1
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Thrasher CJ, Jia F, Yee DW, Kubiak JM, Wang Y, Lee MS, Onoda M, Hart AJ, Macfarlane RJ. Rationally Designing the Supramolecular Interfaces of Nanoparticle Superlattices with Multivalent Polymers. J Am Chem Soc 2024. [PMID: 38622048 DOI: 10.1021/jacs.4c02617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
In supramolecular materials, multiple weak binding groups can act as a single collective unit when confined to a localized volume, thereby producing strong but dynamic bonds between material building blocks. This principle of multivalency provides a versatile means of controlling material assembly, as both the number and the type of supramolecular moieties become design handles to modulate the strength of intermolecular interactions. However, in materials with building blocks significantly larger than individual supramolecular moieties (e.g., polymer or nanoparticle scaffolds), the degree of multivalency is difficult to predict or control, as sufficiently large scaffolds inherently preclude separated supramolecular moieties from interacting. Because molecular models commonly used to examine supramolecular interactions are intrinsically unable to examine any trends or emergent behaviors that arise due to nanoscale scaffold geometry, our understanding of the thermodynamics of these massively multivalent systems remains limited. Here we address this challenge via the coassembly of polymer-grafted nanoparticles and multivalent polymers, systematically examining how multivalent scaffold size, shape, and spacing affect their collective thermodynamics. Investigating the interplay of polymer structure and supramolecular group stoichiometry reveals complicated but rationally describable trends that demonstrate how the supramolecular scaffold design can modulate the strength of multivalent interactions. This approach to self-assembled supramolecular materials thus allows for the manipulation of polymer-nanoparticle composites with controlled thermal stability, nanoparticle organization, and tailored meso- to microscopic structures. The sophisticated control of multivalent thermodynamics through precise modulation of the nanoscale scaffold geometry represents a significant advance in the ability to rationally design complex hierarchically structured materials via self-assembly.
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Affiliation(s)
- Carl J Thrasher
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Fei Jia
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Daryl W Yee
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Joshua M Kubiak
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yuping Wang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Margaret S Lee
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michika Onoda
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - A John Hart
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert J Macfarlane
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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2
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MoSnf5 Regulates Fungal Virulence, Growth, and Conidiation in Magnaporthe oryzae. J Fungi (Basel) 2022; 9:jof9010018. [PMID: 36675839 PMCID: PMC9861326 DOI: 10.3390/jof9010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Snf5 (sucrose nonfermenting) is a core component of the SWI/SNF complexes and regulates diverse cellular processes in model eukaryotes. In plant pathogenic fungi, its biological function and underlying mechanisms remain unexplored. In this study, we investigated the biological roles of MoSnf5 in plant infection and fungal development in the rice blast pathogen Magnaporthe oryzae. The gene deletion mutants of MoSNF5 exhibited slower vegetative hyphal growth, severe defects in conidiogenesis, and impaired virulence and galactose utilization capacities. Domain dissection assays showed that the Snf5 domain and the N- and C-termini of MoSnf5 were all required for its full functions. Co-immunoprecipitation and yeast two-hybrid assays showed that MoSnf5 physically interacts with four proteins, including a transcription initiation factor MoTaf14. Interestingly, the ∆MoTaf14 mutants showed similar phenotypes as the ∆Mosnf5 mutants on fungal virulence and development. Moreover, assays on GFP-MoAtg8 expression and localization showed that both the ∆Mosnf5 and ∆MoTaf14 mutants were defective in autophagy. Taken together, MoSnf5 regulates fungal virulence, growth, and conidiation, possibly through regulating galactose utilization and autophagy in M. oryzae.
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3
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Luo YY, Wu JJ, Li YM. Regulation of liquid-liquid phase separation with focus on post-translational modifications. Chem Commun (Camb) 2021; 57:13275-13287. [PMID: 34816836 DOI: 10.1039/d1cc05266g] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid-liquid phase separation (LLPS), a type of phase transition that is important in organisms, is a unique means of forming biomolecular condensates. LLPS plays a significant role in transcription, genome organisation, immune response and cell signaling, and its dysregulation may cause neurodegenerative diseases and cancers. Exploring the regulatory mechanism of LLPS contributes to the understanding of the pathogenic mechanism of abnormal phase transition and enables potential therapeutic targets to be proposed. Many factors have been found to regulate LLPS, of which post-translational modification (PTM) is among the most important. PTMs can change the structure, charge, hydrophobicity and other properties of the proteins involved in phase separation and thereby affect the phase transition behaviour. In this review, we discuss LLPS and the regulatory effects of PTMs, RNA and molecular chaperones in a phase separation system. We introduce several common PTMs (including phosphorylation, arginine methylation, arginine citrullination, acetylation, ubiquitination and poly(ADP-ribosyl)ation), highlight recent advances regarding their roles in LLPS and describe the regulatory mechanisms behind these features. This review provides a detailed overview of the field that will help further the understanding of and interventions in LLPS.
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Affiliation(s)
- Yun-Yi Luo
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Jun-Jun Wu
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China. .,Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, P. R. China
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China. .,Beijing Institute for Brain Disorders, Beijing 100069, P. R. China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, P. R. China
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4
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Petell CJ, Randene K, Pappas M, Sandoval D, Strahl BD, Harrison JS, Steimel JP. Mechanically transduced immunosorbent assay to measure protein-protein interactions. eLife 2021; 10:67525. [PMID: 34581668 PMCID: PMC8479797 DOI: 10.7554/elife.67525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus producing a mechanical signal when a binding event occurs. The METRIS assay uses as little as 20 pmols of reagents to measure a wide range of affinities while exhibiting a high resolution and sensitivity. We use METRIS to measure several PPIs that were previously inaccessible using traditional methods, providing new insights into epigenetic recognition.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Kathyrn Randene
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Michael Pappas
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Diego Sandoval
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, United States
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5
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Uev1A amino terminus stimulates poly-ubiquitin chain assembly and is required for NF-κB activation. Cell Signal 2020; 74:109712. [DOI: 10.1016/j.cellsig.2020.109712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 12/20/2022]
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6
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Lu X, Ebelle DL, Matsuo H, Walters KJ. An Extended Conformation for K48 Ubiquitin Chains Revealed by the hRpn2:Rpn13:K48-Diubiquitin Structure. Structure 2020; 28:495-506.e3. [PMID: 32160516 DOI: 10.1016/j.str.2020.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/06/2020] [Accepted: 02/26/2020] [Indexed: 12/24/2022]
Abstract
Rpn13/Adrm1 is recruited to the proteasome by PSMD1/Rpn2, where it serves as a substrate receptor that binds preferentially to K48-linked ubiquitin chains, an established signal for protein proteolysis. Here, we use NMR to solve the structure of hRpn13 Pru:hRpn2 (940-953):K48-diubiquitin. Surprisingly, hRpn2-bound hRpn13 selects a dynamic, extended conformation of K48-diubiquitin that is unique from previously determined structures. NMR experiments on free K48-diubiquitin demonstrate the presence of the reported "closed" conformation observed by crystallography, but also this more extended state, in which the hRpn13-binding surface is exposed. This extended K48-diubiquitin conformation is defined by interactions between L73 from G76-linked (distal) ubiquitin and a Y59-centered surface of K48-linked (proximal) ubiquitin. Furthermore, hRpn13 exchanges between the two ubiquitins within 100 ms, although prefers the proximal ubiquitin due to interactions with the K48 linker region. Altogether, these data lead to a revised model of how ubiquitinated substrates interact with the proteasome.
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Affiliation(s)
- Xiuxiu Lu
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Danielle L Ebelle
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hiroshi Matsuo
- Basic Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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7
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Ali MAM, Strickfaden H, Lee BL, Spyracopoulos L, Hendzel MJ. RYBP Is a K63-Ubiquitin-Chain-Binding Protein that Inhibits Homologous Recombination Repair. Cell Rep 2019; 22:383-395. [PMID: 29320735 DOI: 10.1016/j.celrep.2017.12.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/07/2017] [Accepted: 12/13/2017] [Indexed: 12/14/2022] Open
Abstract
Ring1-YY1-binding protein (RYBP) is a member of the non-canonical polycomb repressive complex 1 (PRC1), and like other PRC1 members, it is best described as a transcriptional regulator. However, several PRC1 members were recently shown to function in DNA repair. Here, we report that RYBP preferentially binds K63-ubiquitin chains via its Npl4 zinc finger (NZF) domain. Since K63-linked ubiquitin chains are assembled at DNA double-strand breaks (DSBs), we examined the contribution of RYBP to DSB repair. Surprisingly, we find that RYBP is K48 polyubiquitylated by RNF8 and rapidly removed from chromatin upon DNA damage by the VCP/p97 segregase. High expression of RYBP competitively inhibits recruitment of BRCA1 repair complex to DSBs, reducing DNA end resection and homologous recombination (HR) repair. Moreover, breast cancer cell lines expressing high endogenous RYBP levels show increased sensitivity to DNA-damaging agents and poly ADP-ribose polymerase (PARP) inhibition. These data suggest that RYBP negatively regulates HR repair by competing for K63-ubiquitin chain binding.
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Affiliation(s)
- Mohammad A M Ali
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 2H7, Canada
| | - Hilmar Strickfaden
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 2H7, Canada
| | - Brian L Lee
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 2H7, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 2H7, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 2H7, Canada.
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8
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Dynamic recognition and linkage specificity in K63 di-ubiquitin and TAB2 NZF domain complex. Sci Rep 2018; 8:16478. [PMID: 30405169 PMCID: PMC6220233 DOI: 10.1038/s41598-018-34605-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/18/2018] [Indexed: 12/16/2022] Open
Abstract
Poly-ubiquitin (poly-Ub) is involved in various cellular processes through the linkage-specific recognition of Ub-binding domains (UBD). In this study, using molecular dynamics (MD) simulation together with an enhanced sampling method, we demonstrated that K63-linked di-Ub recognizes the NZF domain of TAB2, a zinc finger UBD, in an ensemble of highly dynamic structures that form from the weak interactions between UBD and the flexible linker connecting the two Ubs. However, the K63 di-Ub/TAB2 NZF complex showed a much more compact and stable ensemble than the non-native complexes, linear di-Ub/TAB2 NZF and K33 di-Ub/TAB2 NZF, that were modeled from linear di-Ub/HOIL-1L NZF and K33 di-Ub/TRABID NZF1, respectively. We further demonstrated the importance of the length and position of the Ub-Ub linker in the results of MD simulations of K63 di-Ub/TAB2 NZF by changing the Ub linkage from the native K63 to four different non-native linkages, linear, K6, K11, and K48, while maintaining inter-molecular contacts in the native complex. No systems with non-native linkage maintained the native binding configuration. These simulation results provide an atomistic picture of the linkage specific recognition of poly-Ubs leading to the biological functions such as cellular colocalization of various component proteins in the signal transduction pathways.
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9
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Wilson RH, Zamfir S, Sumner I. Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme. J Mol Graph Model 2017; 76:403-411. [DOI: 10.1016/j.jmgm.2017.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 11/28/2022]
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10
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Lee BL, Singh A, Mark Glover JN, Hendzel MJ, Spyracopoulos L. Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics. J Mol Biol 2017; 429:3409-3429. [PMID: 28587922 DOI: 10.1016/j.jmb.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/20/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022]
Abstract
Cells are exposed to thousands of DNA damage events on a daily basis. This damage must be repaired to preserve genetic information and prevent development of disease. The most deleterious damage is a double-strand break (DSB), which is detected and repaired by mechanisms known as non-homologous end-joining (NHEJ) and homologous recombination (HR), which are components of the DNA damage response system. NHEJ is an error-prone first line of defense, whereas HR invokes error-free repair and is the focus of this review. The functions of the protein components of HR-driven DNA repair are regulated by the coordinated action of post-translational modifications including lysine acetylation, phosphorylation, ubiquitination, and SUMOylation. The latter two mechanisms are fundamental for recognition of DSBs and reorganizing chromatin to facilitate repair. We focus on the structures and molecular mechanisms for the protein components underlying synthesis, recognition, and cleavage of K63-linked ubiquitin chains, which are abundant at damage sites and obligatory for DSB repair. The forward flux of the K63-linked ubiquitination cascade is driven by the combined activity of E1 enzyme, the heterodimeric E2 Mms2-Ubc13, and its cognate E3 ligases RNF8 and RNF168, which is balanced through the binding and cleavage of chains by the deubiquitinase BRCC36, and the proteasome, and through the binding of chains by recognition modules on repair proteins such as RAP80. We highlight a number of aspects regarding our current understanding for the role of kinetics and dynamics in determining the function of the enzymes and chain recognition modules that drive K63 ubiquitination.
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Affiliation(s)
- Brian L Lee
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Anamika Singh
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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11
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Anamika, Spyracopoulos L. Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80. J Biol Chem 2015; 291:4417-28. [PMID: 26719330 DOI: 10.1074/jbc.m115.705061] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Indexed: 01/04/2023] Open
Abstract
Recognition and repair of double-stranded DNA breaks (DSB) involves the targeted recruitment of BRCA tumor suppressors to damage foci through binding of both ubiquitin (Ub) and the Ub-like modifier SUMO. RAP80 is a component of the BRCA1 A complex, and plays a key role in the recruitment process through the binding of Lys(63)-linked poly-Ub chains by tandem Ub interacting motifs (UIM). RAP80 also contains a SUMO interacting motif (SIM) just upstream of the tandem UIMs that has been shown to specifically bind the SUMO-2 isoform. The RAP80 tandem UIMs and SIM function collectively for optimal recruitment of BRCA1 to DSBs, although the molecular basis of this process is not well understood. Using NMR spectroscopy, we demonstrate that the RAP80 SIM binds SUMO-2, and that both specificity and affinity are enhanced through phosphorylation of the canonical CK2 site within the SIM. The affinity increase results from an enhancement of electrostatic interactions between the phosphoserines of RAP80 and the SIM recognition module within SUMO-2. The NMR structure of the SUMO-2·phospho-RAP80 complex reveals that the molecular basis for SUMO-2 specificity is due to isoform-specific sequence differences in electrostatic SIM recognition modules.
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Affiliation(s)
- Anamika
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leo Spyracopoulos
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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12
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Hodge CD, Edwards RA, Markin CJ, McDonald D, Pulvino M, Huen MSY, Zhao J, Spyracopoulos L, Hendzel MJ, Glover JNM. Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting. ACS Chem Biol 2015; 10:1718-28. [PMID: 25909880 DOI: 10.1021/acschembio.5b00222] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here, we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage and NF-κB signaling in human cells. NSC697923 and BAY 11-7082 both inhibit Ubc13 by covalent adduct formation through a Michael addition at the Ubc13 active site cysteine. The resulting adducts of both compounds exploit a binding groove unique to Ubc13. We developed a Ubc13 mutant which resists NSC697923 inhibition and, using this mutant, we show that the inhibition of cellular DNA damage and NF-κB signaling by NSC697923 is largely due to specific Ubc13 inhibition. We propose that unique structural features near the Ubc13 active site could provide a basis for the rational development and design of specific Ubc13 inhibitors.
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Affiliation(s)
- Curtis D. Hodge
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Ross A. Edwards
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Craig J. Markin
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Darin McDonald
- Department
of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 1Z2
| | - Mary Pulvino
- Department
of Biomedical Genetics, University of Rochester, Rochester, New York 14642, United States
| | - Michael S. Y. Huen
- Department
of Anatomy and Centre for Cancer Research, The University of Hong Kong, Hong
Kong, China
| | - Jiyong Zhao
- Department
of Biomedical Genetics, University of Rochester, Rochester, New York 14642, United States
| | - Leo Spyracopoulos
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Michael J. Hendzel
- Department
of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 1Z2
| | - J. N. Mark Glover
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
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13
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Similarities and differences between Arabidopsis PCNA1 and PCNA2 in complementing the yeast DNA damage tolerance defect. DNA Repair (Amst) 2015; 28:28-36. [DOI: 10.1016/j.dnarep.2015.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/01/2015] [Accepted: 02/03/2015] [Indexed: 11/23/2022]
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14
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Rout MK, Hodge CD, Markin CJ, Xu X, Glover JNM, Xiao W, Spyracopoulos L. Stochastic Gate Dynamics Regulate the Catalytic Activity of Ubiquitination Enzymes. J Am Chem Soc 2014; 136:17446-58. [DOI: 10.1021/ja505440b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Manoj K. Rout
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Curtis D. Hodge
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Craig J. Markin
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Xin Xu
- College
of Life Sciences, Capital Normal University, Beijing 100048, China
| | - J. N. Mark Glover
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Wei Xiao
- College
of Life Sciences, Capital Normal University, Beijing 100048, China
- Department
of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Leo Spyracopoulos
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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15
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Erpapazoglou Z, Walker O, Haguenauer-Tsapis R. Versatile roles of k63-linked ubiquitin chains in trafficking. Cells 2014; 3:1027-88. [PMID: 25396681 PMCID: PMC4276913 DOI: 10.3390/cells3041027] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/14/2014] [Accepted: 10/21/2014] [Indexed: 12/11/2022] Open
Abstract
Modification by Lys63-linked ubiquitin (UbK63) chains is the second most abundant form of ubiquitylation. In addition to their role in DNA repair or kinase activation, UbK63 chains interfere with multiple steps of intracellular trafficking. UbK63 chains decorate many plasma membrane proteins, providing a signal that is often, but not always, required for their internalization. In yeast, plants, worms and mammals, this same modification appears to be critical for efficient sorting to multivesicular bodies and subsequent lysosomal degradation. UbK63 chains are also one of the modifications involved in various forms of autophagy (mitophagy, xenophagy, or aggrephagy). Here, in the context of trafficking, we report recent structural studies investigating UbK63 chains assembly by various E2/E3 pairs, disassembly by deubiquitylases, and specifically recognition as sorting signals by receptors carrying Ub-binding domains, often acting in tandem. In addition, we address emerging and unanticipated roles of UbK63 chains in various recycling pathways that function by activating nucleators required for actin polymerization, as well as in the transient recruitment of signaling molecules at the plasma or ER membrane. In this review, we describe recent advances that converge to elucidate the mechanisms underlying the wealth of trafficking functions of UbK63 chains.
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Affiliation(s)
- Zoi Erpapazoglou
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
| | - Olivier Walker
- Institut des Sciences Analytiques, UMR5280, Université de Lyon/Université Lyon 1, 69100 Villeurbanne, France.
| | - Rosine Haguenauer-Tsapis
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
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16
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Anamika, Markin CJ, Rout MK, Spyracopoulos L. Molecular basis for impaired DNA damage response function associated with the RAP80 ΔE81 defect. J Biol Chem 2014; 289:12852-62. [PMID: 24627472 DOI: 10.1074/jbc.m113.538280] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signal transduction within the DNA damage response is driven by the flux of protein-protein interaction cascades that ultimately recruit repair complexes to sites of damage. The protein RAP80 plays a central role in the damage response by targeting BRCA1/BRCA2 tumor suppressors to DNA damage foci through multivalent binding of Lys-63-linked polyubiquitin chains. Mutations within the high penetrance BRCA1/BRCA2 genes account for ∼20% of familial breast cancers. The genetic basis for the remaining cancers remains unknown, but may involve defects in binding partners for BRCA1 and BRCA2 that lead to impaired targeting to foci and a concomitant role in the pathogenesis of cancer. Recently, an in-frame deletion mutation (ΔE81) in a conserved region from the first ubiquitin interaction motif of RAP80 has been linked to an increase in chromosomal abnormalities. Using NMR spectroscopy, we demonstrate that the N-cap motif within the α-helix of the first ubiquitin interaction motif from ΔE81 undergoes a structural frameshift that leads to abolishment of multivalent binding of polyubiquitin chains. Loss of this single glutamate residue disrupts favorable electrostatic interactions between RAP80 and ubiquitin, establishing a plausible molecular basis for a potential predisposition to cancer unrelated to mutations within BRCA1/BRCA2 genes.
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Affiliation(s)
- Anamika
- From the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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17
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Bai JJ, Safadi SS, Mercier P, Barber KR, Shaw GS. Ataxin-3 is a multivalent ligand for the parkin Ubl domain. Biochemistry 2013; 52:7369-76. [PMID: 24063750 PMCID: PMC3807529 DOI: 10.1021/bi400780v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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The
ubiquitin signaling pathway consists of hundreds of enzymes
that are tightly regulated for the maintenance of cell homeostasis.
Parkin is an E3 ubiquitin ligase responsible for conjugating ubiquitin
onto a substrate protein, which itself can be ubiquitinated. Ataxin-3
performs the opposing function as a deubiquitinating enzyme that can
remove ubiquitin from parkin. In this work, we have identified the
mechanism of interaction between the ubiquitin-like (Ubl) domain from
parkin and three C-terminal ubiquitin-interacting motifs (UIMs) in
ataxin-3. 1H–15N heteronuclear single-quantum
coherence titration experiments revealed that there are weak direct
interactions between all three individual UIM regions of ataxin-3
and the Ubl domain. Each UIM utilizes the exposed β-grasp surface
of the Ubl domain centered around the I44 patch that did not vary
in the residues involved or the surface size as a function of the
number of ataxin-3 UIMs involved. Further, the apparent dissociation
constant for ataxin-3 decreased as a function of the number of UIM
regions used in experiments. A global multisite fit of the nuclear
magnetic resonance titration data, based on three identical binding
ligands, resulted in a KD of 669 ±
62 μM for each site. Our observations support a multivalent
ligand binding mechanism employed by the parkin Ubl domain to recruit
multiple UIM regions in ataxin-3 and provide insight into how these
two proteins function together in ubiquitination–deubiquitination
pathways.
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Affiliation(s)
- Jane J Bai
- Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario , London, Ontario, Canada N6A 5C1
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18
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Structural and functional implication of RAP80 ΔGlu81 mutation. PLoS One 2013; 8:e72707. [PMID: 24039796 PMCID: PMC3767628 DOI: 10.1371/journal.pone.0072707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/15/2013] [Indexed: 11/22/2022] Open
Abstract
Receptor Associated Protein 80 (RAP80) is a member of RAP80-BRCA1-CCDC98 complex family and helps in its recruitment to the DNA damage site for effective homologous recombination repair. It encompasses two tandem UIMs (UIM1 and UIM2) motif at its N-terminus, which interact with K-63 linked polyubiquitin chain(s) on H2AX and thereby assemble the RAP80-BRCA1 complex at the damage site. Nevertheless, how RAP80 helps in the structural integrity of BRCA1 complex is still elusive. Considering the role of RAP80 in the recruitment of BRCA1 complex at the DNA damage site, we attempted to explore the molecular mechanism associated with RAP80 and mutation that causes chromosomal aberrations due to its loss of function. There is a significant loss in structural characteristics of RAP80 ΔE81, which impairs its binding affinity with the polyubiquitin chain. This leads to the defective recruitment of RAP80 and BRCA1 complex at the DNA damage site. The results presented here are very useful in understanding the cause of various repair defects (chromosomal aberration) that arise due to this mutation. Comparative study of wild type and ΔE81 could be helpful in designing the small molecules that can potentially compensate the deleterious effect(s) of ΔE81 and hence useful for therapeutic application.
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19
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Lian LY. NMR studies of weak protein-protein interactions. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:59-72. [PMID: 23611315 DOI: 10.1016/j.pnmrs.2012.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Accepted: 11/22/2012] [Indexed: 06/02/2023]
Affiliation(s)
- Lu-Yun Lian
- NMR Centre for Structural Biology, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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20
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Munoz EM, Correa J, Riguera R, Fernandez-Megia E. Real-Time Evaluation of Binding Mechanisms in Multivalent Interactions: A Surface Plasmon Resonance Kinetic Approach. J Am Chem Soc 2013; 135:5966-9. [DOI: 10.1021/ja400951g] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Eva Maria Munoz
- Department of Organic
Chemistry and Center for Research
in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Jenaro de la
Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan Correa
- Department of Organic
Chemistry and Center for Research
in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Jenaro de la
Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Ricardo Riguera
- Department of Organic
Chemistry and Center for Research
in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Jenaro de la
Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Eduardo Fernandez-Megia
- Department of Organic
Chemistry and Center for Research
in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Jenaro de la
Fuente s/n, 15782 Santiago de Compostela, Spain
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21
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Markin CJ, Spyracopoulos L. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations. JOURNAL OF BIOMOLECULAR NMR 2012; 54:355-376. [PMID: 23086713 DOI: 10.1007/s10858-012-9678-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/10/2012] [Indexed: 06/01/2023]
Abstract
NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements from NMR-monitored chemical shift titrations, for which the dependence of K ( D ) on the chemical shift difference (Δω) between free and bound states is extrapolated to Δω = 0. The demonstrated accuracy and precision for k ( off ) will be valuable for the interpretation of biological kinetics in weakly interacting protein-protein networks, where a small change in the magnitude of the underlying kinetics of a given pathway may lead to large changes in the associated downstream signaling cascade.
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Affiliation(s)
- Craig J Markin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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22
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Markin CJ, Spyracopoulos L. Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations. JOURNAL OF BIOMOLECULAR NMR 2012; 53:125-138. [PMID: 22534787 DOI: 10.1007/s10858-012-9630-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 04/11/2012] [Indexed: 05/31/2023]
Abstract
NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from ~2 μM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K ( D )) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K ( D ), and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K ( D ) and the maximum chemical shift change (Δδ(max)). During a typical NMR titration, the initial protein concentration, [P (0)], is held nearly constant. For this condition, to determine the most accurate parameters for K ( D ) and Δδ(max) from nonlinear least squares analyses requires initial protein concentrations that are ~0.5 × K ( D ), and a maximum concentration for the ligand, or titrant, of ~10 × [P (0)]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K ( D ) and Δδ(max) values when [P (0)] > K ( D ). Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K ( D ) and Δδ(max)) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.
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Affiliation(s)
- Craig J Markin
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
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23
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Mok MT, Henderson BR. The In Vivo Dynamic Organization of BRCA1-A Complex Proteins at DNA Damage-Induced Nuclear Foci. Traffic 2012; 13:800-14. [DOI: 10.1111/j.1600-0854.2012.01355.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 03/13/2012] [Accepted: 03/15/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Myth T.S. Mok
- Westmead Institute for Cancer Research; The University of Sydney, Westmead Millennium Institute at Westmead Hospital; Westmead; NSW; 2145; Australia
| | - Beric R. Henderson
- Westmead Institute for Cancer Research; The University of Sydney, Westmead Millennium Institute at Westmead Hospital; Westmead; NSW; 2145; Australia
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24
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Lange A, Castañeda C, Hoeller D, Lancelin JM, Fushman D, Walker O. Evidence for cooperative and domain-specific binding of the signal transducing adaptor molecule 2 (STAM2) to Lys63-linked diubiquitin. J Biol Chem 2012; 287:18687-99. [PMID: 22493438 DOI: 10.1074/jbc.m111.324954] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As the upstream component of the ESCRT (endosomal sorting complexes required for transport) machinery, the ESCRT-0 complex is responsible for directing ubiquitinated membrane proteins to the multivesicular body pathway. ESCRT-0 is formed by two subunits known as Hrs (hepatocyte growth factor-regulated substrate) and STAM (signal transducing adaptor molecule), both of which harbor multiple ubiquitin-binding domains (UBDs). In particular, STAM2 possesses two UBDs, the VHS (Vps27/Hrs/Stam) and UIM (ubiquitin interacting motif) domains, connected by a 20-amino acid flexible linker. In the present study, we report the interactions of the UIM domain and VHS-UIM construct of STAM2 with monoubiquitin (Ub), Lys(48)- and Lys(63)-linked diubiquitins. Our results demonstrate that the UIM domain alone binds monoubiquitin, Lys(48)- and Lys(63)-linked diubiquitins with the same affinity and in the same binding mode. Interestingly, binding of VHS-UIM to Lys(63)-linked diubiquitin is not only avid, but also cooperative. We also show that the distal domain of Lys(63)-linked diubiquitin stabilizes the helical structure of the UIM domain and that the corresponding complex adopts a specific structural organization responsible for its greater affinity. In contrast, binding of VHS-UIM to Lys(48)-linked diubiquitin and monoubiquitin is not cooperative and does not show any avidity. These results may explain the better sorting efficiency of some cargoes polyubiquitinated with Lys(63)-linked chains over monoubiquitinated cargoes or those tagged with Lys(48)-linked chains.
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Affiliation(s)
- Anja Lange
- Université de Lyon, CNRS, UMR 5280 Institut des Sciences Analytiques, 69622 Villeurbanne, France
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25
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Sekiyama N, Jee J, Isogai S, Akagi KI, Huang TH, Ariyoshi M, Tochio H, Shirakawa M. NMR analysis of Lys63-linked polyubiquitin recognition by the tandem ubiquitin-interacting motifs of Rap80. JOURNAL OF BIOMOLECULAR NMR 2012; 52:339-350. [PMID: 22350954 DOI: 10.1007/s10858-012-9614-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 01/31/2012] [Indexed: 05/31/2023]
Abstract
Ubiquitin is a post-translational modifier that is involved in cellular functions through its covalent attachment to target proteins. Ubiquitin can also be conjugated to itself at seven lysine residues and at its amino terminus to form eight linkage-specific polyubiquitin chains for individual cellular processes. The Lys63-linked polyubiquitin chain is recognized by tandem ubiquitin-interacting motifs (tUIMs) of Rap80 for the regulation of DNA repair. To understand the recognition mechanism between the Lys63-linked diubiquitin (K63-Ub(2)) and the tUIMs in solution, we determined the solution structure of the K63-Ub(2):tUIMs complex by using NOE restraints and RDC data derived from NMR spectroscopy. The structure showed that the tUIMs adopts a nearly straight and single continuous α-helix, and the two ubiquitin units of the K63-Ub(2) separately bind to each UIM motif. The interfaces are formed between Ile44-centered patches of the two ubiquitin units and the hydrophobic residues of the tUIMs. We also showed that the linker region between the two UIM motifs possesses a random-coil conformation in the free state, but undergoes the coil-to-helix transition upon complex formation, which simultaneously fixes the relative position of ubiquitin subunits. These data suggest that the relative position of ubiquitin subunits in the K63-Ub(2):tUIMs complex is essential for linkage-specific binding of Rap80 tUIMs.
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Affiliation(s)
- Naotaka Sekiyama
- Graduate School of Engineering, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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26
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Choi H, Han S, Shin D, Lee S. Polyubiquitin recognition by AtSAP5, an A20-type zinc finger containing protein from Arabidopsis thaliana. Biochem Biophys Res Commun 2012; 419:436-40. [PMID: 22366090 DOI: 10.1016/j.bbrc.2012.02.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Accepted: 02/07/2012] [Indexed: 10/14/2022]
Abstract
Stress associated proteins (SAPs) in plants contain A20-type zinc finger (A20_ZF) domains and are involved with abiotic stress response. A20-type zinc finger domains in animals reportedly recognize ubiquitin as a regulatory signal in cell. However, it remains unclear whether A20_ZF domains in plants perform similar roles. AtSAP5, a SAP from Arabidopsis thaliana, exhibits a unique sequence feature among 10 AtSAPs harboring A20_ZF domains. The highly conserved diaromatic patch is replaced by the dialipathic patch. Here we investigated whether AtSAP5 recognizes ubiquitin and the roles of the dialipathic patch in ubiquitin binding in vitro. GST pulldown assay reveals that AtSAP5 binds polyubiquitin rather than monoubiquitin. AtSAP5 shows preferences for linear and K63-linked polyubiquitin chains to K48-linked one. The A20_ZF domain of AtSAP5 is sufficient for linkage-specific polyubiquitin recognition. The dialipathic patch in AtSAP5 plays an important role in K48-linked polyubiquitin recognition. Taken together, our results suggest that AtSAP5 participates in polyubiquitin recognition in plants and that the dialipathic patch in AtSAP5 is critical in binding K48-linked polyubiquitn chains.
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Affiliation(s)
- Hoon Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Republic of Korea
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27
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Fushman D, Wilkinson KD. Structure and recognition of polyubiquitin chains of different lengths and linkage. F1000 BIOLOGY REPORTS 2011; 3:26. [PMID: 22162729 PMCID: PMC3229271 DOI: 10.3410/b3-26] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The polyubiquitin signal is post-translationally attached to a large number of proteins, often directing formation of macromolecular complexes resulting in the translocation, assembly or degradation of the attached protein. Recent structural and functional studies reveal general mechanisms by which different architectures and length of the signal are distinguished.
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Affiliation(s)
- David Fushman
- Department of Chemistry and Biochemistry, University of MarylandCollege Park, MD 20742USA
| | - Keith D. Wilkinson
- Department of Biochemistry, Emory University School of MedicineAtlanta, GA 30322USA
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28
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Trempe JF. Reading the ubiquitin postal code. Curr Opin Struct Biol 2011; 21:792-801. [PMID: 22036065 DOI: 10.1016/j.sbi.2011.09.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/16/2011] [Accepted: 09/29/2011] [Indexed: 10/15/2022]
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