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Chavan T, Kanabar D, Patel K, Laflamme TM, Riyazi M, Spratt DE, Muth A. Structural modification of the propyl linker of cjoc42 in combination with sulfonate ester and triazole replacements for enhanced gankyrin binding and anti-proliferative activity. Bioorg Med Chem 2024; 110:117836. [PMID: 39029437 PMCID: PMC11342405 DOI: 10.1016/j.bmc.2024.117836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/28/2024] [Accepted: 07/09/2024] [Indexed: 07/21/2024]
Abstract
Liver cancer is a complex disease that involves various oncoproteins and the inactivation of tumor suppressor proteins (TSPs). Gankyrin is one such oncoprotein, first identified in human hepatocellular carcinoma, that is known to inactivate multiple TSPs, leading to proliferation and metastasis of tumor cells. Despite this, there has been limited development of small molecule gankyrin binders for the treatment of liver cancer. In this study, we are reporting the structure-based design of gankyrin-binding small molecules which inhibit the proliferation of HuH6 and HepG2 cells while also increasing the levels of certain TSPs, such as Rb and p53. Interestingly the first molecule to exhibit inhibition by 3D structure stabilization is seen. These results suggest a possible mechanism for small-molecule inhibition of gankyrin and demonstrate that gankyrin is a viable therapeutic target for the treatment of liver cancer.
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Affiliation(s)
- Tejashri Chavan
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, USA
| | - Dipti Kanabar
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, USA
| | - Kinjal Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, USA
| | - Taylor M Laflamme
- Gustaf H. Carlson School of Chemistry & Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Maryam Riyazi
- Gustaf H. Carlson School of Chemistry & Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Donald E Spratt
- Gustaf H. Carlson School of Chemistry & Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Aaron Muth
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, USA.
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2
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Kanabar D, Kane EI, Chavan T, Laflamme TM, Suarez E, Goyal M, Gupta V, Spratt DE, Muth A. Synthesis and evaluation of 2,5-substituted pyrimidines as small-molecule gankyrin binders. Future Med Chem 2024; 16:239-251. [PMID: 38205637 PMCID: PMC10853842 DOI: 10.4155/fmc-2023-0124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/06/2023] [Indexed: 01/12/2024] Open
Abstract
Background: Gankyrin is an ankyrin-repeat protein that promotes cell proliferation, tumor development and cancer progression when overexpressed. Aim: To design and synthesize a novel series of gankyrin-binding small molecules predicated on a 2,5-pyrimidine scaffold. Materials & methods: The synthesized compounds were evaluated for their antiproliferative activity, ability to bind gankyrin and effects on cell cycle progression and the proteasomal degradation pathway. Results: Compounds 188 and 193 demonstrated the most potent antiproliferative activity against MCF7 and A549 cells, respectively. Both compounds also demonstrated the ability to effectively bind gankyrin, disrupt proteasomal degradation and inhibit cell cycle progression. Conclusion: The 2,5-pyrimidine scaffold exhibits a novel and promising strategy for binding gankyrin and inhibiting cancer cell proliferation.
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Affiliation(s)
- Dipti Kanabar
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Emma I Kane
- Gustaf H. Carlson School of Chemistry & Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Tejashri Chavan
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Taylor M Laflamme
- Gustaf H. Carlson School of Chemistry & Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Ethan Suarez
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Mimansa Goyal
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Vivek Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Donald E Spratt
- Gustaf H. Carlson School of Chemistry & Biochemistry, Clark University, Worcester, MA 01610, USA
| | - Aaron Muth
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, St. John's University, Queens, NY 11439, USA
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Kashyap D, Roy R, Varshney N, Baral B, Bagde PH, Kandpal M, Kumar S, Kar P, Jha HC. Withania somnifera extract reduces gastric cancerous properties through inhibition of gankyrin in cellular milieu produced by Helicobacter pylori and Epstein Barr virus. J Biomol Struct Dyn 2023:1-17. [PMID: 37655681 DOI: 10.1080/07391102.2023.2252096] [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: 02/07/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
Helicobacter pylori and Epstein Barr virus (EBV) are group1 carcinogens and their role in Gastric cancer (GC) is well established. Previously we have shown that H. pylori and EBV appears to support aggressive gastric oncogenesis through the upregulation of oncoprotein Gankyrin. Natural plant active molecules have the potential to interrupt oncogenesis. Herein, we investigated the potential of Withania somnifera root extract (WSE) as a possible chemotherapeutic agent against host oncoprotein Gankyrin whose expression was altered by H. pylori and EBV-associated modified cellular milieu. The results show that WSE does not have any inhibitory effect on H. pylori and EBV-associated gene transcripts except for the lmps (lmp1, lmp2a, and lmp2B). Moreover, the WSE exert their anticancer activity via host cellular response and decreased the expression of cell-migratory (mmp3 and mmp7); cell-cycle regulator (pcna); antiapoptotic gene (bcl2); increased the expression of the proapoptotic gene (apaf1 and bax); and tumor suppressor (p53, prb, and pten). Knockdown of Gankyrin followed by the treatment of WSE also decreases the expression of TNF-ɑ, Akt, and elevated the expression of NFkB, PARP, Casp3, and Casp9. WSE also reduces cell migration, and genomic instability and forced the cells to commit programmed cell death. Moreover, molecular simulation studies revealed that out of eight active compounds of WSE, only four compounds such as withaferin A (WFA), withanoside IV (WA4), withanolide B (WNB), and withanolide D (WND) showed direct stable interaction with Gankyrin. This article reports for the first time that treatment of WSE decreased the cancerous properties through host cellular response modulation in gastric epithelial cells coinfected with H. pylori and EBV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dharmendra Kashyap
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Nidhi Varshney
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Budhadev Baral
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Pranit Hemant Bagde
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Meenakshi Kandpal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Sachin Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Dehradun, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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Medur Gurushankar MS, Dalvi S, Venkatraman P. Snapshots of urea-induced early structural changes and unfolding of an ankyrin repeat protein at atomic resolution. Protein Sci 2022; 31:e4515. [PMID: 36382986 PMCID: PMC9703593 DOI: 10.1002/pro.4515] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022]
Abstract
Protein folding and unfolding is a complex process, underscored by the many proteotoxic diseases associated with misfolded proteins. Mapping pathways from a native structure to an unfolded protein or vice versa, identifying the intermediates, and defining the role of sequence and structure en route remain outstanding problems in the field. It is even more challenging to capture the events at atomistic resolution. X-ray diffraction has so far been used to understand how urea interacts with and unfolds two stable globular proteins. Here, we present the case study on PSMD10Gankyrin , a prototype for a moderately stable, non-globular repeat protein, long and rigid, with its termini located at either end. We define structural changes in the time dimension using low urea concentrations to arrive at the following conclusions. (a) Unfolding is rapidly initiated at the C-terminus, slowly at the N-terminus, and proceeds inwards from both ends. (b) C-terminus undergoes an α to 310 helix transition, representing the structure of a potential early unfolding intermediate before disorder sets in. (c) Distinct and progressive changes in the electrostatic landscape of PSMD10Gankyrin were observed, indicative of conformational changes in the seemingly inflexible motif involved in protein-protein interaction. We believe this unique study will open up the field for better and bolder queries and increase the choice of model proteins for a better understanding of the challenging problems of protein folding, protein interactions, protein degradation, and diseases associated with misfolding.
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Affiliation(s)
- Mukund Sudharsan Medur Gurushankar
- Protein Interactome Laboratory for Structural and Functional BiologyAdvanced Centre for Treatment, Research and Education in CancerNavi MumbaiMaharashtraIndia
- Department of Biochemistry and PharmacologyBio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoriaAustralia
| | - Somavally Dalvi
- Protein Interactome Laboratory for Structural and Functional BiologyAdvanced Centre for Treatment, Research and Education in CancerNavi MumbaiMaharashtraIndia
- Department of Biochemistry and PharmacologyBio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoriaAustralia
- Present address:
Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneVictoriaAustralia
| | - Prasanna Venkatraman
- Protein Interactome Laboratory for Structural and Functional BiologyAdvanced Centre for Treatment, Research and Education in CancerNavi MumbaiMaharashtraIndia
- Homi Bhabha National InstituteMumbaiMaharashtraIndia
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M G MS, Chikhale R, Nanaware PP, Dalvi S, Venkatraman P. A druggable pocket on PSMD10 Gankyrin that can accommodate an interface peptide and doxorubicin. Eur J Pharmacol 2022; 915:174718. [PMID: 34953804 DOI: 10.1016/j.ejphar.2021.174718] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND PSMD10Gankyrin, a proteasomal chaperone is also an oncoprotein. Overexpression of PSMD10Gankyrin is associated with poor prognosis and survival in many cancers. Therefore, PSMD10Gankyrin is a sought-after drug target in many hard-to-treat cancers. However, its surface appears flat and undruggable. Here, we build on our earlier discovery of a common hot spot region that defined the interface of multiple interacting partners of PSMD10Gankyrin to expose vulnerable spots for a peptide and a small molecule inhibitor. METHODS High throughput virtual screening was used to screen compounds against PSMD10Gankyrin. Interaction of PSMD10Gankyrin with the drug or protein (CLIC1) or peptide was studied using any one or more of these techniques; Microscale Thermophoresis, limited trypsinolysis, SPR and ITC. Cytotoxic effect of doxorubicin was evaluated using MTT assay. RESULTS We identified doxorubicin as the first-generation small molecule inhibitor of PSMD10Gankyrin. K116 and to a lesser extent R41 on PSMD10Gankyrin contribute to the bulk of binding energy for the peptide EEVD, CLIC1 and doxorubicin. We further demonstrate that PSMD10Gankyrin is an intended target for doxorubicin in cells. GENERAL SIGNIFICANCE Drug design against protein interactions in general and PSMD10Gankyrin in particular, remains a challenge. We provide consolidated biophysical evidence for the use of a shared interface motif EEVD as a possible inhibitor of interaction network in cancers driven by PSMD10Gankyrin. We identify a chemical scaffold for designing novel inhibitors of PSMD10Gankyrin. These findings will impact the field of protein interactions in the context of disease biology/drug discovery.
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Affiliation(s)
- Mukund Sudharsan M G
- Protein Interaction Laboratory for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 41210, India; Homi Bhabha National Institute, 2nd Floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India
| | - Rupesh Chikhale
- Protein Interaction Laboratory for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 41210, India
| | - Padma P Nanaware
- Protein Interaction Laboratory for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 41210, India
| | - Somavally Dalvi
- Protein Interaction Laboratory for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 41210, India
| | - Prasanna Venkatraman
- Protein Interaction Laboratory for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 41210, India; Homi Bhabha National Institute, 2nd Floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India.
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6
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Folding and Stability of Ankyrin Repeats Control Biological Protein Function. Biomolecules 2021; 11:biom11060840. [PMID: 34198779 PMCID: PMC8229355 DOI: 10.3390/biom11060840] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
Ankyrin repeat proteins are found in all three kingdoms of life. Fundamentally, these proteins are involved in protein-protein interaction in order to activate or suppress biological processes. The basic architecture of these proteins comprises repeating modules forming elongated structures. Due to the lack of long-range interactions, a graded stability among the repeats is the generic properties of this protein family determining both protein folding and biological function. Protein folding intermediates were frequently found to be key for the biological functions of repeat proteins. In this review, we discuss most recent findings addressing this close relation for ankyrin repeat proteins including DARPins, Notch receptor ankyrin repeat domain, IκBα inhibitor of NFκB, and CDK inhibitor p19INK4d. The role of local folding and unfolding and gradual stability of individual repeats will be discussed during protein folding, protein-protein interactions, and post-translational modifications. The conformational changes of these repeats function as molecular switches for biological regulation, a versatile property for modern drug discovery.
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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8
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Structural Insights into Ankyrin Repeat-Containing Proteins and Their Influence in Ubiquitylation. Int J Mol Sci 2021; 22:ijms22020609. [PMID: 33435370 PMCID: PMC7826745 DOI: 10.3390/ijms22020609] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Ankyrin repeat (AR) domains are considered the most abundant repeat motif found in eukaryotic proteins. AR domains are predominantly known to mediate specific protein-protein interactions (PPIs) without necessarily recognizing specific primary sequences, nor requiring strict conformity within its own primary sequence. This promiscuity allows for one AR domain to recognize and bind to a variety of intracellular substrates, suggesting that AR-containing proteins may be involved in a wide array of functions. Many AR-containing proteins serve a critical role in biological processes including the ubiquitylation signaling pathway (USP). There is also strong evidence that AR-containing protein malfunction are associated with several neurological diseases and disorders. In this review, the structure and mechanism of key AR-containing proteins are discussed to suggest and/or identify how each protein utilizes their AR domains to support ubiquitylation and the cascading pathways that follow upon substrate modification.
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Hao P, Yue F, Xian X, Ren Q, Cui H, Wang Y. Inhibiting effect of MicroRNA-3619-5p/PSMD10 axis on liver cancer cell growth in vivo and in vitro. Life Sci 2020; 254:117632. [PMID: 32437796 DOI: 10.1016/j.lfs.2020.117632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 03/22/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022]
Abstract
AIMS Liver cancer is one of the leading causes of cancer death worldwide owing to its delayed diagnosis and absence of efficient treatment at advanced TNM stages. Increasing evidence demonstrated that microRNAs are implicated in tumorgenesis and cancer development by regulating cancer-related proteins. This study aimed to explore the effect of miR-3619-5p on cell growth in liver cancer. MAIN METHODS The effect of miR-3619-5p on cell proliferation was measured by quantitative real-time PCR, MTT assay, flow cytometry, and Immunofluorescence assay. The interaction between miR-3619-5p and PSMD10 was validated using dual-luciferase. The expression of PSMD10 and Ki67 was further determined by immunohistochemistry. KEY FINDINGS MiR-3619-5p over-expression remarkably inhibited cell proliferation and induced G1 phase arrest, accompanied with reduced expression of proliferating cell nuclear antigen. The expression of miR-3619-5p was negatively correlated to that of PSMD10, and PSMD10 was validated to be a downstream target of miR-3619-5p. Moreover, miR-3619-5p induced suppressed proliferation and G1 phase arrest were abrogated by elevated the expression of PSMD10 in liver cancer cells. PSMD10 over-expression also induced phosphorylation of signal transducer and activator of transcription 3 (STAT3) and retinoblastoma protein (Rb1). Besides, elevated cyclin A, cyclin D1 and cyclin E expression supported that PSMD10 promoted the progress of cell cycle. In addition, miR-3619-5p inhibited tumor growth in vivo by targeting PSMD10, accompanied with blocked cell cycle. SIGNIFICANCE In conclusion, our findings revealed that miR-3619-5p inhibits cancer cell proliferation by targeting PSMD10, and miR-3619-5p as a potential therapeutic target for the treatment of liver cancer.
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Affiliation(s)
- Peipei Hao
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Center of Stem Cell and Immune Cell Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Hebei Research Center for Stem Cell Medical Translational Engineering, Shijiazhuang 050017, People's Republic of China
| | - Fengming Yue
- Center of Stem Cell and Immune Cell Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Hebei Research Center for Stem Cell Medical Translational Engineering, Shijiazhuang 050017, People's Republic of China; Department of Anatomy and Organ Technology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Xian Xian
- Center of Stem Cell and Immune Cell Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Hebei Research Center for Stem Cell Medical Translational Engineering, Shijiazhuang 050017, People's Republic of China; Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang 050017, People's Republic of China
| | - Qian Ren
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Center of Stem Cell and Immune Cell Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Hebei Research Center for Stem Cell Medical Translational Engineering, Shijiazhuang 050017, People's Republic of China
| | - Huixian Cui
- Department of Human Anatomy, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Center of Stem Cell and Immune Cell Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang 050017, People's Republic of China; Hebei Research Center for Stem Cell Medical Translational Engineering, Shijiazhuang 050017, People's Republic of China
| | - Yunpeng Wang
- Department of General Medicine, The Third Hospital of Hebei Medical University, Shijiazhuang 050051, People's Republic of China.
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Kanabar D, Farrales P, Gnanamony M, Almasri J, Abo-Ali EM, Otmankel Y, Shah H, Nguyen D, El Menyewi M, Dukhande VV, D'Souza A, Muth A. Structural modification of the aryl sulfonate ester of cjoc42 for enhanced gankyrin binding and anti-cancer activity. Bioorg Med Chem Lett 2020; 30:126889. [DOI: 10.1016/j.bmcl.2019.126889] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022]
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11
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Cheng L, Wu B, Zhang L, Bian E, An R, Yu S, Liu W, Xiong Z. Gankyrin promotes osteosarcoma tumorigenesis by forming a positive feedback loop with YAP. Cell Signal 2019; 65:109460. [PMID: 31678253 DOI: 10.1016/j.cellsig.2019.109460] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Although gankyrin has been identified as a vital regulator of tumorigenesis, its role and regulatory mechanism in osteosarcoma (OS) remain unclear. METHODS QRT-PCR, western blot and IHC staining were conducted to detect the expression of gankyrin in OS. Pearson's χ² test was adopted to examine the associations between gankyrin expression and clinicopathologic characteristics. Kaplan-Meier method was used to investigate the relationship between gankyrin expression and overall survival of patients with OS. Next, a series of in vitro and in vivo assays were performed to determine the positive feedback loop between gankyrin and YAP in OS. RESULTS We first reported that gankyrin is upregulated in human OS specimens and cell lines and predicts OS progression and poor prognosis. Furthermore, we demonstrated that gankyrin protects miR-200a-mediated yes-associated protein (YAP) downregulation through p53 and establishes a positive feedback loop to regulate YAP signaling in U2OS and MG63 cells. Intriguingly, gankyrin interacts with YAP to promote OS cell growth in vitro. In addition, our results showed that gankyrin promotes OS tumor growth and regulates YAP levels in vivo. Notably, we also observed a positive correlation between gankyrin and YAP expression in human OS tissues, and co-upregulation of gankyrin and YAP indicated a poor prognosis. CONCLUSIONS Our results identify that gankyrin acts as an oncogene in OS by forming a positive feedback loop with YAP, and disrupting the gankyrin-YAP regulation may be beneficial for controlling OS tumorigenesis.
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Affiliation(s)
- Li Cheng
- School of pharmacy, Anhui Medical University, 81 Mei Shan Road, Hefei 230032, Anhui Province, People's Republic of China
| | - Baoming Wu
- School of pharmacy, Anhui Medical University, 81 Mei Shan Road, Hefei 230032, Anhui Province, People's Republic of China
| | - Lei Zhang
- Department of Anesthesiology, First Affiliated Hospital of Anhui Medical University, 218 Ji Xi Road, Hefei 230032, Anhui Province, People's Republic of China
| | - Erbao Bian
- School of pharmacy, Anhui Medical University, 81 Mei Shan Road, Hefei 230032, Anhui Province, People's Republic of China
| | - Ran An
- Department of Biochemistry and Molecular Biology, Anhui Medical University, 81 Mei Shan Road, Hefei 230032, Anhui Province, People's Republic of China
| | - Shuisheng Yu
- Department of Orthopaedics, Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei 230601, Anhui Province, People's Republic of China
| | - Wei Liu
- Department of Orthopaedics, Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei 230601, Anhui Province, People's Republic of China
| | - Zhigang Xiong
- School of pharmacy, Anhui Medical University, 81 Mei Shan Road, Hefei 230032, Anhui Province, People's Republic of China.
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12
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Xu X, Lou Y, Tang J, Teng Y, Zhang Z, Yin Y, Zhuo H, Tan Z. The long non-coding RNA Linc-GALH promotes hepatocellular carcinoma metastasis via epigenetically regulating Gankyrin. Cell Death Dis 2019; 10:86. [PMID: 30692513 PMCID: PMC6349924 DOI: 10.1038/s41419-019-1348-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most prevalent subtype of liver cancer, and it is characterized by high rate of metastasis and recurrence. Recent studies have boosted our understanding that Gankyrin contributes to both of these pathological properties, but the mechanisms underlying its aberrant regulation are poorly understood. Recently, many long noncoding RNAs (lncRNAs) have been reported to be involved in regulating the expression of oncogenes and anti-oncogenes through various mechanisms. Here, using transcriptome microarray analysis, we identified a long intergenic noncoding RNA termed Linc-GALH that was highly expressed and concordance with Gankyrin expression in HCC. In addition, we revealed that Linc-GALH was an independent unfavorable prognostic indicator for HCC, followed functional experiments showed that Linc-GALH promoted HCC cells migration and invasion in vitro, and enhanced lung metastasis ability of HCC cells in vivo. Mechanistically, we found that Linc-GALH could regulate the expression of Gankyrin through controlling the methylation status of Gankyrin by adjusting the ubiquitination status of DNMT1 in HCC. Collectively, our results demonstrated the role and functional mechanism of Linc-GALH in HCC, and indicated that Linc-GALH may act as a prognostic biomarker and potential therapeutic target for HCC.
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Affiliation(s)
- Xiaoliang Xu
- Medical School of Southeast University, Nanjing, Jiangsu, P.R. China.,Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210093, Jiangsu Province, P.R. China
| | - Yun Lou
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210093, Jiangsu Province, P.R. China.,Key Laboratory of Living Donor Liver Transplantation, Department of Liver Surgery, National Health and Family Planning Commission, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Junwei Tang
- Key Laboratory of Living Donor Liver Transplantation, Department of Liver Surgery, National Health and Family Planning Commission, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yue Teng
- Department of Medical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, Jiangsu, P.R. China
| | - Zechuan Zhang
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210093, Jiangsu Province, P.R. China.,Key Laboratory of Living Donor Liver Transplantation, Department of Liver Surgery, National Health and Family Planning Commission, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yin Yin
- Department of Hepatobiliary Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210093, Jiangsu Province, P.R. China
| | - Han Zhuo
- Key Laboratory of Living Donor Liver Transplantation, Department of Liver Surgery, National Health and Family Planning Commission, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Zhongming Tan
- Key Laboratory of Living Donor Liver Transplantation, Department of Liver Surgery, National Health and Family Planning Commission, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P.R. China.
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13
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Taheri T, Jamialahmadi K, Khadijeh F. Unexpected Lower Expression of Oncoprotein Gankyrin in Drug Resistant ABCG2 Overexpressing Breast Cancer Cell Lines. Asian Pac J Cancer Prev 2017; 18:3413-3418. [PMID: 29286612 PMCID: PMC5980903 DOI: 10.22034/apjcp.2017.18.12.3413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: Development of a multidrug resistance (MDR) phenotype to chemotherapy remains a major barrier in
the treatment of cancer. Gankyrin (p28, p28GANK or PSMD10) is an oncoprotein overexpressed in different carcinoma
cell lines. The aim of this study was to compare Gankyrin expression level in MDR cells (MCF-7/ADR and MCF-7/
MX) and non-MDR counterparts (MCF-7). Methods: Gankyrin, MDR1 (also known as ABCB1; the ATP-binding
cassette sub-family B member 1) and ABCG2 (also known as BCRP; the human breast cancer resistance protein)
mRNA levels were analyzed by real-time RT-PCR. Western blot analysis was used to detect the protein expression
levels of Gankyrin. Results: The PCR results showed that the expression of Gankyrin was significantly lower in the
ABCG2 overexpressing cell line MCF-7/MX than in non-resistanct MCF-7 cells. In contrast, there were no significant
differences in mRNA expression of Gankyrin in the MDR1 overexpressing cell line MCF-7/ADR in comparison with
MCF-7 cells. Similarly, Western blot analysis confirmed lower expression of Gankyrin protein in the MCF-7/MX cell
line (26% compared to controls) but not in MCF-7/ADR cells. Conclusion: These findings showed that there may be
a relation between down-regulation of Gankyrin and overexpression of ABCG2 but without any clear relationship with
MDR1 expression in breast cancer cell lines.
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Affiliation(s)
- Taheri Taheri
- Department of Biochemistry, Faculty of Science, Payam Noor University of Mashhad, Mashhad, Iran.,Department of Stem Cells and Developmental Biology, Royan Institute for Stem cell Biology and Technology, ACECR, Tehran, Iran.
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14
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Structural insights on the dynamics of proteasome formation. Biophys Rev 2017; 10:597-604. [PMID: 29243089 DOI: 10.1007/s12551-017-0381-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/27/2017] [Indexed: 12/28/2022] Open
Abstract
Molecular organization in biological systems comprises elaborately programmed processes involving metastable complex formation of biomolecules. This is exemplified by the formation of the proteasome, which is one of the largest and most complicated biological supramolecular complexes. This biomolecular machinery comprises approximately 70 subunits, including structurally homologous, but functionally distinct, ones, thereby exerting versatile proteolytic functions. In eukaryotes, proteasome formation is non-autonomous and is assisted by assembly chaperones, which transiently associate with assembly intermediates, operating as molecular matchmakers and checkpoints for the correct assembly of proteasome subunits. Accumulated data also suggest that eukaryotic proteasome formation involves scrap-and-build mechanisms. However, unlike the eukaryotic proteasome subunits, the archaeal subunits show little structural divergence and spontaneously assemble into functional machinery. Nevertheless, the archaeal genomes encode homologs of eukaryotic proteasome assembly chaperones. Recent structural and functional studies of these proteins have advanced our understanding of the evolution of molecular mechanisms involved in proteasome biogenesis. This knowledge, in turn, provides a guiding principle in designing molecular machineries using protein engineering approaches and de novo synthesis of artificial molecular systems.
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15
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Verardi R, Kim JS, Ghirlando R, Banerjee A. Structural Basis for Substrate Recognition by the Ankyrin Repeat Domain of Human DHHC17 Palmitoyltransferase. Structure 2017; 25:1337-1347.e6. [PMID: 28757145 DOI: 10.1016/j.str.2017.06.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/25/2017] [Accepted: 06/28/2017] [Indexed: 12/01/2022]
Abstract
DHHC enzymes catalyze palmitoylation, a major post-translational modification that regulates a number of key cellular processes. There are up to 24 DHHCs in mammals and hundreds of substrate proteins that get palmitoylated. However, how DHHC enzymes engage with their substrates is still poorly understood. There is currently no structural information about the interaction between any DHHC enzyme and protein substrates. In this study we have investigated the structural and thermodynamic bases of interaction between the ankyrin repeat domain of human DHHC17 (ANK17) and Snap25b. We solved a high-resolution crystal structure of the complex between ANK17 and a peptide fragment of Snap25b. Through structure-guided mutagenesis, we discovered key residues in DHHC17 that are critically important for interaction with Snap25b. We further extended our finding by showing that the same residues are also crucial for the interaction of DHHC17 with Huntingtin, one of its most physiologically relevant substrates.
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Affiliation(s)
- Raffaello Verardi
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA
| | - Jin-Sik Kim
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anirban Banerjee
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA.
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16
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Lu Y, Wu J, Dong Y, Chen S, Sun S, Ma YB, Ouyang Q, Finley D, Kirschner MW, Mao Y. Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle. Mol Cell 2017; 67:322-333.e6. [PMID: 28689658 PMCID: PMC5580496 DOI: 10.1016/j.molcel.2017.06.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 04/14/2017] [Accepted: 06/07/2017] [Indexed: 10/19/2022]
Abstract
The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly.
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Affiliation(s)
- Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jiayi Wu
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Yuanchen Dong
- Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Shuobing Chen
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Shuangwu Sun
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yong-Bei Ma
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Qi Ouyang
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China; Peking-Tsinghua Joint Center for Life Science, Peking University, Beijing 100871, China
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Youdong Mao
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China; Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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17
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Wang C, Cheng L. Gankyrin as a potential therapeutic target for cancer. Invest New Drugs 2017; 35:655-661. [PMID: 28527132 DOI: 10.1007/s10637-017-0474-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/12/2017] [Indexed: 02/07/2023]
Abstract
Gankyrin is an oncoprotein that plays a central role in the development of cancer. Although researchers have increasingly focused on the relationships of gankyrin with carcinogenesis, metastasis and prognosis of different cancers, the molecular mechanisms are still unclear. In recent years, several interacting partners of gankyrin and cell signaling pathways regulated by gankyrin have been elucidated. In addition, accumulating evidence has indicated the contribution of microRNAs to regulating gankyrin expression in tumor cells. In this review, we summarize the major known roles of gankyrin in cancer cells and highlight the potential clinical relevance of targeting gankyrin. Graphical abstract ᅟ.
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Affiliation(s)
- Chongchong Wang
- Department of Oncology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
| | - Li Cheng
- Department of Orthopaedics, the Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China.
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18
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Kurimoto E, Satoh T, Ito Y, Ishihara E, Okamoto K, Yagi-Utsumi M, Tanaka K, Kato K. Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation. Protein Sci 2017; 26:1080-1085. [PMID: 28263418 DOI: 10.1002/pro.3153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 02/28/2017] [Accepted: 02/28/2017] [Indexed: 01/12/2023]
Abstract
The 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome-specific chaperones, i.e., proteasome-assembling chaperons 1-4 (PAC1-4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not. In the present study, we determined a crystal structure of human PAC4 at 1.90-Å resolution. Our crystallographic data identify a hydrophobic surface that is surrounded by charged residues. The hydrophobic surface is complementary to that of its binding partner, PAC3. The surface also exhibits charge complementarity with the proteasomal α4-5 subunits. This will provide insights into human proteasome-assembling chaperones as potential anticancer drug targets.
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Affiliation(s)
- Eiji Kurimoto
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Tadashi Satoh
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan.,JST, PRESTO, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Yuri Ito
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Eri Ishihara
- Faculty of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Kenta Okamoto
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan
| | - Maho Yagi-Utsumi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan.,Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, 467-8603, Japan.,Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, 444-8787, Japan
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19
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Chattopadhyay A, O’Connor CJ, Zhang F, Galvagnion C, Galloway WRJD, Tan YS, Stokes JE, Rahman T, Verma C, Spring DR, Itzhaki LS. Discovery of a small-molecule binder of the oncoprotein gankyrin that modulates gankyrin activity in the cell. Sci Rep 2016; 6:23732. [PMID: 27046077 PMCID: PMC4820706 DOI: 10.1038/srep23732] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/04/2016] [Indexed: 01/04/2023] Open
Abstract
Gankyrin is an ankyrin-repeat oncoprotein whose overexpression has been implicated in the development of many cancer types. Elevated gankyrin levels are linked to aberrant cellular events including enhanced degradation of tumour suppressor protein p53, and inhibition of gankyrin activity has therefore been identified as an attractive anticancer strategy. Gankyrin interacts with several partner proteins, and a number of these protein-protein interactions (PPIs) are of relevance to cancer. Thus, molecules that bind the PPI interface of gankyrin and interrupt these interactions are of considerable interest. Herein, we report the discovery of a small molecule termed cjoc42 that is capable of binding to gankyrin. Cell-based experiments demonstrate that cjoc42 can inhibit gankyrin activity in a dose-dependent manner: cjoc42 prevents the decrease in p53 protein levels normally associated with high amounts of gankyrin, and it restores p53-dependent transcription and sensitivity to DNA damage. The results represent the first evidence that gankyrin is a "druggable" target with small molecules.
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Affiliation(s)
| | | | - Fengzhi Zhang
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | - Yaw Sing Tan
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jamie E. Stokes
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Taufiq Rahman
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Chandra Verma
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - David R. Spring
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Laura S. Itzhaki
- Department of Pharmacology, Tennis Court Road, Cambridge CB2 1PD, UK
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20
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Chapman AM, McNaughton BR. Synthetic Proteins Potently and Selectively Bind the Oncoprotein Gankyrin, Modulate Its Interaction with S6 ATPase, and Suppress Gankyrin/MDM2-Dependent Ubiquitination of p53. ACS Chem Biol 2015; 10:1880-6. [PMID: 25955581 DOI: 10.1021/acschembio.5b00201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Overexpression of the ankyrin repeat oncoprotein gankyrin is directly linked to the onset, proliferation, and/or metastasis of many cancers. The role of gankyrin in multiple disease-relevant biochemical processes is profound. In addition to other cellular processes, gankyrin overexpression leads to decreased cellular levels of p53, through a complex that involves MDM2. Thus, inhibition of this interaction is an attractive strategy for modulating oncogenic phenotypes in gankyrin-overexpressing cells. However, the lack of well-defined, hydrophobic, small-molecule binding pockets on the putative ankyrin repeat binding face presents a challenge to traditional small-molecule drug discovery. In contrast, by virtue of their size and relatively high folding energies, synthetic gankyrin-binding proteins could, in principle, compete with physiologically relevant PPIs involving gankyrin. Previously, we showed that a shape-complementary protein scaffold can be resurfaced to bind gankyrin with moderate affinity (KD ∼6 μM). Here, we used yeast display high-throughput screening, error-prone PCR, DNA shuffling, and protein engineering to optimize this complex. The best of these proteins bind gankyrin with excellent affinity (KD ∼21 nM), selectively co-purifies with gankyrin from a complex cellular milieu, modulates an interaction between gankyrin and a physiological binding partner (S6 ATPase), and suppresses gankyrin/MDM2-dependent ubiquitination of p53.
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Affiliation(s)
- Alex M. Chapman
- Department
of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brian R. McNaughton
- Department
of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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21
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Robin G, Sato Y, Desplancq D, Rochel N, Weiss E, Martineau P. Restricted Diversity of Antigen Binding Residues of Antibodies Revealed by Computational Alanine Scanning of 227 Antibody–Antigen Complexes. J Mol Biol 2014; 426:3729-3743. [DOI: 10.1016/j.jmb.2014.08.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/31/2014] [Accepted: 08/09/2014] [Indexed: 12/28/2022]
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22
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Chapman AM, Rogers BE, McNaughton BR. Characterization of the binding interaction between the oncoprotein gankyrin and a grafted S6 ATPase. Biochemistry 2014; 53:6857-9. [PMID: 25343477 PMCID: PMC4230329 DOI: 10.1021/bi5012354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A complex with the C-terminal portion of the proteosomal subunit S6 ATPase is the only available structure of a protein-protein interaction involving the oncoprotein gankyrin. However, difficulties associated with recombinant expression of S6 ATPase alone, or truncations thereof, have limited our understanding of this assembly. We replaced the C-terminal portion of FtsH from Escherichia coli with the structurally homologous C-terminal portion of S6 ATPase and used this grafted protein to characterize the gankyrin-S6 ATPase binding interaction by isothermal titration calorimetry.
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Affiliation(s)
- Alex M Chapman
- Department of Chemistry and ‡Department of Biochemistry & Molecular Biology, Colorado State University , Fort Collins, Colorado 80523, United States
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23
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Chapman AM, McNaughton BR. Resurfaced shape complementary proteins that selectively bind the oncoprotein gankyrin. ACS Chem Biol 2014; 9:2223-8. [PMID: 25137482 PMCID: PMC4201333 DOI: 10.1021/cb5003834] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increased cellular levels of protein-protein interactions involving the ankyrin repeat oncoprotein gankyrin are directly linked to aberrant cellular events and numerous cancers. Inhibition of these protein-protein interactions is thus an attractive therapeutic strategy. However, the relatively featureless topology of gankyrin's putative binding face and large surface areas involved in gankyrin-dependent protein-protein interactions present a dramatic challenge to small molecule discovery. The size, high folding energies, and well-defined surfaces present in many proteins overcome some of the challenges faced by small molecule discovery. We used split-superpositive Green Fluorescent Protein (split-spGFP) reassembly to screen a 5×10(9) library of resurfaced proteins that are shape complementary to the putative binding face of gankyrin and identified mutants that potently and selectively bind this oncoprotein in vitro and in living cells. Collectively, our findings represent the first synthetic proteins that bind gankyrin and may represent a general strategy for developing protein basic research tools and drug leads that bind disease-relevant ankyrin repeats.
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Affiliation(s)
- Alex M. Chapman
- Department of Chemistry and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brian R. McNaughton
- Department of Chemistry and ‡Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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24
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Diao W, Yang X, Zhou H. Purification, crystallization and preliminary X-ray data collection of the N-terminal domain of the 26S proteasome regulatory subunit p27 and its complex with the ATPase domain of Rpt5 from Mus musculus. Acta Crystallogr F Struct Biol Commun 2014; 70:611-5. [PMID: 24817721 PMCID: PMC4014330 DOI: 10.1107/s2053230x14006815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 03/27/2014] [Indexed: 11/10/2022] Open
Abstract
The protein 26S proteasome regulatory subunit p27 is one of the four chaperones that help in the assembly of the 19S regulatory particle (RP) of the 26S proteasome. In the present work, the N-terminus of p27 (residues 1-128) from Mus musculus was cloned, expressed, purified and crystallized alone and in complex with the C-terminal ATPase domain of Rpt5 (residues 173-442). The crystals of p27((1-128)) diffracted to 1.7 Å resolution and belonged to space group P212121, with unit-cell parameters a = 26.79, b = 30.39, c = 145.06 Å. Resolution-dependent Matthews coefficient probability analysis suggested the presence of only one molecule per asymmetric unit, with 40.5% solvent content and a VM value of 2.02 Å(3) Da(-1). The crystal of the p27((1-128))-Rpt5((173-442)) complex diffracted to 4 Å resolution and belonged to space group P222, with unit-cell parameters a = 75.93, b = 76.08, c = 336.85 Å. The presence of four heterodimers in the asymmetric unit with 53.2% solvent content and a VM value of 2.63 Å(3) Da(-1) or five heterodimers in the asymmetric unit with 41.5% solvent content and a VM value of 2.10 Å(3) Da(-1) is assumed.
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Affiliation(s)
- Wentao Diao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Xue Yang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
| | - Hao Zhou
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
- College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, People’s Republic of China
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25
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Zheng T, Hong X, Wang J, Pei T, Liang Y, Yin D, Song R, Song X, Lu Z, Qi S, Liu J, Sun B, Xie C, Pan S, Li Y, Luo X, Li S, Fang X, Bhatta N, Jiang H, Liu L. Gankyrin promotes tumor growth and metastasis through activation of IL-6/STAT3 signaling in human cholangiocarcinoma. Hepatology 2014; 59:935-46. [PMID: 24037855 DOI: 10.1002/hep.26705] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/21/2013] [Indexed: 12/30/2022]
Abstract
UNLABELLED Although gankyrin is involved in the tumorigenicity and metastasis of some malignancies, the role of gankyrin in cholangiocarcinoma (CCA) is unclear. In this study we investigated the expression of gankyrin in human CCA tissues and cell lines. The effects of gankyrin on CCA tumor growth and metastasis were determined both in vivo and in vitro. The results showed that gankyrin was overexpressed in CCA tissues and cell lines. Gankyrin expression was associated with CCA histological differentiation, TNM stage, and metastasis. The multivariate Cox analysis revealed that gankyrin was an independent prognostic indicator for overall survival. Gankyrin overexpression promoted CCA cell proliferation, migration, and invasion, while gankyrin knockdown inhibited CCA tumor growth, metastasis, and induced Rb-dependent senescence and G1 phase cell cycle arrest. Gankyrin increased the phosphorylation of signal transducer and activator of transcription 3 (STAT3) and promoted the nuclear translocation of p-STAT3. Suppression of STAT3 signaling by small interfering RNA (siRNA) or STAT3 inhibitor interfered with gankyrin-mediated carcinogenesis and metastasis, while interleukin (IL)-6, a known upstream activator of STAT3, could restore the proliferation and migration of gankyrin-silenced CCA cells. The IL-6 level was decreased by gankyrin knockdown, while increased by gankyrin overexpression. Gankyrin regulated IL-6 expression by way of facilitating the phosphorylation of Rb; meanwhile, rIL-6 treatment increased the expression of gankyrin, suggesting that IL-6 was regulated by a positive feedback loop involving gankyrin in CCA. In the xenograft experiments, gankyrin overexpression accelerated tumor formation and increased tumor weight, whereas gankyrin knockdown showed the opposite effects. The in vivo spontaneous metastasis assay revealed that gankyrin promoted CCA metastasis through IL-6/STAT3 signaling pathway. CONCLUSION Gankyrin is crucial for CCA carcinogenesis and metastasis by activating IL-6/STAT3 signaling pathway through down-regulating Rb protein.
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Affiliation(s)
- Tongsen Zheng
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Department of General Surgery, the First Affiliated Hospital of Harbin Medical University, Harbin, China
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26
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Nanaware PP, Ramteke MP, Somavarapu AK, Venkatraman P. Discovery of multiple interacting partners of gankyrin, a proteasomal chaperone and an oncoprotein--evidence for a common hot spot site at the interface and its functional relevance. Proteins 2014; 82:1283-300. [PMID: 24338975 DOI: 10.1002/prot.24494] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/20/2013] [Accepted: 12/09/2013] [Indexed: 12/27/2022]
Abstract
Gankyrin, a non-ATPase component of the proteasome and a chaperone of proteasome assembly, is also an oncoprotein. Gankyrin regulates a variety of oncogenic signaling pathways in cancer cells and accelerates degradation of tumor suppressor proteins p53 and Rb. Therefore gankyrin may be a unique hub integrating signaling networks with the degradation pathway. To identify new interactions that may be crucial in consolidating its role as an oncogenic hub, crystal structure of gankyrin-proteasome ATPase complex was used to predict novel interacting partners. EEVD, a four amino acid linear sequence seems a hot spot site at this interface. By searching for EEVD in exposed regions of human proteins in PDB database, we predicted 34 novel interactions. Eight proteins were tested and seven of them were found to interact with gankyrin. Affinity of four interactions is high enough for endogenous detection. Others require gankyrin overexpression in HEK 293 cells or occur endogenously in breast cancer cell line- MDA-MB-435, reflecting lower affinity or presence of a deregulated network. Mutagenesis and peptide inhibition confirm that EEVD is the common hot spot site at these interfaces and therefore a potential polypharmacological drug target. In MDA-MB-231 cells in which the endogenous CLIC1 is silenced, trans-expression of Wt protein (CLIC1_EEVD) and not the hot spot site mutant (CLIC1_AAVA) resulted in significant rescue of the migratory potential. Our approach can be extended to identify novel functionally relevant protein-protein interactions, in expansion of oncogenic networks and in identifying potential therapeutic targets.
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Affiliation(s)
- Padma P Nanaware
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
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27
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Cohen MR, Moiseenkova-Bell VY. Structure of thermally activated TRP channels. CURRENT TOPICS IN MEMBRANES 2014; 74:181-211. [PMID: 25366237 DOI: 10.1016/b978-0-12-800181-3.00007-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Temperature sensation is important for adaptation and survival of organisms. While temperature has the potential to affect all biological macromolecules, organisms have evolved specific thermosensitive molecular detectors that are able to transduce temperature changes into physiologically relevant signals. Among these thermosensors are ion channels from the transient receptor potential (TRP) family. Prime candidates include TRPV1-4, TRPA1, and TRPM8 (the so-called "thermoTRP" channels), which are expressed in sensory neurons and gated at specific temperatures. Electrophysiological and thermodynamic approaches have been employed to determine the nature by which thermoTRPs detect temperature and couple temperature changes to channel gating. To further understand how thermoTRPs sense temperature, high-resolution structures of full-length thermoTRPs channels will be required. Here, we will discuss current progress in unraveling the structures of thermoTRP channels.
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Affiliation(s)
- Matthew R Cohen
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Vera Y Moiseenkova-Bell
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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28
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Huynh KW, Cohen MR, Chakrapani S, Holdaway HA, Stewart PL, Moiseenkova-Bell VY. Structural insight into the assembly of TRPV channels. Structure 2013; 22:260-8. [PMID: 24373766 DOI: 10.1016/j.str.2013.11.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/01/2013] [Accepted: 11/21/2013] [Indexed: 11/25/2022]
Abstract
Transient receptor potential (TRP) proteins are a large family of polymodal nonselective cation channels. The TRP vanilloid (TRPV) subfamily consists of six homologous members with diverse functions. TRPV1-TRPV4 are nonselective cation channels proposed to play a role in nociception, while TRPV5 and TRPV6 are involved in epithelial Ca²⁺ homeostasis. Here we present the cryo-electron microscopy (cryo-EM) structure of functional, full-length TRPV2 at 13.6 Å resolution. The map reveals that the TRPV2 cytoplasmic domain displays a 4-fold petal-like shape in which high-resolution N-terminal ankyrin repeat domain (ARD) structures can be unambiguously fitted. Fitting of the available ARD structures for other TRPV subfamily members into the TRPV2 EM map suggests that TRPV subfamily members have highly homologous structural topologies. These results allowed us to postulate a structural explanation for the functional diversity among TRPV channels and their differential regulation by proteins and ligands.
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Affiliation(s)
- Kevin W Huynh
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Matthew R Cohen
- Deparment of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Sudha Chakrapani
- Deparment of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Heather A Holdaway
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Phoebe L Stewart
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Vera Y Moiseenkova-Bell
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Deparment of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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29
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Abstract
The proteasome refers to a collection of complexes centered on the 20S proteasome core particle (20S CP), a complex of 28 subunits that houses proteolytic sites in its hollow interior. Proteasomes are found in eukaryotes, archaea, and some eubacteria, and their activity is critical for many cellular pathways. Important recent advances include inhibitor binding studies and the structure of the immunoproteasome, whose specificity is altered by the incorporation of inducible catalytic subunits. The inherent repression of the 20S CP is relieved by the ATP-independent activators 11S and Blm10/PA200, whose structures reveal principles of proteasome mechanism. The structure of the ATP-dependent 19S regulatory particle, which mediates degradation of polyubiquitylated proteins, is being revealed by a combination of crystal or NMR structures of individual subunits and electron microscopy reconstruction of the intact complex. Other recent structural advances inform us about mechanisms of assembly and the role of conformational changes in the functional cycle.
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Affiliation(s)
- Erik Kish-Trier
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650, USA
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30
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Settanni G, Serquera D, Marszalek PE, Paci E, Itzhaki LS. Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin. PLoS Comput Biol 2013; 9:e1002864. [PMID: 23341763 PMCID: PMC3547791 DOI: 10.1371/journal.pcbi.1002864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 11/11/2012] [Indexed: 11/30/2022] Open
Abstract
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical ‘hot spots’ of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress. Here we use molecular dynamics simulation to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with binding partner S6-C. Tandem repeat proteins like Gankyrin comprise tandem arrays of small structural motifs that pack linearly to produce elongated architectures. They are elastic, mechanically weak molecules and they unfold and refold repeat by repeat under force. We show that S6-C binding greatly increases the resistance of Gankyrin to mechanical stress. The enhanced mechanical stability is specific to those ankyrin repeats in contact with S6-C, and the localized nature of the effect results in fundamental changes in the way the protein responds to force. Thus, the forced unfolding of isolated Gankryin involves a diverse set of pathways with a preference for a C- to N-terminus unfolding mechanism whereas this diversity is reduced upon complex formation with the central repeats, which are those most tightly bound to the ligand, tending to unfold last. Our study shows how stepwise unfolding can buffer repeat proteins and their binding partners from mechanical stress in the cell. It also points to a mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.
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Affiliation(s)
- Giovanni Settanni
- Physics Department, Johannes Gutenberg University, Mainz, Germany
- * E-mail: (GS); (EP); (LSI)
| | - David Serquera
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Cambridge, United Kingdom
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, United States of America
| | - Emanuele Paci
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- * E-mail: (GS); (EP); (LSI)
| | - Laura S. Itzhaki
- University of Cambridge Department of Chemistry, Cambridge, United Kingdom
- * E-mail: (GS); (EP); (LSI)
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31
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Dual functions of the Hsm3 protein in chaperoning and scaffolding regulatory particle subunits during the proteasome assembly. Proc Natl Acad Sci U S A 2012; 109:E1001-10. [PMID: 22460800 DOI: 10.1073/pnas.1116538109] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The 26S proteasome, a molecular machine responsible for regulated protein degradation, consists of a proteolytic core particle (20S CP) associated with 19S regulatory particles (19S RPs) subdivided into base and lid subcomplexes. The assembly of 19S RP base subcomplex is mediated by multiple dedicated chaperones. Among these, Hsm3 is important for normal growth and directly targets the carboxyl-terminal (C-terminal) domain of Rpt1 of the Rpt1-Rpt2-Rpn1 assembly intermediate. Here, we report crystal structures of the yeast Hsm3 chaperone free and bound to the C-terminal domain of Rpt1. Unexpectedly, the structure of the complex suggests that within the Hsm3-Rpt1-Rpt2 module, Hsm3 also contacts Rpt2. We show that in both yeast and mammals, Hsm3 actually directly binds the AAA domain of Rpt2. The Hsm3 C-terminal region involved in this interaction is required in vivo for base assembly, although it is dispensable for binding Rpt1. Although Rpt1 and Rpt2 exhibit weak affinity for each other, Hsm3 unexpectedly acts as an essential matchmaker for the Rpt1-Rpt2-Rpn1 assembly by bridging both Rpt1 and Rpt2. In addition, we provide structural and biochemical evidence on how Hsm3/S5b may regulate the 19S RP association to the 20S CP proteasome. Our data point out the diverse functions of assembly chaperones.
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32
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Lee SH, Moon JH, Yoon SK, Yoon JB. Stable incorporation of ATPase subunits into 19 S regulatory particle of human proteasome requires nucleotide binding and C-terminal tails. J Biol Chem 2012; 287:9269-79. [PMID: 22275368 DOI: 10.1074/jbc.m111.316208] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The 26 S proteasome is a large multi-subunit protein complex that degrades ubiquitinated proteins in eukaryotic cells. Proteasome assembly is a complex process that involves formation of six- and seven-membered ring structures from homologous subunits. Here we report that the assembly of hexameric Rpt ring of the 19 S regulatory particle (RP) requires nucleotide binding but not ATP hydrolysis. Disruption of nucleotide binding to an Rpt subunit by mutation in the Walker A motif inhibits the assembly of the Rpt ring without affecting heterodimer formation with its partner Rpt subunit. Coexpression of the base assembly chaperones S5b and PAAF1 with mutant Rpt1 and Rpt6, respectively, relieves assembly inhibition of mutant Rpts by facilitating their interaction with adjacent Rpt dimers. The mutation in the Walker B motif which impairs ATP hydrolysis does not affect Rpt ring formation. Incorporation of a Walker B mutant Rpt subunit abrogates the ATPase activity of the 19 S RP, suggesting that failure of the mutant Rpt to undergo the conformational transition from an ATP-bound to an ADP-bound state impairs conformational changes in the other five wild-type Rpts in the Rpt ring. In addition, we demonstrate that the C-terminal tails of Rpt subunits possessing core particle (CP)-binding affinities facilitate the cellular assembly of the 19 S RP, implying that the 20 S CP may function as a template for base assembly in human cells. Taken together, these results suggest that the ATP-bound conformational state of an Rpt subunit with the exposed C-terminal tail is competent for cellular proteasome assembly.
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Affiliation(s)
- Seung-Hoon Lee
- Department of Biochemistry, Yonsei University, Seoul, Korea
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33
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Wilkins SE, Karttunen S, Hampton-Smith RJ, Murchland I, Chapman-Smith A, Peet DJ. Factor inhibiting HIF (FIH) recognizes distinct molecular features within hypoxia-inducible factor-α (HIF-α) versus ankyrin repeat substrates. J Biol Chem 2012; 287:8769-81. [PMID: 22270367 DOI: 10.1074/jbc.m111.294678] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Factor Inhibiting HIF (FIH) catalyzes the β-hydroxylation of asparagine residues in HIF-α transcription factors as well as ankyrin repeat domain (ARD) proteins such as Notch and Gankyrin. Although FIH-mediated hydroxylation of HIF-α is well characterized, ARDs were only recently identified as substrates, and less is known about their recognition and hydroxylation by FIH. We investigated the molecular determinants of FIH substrate recognition, with a focus on differences between HIF and ARD substrates. We show that for ARD proteins, structural context is an important determinant of FIH-recognition, but analyses of chimeric substrate proteins indicate that the ankyrin fold alone is not sufficient to explain the distinct substrate properties of the ARDs compared with HIF. For both substrates the kinetic parameters of hydroxylation are influenced by the amino acids proximal to the target asparagine. Although FIH tolerates a variety of chemically disparate residues proximal to the asparagine, we demonstrate that certain combinations of amino acids are not permissive to hydroxylation. Finally, we characterize a conserved RLL motif in HIF and demonstrate that it mediates a high affinity interaction with FIH in the presence of cell lysate or macromolecular crowding agents. Collectively, our data highlight the importance of residues proximal to the asparagine in determining hydroxylation, and identify additional substrate-specific elements that contribute to distinct properties of HIF and ARD proteins as substrates for FIH. These distinct features are likely to influence FIH substrate choice in vivo and, therefore, have important consequences for HIF regulation.
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Affiliation(s)
- Sarah E Wilkins
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
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34
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Bar-Nun S, Glickman MH. Proteasomal AAA-ATPases: structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:67-82. [PMID: 21820014 DOI: 10.1016/j.bbamcr.2011.07.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/07/2011] [Accepted: 07/18/2011] [Indexed: 01/18/2023]
Abstract
The 26S proteasome is a chambered protease in which the majority of selective cellular protein degradation takes place. Throughout evolution, access of protein substrates to chambered proteases is restricted and depends on AAA-ATPases. Mechanical force generated through cycles of ATP binding and hydrolysis is used to unfold substrates, open the gated proteolytic chamber and translocate the substrate into the active proteases within the cavity. Six distinct AAA-ATPases (Rpt1-6) at the ring base of the 19S regulatory particle of the proteasome are responsible for these three functions while interacting with the 20S catalytic chamber. Although high resolution structures of the eukaryotic 26S proteasome are not yet available, exciting recent studies shed light on the assembly of the hetero-hexameric Rpt ring and its consequent spatial arrangement, on the role of Rpt C-termini in opening the 20S 'gate', and on the contribution of each individual Rpt subunit to various cellular processes. These studies are illuminated by paradigms generated through studying PAN, the simpler homo-hexameric AAA-ATPase of the archaeal proteasome. The similarities between PAN and Rpts highlight the evolutionary conserved role of AAA-ATPase in protein degradation, whereas unique properties of divergent Rpts reflect the increased complexity and tighter regulation attributed to the eukaryotic proteasome.
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Affiliation(s)
- Shoshana Bar-Nun
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
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35
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Kim YC, DeMartino GN. C termini of proteasomal ATPases play nonequivalent roles in cellular assembly of mammalian 26 S proteasome. J Biol Chem 2011; 286:26652-66. [PMID: 21628461 DOI: 10.1074/jbc.m111.246793] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 26 S proteasome comprises two multisubunit subcomplexes as follows: 20 S proteasome and PA700/19 S regulatory particle. The cellular mechanisms by which these subcomplexes assemble into 26 S proteasome and the molecular determinants that govern the assembly process are poorly defined. Here, we demonstrate the nonequivalent roles of the C termini of six AAA subunits (Rpt1-Rpt6) of PA700 in 26 S proteasome assembly in mammalian cells. The C-terminal HbYX motif (where Hb is a hydrophobic residue, Y is tyrosine, and X is any amino acid) of each of two subunits, Rpt3 and Rpt5, but not that of a third subunit Rpt2, was essential for assembly of 26 S proteasome. The C termini of none of the three non-HbYX motif Rpt subunits were essential for cellular 26 S proteasome assembly, although deletion of the last three residues of Rpt6 destabilized the 20 S-PA700 interaction. Rpt subunits defective for assembly into 26 S proteasome due to C-terminal truncations were incorporated into intact PA700. Moreover, intact PA700 accumulated as an isolated subcomplex when cellular 20 S proteasome content was reduced by RNAi. These results indicate that 20 S proteasome is not an obligatory template for assembly of PA700. Collectively, these results identify specific structural elements of two Rpt subunits required for 26 S proteasome assembly, demonstrate that PA700 can be assembled independently of the 20 S proteasome, and suggest that intact PA700 is a direct intermediate in the cellular pathway of 26 S proteasome assembly.
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Affiliation(s)
- Young-Chan Kim
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
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36
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Sato S, Mimasu S, Sato A, Hino N, Sakamoto K, Umehara T, Yokoyama S. Crystallographic Study of a Site-Specifically Cross-Linked Protein Complex with a Genetically Incorporated Photoreactive Amino Acid,. Biochemistry 2010; 50:250-7. [DOI: 10.1021/bi1016183] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Shin Sato
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shinya Mimasu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Aya Sato
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Nobumasa Hino
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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37
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Wakamori M, Umehara T, Yokoyama S. A series of bacterial co-expression vectors with rare-cutter recognition sequences. Protein Expr Purif 2010; 74:88-98. [DOI: 10.1016/j.pep.2010.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 06/22/2010] [Accepted: 06/23/2010] [Indexed: 10/19/2022]
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38
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Kumar B, Kim YC, DeMartino GN. The C terminus of Rpt3, an ATPase subunit of PA700 (19 S) regulatory complex, is essential for 26 S proteasome assembly but not for activation. J Biol Chem 2010; 285:39523-35. [PMID: 20937828 DOI: 10.1074/jbc.m110.153627] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
PA700, the 19 S regulatory subcomplex of the 26 S proteasome, contains a heterohexameric ring of AAA subunits (Rpt1 to -6) that forms the binding interface with a heteroheptameric ring of α subunits (α1 to -7) of the 20 S proteasome. Binding of these subcomplexes is mediated by interactions of C termini of certain Rpt subunits with cognate binding sites on the 20 S proteasome. Binding of two Rpt subunits (Rpt2 and Rpt5) depends on their last three residues, which share an HbYX motif (where Hb is a hydrophobic amino acid) and open substrate access gates in the center of the α ring. The relative roles of other Rpt subunits for proteasome binding and activation remain poorly understood. Here we demonstrate that the C-terminal HbYX motif of Rpt3 binds to the 20 S proteasome but does not promote proteasome gating. Binding requires the last three residues and occurs at a dedicated site on the proteasome. A C-terminal peptide of Rpt3 blocked ATP-dependent in vitro assembly of 26 S proteasome from PA700 and 20 S proteasome. In HEK293 cells, wild-type Rpt3, but not Rpt3 lacking the HbYX motif was incorporated into 26 S proteasome. These results indicate that the C terminus of Rpt3 was required for cellular assembly of this subunit into 26 S proteasome. Mutant Rpt3 was assembled into intact PA700. This result indicates that intact PA700 can be assembled independently of association with 20 S proteasome and thus may be a direct precursor for 26 S proteasome assembly under normal conditions. These results provide new insights to the non-equivalent roles of Rpt subunits in 26 S proteasome function and identify specific roles for Rpt3.
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Affiliation(s)
- Brajesh Kumar
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
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39
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Fu H, Lin YL, Fatimababy AS. Proteasomal recognition of ubiquitylated substrates. TRENDS IN PLANT SCIENCE 2010; 15:375-86. [PMID: 20399133 DOI: 10.1016/j.tplants.2010.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Revised: 03/10/2010] [Accepted: 03/18/2010] [Indexed: 05/08/2023]
Abstract
Ubiquitin/26S proteasome-mediated proteolysis controls the half-life of numerous critical regulatory proteins and is an intimate regulatory component for nearly all aspects of cellular processes. In addition to ubiquitin conjugation, an additional level of substrate specificity is regulated at the step of proteasomal recognition of ubiquitylated substrates, which serves as an important mechanistic and regulatory component to connect the substrate from the conjugation machinery to the 26S proteasome. In this review, we discuss current knowledge and future challenges relevant to understanding the mechanism, regulation, functions and substrate specificity of proteasomal recognition mediated by a multitude of ubiquitin receptors. The mechanistic details of major recognition pathways for ubiquitylated substrates are clearly divergent within and across species, which implies functional differentiation.
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Affiliation(s)
- Hongyong Fu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 115, ROC.
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40
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Gallastegui N, Groll M. The 26S proteasome: assembly and function of a destructive machine. Trends Biochem Sci 2010; 35:634-42. [PMID: 20541423 DOI: 10.1016/j.tibs.2010.05.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 05/06/2010] [Accepted: 05/11/2010] [Indexed: 11/29/2022]
Abstract
The heart of the ubiquitin-mediated degradation pathway, the 26S proteasome, endoproteolytically cleaves most intracellular proteins, thereby maintaining biological homeostasis and regulating many crucial processes in the cell. This hydrolyzing machine comprises more than 30 different subunits, which perform different functions including the recognition, unfolding, translocating and cleavage of protein substrates. Thus, careful assemblage and regulation of the 26S proteasome is essential to ensure correct positioning and function of each subunit, thereby preserving the delicate cellular balance between protein synthesis and degradation. Here, we review the most current research on the 26S proteasome assembly pathway, and describe the mechanism used by the cell to manage the complex structure and functions of the proteasome.
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Affiliation(s)
- Nerea Gallastegui
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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41
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Kim S, Saeki Y, Fukunaga K, Suzuki A, Takagi K, Yamane T, Tanaka K, Mizushima T, Kato K. Crystal structure of yeast rpn14, a chaperone of the 19 S regulatory particle of the proteasome. J Biol Chem 2010; 285:15159-15166. [PMID: 20236927 PMCID: PMC2865284 DOI: 10.1074/jbc.m110.104042] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 03/06/2010] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin-proteasome pathway is a major proteolytic system in eukaryotic cells and regulates various cellular processes. The 26 S proteasome, the central enzyme of this pathway, consists of a proteolytic core particle and two 19 S regulatory particles (RPs) composed of ATPase (Rpt) and non-ATPase (Rpn) subunits. Growing evidence indicates that proteasome assembly is assisted by a variety of chaperones. In particular, it has been reported recently that Nas2, Nas6, Rpn14, and Hsm3 bind specific Rpt subunits, thereby contributing to the formation of 19 S RP. Rpn14 transiently binds to the C-terminal domain of the Rpt6 subunit (Rpt6-C) during maturation of the ATPase ring of 19 S RP. In this study, we determined the crystal structure of yeast Rpn14 at 2.0 A resolution, which revealed that this chaperone consists of a unique N-terminal domain with unknown function and a C-terminal domain assuming a canonical seven-bladed beta-propeller fold. The Rpt6-binding site on Rpn14 was predicted based on structural comparison with the complex formed between Nas6 and Rpt3-C. The top face of Rpn14 exhibits a highly acidic surface area, whereas the putative interacting surface of Rpt6-C is basic. By inspection of structural data along with genetic and biochemical data, we determined the specific residues of Rpn14 and Rpt6 for complementary charge interactions that are required for 19 S RP assembly.
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Affiliation(s)
- Sangwoo Kim
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603
| | - Yasushi Saeki
- Laboratory of Frontier Science, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506
| | - Keisuke Fukunaga
- Laboratory of Frontier Science, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506
| | - Atsuo Suzuki
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603
| | - Kenji Takagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603
| | - Takashi Yamane
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603
| | - Keiji Tanaka
- Laboratory of Frontier Science, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506
| | - Tsunehiro Mizushima
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603; Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
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Abstract
Gankyrin, a newly defined oncoprotein also known as PSMD10 and P28, functions as a dual-negative regulator of the two most prominent tumor suppressor pathways, the CDK/pRb and HDM2/P53 pathways. Its aberrant expression has been prevalently found in human hepatocellular carcinomas (HCC) and esophagus squamous cell carcinomas (ESCC), indicative of the potential of gankyrin as a rational diagnostic and therapeutic target in cancers. Here, we review the unique structural features and functional diversity of gankyrin, and discuss its implication in cancer diagnostics and therapeutics from the perspective of chemical biology.
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Affiliation(s)
- Junan Li
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH 43210, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Yi Guo
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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43
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Chaperone-mediated pathway of proteasome regulatory particle assembly. Nature 2009; 459:861-5. [PMID: 19412159 PMCID: PMC2727592 DOI: 10.1038/nature08063] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 04/15/2009] [Indexed: 11/21/2022]
Abstract
The proteasome regulatory particle (RP) initiates the degradation of ubiquitin-protein conjugates by unfolding the substrate and translocating it into the proteasome core particle (CP) to be degraded1. Here we show that in yeast three proteins are found associated with RP but not RP-CP holoenzyme: Nas6, Rpn14, and Hsm3. Mutations in these genes confer proteasome loss of function phenotypes, despite their virtual absence from holoenzyme. These effects result from deficient RP assembly. Thus, Nas6, Rpn14, and Hsm3 are RP chaperones. The RP contains six ATPases–the Rpt proteins–and each RP chaperone binds to the C-terminal domain of a specific Rpt. We show in an accompanying study2 that RP assembly is templated through the Rpt C-termini, apparently by their insertion into binding pockets in the CP. Thus, RP chaperones may regulate proteasome assembly by directly restricting the accessibility of Rpt C-termini to the CP. In addition, competition between the CP and RP chaperones for Rpt engagement may explain the release of RP chaperones as proteasomes mature.
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44
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Abstract
The proteasome is an intricate molecular machine, which serves to degrade proteins following their conjugation to ubiquitin. Substrates dock onto the proteasome at its 19-subunit regulatory particle via a diverse set of ubiquitin receptors and are then translocated into an internal chamber within the 28-subunit proteolytic core particle (CP), where they are hydrolyzed. Substrate is threaded into the CP through a narrow gated channel, and thus translocation requires unfolding of the substrate. Six distinct ATPases in the regulatory particle appear to form a ring complex and to drive unfolding as well as translocation. ATP-dependent, degradation-coupled deubiquitination of the substrate is required both for efficient substrate degradation and for preventing the degradation of the ubiquitin tag. However, the proteasome also contains deubiquitinating enzymes (DUBs) that can remove ubiquitin before substrate degradation initiates, thus allowing some substrates to dissociate from the proteasome and escape degradation. Here we examine the key elements of this molecular machine and how they cooperate in the processing of proteolytic substrates.
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Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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45
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Marques AJ, Palanimurugan R, Matias AC, Ramos PC, Dohmen RJ. Catalytic mechanism and assembly of the proteasome. Chem Rev 2009; 109:1509-36. [PMID: 19265443 DOI: 10.1021/cr8004857] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- António J Marques
- Institute for Genetics, University of Cologne, Zulpicher Strasse 47, D-50674 Cologne, Germany
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46
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Multiple Proteasome-Interacting Proteins Assist the Assembly of the Yeast 19S Regulatory Particle. Cell 2009; 137:900-13. [PMID: 19446323 DOI: 10.1016/j.cell.2009.05.005] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 04/27/2009] [Accepted: 05/01/2009] [Indexed: 11/21/2022]
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47
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Kaneko T, Hamazaki J, Iemura SI, Sasaki K, Furuyama K, Natsume T, Tanaka K, Murata S. Assembly Pathway of the Mammalian Proteasome Base Subcomplex Is Mediated by Multiple Specific Chaperones. Cell 2009; 137:914-25. [PMID: 19490896 DOI: 10.1016/j.cell.2009.05.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Revised: 05/01/2009] [Accepted: 05/08/2009] [Indexed: 11/29/2022]
Affiliation(s)
- Takeumi Kaneko
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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48
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Murata S, Yashiroda H, Tanaka K. Molecular mechanisms of proteasome assembly. Nat Rev Mol Cell Biol 2009; 10:104-15. [DOI: 10.1038/nrm2630] [Citation(s) in RCA: 400] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Hume AJ, Kalejta RF. Regulation of the retinoblastoma proteins by the human herpesviruses. Cell Div 2009; 4:1. [PMID: 19146698 PMCID: PMC2636798 DOI: 10.1186/1747-1028-4-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 01/15/2009] [Indexed: 01/21/2023] Open
Abstract
Viruses are obligate intracellular parasites that alter the environment of infected cells in order to replicate more efficiently. One way viruses achieve this is by modulating cell cycle progression. The main regulators of progression out of G0, through G1, and into S phase are the members of the retinoblastoma (Rb) family of tumor suppressors. Rb proteins repress the transcription of genes controlled by the E2F transcription factors. Because the expression of E2F-responsive genes is required for cell cycle progression into the S phase, Rb arrests the cell cycle in G0/G1. A number of viral proteins directly target Rb family members for inactivation, presumably to create an environment more hospitable for viral replication. Such viral proteins include the extensively studied oncoproteins E7 (from human papillomavirus), E1A (from adenovirus), and the large T (tumor) antigen (from simian virus 40). Elucidating how these three viral proteins target and inactivate Rb has proven to be an invaluable approach to augment our understanding of both normal cell cycle progression and carcinogenesis. In addition to these proteins, a number of other virally-encoded inactivators of the Rb family have subsequently been identified including a surprising number encoded by human herpesviruses. Here we review how the human herpesviruses modulate Rb function during infection, introduce the individual viral proteins that directly or indirectly target Rb, and speculate about what roles Rb modulation by these proteins may play in viral replication, pathogenesis, and oncogenesis.
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Affiliation(s)
- Adam J Hume
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53706-1596, USA.
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50
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Sennhauser G, Grütter MG. Chaperone-assisted crystallography with DARPins. Structure 2008; 16:1443-53. [PMID: 18940601 DOI: 10.1016/j.str.2008.08.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/14/2008] [Accepted: 08/18/2008] [Indexed: 11/29/2022]
Abstract
The structure of proteins that are difficult to crystallize can often be solved by forming a noncovalent complex with a helper protein--a crystallization "chaperone." Although several such applications have been described to date, their handling usually is still very laborious. A valuable addition to the present repertoire of binding proteins is the recently developed designed ankyrin repeat protein (DARPin) technology. DARPins are built based on the natural ankyrin repeat protein fold with randomized surface residue positions allowing specific binding to virtually any target protein. The broad potential of these binding proteins for X-ray crystallography is illustrated by five cocrystal structures that have been determined recently comprising target proteins from distinct families, namely a sugar binding protein, two kinases, a caspase, and a membrane protein. This article reviews the opportunities of this technology for structural biology and the structural aspects of the DARPin-protein complexes.
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Affiliation(s)
- Gaby Sennhauser
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
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