain had the weakest promoting effects on COM crystals. In summary, our findings indicate that FL-HSP90 and its four domains (N, LR, M and C) promote COM crystallization, crystal growth, aggregation, adhesion onto renal cells and invasion through the ECM, all of which are the important physical and biological pathogenic processes of kidney stone formation.
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Affiliation(s)
- Sunisa Yoodee
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor-SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand
| | - Paleerath Peerapen
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor-SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand
| | - Sirikanya Plumworasawat
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor-SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, 6th Floor-SiMR Building, 2 Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand.
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9
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Jussupow A, Lopez A, Baumgart M, Mader SL, Sattler M, Kaila VRI. Extended conformational states dominate the Hsp90 chaperone dynamics. J Biol Chem 2022; 298:102101. [PMID: 35667441 PMCID: PMC9251789 DOI: 10.1016/j.jbc.2022.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
The heat shock protein 90 (Hsp90) is a molecular chaperone central to client protein folding and maturation in eukaryotic cells. During its chaperone cycle, Hsp90 undergoes ATPase-coupled large-scale conformational changes between open and closed states, where the N-terminal and middle domains of the protein form a compact dimerized conformation. However, the molecular principles of the switching motion between the open and closed states remain poorly understood. Here we show by integrating atomistic and coarse-grained molecular simulations with small-angle X-ray scattering experiments and NMR spectroscopy data that Hsp90 exhibits rich conformational dynamics modulated by the charged linker, which connects the N-terminal with the middle domain of the protein. We show that the dissociation of these domains is crucial for the conformational flexibility of the open state, with the separation distance controlled by a β-sheet motif next to the linker region. Taken together, our results suggest that the conformational ensemble of Hsp90 comprises highly extended states, which could be functionally crucial for client processing.
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Affiliation(s)
- Alexander Jussupow
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Abraham Lopez
- Center of Integrated Protein Science, Department Chemie, Technische Universität München Lichtenbergstr. 4, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
| | - Mona Baumgart
- Center of Integrated Protein Science, Department Chemie, Technische Universität München Lichtenbergstr. 4, 85747 Garching (Germany)
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Michael Sattler
- Center of Integrated Protein Science, Department Chemie, Technische Universität München Lichtenbergstr. 4, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum Mu¨nchen, Ingolstädter Landstrasse 1, Neuherberg 85764, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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10
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Peng S, Woodruff J, Pathak PK, Matts RL, Deng J. Crystal structure of the middle and C-terminal domains of Hsp90α labeled with a coumarin derivative reveals a potential allosteric binding site as a drug target. Acta Crystallogr D Struct Biol 2022; 78:571-585. [PMID: 35503206 PMCID: PMC9063849 DOI: 10.1107/s2059798322002261] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/26/2022] [Indexed: 12/01/2022] Open
Abstract
The 90 kDa heat-shock protein (Hsp90) is an abundant molecular chaperone that is essential to activate, stabilize and regulate the function of a plethora of client proteins. As drug targets for the treatment of cancer and neurodegenerative diseases, Hsp90 inhibitors that bind to the N-terminal ATP-binding site of Hsp90 have shown disappointing efficacy in clinical trials. Thus, allosteric regulation of the function of Hsp90 by compounds that interact with its middle and C-terminal (MC) domains is now being pursued as a mechanism to inhibit the ATPase activity and client protein-binding activity of Hsp90 without concomitant induction of the heat-shock response. Here, the crystal structure of the Hsp90αMC protein covalently linked to a coumarin derivative, MDCC {7-diethylamino-3-[N-(2-maleimidoethyl)carbamoyl]coumarin}, which is located in a hydrophobic pocket that is formed at the Hsp90αMC hexamer interface, is reported. MDCC binding leads to the hexamerization of Hsp90, and the stabilization and conformational changes of three loops that are critical for its function. A fluorescence competition assay demonstrated that other characterized coumarin and isoflavone-containing Hsp90 inhibitors compete with MDCC binding, suggesting that they could bind at a common site or that they might allosterically alter the structure of the MDCC binding site. This study provides insights into the mechanism by which the coumarin class of allosteric inhibitors potentially disrupt the function of Hsp90 by regulating its oligomerization and the burial of interaction sites involved in the ATP-dependent folding of Hsp90 clients. The hydrophobic binding pocket characterized here will provide new structural information for future drug design.
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Affiliation(s)
- Shuxia Peng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, USA
| | - Jeff Woodruff
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, USA
| | - Prabhat Kumar Pathak
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, USA
| | - Robert L. Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, USA
| | - Junpeng Deng
- Department of Biochemistry and Molecular Biology, Oklahoma State University, 246 Noble Research Center, Stillwater, OK 74078, USA
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11
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Biebl MM, Delhommel F, Faust O, Zak KM, Agam G, Guo X, Mühlhofer M, Dahiya V, Hillebrand D, Popowicz GM, Kampmann M, Lamb DC, Rosenzweig R, Sattler M, Buchner J. NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems. Mol Cell 2022; 82:555-569.e7. [DOI: 10.1016/j.molcel.2021.12.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/03/2021] [Accepted: 12/21/2021] [Indexed: 12/21/2022]
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12
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Lopez A, Dahiya V, Delhommel F, Freiburger L, Stehle R, Asami S, Rutz D, Blair L, Buchner J, Sattler M. Client binding shifts the populations of dynamic Hsp90 conformations through an allosteric network. SCIENCE ADVANCES 2021; 7:eabl7295. [PMID: 34919431 PMCID: PMC8682993 DOI: 10.1126/sciadv.abl7295] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 05/31/2023]
Abstract
Hsp90 is a molecular chaperone that interacts with a specific set of client proteins and assists their folding. The underlying molecular mechanisms, involving dynamic transitions between open and closed conformations, are still enigmatic. Combining nuclear magnetic resonance, small-angle x-ray scattering, and biochemical experiments, we have identified a key intermediate state of Hsp90 induced by adenosine triphosphate (ATP) binding, in which rotation of the Hsp90 N-terminal domain (NTD) yields a domain arrangement poised for closing. This ATP-stabilized NTD rotation is allosterically communicated across the full Hsp90 dimer, affecting distant client sites. By analyzing the interactions of four distinct clients, i.e., steroid hormone receptors (glucocorticoid receptor and mineralocorticoid receptor), p53, and Tau, we show that client-specific interactions with Hsp90 select and enhance the NTD-rotated state and promote closing of the full-length Hsp90 dimer. The p23 co-chaperone shifts the population of Hsp90 toward the closed state, thereby enhancing client interaction and processing.
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Affiliation(s)
- Abraham Lopez
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Vinay Dahiya
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Florent Delhommel
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Lee Freiburger
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ralf Stehle
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Sam Asami
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Daniel Rutz
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
- Roche Diagnostics GmbH, Nonnenwald 2, 82377 Penzberg, Germany
| | - Laura Blair
- USF Health Byrd Institute, Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, FL, USA
| | - Johannes Buchner
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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13
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The Potential of Hsp90 in Targeting Pathological Pathways in Cardiac Diseases. J Pers Med 2021; 11:jpm11121373. [PMID: 34945845 PMCID: PMC8709342 DOI: 10.3390/jpm11121373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone that interacts with up to 10% of the proteome. The extensive involvement in protein folding and regulation of protein stability within cells makes Hsp90 an attractive therapeutic target to correct multiple dysfunctions. Many of the clients of Hsp90 are found in pathways known to be pathogenic in the heart, ranging from transforming growth factor β (TGF-β) and mitogen activated kinase (MAPK) signaling to tumor necrosis factor α (TNFα), Gs and Gq g-protein coupled receptor (GPCR) and calcium (Ca2+) signaling. These pathways can therefore be targeted through modulation of Hsp90 activity. The activity of Hsp90 can be targeted through small-molecule inhibition. Small-molecule inhibitors of Hsp90 have been found to be cardiotoxic in some cases however. In this regard, specific targeting of Hsp90 by modulation of post-translational modifications (PTMs) emerges as an attractive strategy. In this review, we aim to address how Hsp90 functions, where Hsp90 interacts within pathological pathways, and current knowledge of small molecules and PTMs known to modulate Hsp90 activity and their potential as therapeutics in cardiac diseases.
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14
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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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15
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Semenyuk PI. Effect of Polyphosphorylation on Behavior of Protein Disordered Regions. Int J Mol Sci 2021; 22:ijms22157883. [PMID: 34360648 PMCID: PMC8345927 DOI: 10.3390/ijms22157883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/18/2021] [Accepted: 07/20/2021] [Indexed: 11/25/2022] Open
Abstract
Proteins interact with many charged biological macromolecules (polyelectrolytes), including inorganic polyphosphates. Recently a new protein post-translational modification, polyphosphorylation, or a covalent binding of polyphosphate chain to lysine, was demonstrated in human and yeast. Herein, we performed the first molecular modeling study of a possible effect of polyphosphorylation on behavior of the modified protein using replica exchange molecular dynamics simulations in atomistic force field with explicit water. Human endoplasmin (GRP-94), a member of heat shock protein 90 family, was selected as a model protein. Intrinsically disordered region in N-terminal domain serving as a charged linker between domains and containing a polyacidic serine and lysine-rich motif, was selected as a potent polyphosphorylation site according to literature data. Polyphosphorylation, depending on exact modification site, has been shown to influence on the disordered loop flexibility and induce its further expanding, as well as induce changes in interaction with ordered part of the molecule. As a result, polyphosphorylation in N-terminal domain might affect interaction of HSP90 with client proteins since these chaperones play a key role in protein folding.
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Affiliation(s)
- Pavel I Semenyuk
- Belozersky Research Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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16
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Weidenauer L, Quadroni M. Phosphorylation in the Charged Linker Modulates Interactions and Secretion of Hsp90β. Cells 2021; 10:cells10071701. [PMID: 34359868 PMCID: PMC8304327 DOI: 10.3390/cells10071701] [Citation(s) in RCA: 3] [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: 05/18/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/16/2022] Open
Abstract
Hsp90β is a major chaperone involved in numerous cellular processes. Hundreds of client proteins depend on Hsp90β for proper folding and/or activity. Regulation of Hsp90β is critical to coordinate its tasks and is mediated by several post-translational modifications. Here, we focus on two phosphorylation sites located in the charged linker region of human Hsp90β, Ser226 and Ser255, which have been frequently reported but whose function remains unclear. Targeted measurements by mass spectrometry indicated that intracellular Hsp90β is highly phosphorylated on both sites (>90%). The level of phosphorylation was unaffected by various stresses (e.g., heat shock, inhibition with drugs) that impact Hsp90β activity. Mutating the two serines to alanines increased the amount of proteins interacting with Hsp90β globally and increased the sensitivity to tryptic cleavage in the C-terminal domain. Further investigation revealed that phosphorylation on Ser255 and to a lesser extent on Ser226 is decreased in the conditioned medium of cultured K562 cells, and that a non-phosphorylatable double alanine mutant was secreted more efficiently than the wild type. Overall, our results show that phosphorylation events in the charged linker regulate both the interactions of Hsp90β and its secretion, through changes in the conformation of the chaperone.
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17
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López A, Elimelech AR, Klimm K, Sattler M. The Charged Linker Modulates the Conformations and Molecular Interactions of Hsp90. Chembiochem 2021; 22:1084-1092. [PMID: 33147371 PMCID: PMC8048802 DOI: 10.1002/cbic.202000699] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/04/2020] [Indexed: 12/23/2022]
Abstract
The molecular chaperone Hsp90 supports the functional activity of specific substrate proteins (clients). For client processing, the Hsp90 dimer undergoes a series of ATP-driven conformational rearrangements. Flexible linkers connecting the three domains of Hsp90 are crucial to enable dynamic arrangements. The long charged linker connecting the N-terminal (NTD) and middle (MD) domains exhibits additional functions in vitro and in vivo. The structural basis for these functions remains unclear. Here, we characterize the conformation and dynamics of the linker and NTD-MD domain interactions by NMR spectroscopy. Our results reveal two regions in the linker that are dynamic and exhibit secondary structure conformation. We show that these regions mediate transient interactions with strand β8 of the NTD. As a consequence, this strand detaches and exposes a hydrophobic surface patch, which enables binding to the p53 client. We propose that the charged linker plays an important regulatory role by coupling the Hsp90 NTD-MD arrangement with the accessibility of a client binding site on the NTD.
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Affiliation(s)
- Abraham López
- Institute of Structural Biology, Helmholtz Zentrum MünchenIngolstädter Landstrasse 185764NeuherbergGermany
- Bavarian NMR Center and Center for Integrated Protein Science MunichDepartment of ChemistryTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
| | - Annika R. Elimelech
- Bavarian NMR Center and Center for Integrated Protein Science MunichDepartment of ChemistryTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
| | - Karolin Klimm
- Bavarian NMR Center and Center for Integrated Protein Science MunichDepartment of ChemistryTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum MünchenIngolstädter Landstrasse 185764NeuherbergGermany
- Bavarian NMR Center and Center for Integrated Protein Science MunichDepartment of ChemistryTechnical University of MunichLichtenbergstrasse 485747GarchingGermany
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18
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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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