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You P, Lu F, Ouyang C, Yu J, González-García J, Song J, Ni W, Wang J, Yin C, Zhou CQ. Acidic Lysosome-Anchoring Croconium-Based Nanoplatform for Enhanced Triple-Mode Bioimaging and Fe 3+-Triggered Tumor Synergistic Therapy. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39172044 DOI: 10.1021/acsami.4c09587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Metal-modulated croconium dyes with multimodal-imaging and synergistic therapy in the tumor microenvironment have exhibited great potential in tumor theranostics. However, their unideal structure optimization always weakened the efficacy of near-infrared fluorescence-photoacoustic (NIRF/PA) imaging and photothermal therapy (PTT). Here, we screened croconium dye containing two indole groups with better NIRF/PA imaging and PTT in their family, linked to two morpholine rings, and obtained CR-736, as a lysosome-targeting and Fe3+-modulated agent. The established CR-736-Fe3+ nanoplatform was accurately delivered to the breast tumor site, released CR-736 and Fe3+ in the lower acidic lysosome microenvironment, and activated pH-responsive NIRF/PA/magnetic resonance imaging and PTT. Furthermore, ferroptosis generated hydroxyl free radicals and lipid peroxide by consuming GSH and H2O2 by dint of the accumulation of Fe3+ in tumor cells, which resulted in the inhibition of the expression of heat shock proteins and the concomitant recovery of PTT. The synergistic therapy of PTT, ferroptosis, and chemodynamics was further optimized to the maximal extent in tumor lysosome acidic microenvironment and proved both in vitro and a mouse tumor model. This study opens a new avenue in designing excellent and unique croconium-based nanoplatforms, synergizing multiple tumor theranostic methods, and further optimizing the theranostic effects in tumor microenvironment.
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Affiliation(s)
- Peidan You
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening & Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Fei Lu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chengren Ouyang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jielin Yu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jorge González-García
- Instituto de Ciencia Molecular, Departamento de Química Inorgánica, Universidad de Valencia, Paterna 46980, Spain
| | - Jinxin Song
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weitong Ni
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junping Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Caixia Yin
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, China
| | - Chun-Qiong Zhou
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening & Guangdong-Hongkong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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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:S1355-8145(24)00110-X. [PMID: 39142378 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 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, co-chaperones, 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), 20131, Milano, Italy.
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3
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Wang Y, Zhou Y, Qi L, Wang Y, Sun L, Cai M, Fan Q, Zhang L. Visualizing Single-Molecule Protein Conformational Transitions and Free Energy Landscape. Anal Chem 2024; 96:12006-12011. [PMID: 38993005 DOI: 10.1021/acs.analchem.4c01970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Monitoring the conformational dynamics of individual proteins is essential to understand the relationship between structure and function in molecular regulatory mechanisms. However, the fast dynamics of single proteins remain poorly understood. Here, we construct a single-molecule sensing platform by introducing plasmonic imaging of single nanoparticles to sense and report the protein conformational changes at the single-molecule level. Tracking the fluctuations of individual nanoparticles with high resolution, we detect and characterize distinct conformational states of molecular chaperone heat shock protein 90 (Hsp90). We also explore the conformational changes of Hsp90 in situ under different nucleotide conditions. Analysis of the conformational fluctuations between the open and closed states of single Hsp90 provides important information on free energy profiles, effective spring constants, and multiphase behaviors. This method offers a strategy to visualize the conformational changes of single proteins in real-time and provides insights into the underlying molecular mechanisms.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Yang Zhou
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Liting Qi
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Yamin Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Le Sun
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Miaomiao Cai
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Quli Fan
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Lei Zhang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
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4
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Pöverlein MC, Hulm A, Dietschreit JCB, Kussmann J, Ochsenfeld C, Kaila VRI. QM/MM Free Energy Calculations of Long-Range Biological Protonation Dynamics by Adaptive and Focused Sampling. J Chem Theory Comput 2024; 20:5751-5762. [PMID: 38718352 DOI: 10.1021/acs.jctc.4c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Water-mediated proton transfer reactions are central for catalytic processes in a wide range of biochemical systems, ranging from biological energy conversion to chemical transformations in the metabolism. Yet, the accurate computational treatment of such complex biochemical reactions is highly challenging and requires the application of multiscale methods, in particular hybrid quantum/classical (QM/MM) approaches combined with free energy simulations. Here, we combine the unique exploration power of new advanced sampling methods with density functional theory (DFT)-based QM/MM free energy methods for multiscale simulations of long-range protonation dynamics in biological systems. In this regard, we show that combining multiple walkers/well-tempered metadynamics with an extended system adaptive biasing force method (MWE) provides a powerful approach for exploration of water-mediated proton transfer reactions in complex biochemical systems. We compare and combine the MWE method also with QM/MM umbrella sampling and explore the sampling of the free energy landscape with both geometric (linear combination of proton transfer distances) and physical (center of excess charge) reaction coordinates and show how these affect the convergence of the potential of mean force (PMF) and the activation free energy. We find that the QM/MM-MWE method can efficiently explore both direct and water-mediated proton transfer pathways together with forward and reverse hole transfer mechanisms in the highly complex proton channel of respiratory Complex I, while the QM/MM-US approach shows a systematic convergence of selected long-range proton transfer pathways. In this regard, we show that the PMF along multiple proton transfer pathways is recovered by combining the strengths of both approaches in a QM/MM-MWE/focused US (FUS) scheme and reveals new mechanistic insight into the proton transfer principles of Complex I. Our findings provide a promising basis for the quantitative multiscale simulations of long-range proton transfer reactions in biological systems.
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Affiliation(s)
- Maximilian C Pöverlein
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Andreas Hulm
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
| | - Johannes C B Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
- Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jörg Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), 81377 Munich, Germany
- Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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5
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Rios EI, Gonçalves D, Morano KA, Johnson JL. Quantitative proteomic analysis reveals unique Hsp90 cycle-dependent client interactions. Genetics 2024; 227:iyae057. [PMID: 38606935 PMCID: PMC11151932 DOI: 10.1093/genetics/iyae057] [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: 01/02/2024] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
Hsp90 is an abundant and essential molecular chaperone that mediates the folding and activation of client proteins in a nucleotide-dependent cycle. Hsp90 inhibition directly or indirectly impacts the function of 10-15% of all proteins due to degradation of client proteins or indirect downstream effects. Due to its role in chaperoning oncogenic proteins, Hsp90 is an important drug target. However, compounds that occupy the ATP-binding pocket and broadly inhibit function have not achieved widespread use due to negative effects. More selective inhibitors are needed; however, it is unclear how to achieve selective inhibition. We conducted a quantitative proteomic analysis of soluble proteins in yeast strains expressing wild-type Hsp90 or mutants that disrupt different steps in the client folding pathway. Out of 2,482 proteins in our sample set (approximately 38% of yeast proteins), we observed statistically significant changes in abundance of 350 (14%) of those proteins (log2 fold change ≥ 1.5). Of these, 257/350 (∼73%) with the strongest differences in abundance were previously connected to Hsp90 function. Principal component analysis of the entire dataset revealed that the effects of the mutants could be separated into 3 primary clusters. As evidence that Hsp90 mutants affect different pools of clients, simultaneous co-expression of 2 mutants in different clusters restored wild-type growth. Our data suggest that the ability of Hsp90 to sample a wide range of conformations allows the chaperone to mediate folding of a broad array of clients and that disruption of conformational flexibility results in client defects dependent on those states.
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Affiliation(s)
- Erick I Rios
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Davi Gonçalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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6
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Berisio R, Barra G, Napolitano V, Privitera M, Romano M, Squeglia F, Ruggiero A. HtpG-A Major Virulence Factor and a Promising Vaccine Antigen against Mycobacterium tuberculosis. Biomolecules 2024; 14:471. [PMID: 38672487 PMCID: PMC11048413 DOI: 10.3390/biom14040471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Tuberculosis (TB) is the leading global cause of death f rom an infectious bacterial agent. Therefore, limiting its epidemic spread is a pressing global health priority. The chaperone-like protein HtpG of M. tuberculosis (Mtb) is a large dimeric and multi-domain protein with a key role in Mtb pathogenesis and promising antigenic properties. This dual role, likely associated with the ability of Heat Shock proteins to act both intra- and extra-cellularly, makes HtpG highly exploitable both for drug and vaccine development. This review aims to gather the latest updates in HtpG structure and biological function, with HtpG operating in conjunction with a large number of chaperone molecules of Mtb. Altogether, these molecules help Mtb recovery after exposure to host-like stress by assisting the whole path of protein folding rescue, from the solubilisation of aggregated proteins to their refolding. Also, we highlight the role of structural biology in the development of safer and more effective subunit antigens. The larger availability of structural information on Mtb antigens and a better understanding of the host immune response to TB infection will aid the acceleration of TB vaccine development.
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Affiliation(s)
- Rita Berisio
- Institute of Biostructures and Bioimaging, IBB, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy; (G.B.); (V.N.); (M.P.); (M.R.); (F.S.)
| | | | | | | | | | | | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, IBB, CNR, Via Pietro Castellino 111, I-80131 Naples, Italy; (G.B.); (V.N.); (M.P.); (M.R.); (F.S.)
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7
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Szántó JK, Dietschreit JCB, Shein M, Schütz AK, Ochsenfeld C. Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment. J Chem Theory Comput 2024; 20:2433-2444. [PMID: 38497488 DOI: 10.1021/acs.jctc.3c01280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential. This entails high computational demands for reliable simulations. For NMR measurements in biological systems, a nucleus of major interest is 31P since it is both highly present (e.g., in nucleic acids) and easily observable. The focus of our present study is to develop a robust and computationally cost-efficient framework for simulating 31P NMR chemical shifts of nucleotides. We apply this scheme to study the different stages of the ATP hydrolysis reaction catalyzed by p97. Our methodology is based on MM molecular dynamics (MM-MD) sampling, followed by QM/MM structure optimizations and NMR calculations. Overall, our study is one of the most comprehensive QM-based 31P studies in a protein environment and the first to provide computed NMR chemical shifts for multiple nucleotide states in a protein environment. This study sheds light on a process that is challenging to probe experimentally and aims to bridge the gap between measured and calculated NMR spectroscopic properties.
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Affiliation(s)
- Judit Katalin Szántó
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
| | - Johannes C B Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mikhail Shein
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 München, Germany
| | - Anne K Schütz
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 München, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 München, Germany
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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8
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Meng X, Wu J, Hu Z, Zheng X. Intelligent responsive copper-diethyldithiocarbamate-based multifunctional nanomedicine for photothermal-augmented synergistic cancer therapy. J Mater Chem B 2024; 12:1285-1295. [PMID: 38189142 DOI: 10.1039/d3tb02491a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The design of multifunctional nanomedicine through the combination of multimodal treatments to achieve the optimal antitumor effect is essential for cancer therapy. Herein, we design and develop a multifunctional theranostic nanoplatform using an iron ion-doxorubicin (DOX) nanoscale coordination polymer (Fe/DOX NCP) as a shell coating on the surface of polyvinyl pyrrolidone (PVP) stabilized copper-diethyldithiocarbamate nanoparticles (Cu(DDC)2 NPs) for combined tumor chemo-/photothermal/chemodynamic therapy. The obtained Cu(DDC)2@Fe/DOX NPs display pH/laser dual-responsive degradation behavior and also exhibit favorable photothermal performance. Under 808 nm laser irradiation, Cu(DDC)2@Fe/DOX NPs can convert light into heat, which not only kills tumor cells via hyperthermia in photothermal therapy (PTT), but also accelerates the degradation of Fe/DOX NCPs to release Fe3+ and DOX. The liberated Fe3+ can be used to catalyze hydrogen peroxide via the Fenton reaction to produce highly toxic hydroxyl radicals (˙OH) in chemodynamic therapy (CDT). The released DOX and the exposed Cu(DDC)2 can cause significant cell death in combined chemotherapy via a superimposed effect. In vitro and in vivo results prove that Cu(DDC)2@Fe/DOX NPs with laser irradiation present remarkable anticancer performances in hyperthermia-enhanced chemo-/CDT. Therefore, this study provides a new strategy for highly efficient synergistic cancer therapy.
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Affiliation(s)
- Xiangyu Meng
- Key Laboratory of Advanced Biomaterials and Nanomedicine in Universities of Shandong, Linyi University, Linyi 276000, P. R. China.
- School of Materials Science and Engineering, Linyi University, Linyi 276000, P. R. China
| | - Jiayi Wu
- Key Laboratory of Advanced Biomaterials and Nanomedicine in Universities of Shandong, Linyi University, Linyi 276000, P. R. China.
- School of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, P. R. China
| | - Zunfu Hu
- Key Laboratory of Advanced Biomaterials and Nanomedicine in Universities of Shandong, Linyi University, Linyi 276000, P. R. China.
- School of Materials Science and Engineering, Linyi University, Linyi 276000, P. R. China
| | - Xiuwen Zheng
- Key Laboratory of Advanced Biomaterials and Nanomedicine in Universities of Shandong, Linyi University, Linyi 276000, P. R. China.
- Qilu Normal University, Jinan, 250200, P. R. China
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9
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Carels N, Sgariglia D, Junior MGV, Lima CR, Carneiro FRG, da Silva GF, da Silva FAB, Scardini R, Tuszynski JA, de Andrade CV, Monteiro AC, Martins MG, da Silva TG, Ferraz H, Finotelli PV, Balbino TA, Pinto JC. A Strategy Utilizing Protein-Protein Interaction Hubs for the Treatment of Cancer Diseases. Int J Mol Sci 2023; 24:16098. [PMID: 38003288 PMCID: PMC10671768 DOI: 10.3390/ijms242216098] [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: 07/23/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 11/26/2023] Open
Abstract
We describe a strategy for the development of a rational approach of neoplastic disease therapy based on the demonstration that scale-free networks are susceptible to specific attacks directed against its connective hubs. This strategy involves the (i) selection of up-regulated hubs of connectivity in the tumors interactome, (ii) drug repurposing of these hubs, (iii) RNA silencing of non-druggable hubs, (iv) in vitro hub validation, (v) tumor-on-a-chip, (vi) in vivo validation, and (vii) clinical trial. Hubs are protein targets that are assessed as targets for rational therapy of cancer in the context of personalized oncology. We confirmed the existence of a negative correlation between malignant cell aggressivity and the target number needed for specific drugs or RNA interference (RNAi) to maximize the benefit to the patient's overall survival. Interestingly, we found that some additional proteins not generally targeted by drug treatments might justify the addition of inhibitors designed against them in order to improve therapeutic outcomes. However, many proteins are not druggable, or the available pharmacopeia for these targets is limited, which justifies a therapy based on encapsulated RNAi.
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Affiliation(s)
- Nicolas Carels
- Platform of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (C.R.L.); (G.F.d.S.)
| | - Domenico Sgariglia
- Engenharia de Sistemas e Computação, Instituto Alberto Luiz Coimbra de Pós-Graduação e Pesquisa de Engenharia (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-972, RJ, Brazil;
| | - Marcos Guilherme Vieira Junior
- Computational Modeling of Biological Systems, Scientific Computing Program (PROCC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil or (M.G.V.J.); (F.A.B.d.S.)
| | - Carlyle Ribeiro Lima
- Platform of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (C.R.L.); (G.F.d.S.)
| | - Flávia Raquel Gonçalves Carneiro
- Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (F.R.G.C.); (R.S.)
- Laboratório Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20231-050, RJ, Brazil
| | - Gilberto Ferreira da Silva
- Platform of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (C.R.L.); (G.F.d.S.)
| | - Fabricio Alves Barbosa da Silva
- Computational Modeling of Biological Systems, Scientific Computing Program (PROCC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil or (M.G.V.J.); (F.A.B.d.S.)
| | - Rafaela Scardini
- Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil; (F.R.G.C.); (R.S.)
- Program of Immunology and Tumor Biology, Brazilian National Cancer Institute (INCA), Rio de Janeiro 20231-050, RJ, Brazil
- Centro de Ciências Biológicas e da Saúde (CCBS), Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro 22290-255, RJ, Brazil
| | - Jack Adam Tuszynski
- Dipartimento di Ingegneria Meccanica e Aerospaziale (DIMEAS), Politecnico di Torino, 10129 Turin, Italy;
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
- Department of Physics, University of Alberta, Edmonton, AB T6G 2J1, Canada
| | - Cecilia Vianna de Andrade
- Department of Pathology, Instituto Fernandes Figueira, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 22250-020, RJ, Brazil;
| | - Ana Carolina Monteiro
- Laboratory of Osteo and Tumor Immunology, Department of Immunobiology, Fluminense Federal University, Rio de Janeiro 24210-201, RJ, Brazil;
| | - Marcel Guimarães Martins
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
| | - Talita Goulart da Silva
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
| | - Helen Ferraz
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
| | - Priscilla Vanessa Finotelli
- Laboratório de Nanotecnologia Biofuncional, Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, RJ, Brazil;
| | - Tiago Albertini Balbino
- Nanotechnology Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil;
| | - José Carlos Pinto
- Chemical Engineering Program, Alberto Luiz Coimbra Institute for Graduate Studies and Research in Engineering (COPPE), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-594, RJ, Brazil; (M.G.M.); (T.G.d.S.); (H.F.); (J.C.P.)
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10
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Peng S, Matts R, Deng J. Structural basis of the key residue W320 responsible for Hsp90 conformational change. J Biomol Struct Dyn 2023; 41:9745-9755. [PMID: 36373326 PMCID: PMC10183053 DOI: 10.1080/07391102.2022.2146197] [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: 07/07/2022] [Accepted: 11/06/2022] [Indexed: 11/16/2022]
Abstract
The 90-kDa heat shock protein (Hsp90) is a homodimeric molecular chaperone with ATPase activity, which has become an intensely studied target for the development of drugs for the treatment of cancer, neurodegenerative and infectious diseases. The equilibrium between Hsp90 dimers and oligomers is important for modulating its function. In the absence of ATP, the passive chaperone activity of Hsp90 dimers and oligomers has been shown to stabilize client proteins as a holdase, which enhances substrate binding and prevents irreversible aggregation and precipitation of the substrate proteins. In the presence of ATP and its associated cochaperones, Hsp90 homodimers act as foldases with the binding and hydrolysis of ATP driving conformational changes that mediate client folding. Crystal structures of both wild type and W320A mutant Hsp90αMC (middle/C-terminal domain) have been determined, which displayed a preference for hexameric and dimeric states, respectively. Structural analysis showed that W320 is a key residue for Hsp90 oligomerization by forming intermolecular interactions at the Hsp90 hexameric interface through cation-π interactions with R367. W320A substitution results in the formation of a more open conformation of Hsp90, which has not previously been reported, and the induction of a conformational change in the catalytic loop. The structures provide new insights into the mechanism by which W320 functions as a key switch for conformational changes in Hsp90 self-oligomerization, and binding cochaperones and client proteins.Communicated by Ramaswamy H. Sarma.
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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
| | - Robert 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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Kim H, Saura P, Pöverlein MC, Gamiz-Hernandez AP, Kaila VRI. Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I. J Am Chem Soc 2023; 145:17075-17086. [PMID: 37490414 PMCID: PMC10416309 DOI: 10.1021/jacs.3c03086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Indexed: 07/27/2023]
Abstract
Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes.
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Affiliation(s)
- Hyunho Kim
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Patricia Saura
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | | | - Ana P. Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 10691, Sweden
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12
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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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13
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Ramirez LM, Zweckstetter M. Molecular-level interplay between intrinsically disordered clients and Hsp90. Curr Opin Chem Biol 2023; 74:102304. [PMID: 37068388 DOI: 10.1016/j.cbpa.2023.102304] [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: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 04/19/2023]
Abstract
Proteostasis is maintained by a network of molecular chaperones, a prominent member of which is the 90-kilodalton heat shock protein Hsp90. The chaperone function of Hsp90 has been extensively reviewed previously, emphasizing its ATPase activity and remodeling of folded client proteins. Experimental evidence implicating Hsp90 in neurodegenerative diseases has bolstered interest in the noncanonical chaperoning of intrinsically disordered protein (IDPs), however the interplay between Hsp90 and its disordered clients remains poorly understood. In this review we describe recent advances that have contributed to our understanding of the intricate mechanisms characterizing Hsp90-mediated chaperoning of the IDPs tau and α-synuclein and survey emerging insights into the modulation of the chaperone-client interplay in the context of neurodegeneration.
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Affiliation(s)
- Lisa Marie Ramirez
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Gӧttingen, Germany; Department for NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Gӧttingen, Germany.
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14
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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: 12] [Impact Index Per Article: 12.0] [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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15
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Chowdhury SR, Koley T, Singh M, Samath EA, Kaur P. Association of Hsp90 with p53 and Fizzy related homolog (Fzr) synchronizing Anaphase Promoting Complex (APC/C): An unexplored ally towards oncogenic pathway. Biochim Biophys Acta Rev Cancer 2023; 1878:188883. [PMID: 36972769 DOI: 10.1016/j.bbcan.2023.188883] [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: 09/03/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/29/2023]
Abstract
The intricate molecular interactions leading to the oncogenic pathway are the consequence of cell cycle modification controlled by a bunch of cell cycle regulatory proteins. The tumor suppressor and cell cycle regulatory proteins work in coordination to maintain a healthy cellular environment. The integrity of this cellular protein pool is perpetuated by heat shock proteins/chaperones, which assist in proper protein folding during normal and cellular stress conditions. Among these versatile groups of chaperone proteins, Hsp90 is one of the significant ATP-dependent chaperones that aid in stabilizing many tumor suppressors and cell cycle regulator protein targets. Recently, studies have revealed that in cancerous cell lines, Hsp90 stabilizes mutant p53, 'the guardian of the genome.' Hsp90 also has a significant impact on Fzr, an essential regulator of the cell cycle having an important role in the developmental process of various organisms, including Drosophila, yeast, Caenorhabditis elegans, and plants. During cell cycle progression, p53 and Fzr coordinately regulate the Anaphase Promoting Complex (APC/C) from metaphase to anaphase transition up to cell cycle exit. APC/C mediates proper centrosome function in the dividing cell. The centrosome acts as the microtubule organizing center for the correct segregation of the sister chromatids to ensure perfect cell division. This review examines the structure of Hsp90 and its co-chaperones, which work in synergy to stabilize proteins such as p53 and Fizzy-related homolog (Fzr) to synchronize the Anaphase Promoting Complex (APC/C). Dysfunction of this process activates the oncogenic pathway leading to the development of cancer. Additionally, an overview of current drugs targeting Hsp90 at various phases of clinical trials has been included.
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Affiliation(s)
- Sanghati Roy Chowdhury
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tirthankar Koley
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | | | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.
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16
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Yin W, Chang J, Sun J, Zhang T, Zhao Y, Li Y, Dong H. Nanomedicine-mediated ferroptosis targeting strategies for synergistic cancer therapy. J Mater Chem B 2023; 11:1171-1190. [PMID: 36650960 DOI: 10.1039/d2tb02161g] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Apoptosis-based treatment plays an important role in regulating the death of tumor cells (e.g., chemotherapy, radiotherapy, and immunotherapy). Nevertheless, cancer cells can escape surveillance from apoptosis-associated signaling by bypassing other biological pathways and thus result in considerable resistance to therapies. Significantly, ferroptosis, a newly identified type of regulated cell death that is characterized by iron-dependent and lipid peroxidation accumulation, has aroused great research interest in cancer therapy. Increasing approaches have been developed to induce ferroptosis of tumor cells, including using clinically approved drugs, experimentally used compounds, and nanomedicine formulations. More importantly, the emerging nanomedicine-based strategy has made great advances in tumor treatment because of the promising targeting efficacy and enhanced therapeutic effects. In this review, we mainly overview state-of-the-art research on nanomedicine-mediated ferroptosis targeting strategies for synergistic cancer therapies, such as immunotherapy, chemotherapy, radiotherapy, and photothermal therapy. The potential targeting mechanism of nanomedicine for ferroptosis induction was also included. Finally, the future development of nanomedicine in the field of ferroptosis-based cell death in tumor treatment will be envisioned, aiming to provide new insight for tumor treatment in the clinic.
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Affiliation(s)
- Weimin Yin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration, Ministry of Education, Tongji Hospital, The Institute for Biomedical Engineering & Nano Science (iNANO), School of Medicine, Tongji University, 389 Xincun Road, Shanghai 200065, China.
| | - Jiao Chang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jiuyuan Sun
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Tingting Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yuge Zhao
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yongyong Li
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Haiqing Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration, Ministry of Education, Tongji Hospital, The Institute for Biomedical Engineering & Nano Science (iNANO), School of Medicine, Tongji University, 389 Xincun Road, Shanghai 200065, China.
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17
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Carney TD, Hebalkar RY, Edeleva E, Çiçek IÖ, Shcherbata HR. Signaling through the dystrophin glycoprotein complex affects the stress-dependent transcriptome in Drosophila. Dis Model Mech 2023; 16:286223. [PMID: 36594281 PMCID: PMC9922874 DOI: 10.1242/dmm.049862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/22/2022] [Indexed: 01/04/2023] Open
Abstract
Deficiencies in the human dystrophin glycoprotein complex (DGC), which links the extracellular matrix with the intracellular cytoskeleton, cause muscular dystrophies, a group of incurable disorders associated with heterogeneous muscle, brain and eye abnormalities. Stresses such as nutrient deprivation and aging cause muscle wasting, which can be exacerbated by reduced levels of the DGC in membranes, the integrity of which is vital for muscle health and function. Moreover, the DGC operates in multiple signaling pathways, demonstrating an important function in gene expression regulation. To advance disease diagnostics and treatment strategies, we strive to understand the genetic pathways that are perturbed by DGC mutations. Here, we utilized a Drosophila model to investigate the transcriptomic changes in mutants of four DGC components under temperature and metabolic stress. We identified DGC-dependent genes, stress-dependent genes and genes dependent on the DGC for a proper stress response, confirming a novel function of the DGC in stress-response signaling. This perspective yields new insights into the etiology of muscular dystrophy symptoms, possible treatment directions and a better understanding of DGC signaling and regulation under normal and stress conditions.
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Affiliation(s)
- Travis D. Carney
- Hannover Medical School, Research Group Gene Expression and Signaling, Institute of Cell Biochemistry, Hannover 30625, Germany,Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA
| | - Rucha Y. Hebalkar
- Hannover Medical School, Research Group Gene Expression and Signaling, Institute of Cell Biochemistry, Hannover 30625, Germany
| | | | | | - Halyna R. Shcherbata
- Hannover Medical School, Research Group Gene Expression and Signaling, Institute of Cell Biochemistry, Hannover 30625, Germany,Mount Desert Island Biological Laboratory, Bar Harbor, ME 04609, USA,Author for correspondence ()
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18
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A Structural View at Vaccine Development against M. tuberculosis. Cells 2023; 12:cells12020317. [PMID: 36672252 PMCID: PMC9857197 DOI: 10.3390/cells12020317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Tuberculosis (TB) is still the leading global cause of death from an infectious bacterial agent. Limiting tuberculosis epidemic spread is therefore an urgent global public health priority. As stated by the WHO, to stop the spread of the disease we need a new vaccine, with better coverage than the current Mycobacterium bovis BCG vaccine. This vaccine was first used in 1921 and, since then, there are still no new licensed tuberculosis vaccines. However, there is extremely active research in the field, with a steep acceleration in the past decades, due to the advance of technologies and more rational vaccine design strategies. This review aims to gather latest updates in vaccine development in the various clinical phases and to underline the contribution of Structural Vaccinology (SV) to the development of safer and effective antigens. In particular, SV and the development of vaccine adjuvants is making the use of subunit vaccines, which are the safest albeit the less antigenic ones, an achievable goal. Indeed, subunit vaccines overcome safety concerns but need to be rationally re-engineered to enhance their immunostimulating effects. The larger availability of antigen structural information as well as a better understanding of the complex host immune response to TB infection is a strong premise for a further acceleration of TB vaccine development.
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19
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Muduli S, Mishra S. Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations. Proteins 2023; 91:781-797. [PMID: 36633566 DOI: 10.1002/prot.26466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/20/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023]
Abstract
The microbial enzyme DapE plays a critical role in the lysine biosynthetic pathway and is considered as a potentially safe antibiotic target. In this study, atomistic simulations are employed to identify the modes of essential dynamics that define the conformational response of the enzyme to ligand binding and unbinding. The binding modes and the binding affinities of the products to the DapE enzyme are estimated from the MM-PBSA method, and the residues contributing to the ligand binding are identified. Various structural analyses and the principal component analysis of the molecular dynamics trajectories reveal that the removal of products from the active site causes a significant change in the overall enzyme structure. Both Cartesian and dihedral principal component analyses are used to characterize the structural changes in terms of domain unfolding and domain twisting motions. In the most dominant mode, that is, the domain unfolding motion, the two catalytic domains move away from the two dimerization domains of the dimeric enzyme, representing a closed-to-open conformational change. The conformational changes are initiated by the coordinated movement of three loops (Asp75-Pro82, Gly240-Asn244, and Thr347-Glu353) that trigger a domain-level movement. From multiple short trajectories, the time constant associated with the domain opening motion is estimated as 43.6 ns. Physiologically, this close-to-open conformational change is essential for the regeneration of the initial state of the enzyme for the subsequent cycle of catalytic action and provides the apo enzyme enough flexibility for efficient substrate binding.
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Affiliation(s)
- Sunita Muduli
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
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20
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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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21
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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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22
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Fangaria N, Rani K, Singh P, Dey S, Kumar KA, Bhattacharyya S. DNA damage-induced nuclear import of HSP90α is promoted by Aha1. Mol Biol Cell 2022; 33:ar140. [PMID: 36260391 PMCID: PMC9727810 DOI: 10.1091/mbc.e21-11-0554] [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] [Indexed: 02/04/2023] Open
Abstract
The interplay between yHSP90α (Hsp82) and Rad51 has been implicated in the DNA double-strand break repair (DSB) pathway in yeast. Here we report that nuclear translocation of yHSP90α and its recruitment to the DSB end are essential for homologous recombination (HR)-mediated DNA repair in yeast. The HsHSP90α possesses an amino-terminal extension which is phosphorylated upon DNA damage. We find that the absence of the amino-terminal extension in yHSP90α does not compromise its nuclear import, and the nonphosphorylatable-mutant HsHSP90αT7A could be imported to the yeast nucleus upon DNA damage. Interestingly, the flexible charged-linker (CL) domains of both yHSP90α and HsHSP90α play a critical role during their nuclear translocation. The conformational restricted CL mutant yHSP90α∆(211-259), but not a shorter deletion version yHSP90α∆(211-242), fails to reach the nucleus. As the CL domain of yHSP90α is critical for its interaction with Aha1, we investigated whether Aha1 promotes the nuclear import of yHSP90α. We found that the nuclear import of yHSP90α is severely affected in ∆aha1 strain. Moreover, Aha1 is accumulated in the nucleus during DNA damage. Hence Aha1 may serve as a potential target for inhibiting nuclear function of yHSP90α. The increased sensitivity of ∆aha1 strain to genotoxic agents strengthens this notion.
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Affiliation(s)
- Nupur Fangaria
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Khushboo Rani
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Priyanka Singh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Sandeep Dey
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Kota Arun Kumar
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India,*Address correspondence to: Sunanda Bhattacharyya (; )
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Stuehr DJ, Dai Y, Biswas P, Sweeny EA, Ghosh A. New roles for GAPDH, Hsp90, and NO in regulating heme allocation and hemeprotein function in mammals. Biol Chem 2022; 403:1005-1015. [PMID: 36152339 PMCID: PMC10184026 DOI: 10.1515/hsz-2022-0197] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 12/23/2022]
Abstract
The intracellular trafficking of mitochondrial heme presents a fundamental challenge to animal cells. This article provides some background on heme allocation, discusses some of the concepts, and then reviews research done over the last decade, much in the author's laboratory, that is uncovering unexpected and important roles for glyceraldehyde 3-phosphate dehydrogenase (GAPDH), heat shock protein 90 (hsp90), and nitric oxide (NO) in enabling and regulating the allocation of mitochondrial heme to hemeproteins that mature and function outside of the mitochondria. A model for how hemeprotein functions can be regulated in cells through the coordinate participation of GAPDH, hsp90, and NO in allocating cellular heme is presented.
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Affiliation(s)
- Dennis J Stuehr
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Yue Dai
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Pranjal Biswas
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Elizabeth A Sweeny
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Arnab Ghosh
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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24
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Tang L, Ling M, Syeda MZ, Sun R, He M, Mu Q, Zhu X, Huang C, Cui L. A smart nanoplatform for enhanced photo-ferrotherapy of hepatocellular carcinoma. Front Bioeng Biotechnol 2022; 10:1022330. [PMID: 36204469 PMCID: PMC9530464 DOI: 10.3389/fbioe.2022.1022330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. Emerging therapies, such as ferroptosis mediated cancer therapy and phototherapy, offer new opportunities for HCC treatment. The combination of multiple treatments is often more effective than monotherapy, but many of the current treatments are prone to serious side effects, resulting in a serious decline in patients’ quality of life. Therefore, the combination therapy of tumor in situ controllable activation will improve the efficacy and reduce side effects for precise treatment of tumor. Herein, we synthesized a GSH-activatable nanomedicine to synergize photothermal therapy (PTT) and ferrotherapy. We utilized a near-infrared dye SQ890 as both an iron-chelating and a photothermal converter agent, which was encapsulated with a GSH-sensitive polymer (PLGA-SS-mPEG), to attain the biocompatible SQ890@Fe nanoparticles (NPs). In the tumor microenvironment (TME), SQ890@Fe NPs showed a GSH-activated photothermal effect that could increase the Fenton reaction rate. Meanwhile, the depletion of GSH could further increase ferroptosis effect. In turn, the increasing radical generated by ferrotherapy could impair the formation of heat shock proteins (HSPs) which could amplify PTT effects by limiting the self-protection mechanism. Overall, the intelligent nanomedicine SQ890@Fe NPs combines ferrotherapy and PTT to enhance the efficacy and safety of cancer treatment through the mutual promotion of the two treatment mechanisms, providing a new dimension for tumor combination therapy.
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Affiliation(s)
- Longguang Tang
- The People’s Hospital of Gaozhou, Guangdong Medical University, Maoming, China
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, and School of Pharmacy, Guangdong Medical University, Dongguan, China
- *Correspondence: Longguang Tang, ; Chunming Huang, ; Liao Cui,
| | - Mingjian Ling
- Southern Medical University Shenzhen Stomatology Hospital (Pingshan), Shenzhen, China
| | - Madiha Zahra Syeda
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Zhejiang University School of Medicine, Key Laboratory of Respiratory Disease of Zhejiang Province, Hangzhou, China
| | - Rui Sun
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, China
| | - Minghui He
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Qingchun Mu
- The People’s Hospital of Gaozhou, Guangdong Medical University, Maoming, China
| | - Xiulong Zhu
- The People’s Hospital of Gaozhou, Guangdong Medical University, Maoming, China
| | - Chunming Huang
- The People’s Hospital of Gaozhou, Guangdong Medical University, Maoming, China
- *Correspondence: Longguang Tang, ; Chunming Huang, ; Liao Cui,
| | - Liao Cui
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, and School of Pharmacy, Guangdong Medical University, Dongguan, China
- *Correspondence: Longguang Tang, ; Chunming Huang, ; Liao Cui,
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25
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Ruggiero A, Choi HG, Barra G, Squeglia F, Back YW, Kim HJ, Berisio R. Structure based design of effective HtpG-derived vaccine antigens against M. tuberculosis. Front Mol Biosci 2022; 9:964645. [PMID: 36032688 PMCID: PMC9403545 DOI: 10.3389/fmolb.2022.964645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/15/2022] [Indexed: 12/03/2022] Open
Abstract
Vaccine development against Tuberculosis is a strong need, given the low efficacy of the sole vaccine hitherto used, the Bacillus Calmette–Guérin (BCG) vaccine. The chaperone-like protein HtpGMtb of M. tuberculosis is a large dimeric and multi-domain protein with promising antigenic properties. We here used biophysical and biochemical studies to improve our understanding of the structural basis of HtpGMtb functional role and immunogenicity, a precious information to engineer improved antigens. We showed that HtpGMtb is a dimeric nucleotide-binding protein and identified the dimerisation interface on the C-terminal domain of the protein. We also showed that the most immunoreactive regions of the molecule are located on the C-terminal and middle domains of the protein, whereas no role is played by the catalytic N-terminal domain in the elicitation of the immune response. Based on these observations, we experimentally validated our predictions in mice, using a plethora of immunological assays. As an outcome, we designed vaccine antigens with enhanced biophysical properties and ease of production, albeit conserved or enhanced antigenic properties. Our results prove the efficacy of structural vaccinology approaches in improving our understanding of the structural basis of immunogenicity, a precious information to engineer more stable, homogeneous, efficiently produced, and effective vaccine antigens.
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Affiliation(s)
- Alessia Ruggiero
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
| | - Han-Gyu Choi
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Giovanni Barra
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
| | - Young Woo Back
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hwa-Jung Kim
- Department of Microbiology and Medical Science, College of Medicine, Chungnam National University, Daejeon, South Korea
- *Correspondence: Hwa-Jung Kim, ; Rita Berisio,
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, IBB, CNR, Napoli, Italy
- *Correspondence: Hwa-Jung Kim, ; Rita Berisio,
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26
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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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27
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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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28
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Liew HY, Tan XY, Chan HH, Khaw KY, Ong YS. Natural HSP90 inhibitors as a potential therapeutic intervention in treating cancers: A comprehensive review. Pharmacol Res 2022; 181:106260. [DOI: 10.1016/j.phrs.2022.106260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 10/18/2022]
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29
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Allgöwer F, Gamiz-Hernandez AP, Rutherford AW, Kaila VRI. Molecular Principles of Redox-Coupled Protonation Dynamics in Photosystem II. J Am Chem Soc 2022; 144:7171-7180. [PMID: 35421304 PMCID: PMC9052759 DOI: 10.1021/jacs.1c13041] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Photosystem II (PSII) catalyzes light-driven water oxidization, releasing O2 into the atmosphere and transferring the electrons for the synthesis of biomass. However, despite decades of structural and functional studies, the water oxidation mechanism of PSII has remained puzzling and a major challenge for modern chemical research. Here, we show that PSII catalyzes redox-triggered proton transfer between its oxygen-evolving Mn4O5Ca cluster and a nearby cluster of conserved buried ion-pairs, which are connected to the bulk solvent via a proton pathway. By using multi-scale quantum and classical simulations, we find that oxidation of a redox-active Tyrz (Tyr161) lowers the reaction barrier for the water-mediated proton transfer from a Ca2+-bound water molecule (W3) to Asp61 via conformational changes in a nearby ion-pair (Asp61/Lys317). Deprotonation of this W3 substrate water triggers its migration toward Mn1 to a position identified in recent X-ray free-electron laser (XFEL) experiments [Ibrahim et al. Proc. Natl. Acad. Sci. USA 2020, 117, 12,624-12,635]. Further oxidation of the Mn4O5Ca cluster lowers the proton transfer barrier through the water ligand sphere of the Mn4O5Ca cluster to Asp61 via a similar ion-pair dissociation process, while the resulting Mn-bound oxo/oxyl species leads to O2 formation by a radical coupling mechanism. The proposed redox-coupled protonation mechanism shows a striking resemblance to functional motifs in other enzymes involved in biological energy conversion, with an interplay between hydration changes, ion-pair dynamics, and electric fields that modulate the catalytic barriers.
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Affiliation(s)
- Friederike Allgöwer
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - A William Rutherford
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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30
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Zeng F, Tang L, Zhang Q, Shi C, Huang Z, Nijiati S, Chen X, Zhou Z. Coordinating the Mechanisms of Action of Ferroptosis and the Photothermal Effect for Cancer Theranostics. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fantian Zeng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University Xiamen 361102 P. R. China
| | - Longguang Tang
- International Institutes of Medicine The Fourth Affiliated Hospital of Zhejiang University School of Medicine Yiwu, Zhejiang 322000 P. R. China
| | - Qianyu Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University Xiamen 361102 P. R. China
| | - Changrong Shi
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University Xiamen 361102 P. R. China
| | - Zicheng Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University Xiamen 361102 P. R. China
| | - Sureya Nijiati
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University Xiamen 361102 P. R. China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, and Surgery Clinical Imaging Research Centre Centre for Translational Medicine Nanomedicine Translational Research Program NUS Center for Nanomedicine Yong Loo Lin School of Medicine Departments of Chemical and Biomolecular Engineering and Biomedical Engineering Faculty of Engineering National University of Singapore Singapore 117597 Singapore
| | - Zijian Zhou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics Center for Molecular Imaging and Translational Medicine School of Public Health Xiamen University Xiamen 361102 P. R. China
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31
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Zeng F, Tang L, Zhang Q, Shi C, Huang Z, Nijiati S, Chen X, Zhou Z. Coordinating the mechanism of actions of ferroptosis and photothermal effect for cancer theranostics. Angew Chem Int Ed Engl 2021; 61:e202112925. [PMID: 34932846 DOI: 10.1002/anie.202112925] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 11/07/2022]
Abstract
Combination therapy based on different mechanisms of cell death has shown promises in tumor therapy. However, design considerations for integrating different modalities are often lack of rationale to synergize the therapeutic effects to the maximal extent. Here, we report a cancer theranostic nanomedicine formula by attentively considering the mechanisms of action of ferroptosis and photothermal effect in combination therapy. We applied the croconaine molecule as both a photothermal converter and an iron-chelating agent which could be readily encapsulated with BSA thus attaining biocompatible and stable Cro-Fe@BSA nanoparticles. The Cro-Fe@BSA nanoprticles in the tumor milieu showed an activated photothermal effect which could enhance the radical formation due to the temperature-dependent Fenton reaction kinetics, while the radical formation during ferroptosis could in turn destruct the heat-induced formation of heat shock proteins, thus preventing the self-protection mechanism of cancer cells in response to heat. This mutually beneficial strategy led to an efficient anticancer effect both in vitro and in a subcutaneous mouse tumor model. Furthermore, the activatable photoacoustic and magnetic resonance imaging performance of the Cro-Fe@BSA nanoparticles provided an intelligent paradigm for safe and reliable cancer theranostics. This study may open up new avenues in designing nanomedicines from a vantage point of synergizing different therapeutic modalities.
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Affiliation(s)
- Fantian Zeng
- Xiamen University, School of Public health, CHINA
| | | | - Qianyu Zhang
- Xiamen University, School of Public health, CHINA
| | | | | | | | - Xiaoyuan Chen
- National University of Singapore, School of Medicine and Faculty of Engineering, 10 Medical Dr, 117597, Singapore, SINGAPORE
| | - Zijian Zhou
- Xiamen University, School of Public health, CHINA
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32
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Kaila VRI. Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I. Acc Chem Res 2021; 54:4462-4473. [PMID: 34894649 PMCID: PMC8697550 DOI: 10.1021/acs.accounts.1c00524] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
Biological energy conversion is catalyzed by membrane-bound proteins
that transduce chemical or light energy into energy forms that power
endergonic processes in the cell. At a molecular level, these catalytic
processes involve elementary electron-, proton-, charge-, and energy-transfer
reactions that take place in the intricate molecular machineries of
cell respiration and photosynthesis. Recent developments in structural
biology, particularly cryo-electron microscopy (cryoEM), have resolved
the molecular architecture of several energy transducing proteins,
but detailed mechanistic principles of their charge transfer reactions
still remain poorly understood and a major challenge for modern biochemical
research. To this end, multiscale molecular simulations provide a
powerful approach to probe mechanistic principles on a broad range
of time scales (femtoseconds to milliseconds) and spatial resolutions
(101–106 atoms), although technical challenges
also require balancing between the computational accuracy, cost, and
approximations introduced within the model. Here we discuss how the
combination of atomistic (aMD) and hybrid quantum/classical molecular
dynamics (QM/MM MD) simulations with free energy (FE) sampling methods
can be used to probe mechanistic principles of enzymes responsible
for biological energy conversion. We present mechanistic explorations
of long-range proton-coupled electron transfer (PCET) dynamics in
the highly intricate respiratory chain enzyme Complex I, which functions
as a redox-driven proton pump in bacterial and mitochondrial respiratory
chains by catalyzing a 300 Å fully reversible PCET process. This
process is initiated by a hydride (H–) transfer
between NADH and FMN, followed by long-range (>100 Å) electron
transfer along a wire of 8 FeS centers leading to a quinone biding
site. The reduction of the quinone to quinol initiates dissociation
of the latter to a second membrane-bound binding site, and triggers
proton pumping across the membrane domain of complex I, in subunits
up to 200 Å away from the active site. Our simulations across
different size and time scales suggest that transient charge transfer
reactions lead to changes in the internal hydration state of key regions,
local electric fields, and the conformation of conserved ion pairs,
which in turn modulate the dynamics of functional steps along the
reaction cycle. Similar functional principles, which operate on much
shorter length scales, are also found in some unrelated proteins,
suggesting that enzymes may employ conserved principles in the catalysis
of biological energy transduction processes.
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Affiliation(s)
- Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
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33
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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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34
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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: 8] [Impact Index Per Article: 2.7] [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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Two-colour single-molecule photoinduced electron transfer fluorescence imaging microscopy of chaperone dynamics. Nat Commun 2021; 12:6964. [PMID: 34845214 PMCID: PMC8630005 DOI: 10.1038/s41467-021-27286-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/11/2021] [Indexed: 11/20/2022] Open
Abstract
Many proteins are molecular machines, whose function is dependent on multiple conformational changes that are initiated and tightly controlled through biochemical stimuli. Their mechanistic understanding calls for spectroscopy that can probe simultaneously such structural coordinates. Here we present two-colour fluorescence microscopy in combination with photoinduced electron transfer (PET) probes as a method that simultaneously detects two structural coordinates in single protein molecules, one colour per coordinate. This contrasts with the commonly applied resonance energy transfer (FRET) technique that requires two colours per coordinate. We demonstrate the technique by directly and simultaneously observing three critical structural changes within the Hsp90 molecular chaperone machinery. Our results reveal synchronicity of conformational motions at remote sites during ATPase-driven closure of the Hsp90 molecular clamp, providing evidence for a cooperativity mechanism in the chaperone’s catalytic cycle. Single-molecule PET fluorescence microscopy opens up avenues in the multi-dimensional exploration of protein dynamics and allosteric mechanisms. Revealing mechanisms of complex protein machines requires simultaneous exploration of multiple structural coordinates. Here the authors report two-colour fluorescence microscopy combined with photoinduced electron transfer probes to simultaneously detect two structural coordinates in single protein molecules.
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36
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Cao J, Lian G, Qi X, Jin G. Design synthesis and photophysical properties of a novel antitumor fluorescence agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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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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Ohminato N, Nagayasu M, Ozeki K, Saitoh R, Ono N, Shibahara N, Suda A, Yoshinari K. In vivo- in vitro correlation of antitumor activity of heat shock protein 90 (HSP90) inhibitors with a pharmacokinetics/pharmacodynamics analysis using NCI-N87 xenograft mice. Xenobiotica 2021; 51:968-976. [PMID: 34134599 DOI: 10.1080/00498254.2021.1942588] [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: 10/21/2022]
Abstract
The in vitro antitumor activity (e.g. IC50) of anticancer drugs is important for selecting candidate compounds for in vivo drug efficacy study in the early stage of drug discovery. In this study, we investigated the relationship between in vitro IC50 and in vivo EC50 using six heat shock protein 90 (HSP90) inhibitors.IC50 of each compound was calculated from in vitro cell proliferation assays using the NCI-N87 cancer cell line. Each compound was administered to NCI-N87 xenograft mice, and EC50 and the maximum tumour-killing rate constant were calculated from pharmacokinetics/pharmacodynamics analyses using plasma concentrations and tumour volumes.IC50 obtained in vitro was poorly correlated with EC50 obtained in vivo, while a good correlation (r = 0.856) was observed between them when corrected with the unbound fraction ratio.The results of this study using of HSP90 inhibitors as model compounds suggest importance of the consideration of an unbound fraction to evaluate the relationship between IC50 and EC50. These results will contribute to improvement in the prediction accuracy of in vivo drug efficacy from in vitro activity and the efficiency of drug discovery research.
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Affiliation(s)
- Noriaki Ohminato
- Chugai Research Institute for Medical Science, Inc., Gotemba, Shizuoka, Japan.,Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Miho Nagayasu
- Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Kazuhisa Ozeki
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Ryoichi Saitoh
- Research Division, Chugai Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan; f Sustainability Department, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan
| | - Naomi Ono
- Research Division, Chugai Pharmaceutical Co., Ltd., Fujisawa, Kanagawa, Japan; f Sustainability Department, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan
| | - Norihito Shibahara
- Translational Research Division, Chugai Pharmaceutical Co., Ltd., Gotemba, Shizuoka, Japan
| | - Atsushi Suda
- Sustainability Department, Chugai Pharmaceutical Co., Ltd., Chuo-ku, Tokyo, Japan
| | - Kouichi Yoshinari
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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39
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Abstract
Background Ocular adverse events are common dose-limiting toxicities in cancer patients treated with HSP90 inhibitors, such as AUY922; however, the pathology and molecular mechanisms that mediate AUY922-induced retinal toxicity remain undescribed. Methods The impact of AUY922 on mouse retinas and cell lines was comprehensively investigated using isobaric tags for relative and absolute quantitation (iTRAQ)‑based proteomic profiling and pathway enrichment analysis, immunohistochemistry and immunofluorescence staining, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, MTT assay, colony formation assay, and western blot analysis. The effect of AUY922 on the Transient Receptor Potential cation channel subfamily M member 1 (TRPM1)-HSP90 chaperone complex was characterized by coimmunoprecipitation. TRPM1-regulated gene expression was analyzed by RNAseq analysis and gene set enrichment analysis (GSEA). The role of TRPM1 was assessed using both loss-of-function and gain-of-function approaches. Results Here, we show that the treatment with AUY922 induced retinal damage and cell apoptosis, dysregulated the photoreceptor and retinal pigment epithelium (RPE) layers, and reduced TRPM1 expression. Proteomic profiling and functional annotation of differentially expressed proteins reveals that those related to stress responses, protein folding processes, regulation of apoptosis, cell cycle and growth, reactive oxygen species (ROS) response, cell junction assembly and adhesion regulation, and proton transmembrane transport were significantly enriched in AUY922-treated cells. We found that AUY922 triggered caspase-3-dependent cell apoptosis, increased ROS production and inhibited cell growth. We determined that TRPM1 is a bona fide HSP90 client and characterized that AUY922 may reduce TRPM1 expression by disrupting the CDC37-HSP90 chaperone complex. Additionally, GSEA revealed that TRPM1-regulated genes were associated with retinal morphogenesis in camera-type eyes and the JAK-STAT cascade. Finally, gain-of-function and loss-of-function analyses validated the finding that TRPM1 mediated the cell apoptosis, ROS production and growth inhibition induced by AUY922. Conclusions Our study demonstrates the pathology of AUY922-induced retinal toxicity in vivo. TRPM1 is an HSP90 client, regulates photoreceptor morphology and function, and mediates AUY922-induced cytotoxicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-021-00751-5.
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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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41
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Hohrman K, Gonçalves D, Morano KA, Johnson JL. Disrupting progression of the yeast Hsp90 folding pathway at different transition points results in client-specific maturation defects. Genetics 2021; 217:iyab009. [PMID: 33789348 PMCID: PMC8045699 DOI: 10.1093/genetics/iyab009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/11/2021] [Indexed: 11/12/2022] Open
Abstract
The protein molecular chaperone Hsp90 (Heat shock protein, 90 kilodalton) plays multiple roles in the biogenesis and regulation of client proteins impacting myriad aspects of cellular physiology. Amino acid alterations located throughout Saccharomyces cerevisiae Hsp90 have been shown to result in reduced client activity and temperature-sensitive growth defects. Although some Hsp90 mutants have been shown to affect activity of particular clients more than others, the mechanistic basis of client-specific effects is unknown. We found that Hsp90 mutants that disrupt the early step of Hsp70 and Sti1 interaction, or show reduced ability to adopt the ATP-bound closed conformation characterized by Sba1 and Cpr6 interaction, similarly disrupt activity of three diverse clients, Utp21, Ssl2, and v-src. In contrast, mutants that appear to alter other steps in the folding pathway had more limited effects on client activity. Protein expression profiling provided additional evidence that mutants that alter similar steps in the folding cycle cause similar in vivo consequences. Our characterization of these mutants provides new insight into how Hsp90 and cochaperones identify and interact with diverse clients, information essential for designing pharmaceutical approaches to selectively inhibit Hsp90 function.
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Affiliation(s)
- Kaitlyn Hohrman
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Davi Gonçalves
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Kevin A Morano
- Department of Microbiology and Molecular Genetics, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Jill L Johnson
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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42
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Baumgart M, Röpke M, Mühlbauer ME, Asami S, Mader SL, Fredriksson K, Groll M, Gamiz-Hernandez AP, Kaila VRI. Design of buried charged networks in artificial proteins. Nat Commun 2021; 12:1895. [PMID: 33767131 PMCID: PMC7994573 DOI: 10.1038/s41467-021-21909-7] [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] [Received: 05/30/2020] [Accepted: 02/19/2021] [Indexed: 11/24/2022] Open
Abstract
Soluble proteins are universally packed with a hydrophobic core and a polar surface that drive the protein folding process. Yet charged networks within the central protein core are often indispensable for the biological function. Here, we show that natural buried ion-pairs are stabilised by amphiphilic residues that electrostatically shield the charged motif from its surroundings to gain structural stability. To explore this effect, we build artificial proteins with buried ion-pairs by combining directed computational design and biophysical experiments. Our findings illustrate how perturbation in charged networks can introduce structural rearrangements to compensate for desolvation effects. We validate the physical principles by resolving high-resolution atomic structures of the artificial proteins that are resistant towards unfolding at extreme temperatures and harsh chemical conditions. Our findings provide a molecular understanding of functional charged networks and how point mutations may alter the protein’s conformational landscape. Buried charged networks in proteins are often important for their biological functionality and are believed to destabilise the protein fold. Here, the authors combine computational design, MD simulations, biophysical experiments, NMR and X-ray crystallography to design and characterise artificial 4α-helical proteins with buried charged elements. They analyse their conformational landscapes and observe that the ion-pairs are stabilised by amphiphilic residues that electrostatically shield the charged motif, which increases structural stability.
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Affiliation(s)
- Mona Baumgart
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Michael Röpke
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Max E Mühlbauer
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Sam Asami
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Sophie L Mader
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Kai Fredriksson
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Ana P Gamiz-Hernandez
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.,Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Ville R I Kaila
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany. .,Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden.
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43
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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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44
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Yin L, Yang Y, Zhu W, Xian Y, Han Z, Huang H, Peng L, Zhang K, Zhao Y. Heat Shock Protein 90 Triggers Multi-Drug Resistance of Ovarian Cancer via AKT/GSK3β/β-Catenin Signaling. Front Oncol 2021; 11:620907. [PMID: 33738259 PMCID: PMC7960917 DOI: 10.3389/fonc.2021.620907] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
Ovarian cancer is the most lethal gynaecologic tumor, with which multi-drug resistance as the major therapeutic hindrance. Heat shock protein 90 (Hsp90) has been involved in cancer malignant behaviors. However, its role and mechanism in multi-drug resistance of ovarian cancer remains poorly understood. Our results demonstrated that Hsp90 was overexpressed in multi-drug resistant ovarian cancer cells. Hsp90 downregulation by shHsp90 or inhibitor BIIB021 increased the sensitivity of multi-drug resistant ovarian cancer cells to paclitaxel and cisplatin, and augmented the drugs-induced apoptosis. Hsp90 positively regulated the expressions of multi-drug resistance protein 1 (P-gp/MDR1), breast cancer resistance protein (BCRP), Survivin and Bcl-2 expressions closely associated with multi-drug resistance. Moreover, overexpression of Hsp90 promoted β-catenin accumulation, while Hsp90 downregulation decreased the accumulation, nuclear translocation and transcriptional activity of β-catenin. We also identified that β-catenin was responsible for Hsp90-mediated expressions of P-gp, BCRP, Survivin, and Bcl-2. Furthermore, Hsp90 enhanced the AKT/GSK3β signaling, and AKT signaling played a critical role in Hsp90-induced accumulation and transcriptional activity of β-catenin, as well as multi-drug resistance to paclitaxel and cisplatin. In conclusion, Hsp90 enhanced the AKT/GSK3β/β-catenin signaling to induce multi-drug resistance of ovarian cancer. Suppressing Hsp90 chemosensitized multi-drug resistant ovarian cancer cells via impairing the AKT/GSK3β/β-catenin signaling, providing a promising therapeutic strategy for a successful treatment of ovarian cancer.
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Affiliation(s)
- Lan Yin
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Yuhan Yang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Wanglong Zhu
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Yu Xian
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Zhengyu Han
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Houyi Huang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Liaotian Peng
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Kun Zhang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Ye Zhao
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
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45
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Nanocluster-assisted protein-film voltammetry for direct electrochemical signal acquisition. Anal Bioanal Chem 2021; 413:1665-1673. [PMID: 33501552 DOI: 10.1007/s00216-020-03130-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022]
Abstract
Acquisition of the direct electrochemical response of protein is the cornerstone for the development of the third generation of electrochemical biosensors. In this work, we developed a nanocluster-assisted protein-film voltammetry technique (NCA-PFV) which can achieve the acquisition of the electrochemical signal and maintain the activity without affecting of the protein's structure. With this strategy, a lipid bilayer membrane is used to immobilize the membrane protein so as to maintain its natural state. Copper nanoclusters with a size smaller than most proteins are then used to function at sub-protein scale and to mediate the electron hopping from the electroactive center of the electrode. As a model, the direct electrochemical signal of cyclooxygenase (COX) is successfully obtained, with a pair of well-defined redox peaks located at -0.39 mV and -0.31 mV, which characterize the heme center of the enzyme. Its catalytic activity towards the substrate arachidonic acid (AA) is also retained. The detection range for AA is 10-1000 μM and the detection limit is 2.4 μM. Electrochemical monitoring of the regulation of the catalytic activity by an inhibitor DuP-697 is also achieved. This work provides a powerful tool for the fabrication of enzyme-based electrochemical biosensors, and is also of great significance for promoting the development and application of next-generation electrochemical biosensors.
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46
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Wolf S, Sohmen B, Hellenkamp B, Thurn J, Stock G, Hugel T. Hierarchical dynamics in allostery following ATP hydrolysis monitored by single molecule FRET measurements and MD simulations. Chem Sci 2021; 12:3350-3359. [PMID: 34164105 PMCID: PMC8179424 DOI: 10.1039/d0sc06134d] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/14/2021] [Indexed: 02/06/2023] Open
Abstract
We report on a study that combines advanced fluorescence methods with molecular dynamics (MD) simulations to cover timescales from nanoseconds to milliseconds for a large protein. This allows us to delineate how ATP hydrolysis in a protein causes allosteric changes at a distant protein binding site, using the chaperone Hsp90 as test system. The allosteric process occurs via hierarchical dynamics involving timescales from nano- to milliseconds and length scales from Ångstroms to several nanometers. We find that hydrolysis of one ATP is coupled to a conformational change of Arg380, which in turn passes structural information via the large M-domain α-helix to the whole protein. The resulting structural asymmetry in Hsp90 leads to the collapse of a central folding substrate binding site, causing the formation of a novel collapsed state (closed state B) that we characterise structurally. We presume that similar hierarchical mechanisms are fundamental for information transfer induced by ATP hydrolysis through many other proteins.
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Affiliation(s)
- Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg Freiburg Germany +49 761 203 5883 +49 761 203 5913
| | - Benedikt Sohmen
- Institute of Physical Chemistry, University of Freiburg Freiburg Germany +49 761 203 6192
| | - Björn Hellenkamp
- Engineering and Applied Sciences, Columbia University New York USA
| | - Johann Thurn
- Institute of Physical Chemistry, University of Freiburg Freiburg Germany +49 761 203 6192
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, University of Freiburg Freiburg Germany +49 761 203 5883 +49 761 203 5913
| | - Thorsten Hugel
- Institute of Physical Chemistry, University of Freiburg Freiburg Germany +49 761 203 6192
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg Freiburg Germany
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47
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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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48
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Dutta Gupta S, Pan CH. Recent update on discovery and development of Hsp90 inhibitors as senolytic agents. Int J Biol Macromol 2020; 161:1086-1098. [DOI: 10.1016/j.ijbiomac.2020.06.115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/22/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023]
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49
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HSP90 Inhibition and Modulation of the Proteome: Therapeutical Implications for Idiopathic Pulmonary Fibrosis (IPF). Int J Mol Sci 2020; 21:ijms21155286. [PMID: 32722485 PMCID: PMC7432830 DOI: 10.3390/ijms21155286] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/05/2023] Open
Abstract
Idiopathic Pulmonary fibrosis (IPF) is a catastrophic disease with poor outcomes and limited pharmacological approaches. Heat shock protein 90 (HSP90) has been recently involved in the wound-healing pathological response that leads to collagen deposition in patients with IPF and its inhibition represents an exciting drug target against the development of pulmonary fibrosis. Under physiological conditions, HSP90 guarantees proteostasis through the refolding of damaged proteins and the degradation of irreversibly damaged ones. Additionally, its inhibition, by specific HSP90 inhibitors (e.g., 17 AAG, 17 DAG, and AUY-922) has proven beneficial in different preclinical models of human disease. HSP90 inhibition modulates a complex subset of kinases and interferes with intracellular signaling pathways and proteome regulation. In this review, we evaluated the current evidence and rationale for the use of HSP90 inhibitors in the treatment of pulmonary fibrosis, discussed the intracellular pathways involved, described the limitations of the current understanding and provided insights for future research.
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