1
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Velez-Brochero M, Behera P, Afreen KS, Odle A, Rajsbaum R. Ubiquitination in viral entry and replication: Mechanisms and implications. Adv Virus Res 2024; 119:1-38. [PMID: 38897707 DOI: 10.1016/bs.aivir.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The ubiquitination process is a reversible posttranslational modification involved in many essential cellular functions, such as innate immunity, cell signaling, trafficking, protein stability, and protein degradation. Viruses can use the ubiquitin system to efficiently enter host cells, replicate and evade host immunity, ultimately enhancing viral pathogenesis. Emerging evidence indicates that enveloped viruses can carry free (unanchored) ubiquitin or covalently ubiquitinated viral structural proteins that can increase the efficiency of viral entry into host cells. Furthermore, viruses continuously evolve and adapt to take advantage of the host ubiquitin machinery, highlighting its importance during virus infection. This review discusses the battle between viruses and hosts, focusing on how viruses hijack the ubiquitination process at different steps of the replication cycle, with a specific emphasis on viral entry. We discuss how ubiquitination of viral proteins may affect tropism and explore emerging therapeutics strategies targeting the ubiquitin system for antiviral drug discovery.
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Affiliation(s)
- Maria Velez-Brochero
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Padmanava Behera
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Kazi Sabrina Afreen
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Abby Odle
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States
| | - Ricardo Rajsbaum
- Center for Virus-Host-Innate Immunity and Department of Medicine, Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, NJ, United States.
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2
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Cheng P, Hou Y, Bian M, Fang X, Liu Y, Rao Y, Cao S, Liu Y, Zhang S, Chen Y, Dong X, Liu Z. Parkin-mediated ubiquitination inhibits BAK apoptotic activity by blocking its canonical hydrophobic groove. Commun Biol 2023; 6:1260. [PMID: 38087033 PMCID: PMC10716173 DOI: 10.1038/s42003-023-05650-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BAK permeabilizes the mitochondrial outer membrane, causing apoptosis. This apoptotic activity of BAK is stimulated by binding prodeath activators within its canonical hydrophobic groove. Parkin, an E3 ubiquitin (Ub) ligase, can ubiquitinate BAK, which inhibits BAK apoptotic activity. However, the molecular mechanism underlying the inhibition of ubiquitination remains structurally uncharacterized. Here, we utilize truncated and soluble BAK to construct a mimetic of K113-ubiquitinated BAK (disulfide-linked UbG76C ~ BAKK113C) and further present its NMR-derived structure model. The classical L8-I44-H68-V70 hydrophobic patch of the conjugated Ub subunit binds within the canonical hydrophobic groove of BAK. This Ub occludes the binding of prodeath BID activators in the groove and impairs BID-triggered BAK activation and membrane permeabilization. Reduced interaction between Ub and BAK subunits allows BID to activate K113-ubiquitinated BAK. These mechanistic insights suggest a nonsignaling function of Ub in that it directly antagonizes stimuli targeting Ub-modified proteins rather than by recruiting downstream partners for cellular messaging.
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Affiliation(s)
- Peng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuzhu Hou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingxing Bian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueru Fang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanfang Rao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuo Cao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanjun Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuai Zhang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanke Chen
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xu Dong
- Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074, China.
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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3
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Klonisch T, Logue SE, Hombach-Klonisch S, Vriend J. DUBing Primary Tumors of the Central Nervous System: Regulatory Roles of Deubiquitinases. Biomolecules 2023; 13:1503. [PMID: 37892185 PMCID: PMC10605193 DOI: 10.3390/biom13101503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The ubiquitin proteasome system (UPS) utilizes an orchestrated enzymatic cascade of E1, E2, and E3 ligases to add single or multiple ubiquitin-like molecules as post-translational modification (PTM) to proteins. Ubiquitination can alter protein functions and/or mark ubiquitinated proteins for proteasomal degradation but deubiquitinases (DUBs) can reverse protein ubiquitination. While the importance of DUBs as regulatory factors in the UPS is undisputed, many questions remain on DUB selectivity for protein targeting, their mechanism of action, and the impact of DUBs on the regulation of diverse biological processes. Furthermore, little is known about the expression and role of DUBs in tumors of the human central nervous system (CNS). In this comprehensive review, we have used publicly available transcriptional datasets to determine the gene expression profiles of 99 deubiquitinases (DUBs) from five major DUB families in seven primary pediatric and adult CNS tumor entities. Our analysis identified selected DUBs as potential new functional players and biomarkers with prognostic value in specific subtypes of primary CNS tumors. Collectively, our analysis highlights an emerging role for DUBs in regulating CNS tumor cell biology and offers a rationale for future therapeutic targeting of DUBs in CNS tumors.
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Affiliation(s)
- Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Susan E. Logue
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Jerry Vriend
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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4
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Schneider T, Sawade K, Berner F, Peter C, Kovermann M. Specifying conformational heterogeneity of multi-domain proteins at atomic resolution. Structure 2023; 31:1259-1274.e10. [PMID: 37557171 DOI: 10.1016/j.str.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing a large interdomain mobility. However, molecular recognition and signal transduction are associated with particular conformational substates that are populated in solution. Here, we apply high-resolution NMR spectroscopy in combination with dual-scale MD simulations to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far. We propose a general application of the approach developed here to demystify multi-domain proteins occurring in nature.
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Affiliation(s)
- Tobias Schneider
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kevin Sawade
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Graduate School Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Frederic Berner
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
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5
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Hou XN, Tang C. The pros and cons of ubiquitination on the formation of protein condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1084-1098. [PMID: 37294105 PMCID: PMC10423694 DOI: 10.3724/abbs.2023096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/19/2023] [Indexed: 06/10/2023] Open
Abstract
Ubiquitination, a post-translational modification that attaches one or more ubiquitin (Ub) molecules to another protein, plays a crucial role in the phase-separation processes. Ubiquitination can modulate the formation of membrane-less organelles in two ways. First, a scaffold protein drives phase separation, and Ub is recruited to the condensates. Second, Ub actively phase-separates through the interactions with other proteins. Thus, the role of ubiquitination and the resulting polyUb chains ranges from bystanders to active participants in phase separation. Moreover, long polyUb chains may be the primary driving force for phase separation. We further discuss that the different roles can be determined by the lengths and linkages of polyUb chains which provide preorganized and multivalent binding platforms for other client proteins. Together, ubiquitination adds a new layer of regulation for the flow of material and information upon cellular compartmentalization of proteins.
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Affiliation(s)
- Xue-Ni Hou
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Chun Tang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Center for Quantitate BiologyPKU-Tsinghua Center for Life ScienceAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
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6
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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7
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Czaplewski C, Gong Z, Lubecka EA, Xue K, Tang C, Liwo A. Recent Developments in Data-Assisted Modeling of Flexible Proteins. Front Mol Biosci 2022; 8:765562. [PMID: 35004845 PMCID: PMC8740120 DOI: 10.3389/fmolb.2021.765562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.
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Affiliation(s)
| | - Zhou Gong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland
| | - Kai Xue
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chun Tang
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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8
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022; 283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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9
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Hou XN, Sekiyama N, Ohtani Y, Yang F, Miyanoiri Y, Akagi KI, Su XC, Tochio H. Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins. Chemphyschem 2021; 22:1505-1517. [PMID: 33928740 DOI: 10.1002/cphc.202100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Indexed: 11/06/2022]
Abstract
Linear polyubiquitin chains regulate diverse signaling proteins, in which the chains adopt various conformations to recognize different target proteins. Thus, the structural plasticity of the chains plays an important role in controlling the binding events. Herein, paramagnetic NMR spectroscopy is employed to explore the conformational space sampled by linear diubiquitin, a minimal unit of linear polyubiquitin, in its free state. Rigorous analysis of the data suggests that, regarding the relative positions of the ubiquitin units, particular regions of conformational space are preferentially sampled by the molecule. By combining these results with further data collected for charge-reversal derivatives of linear diubiquitin, structural insights into the factors underlying the binding events of linear diubiquitin are obtained.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yasuko Ohtani
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ken-Ichi Akagi
- NIBIOHN, Section of Laboratory Equipment, Osaka, 567-0085, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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10
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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11
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Alsayyah C, Ozturk O, Cavellini L, Belgareh-Touzé N, Cohen MM. The regulation of mitochondrial homeostasis by the ubiquitin proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148302. [PMID: 32861697 DOI: 10.1016/j.bbabio.2020.148302] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/05/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
From mitochondrial quality control pathways to the regulation of specific functions, the Ubiquitin Proteasome System (UPS) could be compared to a Swiss knife without which mitochondria could not maintain its integrity in the cell. Here, we review the mechanisms that the UPS employs to regulate mitochondrial function and efficiency. For this purpose, we depict how Ubiquitin and the Proteasome participate in diverse quality control pathways that safeguard entry into the mitochondrial compartment. A focus is then achieved on the UPS-mediated control of the yeast mitofusin Fzo1 which provides insights into the complex regulation of this particular protein in mitochondrial fusion. We ultimately dissect the mechanisms by which the UPS controls the degradation of mitochondria by autophagy in both mammalian and yeast systems. This organization should offer a useful overview of this abundant but fascinating literature on the crosstalks between mitochondria and the UPS.
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Affiliation(s)
- Cynthia Alsayyah
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, F-75005 Paris, France
| | - Oznur Ozturk
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, F-75005 Paris, France
| | - Laetitia Cavellini
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, F-75005 Paris, France
| | - Naïma Belgareh-Touzé
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, F-75005 Paris, France
| | - Mickael M Cohen
- Sorbonne Université, CNRS, UMR8226, Institut de Biologie Physico-Chimique, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, F-75005 Paris, France.
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12
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Huang Q, Duan B, Dong X, Fan S, Xia B. GapR binds DNA through dynamic opening of its tetrameric interface. Nucleic Acids Res 2020; 48:9372-9386. [PMID: 32756896 PMCID: PMC7498317 DOI: 10.1093/nar/gkaa644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 07/13/2020] [Accepted: 07/24/2020] [Indexed: 01/27/2023] Open
Abstract
GapR is a nucleoid-associated protein that is an essential regulator of chromosome replication in the cell cycle model Caulobacter crescentus. Here, we demonstrate that free GapR is a homotetramer, but not a dimer as previously reported (Guo et al., Cell 175: 583–597, 2018). We have determined the crystal structure of GapR in complex with a 10-bp A-tract DNA, which has an open tetrameric conformation, different from the closed clamp conformation in the previously reported crystal structure of GapR/DNA complex. The free GapR adopts multiple conformations in dynamic exchange equilibrium, with the major conformation resembling the closed tetrameric conformation, while the open tetrameric conformation is a representative of minor conformers. As it is impossible for the circular genomic DNA to get into the central DNA binding tunnel of the major conformation, we propose that GapR initially binds DNA through the open conformation, and then undergoes structural rearrangement to form the closed conformation which fully encircles the DNA. GapR prefers to bind DNA with 10-bp consecutive A/T base pairs nonselectively (Kd ∼12 nM), while it can also bind GC-rich DNA sequence with a reasonable affinity of about 120 nM. Besides, our results suggest that GapR binding results in widening the minor groove of AT-rich DNA, instead of overtwisting DNA.
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Affiliation(s)
- Qian Huang
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bo Duan
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xianzhi Dong
- Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Shilong Fan
- The Technology Center for Protein Sciences, Tsinghua University, Beijing 100084, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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13
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Jussupow A, Messias AC, Stehle R, Geerlof A, Solbak SMØ, Paissoni C, Bach A, Sattler M, Camilloni C. The dynamics of linear polyubiquitin. SCIENCE ADVANCES 2020; 6:6/42/eabc3786. [PMID: 33055165 PMCID: PMC7556843 DOI: 10.1126/sciadv.abc3786] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/25/2020] [Indexed: 05/17/2023]
Abstract
Polyubiquitin chains are flexible multidomain proteins, whose conformational dynamics enable them to regulate multiple biological pathways. Their dynamic is determined by the linkage between ubiquitins and by the number of ubiquitin units. Characterizing polyubiquitin behavior as a function of their length is hampered because of increasing system size and conformational variability. Here, we introduce a new approach to efficiently integrating small-angle x-ray scattering with simulations allowing us to accurately characterize the dynamics of linear di-, tri-, and tetraubiquitin in the free state as well as of diubiquitin in complex with NEMO, a central regulator in the NF-κB pathway. Our results show that the behavior of the diubiquitin subunits is independent of the presence of additional ubiquitin modules and that the dynamics of polyubiquitins with different lengths follow a simple model. Together with experimental data from multiple biophysical techniques, we then rationalize the 2:1 NEMO:polyubiquitin binding.
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Affiliation(s)
- Alexander Jussupow
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching 85747, Germany
| | - Ana C Messias
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Sara M Ø Solbak
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Cristina Paissoni
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milano, Italy
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany.
- Center for Integrated Protein Science Munich at Department of Chemistry, Technical University of Munich, Garching 85747, Germany
| | - Carlo Camilloni
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching 85747, Germany.
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milano, Italy
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14
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NMR Characterization of Conformational Interconversions of Lys48-Linked Ubiquitin Chains. Int J Mol Sci 2020; 21:ijms21155351. [PMID: 32731397 PMCID: PMC7432494 DOI: 10.3390/ijms21155351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/22/2020] [Accepted: 07/25/2020] [Indexed: 11/17/2022] Open
Abstract
Ubiquitin (Ub) molecules can be enzymatically connected through a specific isopeptide linkage, thereby mediating various cellular processes by binding to Ub-interacting proteins through their hydrophobic surfaces. The Lys48-linked Ub chains, which serve as tags for proteasomal degradation, undergo conformational interconversions between open and closed states, in which the hydrophobic surfaces are exposed and shielded, respectively. Here, we provide a quantitative view of such dynamic processes of Lys48-linked triUb and tetraUb in solution. The native and cyclic forms of Ub chains are prepared with isotope labeling by in vitro enzymatic reactions. Our comparative NMR analyses using monomeric Ub and cyclic diUb as reference molecules enabled the quantification of populations of the open and closed states for each Ub unit of the native Ub chains. The data indicate that the most distal Ub unit in the Ub chains is the most apt to expose its hydrophobic surface, suggesting its preferential involvement in interactions with the Ub-recognizing proteins. We also demonstrate that a mutational modification of the distal end of the Ub chain can remotely affect the solvent exposure of the hydrophobic surfaces of the other Ub units, suggesting that Ub chains could be unique design frameworks for the creation of allosterically controllable multidomain proteins.
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15
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Wakamoto T, Kitazawa S, Kameda T, Kitahara R. Dynamic aspects of pressure and temperature-stabilized intermediates of outer surface protein A. Proteins 2020; 88:1423-1433. [PMID: 32519353 DOI: 10.1002/prot.25962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/05/2020] [Accepted: 06/06/2020] [Indexed: 01/18/2023]
Abstract
Structural characterization of alternatively folded and partially disordered protein conformations remains challenging. Outer surface protein A (OspA) is a pivotal protein in Borrelia infection, which is the etiological agent of Lyme disease. OspA exists in equilibrium with intermediate conformations, in which the central and the C-terminal regions of the protein have lower stabilities than the N-terminal. Here, we characterize pressure- and temperature-stabilized intermediates of OspA by nuclear magnetic resonance spectroscopy combined with paramagnetic relaxation enhancement (PRE). We found that although the C-terminal region of the intermediate was partially disordered, it retains weak specific contact with the N-terminal region, owing to a twist of the central β-sheet and increased flexibility in the polypeptide chain. The disordered C-terminal region of the pressure-stabilized intermediate was more compact than that of the temperature-stabilized form. Further, molecular dynamics simulation demonstrated that temperature-induced disordering of the β-sheet was initiated at the C-terminal region and continued through to the central region. An ensemble of simulation snapshots qualitatively described the PRE data from the intermediate and indicated that the intermediate structures of OspA may expose tick receptor-binding sites more readily than does the basic folded conformation.
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Affiliation(s)
- Takuro Wakamoto
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Ryo Kitahara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Japan
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16
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Integrating Non-NMR Distance Restraints to Augment NMR Depiction of Protein Structure and Dynamics. J Mol Biol 2020; 432:2913-2929. [DOI: 10.1016/j.jmb.2020.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 11/24/2022]
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17
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Paissoni C, Jussupow A, Camilloni C. Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics. J Chem Theory Comput 2020; 16:2825-2834. [PMID: 32119546 PMCID: PMC7997378 DOI: 10.1021/acs.jctc.9b01181] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Small-angle
X-ray scattering (SAXS) experiments provide low-resolution
but valuable information about the dynamics of biomolecular systems,
which could be ideally integrated into molecular dynamics (MD) simulations
to accurately determine conformational ensembles of flexible proteins.
The applicability of this strategy is hampered by the high computational
cost required to calculate scattering intensities from three-dimensional
structures. We previously presented a hybrid resolution method that
makes atomistic SAXS-restrained MD simulation feasible by adopting
a coarse-grained approach to efficiently back-calculate scattering
intensities; here, we extend this technique, applying it in the framework
of metainference with the aim to investigate the dynamical behavior
of flexible biomolecules. The efficacy of the method is assessed on
the K63-diubiquitin, showing that the inclusion of SAXS restraints
is effective in generating a reliable conformational ensemble, improving
the agreement with independent experimental data.
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Affiliation(s)
- Cristina Paissoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
| | - Alexander Jussupow
- Department of Chemistry and Institute of Advanced Study, Technical University of Munich, Garching 85747, Germany
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
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18
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Kliza K, Husnjak K. Resolving the Complexity of Ubiquitin Networks. Front Mol Biosci 2020; 7:21. [PMID: 32175328 PMCID: PMC7056813 DOI: 10.3389/fmolb.2020.00021] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/04/2020] [Indexed: 12/22/2022] Open
Abstract
Ubiquitination regulates nearly all cellular processes by coordinated activity of ubiquitin writers (E1, E2, and E3 enzymes), erasers (deubiquitinating enzymes) and readers (proteins that recognize ubiquitinated proteins by their ubiquitin-binding domains). By differentially modifying cellular proteome and by recognizing these ubiquitin modifications, ubiquitination machinery tightly regulates execution of specific cellular events in space and time. Dynamic and complex ubiquitin architecture, ranging from monoubiquitination, multiple monoubiquitination, eight different modes of homotypic and numerous types of heterogeneous polyubiquitin linkages, enables highly dynamic and complex regulation of cellular processes. We discuss available tools and approaches to study ubiquitin networks, including methods for the identification and quantification of ubiquitin-modified substrates, as well as approaches to quantify the length, abundance, linkage type and architecture of different ubiquitin chains. Furthermore, we also summarize the available approaches for the discovery of novel ubiquitin readers and ubiquitin-binding domains, as well as approaches to monitor and visualize activity of ubiquitin conjugation and deconjugation machineries. We also discuss benefits, drawbacks and limitations of available techniques, as well as what is still needed for detailed spatiotemporal dissection of cellular ubiquitination networks.
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Affiliation(s)
- Katarzyna Kliza
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Medical Faculty, Goethe University, Frankfurt, Germany
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19
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Shahul Hameed D, van Tilburg GBA, Merkx R, Flierman D, Wienk H, El Oualid F, Hofmann K, Boelens R, Ovaa H. Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1. Front Chem 2020; 7:921. [PMID: 32039147 PMCID: PMC6987245 DOI: 10.3389/fchem.2019.00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Ubiquitination is a process in which a protein is modified by the covalent attachment of the C-terminal carboxylic acid of ubiquitin (Ub) to the ε-amine of lysine or N-terminal methionine residue of a substrate protein or another Ub molecule. Each of the seven internal lysine residues and the N-terminal methionine residue of Ub can be linked to the C-terminus of another Ub moiety to form 8 distinct Ub linkages and the resulting differences in linkage types elicit different Ub signaling pathways. Cellular responses are triggered when proteins containing ubiquitin-binding domains (UBDs) recognize and bind to specific polyUb linkage types. To get more insight into the differences between polyUb chains, all of the seven lysine-linked di-ubiquitin molecules (diUbs) were prepared and used as a model to study their structural conformations in solution using NMR spectroscopy. We report the synthesis of diUb molecules, fully 15N-labeled on the distal (N-terminal) Ub moiety and revealed their structural orientation with respect to the proximal Ub. As expected, the diUb molecules exist in different conformations in solution, with multiple conformations known to exist for K6-, K48-, and K63-linked diUb molecules. These multiple conformations allow structural flexibility in binding with UBDs thereby inducing unique responses. One of the well-known but poorly understood UBD-Ub interaction is the recognition of K6 polyubiquitin by the ubiquitin-associated (UBA) domain of UBXN1 in the BRCA-mediated DNA repair pathway. Using our synthetic 15N-labeled diUbs, we establish here how a C-terminally extended UBA domain of UBXN1 confers specificity to K6 diUb while the non-extended version of the domain does not show any linkage preference. We show that the two distinct conformations of K6 diUb that exist in solution converge into a single conformation upon binding to this extended form of the UBA domain of the UBXN1 protein. It is likely that more of such extended UBA domains exist in nature and can contribute to linkage-specificity in Ub signaling. The isotopically labeled diUb compounds described here and the use of NMR to study their interactions with relevant partner molecules will help accelerate our understanding of Ub signaling pathways.
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Affiliation(s)
- Dharjath Shahul Hameed
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Gabrielle B A van Tilburg
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Remco Merkx
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Flierman
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Farid El Oualid
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,UbiQ Bio BV, Amsterdam, Netherlands
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
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20
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Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers. Sci Rep 2019; 9:19991. [PMID: 31882959 PMCID: PMC6934565 DOI: 10.1038/s41598-019-56458-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/03/2019] [Indexed: 11/30/2022] Open
Abstract
Ubiquitylation is an eminent posttranslational modification referring to the covalent attachment of single ubiquitin molecules or polyubiquitin chains to a target protein dictating the fate of such labeled polypeptide chains. Here, we have biochemically produced artificially Lys11-, and Lys27-, and Lys63-linked ubiquitin dimers based on click-chemistry generating milligram quantities in high purity. We show that the artificial linkage used for the conjugation of two ubiquitin moieties represents a fully reliable surrogate of the natural isopeptide bond by acquiring highly resolved nuclear magnetic resonance (NMR) spectroscopic data including ligand binding studies. Extensive coarse grained and atomistic molecular dynamics (MD) simulations allow to extract structures representing the ensemble of domain-domain conformations used to verify the experimental data. Advantageously, this methodology does not require individual isotopic labeling of both ubiquitin moieties as NMR data have been acquired on the isotopically labeled proximal moiety and complementary MD simulations have been used to fully interpret the experimental data in terms of domain-domain conformation. This combined approach intertwining NMR spectroscopy with MD simulations makes it possible to describe the conformational space non-canonically Lys11-, and Lys27-linked ubiquitin dimers occupy in a solution averaged ensemble by taking atomically resolved information representing all residues in ubiquitin dimers into account.
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21
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Requirement for p62 acetylation in the aggregation of ubiquitylated proteins under nutrient stress. Nat Commun 2019; 10:5792. [PMID: 31857589 PMCID: PMC6923396 DOI: 10.1038/s41467-019-13718-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/20/2019] [Indexed: 01/05/2023] Open
Abstract
Autophagy receptor p62/SQSTM1 promotes the assembly and removal of ubiquitylated proteins by forming p62 bodies and mediating their encapsulation in autophagosomes. Here we show that under nutrient-deficient conditions, cellular p62 specifically undergoes acetylation, which is required for the formation and subsequent autophagic clearance of p62 bodies. We identify K420 and K435 in the UBA domain as the main acetylation sites, and TIP60 and HDAC6 as the acetyltransferase and deacetylase. Mechanically, acetylation at both K420 and K435 sites enhances p62 binding to ubiquitin by disrupting UBA dimerization, while K435 acetylation also directly increases the UBA-ubiquitin affinity. Furthermore, we show that acetylation of p62 facilitates polyubiquitin chain-induced p62 phase separation. Our results suggest an essential role of p62 acetylation in the selective degradation of ubiquitylated proteins in cells under nutrient stress, by specifically regulating the assembly of p62 bodies. The autophagy receptor p62 mediates the assembly and removal of ubiquitylated protein aggregates by forming p62 bodies. Here, the authors identify an acetylation-dependent mechanism that regulates formation and autophagic clearance of p62 bodies under nutrient-deficient conditions.
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22
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Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR. BIOPHYSICS REPORTS 2019. [DOI: 10.1007/s41048-019-00099-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
AbstractNMR structure calculation is inherently integrative, and can incorporate new experimental data as restraints. As RNAs have lower proton densities and are more conformational heterogenous than proteins, the refinement of RNA structures can benefit from additional types of restraints. Paramagnetic relaxation enhancement (PRE) provides distance information between a paramagnetic probe and protein or RNA nuclei. However, covalent conjugation of a paramagnetic probe is difficult for RNAs, thus limiting the use of PRE NMR for RNA structure characterization. Here, we show that the solvent PRE can be accurately measured for RNA labile imino protons, simply with the addition of an inert paramagnetic cosolute. Demonstrated on three RNAs that have increasingly complex topologies, we show that the incorporation of the solvent PRE restraints can significantly improve the precision and accuracy of RNA structures. Importantly, the solvent PRE data can be collected for RNAs without isotope enrichment. Thus, the solvent PRE method can work integratively with other biophysical techniques for better characterization of RNA structures.
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23
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Tang C, Zhang WP. How Phosphorylation by PINK1 Remodels the Ubiquitin System: A Perspective from Structure and Dynamics. Biochemistry 2019; 59:26-33. [PMID: 31503455 DOI: 10.1021/acs.biochem.9b00715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ubiquitin is an important signaling protein in cells. It functions by covalent attachment to substrate proteins and by noncovalent interactions with target proteins. Ubiquitins are also concatenated, and the resulting polyubiquitins recognize target proteins multivalently with enhanced specificity. The function of ubiquitin is enabled by the conformational dynamics of ubiquitin and polyubiquitins, which spans over 12 orders of magnitude in a time scale. Recently, it was found that ubiquitin can be phosphorylated by PINK1 at residues S65 and T66. Only sparsely populated for the unmodified ubiquitin, a C-terminally retracted conformation is stabilized for phosphorylated ubiquitin and is further enriched at an increasing pH. The modulation of tertiary structure further impacts the quaternary arrangements of ubiquitin subunits in polyubiquitins. Additionally, ubiquitin phosphorylation inhibits the activities of many enzymes responsible for attaching and removing polyubiquitins, thus remodeling the composition and length of polyubiquitins. The phosphorylation-remolded polyubiquitins can then recognize different target proteins. As PINK1 and ubiquitin phosphorylation levels are up-regulated under certain pathophysiological conditions, the remodeled ubiquitin system may be involved in the divergence of cell fate.
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Affiliation(s)
- Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan , Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan , Hubei 430071 , China
| | - Wei-Ping Zhang
- Department of Pharmacology, Key Laboratory of Medical Neurobiology of Ministry of Health of China , Zhejiang University School of Medicine , Hangzhou , Zhejiang 310058 , China
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24
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Matsumoto ML, Castellanos ER, Zeng YJ, Kirkpatrick DS. Interpreting the Language of Polyubiquitin with Linkage-Specific Antibodies and Mass Spectrometry. Methods Mol Biol 2019; 1844:385-400. [PMID: 30242722 DOI: 10.1007/978-1-4939-8706-1_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Posttranslational modification of cellular proteins by ubiquitin serves a variety of functions. Among the multitude of ubiquitin substrates, ubiquitin itself is the most prevalent. For many years, the direct detection of polyubiquitin chains attached to cellular substrates was not practical, with cell biologists relegated to indirect approaches involving site-directed mutagenesis or in vitro biochemistry. Recent advances in two technologies-polyubiquitin linkage-specific antibodies and mass spectrometry proteomics, have overcome that limitation. Using one or both of these, the direct analysis of polyubiquitin chain linkages on cellular substrate proteins may be performed. This paper describes the complimentary nature of linkage-specific antibodies and mass spectrometry proteomics for the characterization of complex ubiquitin signals using lessons learned in early development of both technologies.
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Affiliation(s)
- Marissa L Matsumoto
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA.
| | - Erick R Castellanos
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA, USA
| | - Yi Jimmy Zeng
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South San Francisco, CA, USA.
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25
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Berg A, Peter C. Simulating and analysing configurational landscapes of protein-protein contact formation. Interface Focus 2019; 9:20180062. [PMID: 31065336 DOI: 10.1098/rsfs.2018.0062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 01/04/2023] Open
Abstract
Interacting proteins can form aggregates and protein-protein interfaces with multiple patterns and different stabilities. Using molecular simulation one would like to understand the formation of these aggregates and which of the observed states are relevant for protein function and recognition. To characterize the complex configurational ensemble of protein aggregates, one needs a quantitative measure for the similarity of structures. We present well-suited descriptors that capture the essential features of non-covalent protein contact formation and domain motion. This set of collective variables is used with a nonlinear multi-dimensional scaling-based dimensionality reduction technique to obtain a low-dimensional representation of the configurational landscape of two ubiquitin proteins from coarse-grained simulations. We show that this two-dimensional representation is a powerful basis to identify meaningful states in the ensemble of aggregated structures and to calculate distributions and free energy landscapes for different sets of simulations. By using a measure to quantitatively compare free energy landscapes we can show how the introduction of a covalent bond between two ubiquitin proteins at different positions alters the configurational states of these dimers.
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Affiliation(s)
- Andrej Berg
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
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26
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Liu Z, Dong X, Yi HW, Yang J, Gong Z, Wang Y, Liu K, Zhang WP, Tang C. Structural basis for the recognition of K48-linked Ub chain by proteasomal receptor Rpn13. Cell Discov 2019; 5:19. [PMID: 30962947 PMCID: PMC6443662 DOI: 10.1038/s41421-019-0089-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 01/18/2023] Open
Abstract
The interaction between K48-linked ubiquitin (Ub) chain and Rpn13 is important for proteasomal degradation of ubiquitinated substrate proteins. Only the complex structure between the N-terminal domain of Rpn13 (Rpn13NTD) and Ub monomer has been characterized, while it remains unclear how Rpn13 specifically recognizes K48-linked Ub chain. Using single-molecule FRET, here we show that K48-linked diubiquitin (K48-diUb) fluctuates among distinct conformational states, and a preexisting compact state is selectively enriched by Rpn13NTD. The same binding mode is observed for full-length Rpn13 and longer K48-linked Ub chain. Using solution NMR spectroscopy, we have determined the complex structure between Rpn13NTD and K48-diUb. In this structure, Rpn13NTD simultaneously interacts with proximal and distal Ub subunits of K48-diUb that remain associated in the complex, thus corroborating smFRET findings. The proximal Ub interacts with Rpn13NTD similarly as the Ub monomer in the known Rpn13NTD:Ub structure, while the distal Ub binds to a largely electrostatic surface of Rpn13NTD. Thus, a charge-reversal mutation in Rpn13NTD weakens the interaction between Rpn13 and K48-linked Ub chain, causing accumulation of ubiquitinated proteins. Moreover, physical blockage of the access of the distal Ub to Rpn13NTD with a proximity-attached Ub monomer can disrupt the interaction between Rpn13 and K48-diUb. Taken together, the bivalent interaction of K48-linked Ub chain with Rpn13 provides the structural basis for Rpn13 linkage selectivity, which opens a new window for modulating proteasomal function.
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Affiliation(s)
- Zhu Liu
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,2National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xu Dong
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China
| | - Hua-Wei Yi
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,3University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ju Yang
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,3University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhou Gong
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China
| | - Yi Wang
- 4Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310027 China
| | - Kan Liu
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China
| | - Wei-Ping Zhang
- 4Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310027 China
| | - Chun Tang
- 1CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071 China.,3University of Chinese Academy of Sciences, Beijing, 100049 China.,5Wuhan National Laboratory for Optoelectronics, Wuhan, Hubei Province 430074 China
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27
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Berg A, Kukharenko O, Scheffner M, Peter C. Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers. PLoS Comput Biol 2018; 14:e1006589. [PMID: 30444864 PMCID: PMC6268000 DOI: 10.1371/journal.pcbi.1006589] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/30/2018] [Accepted: 10/22/2018] [Indexed: 12/25/2022] Open
Abstract
Covalent modification of proteins by ubiquitin or ubiquitin chains is one of the most prevalent post-translational modifications in eukaryotes. Different types of ubiquitin chains are assumed to selectively signal respectively modified proteins for different fates. In support of this hypothesis, structural studies have shown that the eight possible ubiquitin dimers adopt different conformations. However, at least in some cases, these structures cannot sufficiently explain the molecular basis of the selective signaling mechanisms. This indicates that the available structures represent only a few distinct conformations within the entire conformational space adopted by a ubiquitin dimer. Here, molecular simulations on different levels of resolution can complement the structural information. We have combined exhaustive coarse grained and atomistic simulations of all eight possible ubiquitin dimers with a suitable dimensionality reduction technique and a new method to characterize protein-protein interfaces and the conformational landscape of protein conjugates. We found that ubiquitin dimers exhibit characteristic linkage type-dependent properties in solution, such as interface stability and the character of contacts between the subunits, which can be directly correlated with experimentally observed linkage-specific properties. Post-translational modification of proteins by covalent attachment of ubiquitin is a key cellular process, regulating for example the fate and recycling of proteins. We present a new method to combine multiscale simulation with advanced analysis methods to characterize the states of ubiquitin-ubiquitin conjugates. We found that the linkage position affects the conformational space of ubiquitin dimers, determining the number and stability of relevant states, the character of subunit contacts and the nature of the surface exposed to possible binding partners.
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Affiliation(s)
- Andrej Berg
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | | | - Martin Scheffner
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz, Germany
- * E-mail:
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28
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Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS. Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biol Open 2018; 7:7/7/bio036103. [PMID: 30037883 PMCID: PMC6078352 DOI: 10.1242/bio.036103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our experiments have identified eight new sensitizing conditions for Lys63 and uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.
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Affiliation(s)
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kyle A Barlow
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Daniel Asarnow
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Yuliya Birman
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Derek Britain
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Evan M Green
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Charlotte A Nelson
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Pooja Suresh
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ruilin Tian
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taylor Arhar
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Beatrice E Ary
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - David P Bauer
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ian D Bergman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Rachel M Brunetti
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Cynthia M Chio
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Shizhong A Dai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Miles S Dickinson
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Susanna K Elledge
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Cole V M Helsell
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nathan L Hendel
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Emily Kang
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Nadja Kern
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Matvei S Khoroshkin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Lisa L Kirkemo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Greyson R Lewis
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Kevin Lou
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Wesley M Marin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Alison M Maxwell
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter F McTigue
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | | | - Tamas L Nagy
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Andrew M Natale
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sergei Pourmal
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Gabriel K Reder
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Nicholas J Rettko
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Peter J Rohweder
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Daniel M C Schwarz
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Sophia K Tan
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Paul V Thomas
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Ryan W Tibble
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Jason P Town
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
| | - Mary K Tsai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Douglas R Wassarman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Alexander M Wolff
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
| | - Taia S Wu
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
| | - Derek Bogdanoff
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Jennifer Li
- Department of Chemistry Undergraduate Program, University of California, Davis 95616, USA
| | - Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Shane O'Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
| | - Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA .,Institute for Neurodegenerative Diseases, University of California, San Francisco 94158, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
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29
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Olivieri C, Subrahmanian MV, Xia Y, Kim J, Porcelli F, Veglia G. Simultaneous detection of intra- and inter-molecular paramagnetic relaxation enhancements in protein complexes. JOURNAL OF BIOMOLECULAR NMR 2018; 70:133-140. [PMID: 29396770 PMCID: PMC6029865 DOI: 10.1007/s10858-018-0165-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/19/2018] [Indexed: 05/16/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) measurements constitute a powerful approach for detecting both permanent and transient protein-protein interactions. Typical PRE experiments require an intrinsic or engineered paramagnetic site on one of the two interacting partners; while a second, diamagnetic binding partner is labeled with stable isotopes (15N or 13C). Multiple paramagnetic labeled centers or reversed labeling schemes are often necessary to obtain sufficient distance restraints to model protein-protein complexes, making this approach time consuming and expensive. Here, we show a new strategy that combines a modified pulse sequence (1HN-Γ2-CCLS) with an asymmetric labeling scheme to enable the detection of both intra- and inter-molecular PREs simultaneously using only one sample preparation. We applied this strategy to the non-covalent dimer of ubiquitin. Our method confirmed the previously identified binding interface for the transient di-ubiquitin complex, and at the same time, unveiled the internal structural dynamics rearrangements of ubiquitin upon interaction. In addition to reducing the cost of sample preparation and speed up PRE measurements, by detecting the intra-molecular PRE this new strategy will make it possible to measure and calibrate inter-molecular distances more accurately for both symmetric and asymmetric protein-protein complexes.
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Affiliation(s)
- Cristina Olivieri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Manu Veliparambil Subrahmanian
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Youlin Xia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jonggul Kim
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA
| | - Fernando Porcelli
- DIBAF - University of Tuscia - Largo dell'Università, Blocco D, 01100, Viterbo, Italy
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN, 55455, USA.
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30
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Gong Z, Liu Z, Dong X, Ding YH, Dong MQ, Tang C. Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL. BIOPHYSICS REPORTS 2017; 3:100-108. [PMID: 29238747 PMCID: PMC5719800 DOI: 10.1007/s41048-017-0044-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/18/2017] [Indexed: 12/16/2022] Open
Abstract
Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigid-body refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein–protein complexes, and is freely available at www.tanglab.org/resources.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
| | - Zhu Liu
- Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou, 310057 China
| | - Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
| | - Yue-He Ding
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605 USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206 China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
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31
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Liu Z, Gong Z, Cao Y, Ding YH, Dong MQ, Lu YB, Zhang WP, Tang C. Characterizing Protein Dynamics with Integrative Use of Bulk and Single-Molecule Techniques. Biochemistry 2017; 57:305-313. [PMID: 28945353 DOI: 10.1021/acs.biochem.7b00817] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protein dynamically samples multiple conformations, and the conformational dynamics enables protein function. Most biophysical measurements are ensemble-based, with the observables averaged over all members of the ensemble. Though attainable, the decomposition of the observables to the constituent conformational states can be computationally expensive and ambiguous. Here we show that the incorporation of single-molecule fluorescence resonance energy transfer (smFRET) data resolves the ambiguity and affords protein ensemble structures that are more precise and accurate. Using K63-linked diubiquitin, we characterize the dynamic domain arrangements of the model system, with the use of chemical cross-linking coupled with mass spectrometry (CXMS), small-angle X-ray scattering (SAXS), and smFRET techniques. CXMS allows the modeling of protein conformational states that are alternatives to the crystal structure. SAXS provides ensemble-averaged low-resolution shape information. Importantly, smFRET affords state-specific populations, and the FRET distances validate the ensemble structures obtained by refining against CXMS and SAXS restraints. Together, the integrative use of bulk and single-molecule techniques affords better insight into protein dynamics and shall be widely implemented in structural biology.
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Affiliation(s)
- Zhu Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan, Hubei 430071, China.,Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine , Hangzhou, Zhejiang 310058, China
| | - Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan, Hubei 430071, China
| | - Yong Cao
- National Institute of Biological Sciences , Beijing 102206, China
| | - Yue-He Ding
- National Institute of Biological Sciences , Beijing 102206, China.,RNA Therapeutics Institute, University of Massachusetts Medical School , 368 Plantation Street, Worcester, Massachusetts 01605, United States
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing 102206, China
| | - Yun-Bi Lu
- Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine , Hangzhou, Zhejiang 310058, China
| | - Wei-Ping Zhang
- Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of Ministry of Health of China, and Zhejiang Province Key Laboratory of Mental Disorder's Management, Zhejiang University School of Medicine , Hangzhou, Zhejiang 310058, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences , Wuhan, Hubei 430071, China
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32
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Wagner ND, Clemmer DE, Russell DH. ESI-IM-MS and Collision-Induced Unfolding That Provide Insight into the Linkage-Dependent Interfacial Interactions of Covalently Linked Diubiquitin. Anal Chem 2017; 89:10094-10103. [DOI: 10.1021/acs.analchem.7b02932] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole D. Wagner
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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33
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Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch. Proc Natl Acad Sci U S A 2017; 114:6770-6775. [PMID: 28611216 DOI: 10.1073/pnas.1705718114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin (Ub) is an important signaling protein. Recent studies have shown that Ub can be enzymatically phosphorylated at S65, and that the resulting pUb exhibits two conformational states-a relaxed state and a retracted state. However, crystallization efforts have yielded only the structure for the relaxed state, which was found similar to that of unmodified Ub. Here we present the solution structures of pUb in both states obtained through refinement against state-specific NMR restraints. We show that the retracted state differs from the relaxed state by the retraction of the last β-strand and by the extension of the second α-helix. Further, we show that at 7.2, the pKa value for the phosphoryl group in the relaxed state is higher by 1.4 units than that in the retracted state. Consequently, pUb exists in equilibrium between protonated and deprotonated forms and between retracted and relaxed states, with protonated/relaxed species enriched at slightly acidic pH and deprotonated/retracted species enriched at slightly basic pH. The heterogeneity of pUb explains the inability of phosphomimetic mutants to fully mimic pUb. The pH-sensitive conformational switch is likely preserved for polyubiquitin, as single-molecule FRET data indicate that pH change leads to quaternary rearrangement of a phosphorylated K63-linked diubiquitin. Because cellular pH varies among compartments and changes upon pathophysiological insults, our finding suggests that pH and Ub phosphorylation confer additional target specificities and enable an additional layer of modulation for Ub signals.
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34
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Abstract
Ubiquitylation is essential for signal transduction as well as cell division and differentiation in all eukaryotes. Substrate modifications range from a single ubiquitin molecule to complex polymeric chains, with different types of ubiquitylation often eliciting distinct outcomes. The recent identification of novel chain topologies has improved our understanding of how ubiquitylation establishes precise communication within cells. Here, we discuss how the increasing complexity of ubiquitylation is employed to ensure robust and faithful signal transduction in eukaryotic cells.
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35
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Bowerman S, Rana ASJB, Rice A, Pham GH, Strieter ER, Wereszczynski J. Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations. J Chem Theory Comput 2017; 13:2418-2429. [PMID: 28482663 DOI: 10.1021/acs.jctc.7b00059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Small-angle X-ray scattering (SAXS) has become an increasingly popular technique for characterizing the solution ensemble of flexible biomolecules. However, data resulting from SAXS is typically low-dimensional and is therefore difficult to interpret without additional structural knowledge. In theory, molecular dynamics (MD) trajectories can provide this information, but conventional simulations rarely sample the complete ensemble. Here, we demonstrate that accelerated MD simulations can be used to produce higher quality models in shorter time scales than standard simulations, and we present an iterative Bayesian Monte Carlo method that is able to identify multistate ensembles without overfitting. This methodology is applied to several ubiquitin trimers to demonstrate the effect of linkage type on the solution states of the signaling protein. We observe that the linkage site directly affects the solution flexibility of the trimer and theorize that this difference in plasticity contributes to their disparate roles in vivo.
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Affiliation(s)
- Samuel Bowerman
- Department of Physics and Center for the Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago, Illinois 60616, United States
| | - Ambar S J B Rana
- Department of Chemistry, University of Massachusetts-Amherst , Amherst, Massachusetts 01003, United States.,Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Amy Rice
- Department of Physics and Center for the Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago, Illinois 60616, United States
| | - Grace H Pham
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts-Amherst , Amherst, Massachusetts 01003, United States.,Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst , Amherst, Massachusetts 01003, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for the Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , Chicago, Illinois 60616, United States
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36
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Abstract
The ubiquitin proteasome system controls the concentrations of regulatory proteins and removes damaged and misfolded proteins from cells. Proteins are targeted to the protease at the center of this system, the proteasome, by ubiquitin tags, but ubiquitin is also used as a signal in other cellular processes. Specificity is conferred by the size and structure of the ubiquitin tags, which are recognized by receptors associated with the different cellular processes. However, the ubiquitin code remains ambiguous, and the same ubiquitin tag can target different proteins to different fates. After binding substrate protein at the ubiquitin tag, the proteasome initiates degradation at a disordered region in the substrate. The proteasome has pronounced preferences for the initiation site, and its recognition represents a second component of the degradation signal.
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Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
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37
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Kristariyanto YA, Abdul Rehman SA, Weidlich S, Knebel A, Kulathu Y. A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. EMBO Rep 2017; 18:392-402. [PMID: 28082312 DOI: 10.15252/embr.201643205] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022] Open
Abstract
The eight different types of ubiquitin (Ub) chains that can be formed play important roles in diverse cellular processes. Linkage-selective recognition of Ub chains by Ub-binding domain (UBD)-containing proteins is central to coupling different Ub signals to specific cellular responses. The motif interacting with ubiquitin (MIU) is a small UBD that has been characterized for its binding to monoUb. The recently discovered deubiquitinase MINDY-1/FAM63A contains a tandem MIU repeat (tMIU) that is highly selective at binding to K48-linked polyUb. We here identify that this linkage-selective binding is mediated by a single MIU motif (MIU2) in MINDY-1. The crystal structure of MIU2 in complex with K48-linked polyubiquitin chains reveals that MIU2 on its own binds to all three Ub moieties in an open conformation that can only be accommodated by K48-linked triUb. The weak Ub binder MIU1 increases overall affinity of the tMIU for polyUb chains without affecting its linkage selectivity. Our analyses reveal new concepts for linkage selectivity and polyUb recognition by UBDs.
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Affiliation(s)
- Yosua Adi Kristariyanto
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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38
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Wagner ND, Russell DH. Defining Noncovalent Ubiquitin Homodimer Interfacial Interactions through Comparisons with Covalently Linked Diubiquitin. J Am Chem Soc 2016; 138:16588-16591. [PMID: 27977175 DOI: 10.1021/jacs.6b09829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covalently linked diubiquitin (diUbq) is known to adopt specific interfacial interactions owing to steric hindrance induced by the covalent tether. K48-linked diUbq preferentially forms hydrophobic interfacial interactions between the two I44 faces under physiological conditions, whereas K63-linked diUbq preferentially forms electrostatic interfacial interactions. Here, we show using collision-induced unfolding ion mobility-mass spectrometry that the recently reported noncovalent dimer of ubiquitin exhibits structural preferences and interfacial interactions that are most similar to that of K48-linked diUbq.
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Affiliation(s)
- Nicole D Wagner
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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39
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Abstract
In this issue of Structure, Castañeda et al. (2016b) use multi-disciplinary approaches including NMR techniques, small-angle neutron scattering, and docking to convincingly demonstrate that K27-linked diubiquitin is relatively rigid with unexpected similarity to the conformation of K48-linked diubiquitin bound to the UBA2 domain of hHR23a.
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Affiliation(s)
- Paola Di Lello
- Department of Protein Chemistry & Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah G Hymowitz
- Department of Protein Chemistry & Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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40
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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Mavor D, Barlow K, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate RE, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo EC, See SK, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. eLife 2016; 5. [PMID: 27111525 PMCID: PMC4862753 DOI: 10.7554/elife.15802] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 04/06/2016] [Indexed: 12/31/2022] Open
Abstract
Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum. DOI:http://dx.doi.org/10.7554/eLife.15802.001 The ability of an organism to grow and reproduce, that is, it’s “fitness”, is determined by how its genes interact with the environment. Yeast is a model organism in which researchers can control the exact mutations present in the yeast’s genes (its genotype) and the conditions in which the yeast cells live (their environment). This allows researchers to measure how a yeast cell’s genotype and environment affect its fitness. Ubiquitin is a protein that many organisms depend on to manage cell stress by acting as a tag that targets other proteins for degradation. Essential proteins such as ubiquitin often remain unchanged by mutation over long periods of time. As a result, these proteins evolve very slowly. Like all proteins, ubiquitin is built from a chain of amino acid molecules linked together, and the ubiquitin proteins of yeast and humans are made of almost identical sequences of amino acids. Although ubiquitin has barely changed its sequence over evolution, previous studies have shown that – under normal growth conditions in the laboratory – most amino acids in ubiquitin can be mutated without any loss of cell fitness. This led Mavor et al. to hypothesize that treating the yeast cells with chemicals that cause cell stress might lead to amino acids in ubiquitin becoming more sensitive to mutation. To test this idea, a class of graduate students at the University of California, San Francisco grew yeast cells with different ubiquitin mutations together, and with different chemicals that induce cell stress, and measured their growth rates. Sequencing the ubiquitin gene in the thousands of tested yeast cells revealed that three of the chemicals cause a shared set of amino acids in ubiquitin to become more sensitive to mutation. This result suggests that these amino acids are important for the stress response, possibly by altering the ability of yeast cells to target certain proteins for degradation. Conversely, another chemical causes yeast to become more tolerant to changes in the ubiquitin sequence. The experiments also link changes in particular amino acids in ubiquitin to specific stress responses. Mavor et al. show that many of ubquitin’s amino acids are sensitive to mutation under different stress conditions, while others can be mutated to form different amino acids without effecting fitness. By testing the effects of other chemicals, future experiments could further characterize how the yeast’s genotype and environment interact. DOI:http://dx.doi.org/10.7554/eLife.15802.002
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Affiliation(s)
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Kyle Barlow
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Samuel Thompson
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Benjamin A Barad
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Alain R Bonny
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Clinton L Cario
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Garrett Gaskins
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Zairan Liu
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Laura Deming
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Seth D Axen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Elena Caceres
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Adolfo Cuesta
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Rachel E Gate
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Evan M Green
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Kaitlin R Hulce
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Weiyue Ji
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Steven M Moss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Marco Mravic
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Ryan K Muir
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stefan Niekamp
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Chimno I Nnadi
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Eugene Palovcak
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Tyler D Ross
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Eugenia C Salcedo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Stephanie K See
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Meena Subramaniam
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
| | - Allison W Wong
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
| | - Jennifer Li
- UCSF Science and Health Education Partnership, University of California, San Francisco, San Francisco, United States
| | - Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Shane Ó Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
| | - Benjamin P Roscoe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Center for Advanced Technology, University of California, San Francisco, San Francisco, United States
| | - Joseph L DeRisi
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
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42
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Liu Z, Tang C. Ensemble structure description of Lys63-linked diubiquitin. Data Brief 2016; 7:81-8. [PMID: 26955652 PMCID: PMC4761699 DOI: 10.1016/j.dib.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/15/2015] [Accepted: 02/01/2016] [Indexed: 12/03/2022] Open
Abstract
The data described herein are related to the article entitled “Lys63-linked ubiquitin chain adopts multiple conformational states for specific target recognition” [1], and to the coordinates for the ensemble structure of Lys63-linked diubiquitin (PDB code 2N2K). A Lys63-linked diubiquitin exists in three conformational states with different orientations for the two subunits, each responsible for binding to a target protein and encoding a specific cell signal. An atomic entry in the ensemble structure file consists multiple lines, representing alternative locations of the atom and recapitulating the dynamics of the protein. Experimental details about obtaining strictly intramolecular paramagnetic restraints and determining the relative occupancies of the conformational states are presented. The experimental design and procedures in this Data article can be useful for characterizing the structure and dynamics of other multi-domain proteins.
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Affiliation(s)
- Zhu Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310028, China
| | - Chun Tang
- Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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43
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Pham GH, Rana ASJB, Korkmaz EN, Trang VH, Cui Q, Strieter ER. Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities. Protein Sci 2016; 25:456-71. [PMID: 26506216 DOI: 10.1002/pro.2834] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 12/11/2022]
Abstract
Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.
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Affiliation(s)
- Grace H Pham
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Ambar S J B Rana
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - E Nihal Korkmaz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Vivian H Trang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Eric R Strieter
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
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