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Xu P, Liu Y, Liu C, Guey B, Li L, Melenec P, Ricci J, Ablasser A. The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation. Nature 2024; 627:873-879. [PMID: 38418882 PMCID: PMC10972748 DOI: 10.1038/s41586-024-07112-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2'3'-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA demands tight regulatory mechanisms that are necessary to maintain cell and tissue homeostasis under normal conditions. Inside the cell nucleus, anchoring to nucleosomes and competition with chromatin architectural proteins jointly prohibit cGAS activation by genomic DNA8-15. However, the fate of nuclear cGAS and its role in cell physiology remains unclear. Here we show that the ubiquitin proteasomal system (UPS) degrades nuclear cGAS in cycling cells. We identify SPSB3 as the cGAS-targeting substrate receptor that associates with the cullin-RING ubiquitin ligase 5 (CRL5) complex to ligate ubiquitin onto nuclear cGAS. A cryo-electron microscopy structure of nucleosome-bound cGAS in a complex with SPSB3 reveals a highly conserved Asn-Asn (NN) minimal degron motif at the C terminus of cGAS that directs SPSB3 recruitment, ubiquitylation and cGAS protein stability. Interference with SPSB3-regulated nuclear cGAS degradation primes cells for type I interferon signalling, conferring heightened protection against infection by DNA viruses. Our research defines protein degradation as a determinant of cGAS regulation in the nucleus and provides structural insights into an element of cGAS that is amenable to therapeutic exploitation.
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Affiliation(s)
- Pengbiao Xu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Ying Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- School of Medicine, Jiangnan University, Wuxi, China
| | - Chong Liu
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Baptiste Guey
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Lingyun Li
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Pauline Melenec
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Jonathan Ricci
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Ablasser
- Global Health Institute, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- Institute for Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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2
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Mi T, Siriwibool S, Burgess K. Streamlined Protein-Protein Interface Loop Mimicry. Angew Chem Int Ed Engl 2023; 62:e202307092. [PMID: 37849440 DOI: 10.1002/anie.202307092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Cyclic peptides comprising endocyclic organic fragments, "cyclo-organopeptides", can be probes for perturbing protein-protein interactions (PPIs). Finding loop mimics is difficult because of high conformational variability amongst targets. Backbone Matching (BM), introduced here, helps solve this problem in the illustrative cases by facilitating efficient evaluation of virtual cyclo-organopeptide core-structure libraries. Thus, 86 rigid organic fragments were selected to build a library of 602 cyclo-organopeptides comprising Ala and organic parts: "cyclo-{-(Ala)n -organo-}". The central hypothesis is "hit" library members have accessible low energy conformers corresponding to backbone structures of target protein loops, while library members which cannot attain this conformation are probably unworthy of further evaluation. BM thereby prioritizes candidate loop mimics, so that less than 10 cyclo-organopeptides are needed to be prepared to find leads for two illustrative PPIs: iNOS ⋅ SPSB2, and uPA ⋅ uPAR.
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Affiliation(s)
- Tianxiong Mi
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
| | - Siriwalee Siriwibool
- School of Chemistry, Institute of Science, Suranaree University of Technology, 30000, Nakhon Ratchasima, Thailand
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, 77842, College Station, TX, USA
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3
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Rahman A, Matthews MA, Nowell CJ, Chalmers DK, Thompson PE, Nicholson SE, Barlow N, Norton RS. Enhanced nitric oxide production by macrophages treated with a cell-penetrating peptide conjugate. Bioorg Chem 2022; 123:105763. [DOI: 10.1016/j.bioorg.2022.105763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/02/2022]
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4
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Li K, You T, Zhao P, Luo Y, Zhang D, Wei H, Wang Y, Yang J, Guan X, Kuang Z. Structural basis for the regulation of inducible nitric oxide synthase by the SPRY domain-containing SOCS box protein SPSB2, an E3 ubiquitin ligase. Nitric Oxide 2021; 113-114:1-6. [PMID: 33862200 DOI: 10.1016/j.niox.2021.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/12/2021] [Accepted: 04/09/2021] [Indexed: 11/28/2022]
Abstract
Relatively high concentration of nitric oxide (NO) produced by inducible nitric oxide synthase (iNOS) in response to a variety of stimuli is a source of reactive nitrogen species, an important weapon of host innate immune defense. The SPRY domain-containing SOCS box protein 2 (SPSB2) is an E3 ubiquitin ligase that regulates the lifetime of iNOS. SPSB2 interacts with the N-terminal region of iNOS via a binding site on the SPRY domain of SPSB2, and recruits an E3 ubiquitin ligase complex to polyubiquitinate iNOS, leading to its proteasomal degradation. Although critical residues for the SPSB2-iNOS interaction have been identified, structural basis for the interaction remains to be explicitly determined. In this study, we have determined a crystal structure of the N-terminal region of iNOS in complex with the SPRY domain of SPSB2 at 1.24 Å resolution. We have resolved the roles of some flanking residues, whose contribution to the SPSB2-iNOS interaction was structurally unclear previously. Furthermore, we have evaluated the effects of SPSB2 inhibitors on NO production using transient transfection and cell-penetrating peptide approaches, and found that such inhibitors can elevate NO production in RAW264.7 macrophages. These results thus provide a useful basis for the development of potent SPSB2 inhibitors as well as recruiting ligands for proteolysis targeting chimera (PROTAC) design.
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Affiliation(s)
- Kefa Li
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Tingting You
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Panqi Zhao
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Yanhong Luo
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Danting Zhang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Huan Wei
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Yuhui Wang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Jinjin Yang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Xueyan Guan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China
| | - Zhihe Kuang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China; Guangdong Provincial Biotechnology Drug and Engineering Technology Research Center, Guangzhou, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou, 510632, China.
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5
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Ishida T, Ciulli A. E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones. SLAS Discov 2021; 26:484-502. [PMID: 33143537 PMCID: PMC8013866 DOI: 10.1177/2472555220965528] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.
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Affiliation(s)
- Tasuku Ishida
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
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6
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Muñoz Sosa CJ, Issoglio FM, Carrizo ME. Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1. J Biol Chem 2021; 296:100772. [PMID: 33989636 PMCID: PMC8203840 DOI: 10.1016/j.jbc.2021.100772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 01/01/2023] Open
Abstract
Tripartite motif (TRIM)7 is an E3 ubiquitin ligase that was first identified through its interaction with glycogenin-1 (GN1), the autoglucosyltransferase that initiates glycogen biosynthesis. A growing body of evidence indicates that TRIM7 plays an important role in cancer development, viral pathogenesis, and atherosclerosis and, thus, represents a potential therapeutic target. TRIM family proteins share a multidomain architecture with a conserved N-terminal TRIM and a variable C-terminal domain. Human TRIM7 contains the canonical TRIM motif and a B30.2 domain at the C terminus. To contribute to the understanding of the mechanism of action of TRIM7, we solved the X-ray crystal structure of its B30.2 domain (TRIM7B30.2) in two crystal forms at resolutions of 1.6 Å and 1.8 Å. TRIM7B30.2 exhibits the typical B30.2 domain fold, consisting of two antiparallel β-sheets of seven and six strands, arranged as a distorted β-sandwich. Furthermore, two long loops partially cover the concave face of the β-sandwich defined by the β-sheet of six strands, thus forming a positively charged cavity. We used sequence conservation and mutational analyses to provide evidence of a putative binding interface for GN1. These studies showed that Leu423, Ser499, and Cys501 of TRIM7B30.2 and the C-terminal 33 amino acids of GN1 are critical for this binding interaction. Molecular dynamics simulations also revealed that hydrogen bond and hydrophobic interactions play a major role in the stability of a modeled TRIM7B30.2-GN1 C-terminal peptide complex. These data provide useful information that could be used to target this interaction for the development of potential therapeutic agents.
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Affiliation(s)
- Christian J Muñoz Sosa
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) - CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Federico M Issoglio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) - CONICET and Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María E Carrizo
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) - CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
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7
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Babu Reddiar S, Al-Wassiti H, Pouton CW, Nowell CJ, Matthews MA, Rahman A, Barlow N, Norton RS. Assessing the cellular toxicity of peptide inhibitors of intracellular protein-protein interactions by microinjection. Bioorg Med Chem 2021; 29:115906. [PMID: 33310547 DOI: 10.1016/j.bmc.2020.115906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 10/22/2022]
Abstract
Inhibitors of protein-protein interactions can be developed through a number of technologies to provide leads that include cell-impermeable molecules. Redesign of these impermeable leads to provide cell-permeable derivatives can be challenging and costly. We hypothesised that intracellular toxicity of leads could be assessed by microinjection prior to investing in the redesign process. We demonstrate this approach for our development of inhibitors of the protein-protein interaction between inducible nitric-oxide synthase (iNOS) and SPRY domain-containing SOCS box proteins (SPSBs). We microinjected a lead molecule into AD-293 cells and were able to perform an intracellular toxicity assessment. We also investigated the intracellular distribution and localisation of injected inhibitor using a fluorescently-labelled analogue. Our findings show that a lead peptide inhibitor, CP2, had no toxicity even at intracellular concentrations four orders of magnitude higher than its Kd for binding to SPSB2. This early toxicity assessment justifies further development of this cell-impermeable lead to confer cell permeability. Our investigation highlights the utility of microinjection as a tool for assessing toxicity during development of drugs targeting protein-protein interactions.
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Affiliation(s)
- Sanjeevini Babu Reddiar
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Hareth Al-Wassiti
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Colin W Pouton
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Cameron J Nowell
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Macgregor A Matthews
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Arfatur Rahman
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia.
| | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic, Australia; ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia.
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8
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Yang J, Guan X, Zhang D, Zhao P, Guo S, Kuang Z. Crystal structure of the SPRY domain-containing protein 7 reveals unique structural features. Biochem Biophys Res Commun 2020; 531:350-356. [PMID: 32800543 DOI: 10.1016/j.bbrc.2020.07.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Abstract
The SPRY/B30.2 domain is one of the most abundant protein domains found in eukaryotes. Vast majority of the SPRY domain-containing proteins are multi-domain proteins. The SPRY domain-containing protein 7 (SPRY7, also named C13orf1, and named chronic lymphocytic leukemia deletion region gene 6 protein, CCLD6, encoded by the spryd7 gene) is the smallest SPRY domain protein in human that does not contain other accessory domains. Here we have determined the crystal structure of human SPRY7 at a resolution of 1.62 Å and found that SPRY7 has some unique structural features that are not present in other previously reported SRPY domain structures. Overall, SPRY7 may represent an evolutionary early version of the SPRY domain, and subsequent loop insertions and expansions, residue substitutions, as well as domain combinations have rendered the SPRY domain versatile binding specificities and broad biological functions. These results serve as a useful basis for a profound characterization of the molecular interactions of SPRY7.
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Affiliation(s)
- Jinjin Yang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Xueyan Guan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Danting Zhang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Panqi Zhao
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Shujun Guo
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Zhihe Kuang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China.
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9
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Shinjo K, Hara K, Nagae G, Umeda T, Katsushima K, Suzuki M, Murofushi Y, Umezu Y, Takeuchi I, Takahashi S, Okuno Y, Matsuo K, Ito H, Tajima S, Aburatani H, Yamao K, Kondo Y. A novel sensitive detection method for DNA methylation in circulating free DNA of pancreatic cancer. PLoS One 2020; 15:e0233782. [PMID: 32520974 PMCID: PMC7286528 DOI: 10.1371/journal.pone.0233782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/12/2020] [Indexed: 12/26/2022] Open
Abstract
Despite recent advances in clinical treatment, pancreatic cancer remains a highly lethal malignancy. In order to improve the survival rate of patients with pancreatic cancer, the development of non-invasive diagnostic methods using effective biomarkers is urgently needed. Here, we developed a highly sensitive method to detect DNA methylation in cell-free (cf)DNA samples based on the enrichment of methyl-CpG binding (MBD) protein coupled with a digital PCR method (MBD–ddPCR). Five DNA methylation markers for the diagnosis of pancreatic cancer were identified through DNA methylation microarray analysis in 37 pancreatic cancers. The sensitivity and specificity of the five markers were validated in another independent cohort of pancreatic cancers (100% and 100%, respectively; n = 46) as well as in The Cancer Genome Atlas data set (96% and 90%, respectively; n = 137). MBD–ddPCR analysis revealed that DNA methylation in at least one of the five markers was detected in 23 (49%) samples of cfDNA from 47 patients with pancreatic cancer. Further, a combination of DNA methylation markers and the KRAS mutation status improved the diagnostic capability of this method (sensitivity and specificity, 68% and 86%, respectively). Genome-wide MBD-sequencing analysis in cancer tissues and corresponding cfDNA revealed that more than 80% of methylated regions were overlapping; DNA methylation profiles of cancerous tissues and cfDNA significantly correlated with each other (R = 0.97). Our data indicate that newly developed MBD–ddPCR is a sensitive method to detect cfDNA methylation and that using five marker genes plus KRAS mutations may be useful for the detection of pancreatic cancers.
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Affiliation(s)
- Keiko Shinjo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuo Hara
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Genta Nagae
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Umeda
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Keisuke Katsushima
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miho Suzuki
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiteru Murofushi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuta Umezu
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,School of Information and Data Sciences, Nagasaki University, Nagasaki, Japan
| | - Ichiro Takeuchi
- Department of Computer Science, Nagoya Institute of Technology, Nagoya, Japan.,RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan.,Department of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hiroyuki Aburatani
- Genome Science Laboratory, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kenji Yamao
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya, Japan.,Department of Gastroenterology, Narita Memorial Hospital, Toyohashi, Japan
| | - Yutaka Kondo
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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10
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Bai P, Lu X, Lan Y, Chen Z, Patnaik D, Fiedler S, Striar R, Haggarty SJ, Wang C. Radiosynthesis and in vivo evaluation of a new positron emission tomography radiotracer targeting bromodomain and extra-terminal domain (BET) family proteins. Nucl Med Biol 2020; 84-85:96-101. [PMID: 32320910 DOI: 10.1016/j.nucmedbio.2020.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Bromodomain and extra-terminal domain (BET) family proteins play a vital role in the epigenetic regulation process by interacting with acetylated lysine (Ac-K) residues in histones. BET inhibitors have become promising candidates to treat various diseases through the inhibition of the interaction between BET bromodomains and Ac-K of histone tails. With a molecular imaging probe, noninvasive imaging such as positron emission tomography (PET) can visualize the distribution and roles of BET family proteins in vivo and enlighten our understanding of BET protein function in both healthy and diseased tissue. METHODS We radiolabeled the potent BET inhibitor INCB054329 by N-methylation to make [11C]PB003 as a BET PET radiotracer. The bioactivity evaluation of unlabeled PB003 in vitro was performed to confirm its binding affinity for BRDs, then the PET/CT imaging in rodents was performed to evaluate the bioactivity of [11C]PB003 in vivo. RESULTS In our in vitro evaluation, PB003 showed a high BET binding affinity for BRDs (Kd = 2 nM, 1.2 nM, and 1.2 nM for BRD2, BRD3, and BRD4, respectively). In vivo PET/CT imaging demonstrated that [11C]PB003 has favorable uptake with appropriate kinetics and distributions in main peripheral organs. Besides, the blockade of [11C]PB003 binding was found in our blocking study which indicated the specificity of [11C]PB003. However, the BBB penetration and brain uptake of [11C]PB003 was limited, with only a maximum 0.2% injected dose/g at ~2 min post-injection. CONCLUSION The imaging results in rodents in vivo demonstrate that [11C]PB003 binds to BET with high selectivity and specificity and has favorable uptake in peripheral organs. However, the low brain uptake of [11C]PB003 limits the visualization of brain regions indicating the efforts are still needed to discover the new BET imaging probes for brain visualization.
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Affiliation(s)
- Ping Bai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xiaoxia Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yu Lan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Zude Chen
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Debasis Patnaik
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Stephanie Fiedler
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Robin Striar
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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11
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Jin X, Li J, Li W, Wang X, Du C, Geng Z, Geng Y, Kang L, Zhang X, Wang M, Tian S. Weighted gene co-expression network analysis reveals specific modules and biomarkers in Parkinson's disease. Neurosci Lett 2020; 728:134950. [PMID: 32276105 DOI: 10.1016/j.neulet.2020.134950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Parkinson's disease (PD) ranks as the second most frequently occurring neurodegenerative disease. The precise pathogenic mechanism of this disease remains unknown. The aim of the present study was to identify the biomarkers in PD and classify the primary differentially expressed genes (DEGs). METHODS The present study searched for and downloaded mRNA expression data from the Gene Expression Omnibus database to identify differences in mRNA expression in the substantia nigra (SN) and blood of patients with PD and healthy controls. In addition, in order to investigate the biological functions of the classified dysregulated genes, the present study utilized Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO), reverse transcription-quantitative PCR (RT-qPCR), gene co-expression network analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A receiver operating characteristic (ROC) curve was applied to assay TMEM243 as a diagnostic marker. RESULTS Between PD and controls in GSE20292, the present study identified 1862 DEGs. Using the weighted gene co-expression network analysis, the present study identified 15 modules in PD. The module preservation analysis revealed that the tan, blue and green-yellow modules were the most stable. KEGG pathway analysis revealed that five DEGs in the black module were significantly enriched in the ubiquitin-mediated proteolysis pathway, nucleotide excision repair pathway, mismatch repair pathway. The present study selected 303 genes with high connectivity in blue, green-yellow and tan modules as hub genes, where 58 were differentially expressed in both the GSE20292 and GSE54536 datasets. In the SN and blood, 11 genes exhibited the same trend of expression. Furthermore, in the blood samples of patients with PD, the results displayed a significant upregulation of TMEM243. The expression levels of CCR4, CAMK1D, ACTR1B and SPSB3 increased, while both the levels of INA and PSMD4 decreased. These findings are consistent with the bioinformatics analysis results but are not statistically significant. TMEM243 can be considered as a diagnostic biomarker (area under the curve = 0.694; sensitivity, 80 %; specificity, 56 %; P < 0.018). CONCLUSION TMEM243 was distinctly upregulated in the blood samples of patients with PD, as validated via RT-qPCR, and was highly sensitive, revealing its potential as a biomarker for the future diagnosis of PD.
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12
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Guéret SM, Thavam S, Carbajo RJ, Potowski M, Larsson N, Dahl G, Dellsén A, Grossmann TN, Plowright AT, Valeur E, Lemurell M, Waldmann H. Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments. J Am Chem Soc 2020; 142:4904-4915. [PMID: 32058716 PMCID: PMC7307906 DOI: 10.1021/jacs.0c00269] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
“Hot
loop” protein segments have variable structure
and conformation and contribute crucially to protein–protein
interactions. We describe a new hot loop mimicking modality, termed
PepNats, in which natural product (NP)-inspired structures are incorporated
as conformation-determining and -restricting structural elements into
macrocyclic hot loop-derived peptides. Macrocyclic PepNats representing
hot loops of inducible nitric oxide synthase (iNOS) and human agouti-related
protein (AGRP) were synthesized on solid support employing macrocyclization
by imine formation and subsequent stereoselective 1,3-dipolar cycloaddition
as key steps. PepNats derived from the iNOS DINNN hot loop and the
AGRP RFF hot spot sequence yielded novel and potent ligands of the
SPRY domain-containing SOCS box protein 2 (SPSB2) that binds to iNOS,
and selective ligands for AGRP-binding melanocortin (MC) receptors.
NP-inspired fragment absolute configuration determines the conformation
of the peptide part responsible for binding. These results demonstrate
that combination of NP-inspired scaffolds with peptidic epitopes enables
identification of novel hot loop mimics with conformationally constrained
and biologically relevant structure.
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Affiliation(s)
- Stéphanie M Guéret
- Department of Chemical Biology, AstraZeneca-Max Planck Institute Satellite Unit, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Sasikala Thavam
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Rodrigo J Carbajo
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Marco Potowski
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Göran Dahl
- Structure, Biophysics & Fragment Based Lead Generation, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Anita Dellsén
- Mechanistic Biology & Profiling, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Eric Valeur
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Malin Lemurell
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
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13
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Georgana I, Maluquer de Motes C. Cullin-5 Adaptor SPSB1 Controls NF-κB Activation Downstream of Multiple Signaling Pathways. Front Immunol 2020; 10:3121. [PMID: 32038638 PMCID: PMC6985365 DOI: 10.3389/fimmu.2019.03121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/20/2019] [Indexed: 01/03/2023] Open
Abstract
The initiation of innate immune responses against pathogens relies on the activation of pattern-recognition receptors (PRRs) and corresponding intracellular signaling cascades. To avoid inappropriate or excessive activation of PRRs, these responses are tightly controlled. Cullin-RING E3 ubiquitin ligases (CRLs) have emerged as critical regulators of many cellular functions including innate immune activation and inflammation. CRLs form multiprotein complexes in which a Cullin protein acts as a scaffold and recruits specific adaptor proteins, which in turn recognize specific substrate proteins for ubiquitylation, hence providing selectivity. CRLs are divided into 5 main groups, each of which uses a specific group of adaptor proteins. Here, we systematically depleted all predicted substrate adaptors for the CRL5 family (the so-called SOCS-box proteins) and assessed the impact on the activation of the inflammatory transcription factor NF-κB. Depletion of SPSB1 resulted in a significant increase in NF-κB activation, indicating the importance of SPSB1 as an NF-κB negative regulator. In agreement, overexpression of SPSB1 suppressed NF-κB activity in a potent, dose-dependent manner in response to various agonists. Inhibition by SPSB1 was specific to NF-κB, because other transcription factors related to innate immunity and interferon (IFN) responses such as IRF-3, AP-1, and STATs remained unaffected by SPSB1. SPSB1 suppressed NF-κB activation induced via multiple pathways including Toll-like receptors and RNA and DNA sensing adaptors, and required the presence of its SOCS-box domain. To provide mechanistic insight, we examined phosphorylation and degradation of the inhibitor of κB (IκBα) and p65 translocation into the nucleus. Both remained unaffected by SPSB1, indicating that SPSB1 exerts its inhibitory activity downstream, or at the level, of the NF-κB heterodimer. In agreement with this, SPSB1 was found to co-precipitate with p65 after over-expression and at endogenous levels. Additionally, A549 cells stably expressing SPSB1 presented lower cytokine levels including type I IFN in response to cytokine stimulation and virus infection. Taken together, our results reveal novel regulatory mechanisms in innate immune signaling and identify the prominent role of SPSB1 in limiting NF-κB activation. Our work thus provides insights into inflammation and inflammatory diseases and new opportunities for the therapeutic targeting of NF-κB transcriptional activity.
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14
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Chittoor B, Krishnarjuna B, Morales RAV, Norton RS. The Single Disulfide-Directed β-Hairpin Fold: Role of Disulfide Bond in Folding and Effect of an Additional Disulfide Bond on Stability. Aust J Chem 2020. [DOI: 10.1071/ch19386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Disulfide bonds play a key role in the oxidative folding, conformational stability, and functional activity of many peptides. A few disulfide-rich peptides with privileged architecture such as the inhibitor cystine knot motif have garnered attention as templates in drug design. The single disulfide-directed β-hairpin (SDH), a novel fold identified more recently in contryphan-Vc1, has been shown to possess remarkable thermal, conformational, and chemical stability and can accept a short bioactive epitope without compromising the core structure of the peptide. In this study, we demonstrated that the single disulfide bond is critical in maintaining the native fold by replacing both cysteine residues with serine. We also designed an analogue with an additional, non-native disulfide bridge by replacing Gln1 and Tyr9 with Cys. Contryphan-Vc11–22[Q1C, Y9C] was synthesised utilising orthogonal cysteine protection and its solution structure determined using solution NMR spectroscopy. This analogue maintained the overall fold of native contryphan-Vc1. Previous studies had shown that the β-hairpin core of contryphan-Vc1 was resistant to proteolysis by trypsin and α-chymotrypsin but susceptible to cleavage by pepsin. Contryphan-Vc11–22[Q1C, Y9C] proved to be completely resistant to pepsin, thus confirming our design strategy. These results highlight the role of the disulfide bond in maintaining the SDH fold and provide a basis for the design of more stable analogues for peptide epitope grafting.
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15
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Schapira M, Calabrese MF, Bullock AN, Crews CM. Targeted protein degradation: expanding the toolbox. Nat Rev Drug Discov 2019; 18:949-63. [PMID: 31666732 DOI: 10.1038/s41573-019-0047-y] [Citation(s) in RCA: 450] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/19/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) and related molecules that induce targeted protein degradation by the ubiquitin-proteasome system represent a new therapeutic modality and are the focus of great interest, owing to potential advantages over traditional occupancy-based inhibitors with respect to dosing, side effects, drug resistance and modulating 'undruggable' targets. However, the technology is still maturing, and the design elements for successful PROTAC-based drugs are currently being elucidated. Importantly, fewer than 10 of the more than 600 E3 ubiquitin ligases have so far been exploited for targeted protein degradation, and expansion of knowledge in this area is a key opportunity. Here, we briefly discuss lessons learned about targeted protein degradation in chemical biology and drug discovery and systematically review the expression profile, domain architecture and chemical tractability of human E3 ligases that could expand the toolbox for PROTAC discovery.
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16
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Wang M, Wang Y, Liu Y, Wang H, Xin X, Li J, Hao Y, Han L, Yu F, Zheng C, Shen C. SPSB2 inhibits hepatitis C virus replication by targeting NS5A for ubiquitination and degradation. PLoS One 2019; 14:e0219989. [PMID: 31344133 PMCID: PMC6657855 DOI: 10.1371/journal.pone.0219989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/04/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) replication involves many viral and host factors. Host factor SPRY domain- and SOCS box-containing protein 2(SPSB2) belongs to SPSB family, and it recruits target proteins by the SPRY domain and forms E3 ubiquitin ligase complexes by the SOCS box. As an adaptor protein, it can regulate the host’s response to infection, but little is known about whether SPSB2 plays a role in HCV replication. In the present study, we found that HCV infection significantly upregulated the mRNA and protein levels of SPSB2 in HCVcc-infected cells. Exogenous expression of SPSB2 in hepatoma cells decreased HCV RNA and protein levels which depended on the SOCS box, while knockdown of endogenous SPSB2 increased HCV RNA and protein levels. Additionally, we demonstrated that SPSB2 interacted with HCV structural protein E1 and nonstructural protein protein 5A (NS5A) via the C-terminal portion of the SPSB2 SPRY domain. Furthermore, SPSB2 induced NS5A ubiquitination and mediated NS5A degradation. Collectively, this study discovered host factor SPSB2 significantly inhibits HCV replication by interacting and degrading NS5A.
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Affiliation(s)
- Mingzhen Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yu Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yuehong Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Hailong Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiu Xin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiadai Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yao Hao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lingling Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Yu
- Department of Pathology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Congyi Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
| | - Chao Shen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- China Center for Type Culture Collection, Wuhan University, Wuhan, China
- * E-mail:
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17
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Luo Y, Li K, Yang J, Zhang D, Zhou Y, Kuang Z. Crystal structure of the SPRY domain of human SPSB2 in the apo state. Acta Crystallogr F Struct Biol Commun 2019; 75:412-418. [PMID: 31204687 PMCID: PMC6572098 DOI: 10.1107/s2053230x1900623x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/02/2019] [Indexed: 11/10/2022] Open
Abstract
The SPRY domain-containing SOCS box protein 2 (SPSB2) is one of four mammalian SPSB proteins that are characterized by a C-terminal SOCS box and a central SPRY/B30.2 domain. SPSB2 interacts with inducible nitric oxide synthase (iNOS) via the SPRY domain and polyubiquitinates iNOS, resulting in its proteasomal degradation. Inhibitors that can disrupt SPSB2-iNOS interaction and augment NO production may serve as novel anti-infective and anticancer agents. The previously determined murine SPSB2 structure may not reflect the true apo conformation of the iNOS-binding site. Here, the crystal structure of human SPSB2 SPRY domain in the apo state is reported at a resolution of 1.9 Å. Comparison of the apo and ligand-bound structures reveals that the iNOS-binding site is highly preformed and that major conformational changes do not occur upon ligand binding. Moreover, the C-terminal His6 tag of the recombinant protein binds to a shallow pocket adjacent to the iNOS-binding site on a crystallographically related SPSB2 molecule. These findings may help in structure-based and fragment-based SPSB2 inhibitor design in the future.
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Affiliation(s)
- Yanhong Luo
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Kefa Li
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Jinjin Yang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Danting Zhang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Yuying Zhou
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Zhihe Kuang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
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18
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Wang M, Liu C, Wang W, Dong M, Zhang P, Liu Y, Wang L, Song L. A SPRY domain-containing SOCS box protein 3 (SPSB3) involved in the regulation of cytokine production in granulocytes of Crassostrea gigas. Dev Comp Immunol 2019; 95:28-37. [PMID: 30711451 DOI: 10.1016/j.dci.2019.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
The sp1A/ryanodine receptor (SPRY) family members have been reported to involve in important biological pathways, including innate immune signaling, cytokine signaling suppression, development, cell growth, and retroviral restriction. In the present study, a SPRY domain-containing SOCS box protein (named as CgSPSB3) was identified and characterized from oyster Crassostrea gigas. The open reading frame of CgSPSB3 gene was of 699 bp, encoding a polypeptide of 232 amino acid residues with a central SPRY domain and a C-terminal SOCS box motif. CgSPSB3 mRNA transcripts could be detected in all the examined tissues with the highest level in hemocytes, which was about 82.72-fold (p < 0.05) of that in gonad. Furthermore, the expression level of CgSPSB3 mRNA in granulocytes was significantly higher than that in semi-granulocytes and agranulocytes, which was about 2.04-fold (p < 0.05) of the average level of hemocytes. Immunofluorescence assay further revealed that CgSPSB3 protein was mainly distributed in the cytoplasm of granulocytes. The mRNA expression of CgSPSB3 in hemocytes was up-regulated after lipopolysaccharide (LPS) and Vibrio splendidus stimulations. The mRNA expression of CgIFNLP, CgIL17-5 and CgTNF-1 decreased significantly (p < 0.05) at 24 h after the CgSPSB3 mRNA was knocked down by RNAi. These results collectively indicated that CgSPSB3 might play an important role in regulating cytokines production in granulocytes of C. gigas.
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Affiliation(s)
- Min Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Chang Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Disease Control and Prevention of Aquaculture Animals, Dalian Ocean University, Dalian, 116023, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Disease Control and Prevention of Aquaculture Animals, Dalian Ocean University, Dalian, 116023, China
| | - Miren Dong
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
| | - Peng Zhang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
| | - Yu Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Disease Control and Prevention of Aquaculture Animals, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
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19
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Yu Y, Liang L, Jin Y, Yin Y. The TRIM14 PRYSPRY domain mediates protein interaction
via
its basic interface. FEBS Lett 2019; 593:1122-1129. [DOI: 10.1002/1873-3468.13386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/26/2019] [Accepted: 04/05/2019] [Indexed: 01/04/2023]
Affiliation(s)
- Ying Yu
- Institute of Systems Biomedicine Department of Pathology School of Basic Medical Sciences Peking University Health Science Center Beijing China
| | - Ling Liang
- Institute of Systems Biomedicine Department of Pathology School of Basic Medical Sciences Peking University Health Science Center Beijing China
- Department of Biophysics School of Basic Medical Sciences Peking University Health Science Center Beijing China
| | - Yan Jin
- Institute of Systems Biomedicine Department of Pathology School of Basic Medical Sciences Peking University Health Science Center Beijing China
| | - Yuxin Yin
- Institute of Systems Biomedicine Department of Pathology School of Basic Medical Sciences Peking University Health Science Center Beijing China
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20
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Sadek MM, Barlow N, Leung EWW, Williams-Noonan BJ, Yap BK, Shariff FM, Caradoc-Davies TT, Nicholson SE, Chalmers DK, Thompson PE, Law RHP, Norton RS. A Cyclic Peptide Inhibitor of the iNOS-SPSB Protein-Protein Interaction as a Potential Anti-Infective Agent. ACS Chem Biol 2018; 13:2930-2938. [PMID: 30226743 DOI: 10.1021/acschembio.8b00561] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4 interact with inducible nitric oxide synthase (iNOS), causing the iNOS to be polyubiquitinated and targeted for degradation. Inhibition of this interaction increases iNOS levels, and consequently cellular nitric oxide (NO) concentrations, and has been proposed as a potential strategy for killing intracellular pathogens. We previously described two DINNN-containing cyclic peptides (CP1 and CP2) as potent inhibitors of the murine SPSB-iNOS interaction. In this study, we report the crystal structures of human SPSB4 bound to CP1 and CP2 and human SPSB2 bound to CP2. We then used these structures to design a new inhibitor in which an intramolecular hydrogen bond was replaced with a hydrocarbon linkage to form a smaller macrocycle while maintaining the bound geometry of CP2 observed in the crystal structures. This resulting pentapeptide SPSB-iNOS inhibitor (CP3) has a reduced macrocycle ring size, fewer nonbinding residues, and includes additional conformational constraints. CP3 has a greater affinity for SBSB2 ( KD = 7 nM as determined by surface plasmon resonance) and strongly inhibits the SPSB2-iNOS interaction in macrophage cell lysates. We have also determined the crystal structure of CP3 in complex with human SPSB2, which reveals the structural basis for the increased potency of CP3 and validates the original design.
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Affiliation(s)
- Maiada M. Sadek
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
| | - Eleanor W. W. Leung
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
| | - Billy J. Williams-Noonan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
| | - Beow Keat Yap
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
| | - Fairolniza Mohd Shariff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra, 43400 Seri Kembangan, Selangor, Malaysia
| | | | - Sandra E. Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville Victoria 3052, Australia
- The Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - David K. Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
| | - Philip E. Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
| | - Ruby H. P. Law
- Department of Biochemistry and Molecular Biology and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Victoria 3052, Australia
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21
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Abstract
Background Transformation by oncogene Ras overcomes TGF-β mediated growth inhibition in epithelial cells. However, it cooperates with each other to mediate epithelial to mesenchymal transition (EMT). The mechanism of how these two pathways interact with each other is controversial. Methods Molecular techniques were used to engineer expression plasmids for Ras, SPRY, TGF-β receptors, type I and II and ubiquitin. Immunoprecipitation and western blots were employed to determine protein-protein interactions, preotein levels, protein phosphorylation while immunofluorecesent staining for molecular co-localization. TGF-β signalling activities is also determined by its luciferase reporter assay. Trans-well assays were used to measure cell migration and invasion. Results Ras interacts with the SPSB1’s SPRY domain to enhance TGF-β signaling. Ras interacts and colocalizes with the TGF-β type II receptor’s (TβRII) negative regulator SPSB1 on the cell membrane, consequently promoting SPSB1 protein degradation via enhanced mono- and di-ubiquitination. Reduced SPSB1 levels result in the stablization of TβRII, in turn the increase of receptor levels significantly enhance Smad2/3 phosphorylation and signaling. Importantly, forced expression of SPSB1 in Ras transformed cells suppresses TGF-β signaling and its mediated migration and invasion. Conclusion Ras positively cooperates with TGF-β signaling by reducing the cellular protein levels of TβRII negative regualtor SPSB1. Electronic supplementary material The online version of this article (10.1186/s12964-018-0223-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sheng Liu
- Department of Surgery (RMH), The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Josephine Iaria
- Department of Surgery (RMH), The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
| | - Richard J Simpson
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC, Australia
| | - Hong-Jian Zhu
- Department of Surgery (RMH), The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia.
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22
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Juszczak GR, Stankiewicz AM. Glucocorticoids, genes and brain function. Prog Neuropsychopharmacol Biol Psychiatry 2018; 82:136-168. [PMID: 29180230 DOI: 10.1016/j.pnpbp.2017.11.020] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/18/2017] [Accepted: 11/23/2017] [Indexed: 01/02/2023]
Abstract
The identification of key genes in transcriptomic data constitutes a huge challenge. Our review of microarray reports revealed 88 genes whose transcription is consistently regulated by glucocorticoids (GCs), such as cortisol, corticosterone and dexamethasone, in the brain. Replicable transcriptomic data were combined with biochemical and physiological data to create an integrated view of the effects induced by GCs. The most frequently reported genes were Errfi1 and Ddit4. Their up-regulation was associated with the altered transcription of genes regulating growth factor and mTORC1 signaling (Gab1, Tsc22d3, Dusp1, Ndrg2, Ppp5c and Sesn1) and progression of the cell cycle (Ccnd1, Cdkn1a and Cables1). The GC-induced reprogramming of cell function involves changes in the mRNA level of genes responsible for the regulation of transcription (Klf9, Bcl6, Klf15, Tle3, Cxxc5, Litaf, Tle4, Jun, Sox4, Sox2, Sox9, Irf1, Sall2, Nfkbia and Id1) and the selective degradation of mRNA (Tob2). Other genes are involved in the regulation of metabolism (Gpd1, Aldoc and Pdk4), actin cytoskeleton (Myh2, Nedd9, Mical2, Rhou, Arl4d, Osbpl3, Arhgef3, Sdc4, Rdx, Wipf3, Chst1 and Hepacam), autophagy (Eva1a and Plekhf1), vesicular transport (Rhob, Ehd3, Vps37b and Scamp2), gap junctions (Gjb6), immune response (Tiparp, Mertk, Lyve1 and Il6r), signaling mediated by thyroid hormones (Thra and Sult1a1), calcium (Calm2), adrenaline/noradrenaline (Adcy9 and Adra1d), neuropeptide Y (Npy1r) and histamine (Hdc). GCs also affected genes involved in the synthesis of polyamines (Azin1) and taurine (Cdo1). The actions of GCs are restrained by feedback mechanisms depending on the transcription of Sgk1, Fkbp5 and Nr3c1. A side effect induced by GCs is increased production of reactive oxygen species. Available data show that the brain's response to GCs is part of an emergency mode characterized by inactivation of non-core activities, restrained inflammation, restriction of investments (growth), improved efficiency of energy production and the removal of unnecessary or malfunctioning cellular components to conserve energy and maintain nutrient supply during the stress response.
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Affiliation(s)
- Grzegorz R Juszczak
- Department of Animal Behavior, Institute of Genetics and Animal Breeding, Jastrzebiec, ul. Postepu 36A, 05-552 Magdalenka, Poland.
| | - Adrian M Stankiewicz
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Jastrzebiec, ul. Postepu 36A, 05-552 Magdalenka, Poland
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23
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D'Cruz AA, Kershaw NJ, Hayman TJ, Linossi EM, Chiang JJ, Wang MK, Dagley LF, Kolesnik TB, Zhang JG, Masters SL, Griffin MDW, Gack MU, Murphy JM, Nicola NA, Babon JJ, Nicholson SE. Identification of a second binding site on the TRIM25 B30.2 domain. Biochem J 2018; 475:429-440. [PMID: 29259080 PMCID: PMC6200327 DOI: 10.1042/bcj20170427] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 12/29/2022]
Abstract
The retinoic acid-inducible gene-I (RIG-I) receptor recognizes short 5'-di- and triphosphate base-paired viral RNA and is a critical mediator of the innate immune response against viruses such as influenza A, Ebola, HIV and hepatitis C. This response is reported to require an orchestrated interaction with the tripartite motif 25 (TRIM25) B30.2 protein-interaction domain. Here, we present a novel second RIG-I-binding interface on the TRIM25 B30.2 domain that interacts with CARD1 and CARD2 (caspase activation and recruitment domains) of RIG-I and is revealed by the removal of an N-terminal α-helix that mimics dimerization of the full-length protein. Further characterization of the TRIM25 coiled-coil and B30.2 regions indicated that the B30.2 domains move freely on a flexible tether, facilitating RIG-I CARD recruitment. The identification of a dual binding mode for the TRIM25 B30.2 domain is a first for the SPRY/B30.2 domain family and may be a feature of other SPRY/B30.2 family members.
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Affiliation(s)
- Akshay A D'Cruz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Nadia J Kershaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas J Hayman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Edmond M Linossi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, U. S. A
| | - May K Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, U. S. A
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Tatiana B Kolesnik
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Jian-Guo Zhang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Seth L Masters
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | | | - Michaela U Gack
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, U. S. A
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Nicos A Nicola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Jeffrey J Babon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Sandra E Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
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24
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You T, Wang Y, Li K, Zhang D, Wei H, Luo Y, Li H, Lu Y, Su X, Kuang Z. Crystal structure of SPSB2 in complex with a rational designed RGD-containing cyclic peptide inhibitor of SPSB2-iNOS interaction. Biochem Biophys Res Commun 2017; 489:346-352. [DOI: 10.1016/j.bbrc.2017.05.122] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 05/22/2017] [Indexed: 12/24/2022]
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25
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Hebbar N, Burikhanov R, Shukla N, Qiu S, Zhao Y, Elenitoba-Johnson KSJ, Rangnekar VM. A Naturally Generated Decoy of the Prostate Apoptosis Response-4 Protein Overcomes Therapy Resistance in Tumors. Cancer Res 2017. [PMID: 28625975 DOI: 10.1158/0008-5472.can-16-1970] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Primary tumors are often heterogeneous, composed of therapy-sensitive and emerging therapy-resistant cancer cells. Interestingly, treatment of therapy-sensitive tumors in heterogeneous tumor microenvironments results in apoptosis of therapy-resistant tumors. In this study, we identify a prostate apoptosis response-4 (Par-4) amino-terminal fragment (PAF) that is released by diverse therapy-sensitive cancer cells following therapy-induced caspase cleavage of the tumor suppressor Par-4 protein. PAF caused apoptosis in cancer cells resistant to therapy and inhibited tumor growth. A VASA segment of Par-4 mediated its binding and degradation by the ubiquitin ligase Fbxo45, resulting in loss of Par-4 proapoptotic function. Conversely, PAF, which contains this VASA segment, competitively bound to Fbxo45 and rescued Par-4-mediated induction of cancer cell-specific apoptosis. Collectively, our findings identify a molecular decoy naturally generated during apoptosis that inhibits a ubiquitin ligase to overcome therapy resistance in tumors. Cancer Res; 77(15); 4039-50. ©2017 AACR.
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Affiliation(s)
- Nikhil Hebbar
- Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Ravshan Burikhanov
- Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky
| | - Nidhi Shukla
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - Shirley Qiu
- Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky
| | - Yanming Zhao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | | | - Vivek M Rangnekar
- Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky. .,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky.,Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, Kentucky.,L.P. Markey Cancer Center, University of Kentucky, Lexington, Kentucky
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26
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Chittoor B, Krishnarjuna B, Morales RAV, MacRaild CA, Sadek M, Leung EWW, Robinson SD, Pennington MW, Norton RS. The Single Disulfide-Directed β-Hairpin Fold. Dynamics, Stability, and Engineering. Biochemistry 2017; 56:2455-2466. [PMID: 28437072 DOI: 10.1021/acs.biochem.7b00120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Grafting bioactive peptide sequences onto small cysteine-rich scaffolds is a promising strategy for enhancing their stability and value as novel peptide-based therapeutics. However, correctly folded disulfide-rich peptides can be challenging to produce by either recombinant or synthetic means. The single disulfide-directed β-hairpin (SDH) fold, first observed in contryphan-Vc1, provides a potential alternative to complex disulfide-rich scaffolds. We have undertaken recombinant production of full-length contryphan-Vc1 (rCon-Vc1[Z1Q]) and a truncated analogue (rCon-Vc11-22[Z1Q]), analyzed the backbone dynamics of rCon-Vc1[Z1Q], and probed the conformational and proteolytic stability of these peptides to evaluate the potential of contryphan-Vc1 as a molecular scaffold. Backbone 15N relaxation measurements for rCon-Vc1[Z1Q] indicate that the N-terminal domain of the peptide is ordered up to Thr19, whereas the remainder of the C-terminal region is highly flexible. The solution structure of truncated rCon-Vc11-22[Z1Q] was similar to that of the full-length peptide, indicating that the flexible C-terminus does not have any effect on the structured domain of the peptide. Contryphan-Vc1 exhibited excellent proteolytic stability against trypsin and chymotrypsin but was susceptible to pepsin digestion. We have investigated whether contryphan-Vc1 can accept a bioactive epitope while maintaining the structure of the peptide by introducing peptide sequences based on the DINNN motif of inducible nitric oxide synthase. We show that sCon-Vc11-22[NNN12-14] binds to the iNOS-binding protein SPSB2 with an affinity of 1.3 μM while maintaining the SDH fold. This study serves as a starting point in utilizing the SDH fold as a peptide scaffold.
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Affiliation(s)
- Balasubramanyam Chittoor
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Rodrigo A V Morales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Maiada Sadek
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Eleanor W W Leung
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Samuel D Robinson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | | | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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27
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Leung EWW, Mulcair MD, Yap BK, Nicholson SE, Scanlon MJ, Norton RS. Molecular Insights into the Interaction Between the SPRY Domain-Containing SOCS Box Protein SPSB2 and Peptides Based on the Binding Motif from iNOS. Aust J Chem 2017. [DOI: 10.1071/ch16510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SPRY domain-containing SOCS box proteins SPSB1, 2, and 4 mediate the proteasomal degradation of inducible nitric oxide synthase (iNOS) and thereby modulate the amount of NO available for combating infectious organisms. A highly conserved Asp-Ile-Asn-Asn-Asn (DINNN) motif found at the N-terminus of iNOS binds to SPSB2 with nanomolar affinity. The design of specific and potent inhibitors of iNOS–SPSB interactions will be aided by a better understanding of the interactions of this DINNN sequence with SPSB2. Although crystal structures of SPSB complexes with DINNN peptides are available, aspects of the interaction between peptide and protein are still not fully understood. Here, our results from surface plasmon resonance and NMR spectroscopy indicate that residues flanking the DINNN motif, which make no direct contact with SPSB2 in the available crystal structures, nonetheless play an important role in enhancing the binding affinity to SPSB2, by up to 80-fold. Mutational analysis of the DINNN sequence showed that mutation of the Asp or the first Asn residue to Ala reduced the binding affinity by 200- or 600-fold respectively, whereas mutation of the third Asn made binding undetectable. Ala substitution of the second Asn residue caused a 30-fold drop in binding affinity. Substitution of the Ile had very little effect on the binding affinity and substitutions with bulky residues were tolerated. This provides an opportunity for further modification for therapeutic applications. These results highlight the complex interplay of peptide sequence and protein binding and inform efforts to design peptide therapeutics to disrupt the iNOS–SPSB interaction.
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28
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Hong SK, Kim KH, Song EJ, Kim EE. Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development. J Mol Biol 2016; 428:4330-4344. [PMID: 27622290 DOI: 10.1016/j.jmb.2016.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 02/08/2023]
Abstract
RanBPM and RanBP10 are non-canonical members of the Ran binding protein family that lack the Ran binding domain and do not associate with Ran GTPase in vivo. Rather, they have been shown to be scaffolding proteins that are important for a variety of cellular processes, and both of these proteins contain a SPRY domain, which has been implicated in mediating protein-protein interactions with a variety of targets including the DEAD-box containing ATP-dependent RNA helicase (DDX-4). In this study, we have determined the crystal structures of the SPIa and the ryanodine receptor domain and of approximately 70 upstream residues (immediate upstream to SPRY motif) of both RanBPM and RanBP10. They are almost identical, composed of a β-sandwich fold with a set of two helices on each side located at the edge of the sheets. A unique shallow binding surface is formed by highly conserved loops on the surface of the β-sheet with two aspartates on one end, a positive patch on the opposite end, and a tryptophan lining at the bottom of the surface. The 20-mer peptide (residues 228-247) of human DDX-4, an ATP-dependent RNA helicase known to regulate germ cell development, binds to this surface with a KD of ~13μM. The crystal structure of the peptide complex and the mutagenesis studies elucidate how RanBPM can recognize its interaction partners to function in gametogenesis.
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Affiliation(s)
- Seung Kon Hong
- Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu Hwarang-ro 14-gil 5, Seoul 02792, Republic of Korea
| | - Kook-Han Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu Hwarang-ro 14-gil 5, Seoul 02792, Republic of Korea
| | - Eun Joo Song
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seongbuk-gu Hwarang-ro 14-gil 5, Seoul 02792, Republic of Korea
| | - Eunice EunKyeong Kim
- Biomedical Research Institute, Korea Institute of Science and Technology, Seongbuk-gu Hwarang-ro 14-gil 5, Seoul 02792, Republic of Korea.
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29
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Norton RS, Leung EWW, Chandrashekaran IR, MacRaild CA. Applications of (19)F-NMR in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21070860. [PMID: 27438818 PMCID: PMC6273323 DOI: 10.3390/molecules21070860] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 11/16/2022] Open
Abstract
(19)F-NMR has proved to be a valuable tool in fragment-based drug discovery. Its applications include screening libraries of fluorinated fragments, assessing competition among elaborated fragments and identifying the binding poses of promising hits. By observing fluorine in both the ligand and the target protein, useful information can be obtained on not only the binding pose but also the dynamics of ligand-protein interactions. These applications of (19)F-NMR will be illustrated in this review with studies from our fragment-based drug discovery campaigns against protein targets in parasitic and infectious diseases.
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Affiliation(s)
- Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Eleanor W W Leung
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Indu R Chandrashekaran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia.
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30
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Huwe PJ, Xu Q, Shapovalov MV, Modi V, Andrake MD, Dunbrack RL. Biological function derived from predicted structures in CASP11. Proteins 2016; 84 Suppl 1:370-91. [PMID: 27181425 DOI: 10.1002/prot.24997] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 01/10/2016] [Accepted: 01/18/2016] [Indexed: 12/26/2022]
Abstract
In CASP11, the organizers sought to bring the biological inferences from predicted structures to the fore. To accomplish this, we assessed the models for their ability to perform quantifiable tasks related to biological function. First, for 10 targets that were probable homodimers, we measured the accuracy of docking the models into homodimers as a function of GDT-TS of the monomers, which produced characteristic L-shaped plots. At low GDT-TS, none of the models could be docked correctly as homodimers. Above GDT-TS of ∼60%, some models formed correct homodimers in one of the largest docked clusters, while many other models at the same values of GDT-TS did not. Docking was more successful when many of the templates shared the same homodimer. Second, we docked a ligand from an experimental structure into each of the models of one of the targets. Docking to the models with two different programs produced poor ligand RMSDs with the experimental structure. Measures that evaluated similarity of contacts were reasonable for some of the models, although there was not a significant correlation with model accuracy. Finally, we assessed whether models would be useful in predicting the phenotypes of missense mutations in three human targets by comparing features calculated from the models with those calculated from the experimental structures. The models were successful in reproducing accessible surface areas but there was little correlation of model accuracy with calculation of FoldX evaluation of the change in free energy between the wild-type and the mutant. Proteins 2016; 84(Suppl 1):370-391. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Peter J Huwe
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, 19111
| | - Qifang Xu
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, 19111
| | | | - Vivek Modi
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, 19111
| | - Mark D Andrake
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, 19111
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31
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Harjani JR, Yap BK, Leung EWW, Lucke A, Nicholson SE, Scanlon MJ, Chalmers DK, Thompson PE, Norton RS, Baell JB. Design, Synthesis, and Characterization of Cyclic Peptidomimetics of the Inducible Nitric Oxide Synthase Binding Epitope That Disrupt the Protein–Protein Interaction Involving SPRY Domain-Containing Suppressor of Cytokine Signaling Box Protein (SPSB) 2 and Inducible Nitric Oxide Synthase. J Med Chem 2016; 59:5799-809. [DOI: 10.1021/acs.jmedchem.6b00386] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jitendra R. Harjani
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Beow Keat Yap
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Eleanor W. W. Leung
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew Lucke
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Sandra E. Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- The
Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Martin J. Scanlon
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - David K. Chalmers
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Philip E. Thompson
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Raymond S. Norton
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Jonathan B. Baell
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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32
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Yap BK, Harjani JR, Leung EWW, Nicholson SE, Scanlon MJ, Chalmers DK, Thompson PE, Baell JB, Norton RS. Redox-stable cyclic peptide inhibitors of the SPSB2-iNOS interaction. FEBS Lett 2016; 590:696-704. [DOI: 10.1002/1873-3468.12115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Beow Keat Yap
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
| | - Jitendra R. Harjani
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
| | - Eleanor W. W. Leung
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
| | - Sandra E. Nicholson
- The Walter and Eliza Hall Institute of Medical Research; Parkville Vic. Australia
- The Department of Medical Biology; University of Melbourne; Parkville Vic. Australia
| | - Martin J. Scanlon
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
| | - David K. Chalmers
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
| | - Philip E. Thompson
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
| | - Jonathan B. Baell
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
| | - Raymond S. Norton
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Vic. Australia
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33
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Wang H, Morita CT. Sensor Function for Butyrophilin 3A1 in Prenyl Pyrophosphate Stimulation of Human Vγ2Vδ2 T Cells. J Immunol 2015; 195:4583-94. [PMID: 26475929 DOI: 10.4049/jimmunol.1500314] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022]
Abstract
Vγ2Vδ2 T cells play important roles in human immunity to pathogens and in cancer immunotherapy by responding to isoprenoid metabolites, such as (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate and isopentenyl pyrophosphate. The Ig superfamily protein butyrophilin (BTN)3A1 was shown to be required for prenyl pyrophosphate stimulation. We proposed that the intracellular B30.2 domain of BTN3A1 binds prenyl pyrophosphates, resulting in a change in the extracellular BTN3A1 dimer that is detected by Vγ2Vδ2 TCRs. Such B30.2 binding was demonstrated recently. However, other investigators reported that the extracellular BTN3A1 IgV domain binds prenyl pyrophosphates, leading to the proposal that the Vγ2Vδ2 TCR recognizes the complex. To distinguish between these mechanisms, we mutagenized residues in the two binding sites and tested the mutant BTN3A1 proteins for their ability to mediate prenyl pyrophosphate stimulation of Vγ2Vδ2 T cells to proliferate and secrete TNF-α. Mutagenesis of residues in the IgV site had no effect on Vγ2Vδ2 T cell proliferation or secretion of TNF-α. In contrast, mutagenesis of residues within the basic pocket and surrounding V regions of the B30.2 domain abrogated prenyl pyrophosphate-induced proliferation. Mutations of residues making hydrogen bonds to the pyrophosphate moiety also abrogated TNF-α secretion, as did mutation of aromatic residues making contact with the alkenyl chain. Some mutations further from the B30.2 binding site also diminished stimulation, suggesting that the B30.2 domain may interact with a second protein. These findings support intracellular sensing of prenyl pyrophosphates by BTN3A1 rather than extracellular presentation.
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Affiliation(s)
- Hong Wang
- Division of Immunology, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242; Department of Veterans Affairs, Iowa City Health Care System, Iowa City, IA 52246; and
| | - Craig T Morita
- Division of Immunology, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242; Department of Veterans Affairs, Iowa City Health Care System, Iowa City, IA 52246; and Interdisciplinary Graduate Program in Immunology, University of Iowa Carver College of Medicine, Iowa City, IA 52242
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Kellner JN, Meinhart A. Structure of the SPRY domain of the human RNA helicase DDX1, a putative interaction platform within a DEAD-box protein. Acta Crystallogr F Struct Biol Commun 2015; 71:1176-88. [PMID: 26323305 PMCID: PMC4555926 DOI: 10.1107/s2053230x15013709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 07/20/2015] [Indexed: 11/24/2022] Open
Abstract
The human RNA helicase DDX1 in the DEAD-box family plays an important role in RNA processing and has been associated with HIV-1 replication and tumour progression. Whereas previously described DEAD-box proteins have a structurally conserved core, DDX1 shows a unique structural feature: a large SPRY-domain insertion in its RecA-like consensus fold. SPRY domains are known to function as protein-protein interaction platforms. Here, the crystal structure of the SPRY domain of human DDX1 (hDSPRY) is reported at 2.0 Å resolution. The structure reveals two layers of concave, antiparallel β-sheets that stack onto each other and a third β-sheet beneath the β-sandwich. A comparison with SPRY-domain structures from other eukaryotic proteins showed that the general β-sandwich fold is conserved; however, differences were detected in the loop regions, which were identified in other SPRY domains to be essential for interaction with cognate partners. In contrast, in hDSPRY these loop regions are not strictly conserved across species. Interestingly, though, a conserved patch of positive surface charge is found that may replace the connecting loops as a protein-protein interaction surface. The data presented here comprise the first structural information on DDX1 and provide insights into the unique domain architecture of this DEAD-box protein. By providing the structure of a putative interaction domain of DDX1, this work will serve as a basis for further studies of the interaction network within the hetero-oligomeric complexes of DDX1 and of its recruitment to the HIV-1 Rev protein as a viral replication factor.
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Affiliation(s)
- Julian N Kellner
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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Liu S, Nheu T, Luwor R, Nicholson SE, Zhu HJ. SPSB1, a Novel Negative Regulator of the Transforming Growth Factor-β Signaling Pathway Targeting the Type II Receptor. J Biol Chem 2015; 290:17894-17908. [PMID: 26032413 DOI: 10.1074/jbc.m114.607184] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 01/17/2023] Open
Abstract
Appropriate cellular signaling is essential to control cell proliferation, differentiation, and cell death. Aberrant signaling can have devastating consequences and lead to disease states, including cancer. The transforming growth factor-β (TGF-β) signaling pathway is a prominent signaling pathway that has been tightly regulated in normal cells, whereas its deregulation strongly correlates with the progression of human cancers. The regulation of the TGF-β signaling pathway involves a variety of physiological regulators. Many of these molecules act to alter the activity of Smad proteins. In contrast, the number of molecules known to affect the TGF-β signaling pathway at the receptor level is relatively low, and there are no known direct modulators for the TGF-β type II receptor (TβRII). Here we identify SPSB1 (a Spry domain-containing Socs box protein) as a novel regulator of the TGF-β signaling pathway. SPSB1 negatively regulates the TGF-β signaling pathway through its interaction with both endogenous and overexpressed TβRII (and not TβRI) via its Spry domain. As such, TβRII and SPSB1 co-localize on the cell membrane. SPSB1 maintains TβRII at a low level by enhancing the ubiquitination levels and degradation rates of TβRII through its Socs box. More importantly, silencing SPSB1 by siRNA results in enhanced TGF-β signaling and migration and invasion of tumor cells.
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Affiliation(s)
- Sheng Liu
- Departments of Surgery (the Royal Melbourne Hospital), University of Melbourne, Parkville, Victoria 3050, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Thao Nheu
- Departments of Surgery (the Royal Melbourne Hospital), University of Melbourne, Parkville, Victoria 3050, Australia
| | - Rodney Luwor
- Departments of Surgery (the Royal Melbourne Hospital), University of Melbourne, Parkville, Victoria 3050, Australia
| | - Sandra E Nicholson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia; Departments of Medical Biology, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Hong-Jian Zhu
- Departments of Surgery (the Royal Melbourne Hospital), University of Melbourne, Parkville, Victoria 3050, Australia.
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Dong Z, Cheng F, Yuwen Y, Chen J, Li X, Dou H, Zhang H, Chen G, Liu D. Identification and expression analysis of a Spsb gene in planarian Dugesia japonica. Gene 2015; 564:168-75. [DOI: 10.1016/j.gene.2015.03.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 03/02/2015] [Accepted: 03/14/2015] [Indexed: 11/22/2022]
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D'Cruz AA, Babon JJ, Norton RS, Nicola NA, Nicholson SE. Structure and function of the SPRY/B30.2 domain proteins involved in innate immunity. Protein Sci 2014; 22:1-10. [PMID: 23139046 DOI: 10.1002/pro.2185] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/16/2012] [Accepted: 10/19/2012] [Indexed: 11/12/2022]
Abstract
The SPRY domain is a protein interaction module found in 77 murine and ~100 human proteins, and is implicated in important biological pathways, including those that regulate innate and adaptive immunity. The current definition of the SPRY domain is based on a sequence repeat discovered in the splA kinase and ryanodine receptors. The greater SPRY family is divided into the B30.2 (which contains a PRY extension at the N-terminus) and "SPRY-only" sub-families. In this brief review, we examine the current structural and biochemical literature on SPRY/B30.2 domain involvement in key immune processes and highlight a PRY-like 60 amino acid region in the N-terminus of "SPRY-only" proteins. Phylogenetic, structural, and functional analyses suggest that this N-terminal region is related to the PRY region of B30.2 and should be characterized as part of an extended SPRY domain. Greater understanding of the functional importance of the N-terminal region in "SPRY only" proteins will enhance our ability to interrogate SPRY interactions with their respective binding partners.
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Affiliation(s)
- Akshay A D'Cruz
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
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Chung FZ, Sahasrabuddhe AA, Ma K, Chen X, Basrur V, Lim MS, Elenitoba-Johnson KSJ. Fbxo45 inhibits calcium-sensitive proteolysis of N-cadherin and promotes neuronal differentiation. J Biol Chem 2014; 289:28448-59. [PMID: 25143387 DOI: 10.1074/jbc.m114.561241] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Fbxo45 is an atypical E3 ubiquitin ligase, which specifically targets proteins for ubiquitin-mediated degradation. Fbxo45 ablation results in defective neuronal differentiation and abnormal formation of neural connections; however, the mechanisms underlying these defects are poorly understood. Using an unbiased mass spectrometry-based proteomic screen, we show here that N-cadherin is a novel interactor of Fbxo45. N-cadherin specifically interacts with Fbxo45 through two consensus motifs overlapping the site of calcium-binding and dimerization of the cadherin molecule. N-cadherin interaction with Fbxo45 is significantly abrogated by calcium treatment. Surprisingly, Fbxo45 depletion by RNAi-mediated silencing results in enhanced proteolysis of N-cadherin. Conversely, ectopic expression of Fbxo45 results in decreased proteolysis of N-cadherin. Fbxo45 depletion results in dramatic reduction in N-cadherin expression, impaired neuronal differentiation, and diminished formation of neuronal processes. Our studies reveal an unanticipated role for an F-box protein that inhibits proteolysis in the regulation of a critical biological process.
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Affiliation(s)
| | | | - Kaiyu Ma
- From the Department of Pathology
| | | | | | - Megan S Lim
- From the Department of Pathology, the Center for Computational Medicine and Bioinformatics, and
| | - Kojo S J Elenitoba-Johnson
- From the Department of Pathology, the Center for Computational Medicine and Bioinformatics, and the Protein Folding Diseases Initiative, University of Michigan Medical School, Ann Arbor, Michigan 48109
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Yap BK, Leung EWW, Yagi H, Galea CA, Chhabra S, Chalmers DK, Nicholson SE, Thompson PE, Norton RS. A Potent Cyclic Peptide Targeting SPSB2 Protein as a Potential Anti-infective Agent. J Med Chem 2014; 57:7006-15. [DOI: 10.1021/jm500596j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Beow Keat Yap
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Eleanor W. W. Leung
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Hiromasa Yagi
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Charles A. Galea
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Sandeep Chhabra
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - David K. Chalmers
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Sandra E. Nicholson
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia
- The
Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Philip E. Thompson
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Raymond S. Norton
- Medicinal
Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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40
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Qin Y, McAllister SS. SPSB1 may have MET its match during breast cancer recurrence. Cancer Discov 2014; 4:760-1. [PMID: 25002612 DOI: 10.1158/2159-8290.cd-14-0505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
SUMMARY Disease recurrence is the most common cause of death for patients with breast cancer, yet little is known about the molecular mechanisms underlying this process. Using inducible transgenic mouse model systems, Feng and colleagues identified SPSB1 as a determinant of breast cancer recurrence by virtue of its ability to protect tumor cells from apoptosis through c-MET activation.
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Affiliation(s)
- Yuanbo Qin
- Authors' Affiliations:Hematology Division, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School
| | - Sandra S McAllister
- Authors' Affiliations:Hematology Division, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School; Harvard Stem Cell Institute, Boston; and Broad Institute of Harvard and MIT, Cambridge, Massachusetts
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41
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Chen X, Sahasrabuddhe AA, Szankasi P, Chung F, Basrur V, Rangnekar VM, Pagano M, Lim MS, Elenitoba-Johnson KS. Fbxo45-mediated degradation of the tumor-suppressor Par-4 regulates cancer cell survival. Cell Death Differ 2014; 21:1535-45. [PMID: 24992930 DOI: 10.1038/cdd.2014.92] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/09/2014] [Accepted: 05/23/2014] [Indexed: 11/09/2022] Open
Abstract
Prostate apoptosis response protein 4 (Par-4) also known as PRKC apoptosis WT1 regulator is a tumor suppressor that selectively induces apoptosis in cancer cells. However, its post-translational regulation by ubiquitin-mediated proteolysis and the cellular machinery that is responsible for its proteasomal degradation are unknown. Using immunopurification and an unbiased mass spectrometry-based approach, we show that Par-4 interacts with the SPRY-domain containing E3 ubiquitin ligase Fbxo45 through a short consensus sequence motif. Fbxo45 interacts with Par-4 in the cytoplasm and mediates its ubiquitylation and proteasomal degradation. Fbxo45 silencing results in stabilization of Par-4 with increased apoptosis. Importantly, a Par-4 mutant that is unable to bind Fbxo45 is stabilized and further enhances staurosporine-induced apoptosis. Co-expression of Fbxo45 with Par-4 protects cancer cells against Par-4-induced apoptosis. Our studies reveal that Fbxo45 is the substrate-receptor subunit of a functional E3 ligase for Par-4 that has a critical role in cancer cell survival.
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42
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Leung EWW, Yagi H, Harjani JR, Mulcair MD, Scanlon MJ, Baell JB, Norton RS. 19F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY Domain-Containing SOCS Box Protein 2. Chem Biol Drug Des 2014; 84:616-25. [DOI: 10.1111/cbdd.12355] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/12/2014] [Accepted: 04/29/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Eleanor W. W. Leung
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Hiromasa Yagi
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Jitendra R. Harjani
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Mark D. Mulcair
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Martin J. Scanlon
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Jonathan B. Baell
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Raymond S. Norton
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
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43
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D'Cruz AA, Kershaw NJ, Chiang JJ, Wang MK, Nicola NA, Babon JJ, Gack MU, Nicholson SE. Crystal structure of the TRIM25 B30.2 (PRYSPRY) domain: a key component of antiviral signalling. Biochem J 2013; 456:231-40. [PMID: 24015671 DOI: 10.1042/BJ20121425] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TRIM (tripartite motif) proteins primarily function as ubiquitin E3 ligases that regulate the innate immune response to infection. TRIM25 [also known as Efp (oestrogen-responsive finger protein)] has been implicated in the regulation of oestrogen receptor α signalling and in the regulation of innate immune signalling via RIG-I (retinoic acid-inducible gene-I). RIG-I senses cytosolic viral RNA and is subsequently ubiquitinated by TRIM25 at its N-terminal CARDs (caspase recruitment domains), leading to type I interferon production. The interaction with RIG-I is dependent on the TRIM25 B30.2 domain, a protein-interaction domain composed of the PRY and SPRY tandem sequence motifs. In the present study we describe the 1.8 Å crystal structure of the TRIM25 B30.2 domain, which exhibits a typical B30.2/SPRY domain fold comprising two N-terminal α-helices, thirteen β-strands arranged into two β-sheets and loop regions of varying lengths. A comparison with other B30.2/SPRY structures and an analysis of the loop regions identified a putative binding pocket, which is likely to be involved in binding target proteins. This was supported by mutagenesis and functional analyses, which identified two key residues (Asp(488) and Trp(621)) in the TRIM25 B30.2 domain as being critical for binding to the RIG-I CARDs.
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Biris N, Tomashevski A, Bhattacharya A, Diaz-Griffero F, Ivanov DN. Rhesus monkey TRIM5α SPRY domain recognizes multiple epitopes that span several capsid monomers on the surface of the HIV-1 mature viral core. J Mol Biol 2013; 425:5032-44. [PMID: 23886867 DOI: 10.1016/j.jmb.2013.07.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 01/06/2023]
Abstract
The restriction factor TRIM5α binds to the capsid protein of the retroviral core and blocks retroviral replication. The affinity of TRIM5α for the capsid is a major host tropism determinant of HIV and other primate immunodeficiency viruses, but the molecular interface involved in this host-pathogen interaction remains poorly characterized. Here we use NMR spectroscopy to investigate binding of the rhesus TRIM5α SPRY domain to a selection of HIV capsid constructs. The data are consistent with a model in which one SPRY domain interacts with more than one capsid monomer within the assembled retroviral core. The highly mobile SPRY v1 loop appears to span the gap between neighboring capsid hexamers making interhexamer contacts critical for restriction. The interaction interface is extensive, involves mobile loops and multiple epitopes, and lacks interaction hot spots. These properties, which may enhance resistance of TRIM5α to capsid mutations, result in relatively low affinity of the individual SPRY domains for the capsid, and the TRIM5α-mediated restriction depends on the avidity effect arising from the oligomerization of TRIM5α.
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Affiliation(s)
- Nikolaos Biris
- Department of Biochemistry and Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
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Wang H, Henry O, Distefano MD, Wang YC, Räikkönen J, Mönkkönen J, Tanaka Y, Morita CT. Butyrophilin 3A1 plays an essential role in prenyl pyrophosphate stimulation of human Vγ2Vδ2 T cells. J Immunol 2013; 191:1029-42. [PMID: 23833237 DOI: 10.4049/jimmunol.1300658] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Most human γδ T cells express Vγ2Vδ2 TCRs and play important roles in microbial and tumor immunity. Vγ2Vδ2 T cells are stimulated by self- and foreign prenyl pyrophosphate intermediates in isoprenoid synthesis. However, little is known about the molecular basis for this stimulation. We find that a mAb specific for butyrophilin 3 (BTN3)/CD277 Ig superfamily proteins mimics prenyl pyrophosphates. The 20.1 mAb stimulated Vγ2Vδ2 T cell clones regardless of their functional phenotype or developmental origin and selectively expanded blood Vγ2Vδ2 T cells. The γδ TCR mediates 20.1 mAb stimulation because IL-2 is released by β(-) Jurkat cells transfected with Vγ2Vδ2 TCRs. 20.1 stimulation was not due to isopentenyl pyrophosphate (IPP) accumulation because 20.1 treatment of APC did not increase IPP levels. In addition, stimulation was not inhibited by statin treatment, which blocks IPP production. Importantly, small interfering RNA knockdown of BTN3A1 abolished stimulation by IPP that could be restored by re-expression of BTN3A1 but not by BTN3A2 or BTN3A3. Rhesus monkey and baboon APC presented HMBPP and 20.1 to human Vγ2Vδ2 T cells despite amino acid differences in BTN3A1 that localize to its outer surface. This suggests that the conserved inner and/or top surfaces of BTN3A1 interact with its counterreceptor. Although no binding site exists on the BTN3A1 extracellular domains, a model of the intracellular B30.2 domain predicts a basic pocket on its binding surface. However, BTN3A1 did not preferentially bind a photoaffinity prenyl pyrophosphate. Thus, BTN3A1 is required for stimulation by prenyl pyrophosphates but does not bind the intermediates with high affinity.
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Affiliation(s)
- Hong Wang
- Division of Immunology, Department of Internal Medicine, Interdisciplinary Graduate Program in Immunology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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Foster MW, Thompson JW, Forrester MT, Sha Y, McMahon TJ, Bowles DE, Moseley MA, Marshall HE. Proteomic analysis of the NOS2 interactome in human airway epithelial cells. Nitric Oxide 2013; 34:37-46. [PMID: 23438482 DOI: 10.1016/j.niox.2013.02.079] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 02/07/2013] [Accepted: 02/08/2013] [Indexed: 01/22/2023]
Abstract
The cytokine-inducible isoform of nitric oxide synthase (NOS2) is constitutively expressed in human respiratory epithelia and is upregulated in inflammatory lung disease. Here, we sought to better define the protein interactions that may be important for NOS2 activity and stability, as well as to identify potential targets of NOS2-derived NO, in the respiratory epithelium. We overexpressed Flag-tagged, catalytically-inactive NOS2 in A549 cells and used mass spectrometry to qualitatively identify NOS2 co-immunoprecipitating proteins. Stable isotope labeling of amino acids in cell culture (SILAC) was used to quantify the coordinate effects of cytokine stimulation on NOS2-protein interactions. Multi-protein networks dominated the NOS2 interactome, and cytokine-inducible interactions with allosteric activators and with the ubiquitin-proteasome system were correlated with cytokine-dependent increases in NO metabolites and in NOS2 ubiquitination. The ubiquitin ligase scaffolding protein, FBXO45, was identified as a novel, direct NOS2 interactor. Similar to the SPRY domain-containing SOCS box (SPSB) proteins, FBXO45 requires Asn27 in the (23)DINNN(27) motif of NOS2 for its interaction. However, FBXO45 is unique from the SPSBs in that it recruits a distinct E3 ligase complex containing MYCBP2 and SKP1. Collectively, these findings demonstrate the general utility of interaction proteomics for defining new aspects of NOS2 physiology.
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Affiliation(s)
- Matthew W Foster
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University Medical Centers, Durham, NC 27710, United States.
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Perfetto L, Gherardini PF, Davey NE, Diella F, Helmer-Citterich M, Cesareni G. Exploring the diversity of SPRY/B30.2-mediated interactions. Trends Biochem Sci 2013; 38:38-46. [PMID: 23164942 DOI: 10.1016/j.tibs.2012.10.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 10/02/2012] [Accepted: 10/05/2012] [Indexed: 11/21/2022]
Abstract
The SPla/Ryanodine receptor (SPRY)/B30.2 domain is one of the most common folds in higher eukaryotes. The human genome encodes 103 SPRY/B30.2 domains, several of which are involved in the immune response. Approximately 45% of human SPRY/B30.2-containing proteins are E3 ligases. The role and function of the majority of SPRY/B30.2 domains are still poorly understood, however, in several cases mutations in this domain have been linked to congenital disorders. The recent characterization of SPRY/B30.2-mediated protein interactions has provided evidence for a role of this domain as an adaptor module to assemble macromolecular complexes, analogous to Src homology (SH)2, SH3, and WW domains. However, functional and structural evidence suggests that SPRY/B30.2 is a more versatile fold, allowing a wide range of binding modes.
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48
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Biris N, Yang Y, Taylor AB, Tomashevski A, Guo M, Hart PJ, Diaz-Griffero F, Ivanov DN. Structure of the rhesus monkey TRIM5α PRYSPRY domain, the HIV capsid recognition module. Proc Natl Acad Sci U S A 2012; 109:13278-83. [PMID: 22847415 DOI: 10.1073/pnas.1203536109] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tripartite motif protein TRIM5α blocks retroviral replication after cell entry, and species-specific differences in its activity are determined by sequence variations within the C-terminal B30.2/PRYSPRY domain. Here we report a high-resolution structure of a TRIM5α PRYSPRY domain, the PRYSPRY of the rhesus monkey TRIM5α that potently restricts HIV infection, and identify features involved in its interaction with the HIV capsid. The extensive capsid-binding interface maps on the structurally divergent face of the protein formed by hypervariable loop segments, confirming that TRIM5α evolution is largely determined by its binding specificity. Interactions with the capsid are mediated by flexible variable loops via a mechanism that parallels antigen recognition by IgM antibodies, a similarity that may help explain some of the unusual functional properties of TRIM5α. Distinctive features of this pathogen-recognition interface, such as structural plasticity conferred by the mobile v1 segment and interaction with multiple epitopes, may allow restriction of divergent retroviruses and increase resistance to capsid mutations.
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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D’Cruz AA, Linossi EM, Babon JJ, Norton RS, Nicola NA, Nicholson SE. PS2-002. Redefining the SPRY/B30.2 domain and investigating its binding specificities. Cytokine 2011. [DOI: 10.1016/j.cyto.2011.07.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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