1
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Fuxreiter M. Context-dependent, fuzzy protein interactions: Towards sequence-based insights. Curr Opin Struct Biol 2024; 87:102834. [PMID: 38759297 DOI: 10.1016/j.sbi.2024.102834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/19/2024]
Abstract
Predicting protein interactions in the cellular environment still remains a challenge in the AlphaFold era. Protein interactions, similarly to their structures, sample a continuum from ordered to disordered states, with specific partners in many bound configurations. A multiplicity of binding modes (MBM) enables transition between these states under different cellular conditions. This review focuses on how the cellular environment affects protein interactions, highlighting the molecular mechanisms, biophysical origin, and sequence-based principles of context-dependent, fuzzy interactions. It summarises experimental and computational approaches to address the challenge of interaction heterogeneity and its contribution to a wide range of biological functions. These insights will help in understanding complex cellular processes, involving conversions between protein assembly states, such as from liquid-like droplet state to the amyloid state.
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Affiliation(s)
- Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, Italy; Department of Physics and Astronomy, University of Padova, Padova, Italy.
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2
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Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M. Structural Insights into the Roles of PARP4 and NAD + in the Human Vault Cage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601040. [PMID: 38979142 PMCID: PMC11230398 DOI: 10.1101/2024.06.27.601040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Vault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is thought to transport transiently bound "cargo" molecules. Vertebrate vaults house a poly (ADP-ribose) polymerase (known as PARP4 in humans), which is the only MVC with known enzymatic activity. Despite being discovered decades ago, the molecular basis for PARP4's interaction with MVP remains unclear. In this study, we determined the structure of the human vault cage in complex with PARP4 and its enzymatic substrate NAD + . The structures reveal atomic-level details of the protein-binding interface, as well as unexpected NAD + -binding pockets within the interior of the vault cage. In addition, proteomics data show that human vaults purified from wild-type and PARP4-depleted cells interact with distinct subsets of proteins. Our results thereby support a model in which PARP4's specific incorporation into the vault cage helps to regulate vault's selection of cargo and its subcellular localization. Further, PARP4's proximity to MVP's NAD + -binding sites could support its enzymatic function within the vault.
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3
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Ju CC, Liu XX, Liu LH, Guo N, Guan LW, Wu JX, Liu DW. Epigenetic modification: A novel insight into diabetic wound healing. Heliyon 2024; 10:e28086. [PMID: 38533007 PMCID: PMC10963386 DOI: 10.1016/j.heliyon.2024.e28086] [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: 07/05/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024] Open
Abstract
Wound healing is an intricate and fine regulatory process. In diabetic patients, advanced glycation end products (AGEs), excessive reactive oxygen species (ROS), biofilm formation, persistent inflammation, and angiogenesis regression contribute to delayed wound healing. Epigenetics, the fast-moving science in the 21st century, has been up to date and associated with diabetic wound repair. In this review, we go over the functions of epigenetics in diabetic wound repair in retrospect, covering transcriptional and posttranscriptional regulation. Among these, we found that histone modification is widely involved in inflammation and angiogenesis by affecting macrophages and endothelial cells. DNA methylation is involved in factors regulation in wound repair but also affects the differentiation phenotype of cells in hyperglycemia. In addition, noncodingRNA regulation and RNA modification in diabetic wound repair were also generalized. The future prospects for epigenetic applications are discussed in the end. In conclusion, the study suggests that epigenetics is an integral regulatory mechanism in diabetic wound healing.
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Affiliation(s)
- Cong-Cong Ju
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
- Huankui Academy, Nanchang University, Nanchang, Jiangxi, PR China
| | - Xiao-Xiao Liu
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
| | - Li-hua Liu
- Huankui Academy, Nanchang University, Nanchang, Jiangxi, PR China
| | - Nan Guo
- Nanchang University, Nanchang, Jiangxi, PR China
| | - Le-wei Guan
- Huankui Academy, Nanchang University, Nanchang, Jiangxi, PR China
| | - Jun-xian Wu
- Nanchang University, Nanchang, Jiangxi, PR China
| | - De-Wu Liu
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
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4
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Davarinejad H, Arvanitis-Vigneault A, Nygard D, Lavallée-Adam M, Couture JF. Modus operandi: Chromatin recognition by α-helical histone readers. Structure 2024; 32:8-17. [PMID: 37922903 DOI: 10.1016/j.str.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023]
Abstract
Histone reader domains provide a mechanism for sensing states of coordinated nuclear processes marked by histone proteins' post-translational modifications (PTMs). Among a growing number of discovered histone readers, the 14-3-3s, ankyrin repeat domains (ARDs), tetratricopeptide repeats (TPRs), bromodomains (BRDs), and HEAT domains are a group of domains using various mechanisms to recognize unmodified or modified histones, yet they all are composed of an α-helical fold. In this review, we compare how these readers fold to create protein domains that are very diverse in their tertiary structures, giving rise to intriguing peptide binding mechanisms resulting in vastly different footprints of their targets.
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Affiliation(s)
- Hossein Davarinejad
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Alexis Arvanitis-Vigneault
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Dallas Nygard
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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5
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Goswami R, Gupta A, Bednova O, Coulombe G, Patel D, Rotello VM, Leyton JV. Nuclear localization signal-tagged systems: relevant nuclear import principles in the context of current therapeutic design. Chem Soc Rev 2024; 53:204-226. [PMID: 38031452 PMCID: PMC10798298 DOI: 10.1039/d1cs00269d] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Nuclear targeting of therapeutics provides a strategy for enhancing efficacy of molecules active in the nucleus and minimizing off-target effects. 'Active' nuclear-directed transport and efficient translocations across nuclear pore complexes provide the most effective means of maximizing nuclear localization. Nuclear-targeting systems based on nuclear localization signal (NLS) motifs have progressed significantly since the beginning of the current millennium. Here, we offer a roadmap for understanding the basic mechanisms of nuclear import in the context of actionable therapeutic design for developing NLS-therapeutics with improved treatment efficacy.
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Affiliation(s)
- Ritabrita Goswami
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Aarohi Gupta
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Olga Bednova
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec, Canada
| | - Gaël Coulombe
- Service des stages et du développement professionnel, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dipika Patel
- Service des stages et du développement professionnel, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Jeffrey V Leyton
- École des sciences pharmaceutiques, Université d'Ottawa, Ottawa, Ontario, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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6
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Shi Q, Lin M, Cheng X, Zhang Z, Deng S, Lang K, Yang Z, Sun X. KPNB1-mediated nuclear import in cancer. Eur J Pharmacol 2023; 955:175925. [PMID: 37473981 DOI: 10.1016/j.ejphar.2023.175925] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/03/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Dysregulation of nucleocytoplasmic shuttling impairs cellular homeostasis and promotes cancer development. KPNB1 is a member of karyopherin β family, mediating the transportation of proteins from the cytoplasm to the nucleus. In a variety of cancers, the expression of KPNB1 is upregulated to facilitate tumor growth and progression. Both downregulation of KPNB1 level and inhibition of KPNB1 activity prevent the entry of cancer-related transcription factors into the nucleus, subsequently suppressing the proliferation and metastasis of cancer cells. Currently, five KPNB1 inhibitors have been reported and exhibited good efficacy against cancer. This paper provides an overview of the role and mechanism of KPNB1 in different cancers and KPNB1-targeted anticancer compounds which hold promise for the future.
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Affiliation(s)
- Qiwen Shi
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Mengxia Lin
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Xiang Cheng
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Ziyuan Zhang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Shufen Deng
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Ke Lang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Zhikun Yang
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Xuanrong Sun
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China.
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7
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Ding N, Li H, Zhang Z, Jia H. Inhibition of importin-7 attenuates ventilator-induced lung injury by targeting nuclear translocation of p38. Inflamm Res 2023; 72:971-988. [PMID: 37004548 DOI: 10.1007/s00011-023-01727-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/13/2023] [Accepted: 03/26/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND The ability of p38 to phosphorylate substrates in the nucleus and the role of nuclear p38 in the regulation of inflammation have focused attention on the subcellular localization of the kinase. Although it is clear that p38 shuttles to the nucleus upon stimulation, the mechanisms that regulate p38 nuclear input in response to mechanical stretch remain to be determined. METHODS Cyclic stretch (CS)-induced nuclear translocation of p38 was determined by Western blotting and immunofluorescence. The p38 interacting protein was identified using endogenous pull-down and protein binding assays. The potential role of importin-7 (Imp7) in CS-induced nuclear translocation of p38 and p38-dependent gene expression was confirmed using a series of in vitro and in vivo experiments. Furthermore, we tested the therapeutic potential of intratracheal administration of Imp7 siRNA-loaded nanoparticles in the ventilator-induced lung injury (VILI) mouse model. RESULTS We show that CS induced phosphorylation-dependent nuclear translocation of p38, which required the involvement of microtubules and dynein. Endogenous pull-down assay revealed Imp7 to be a potential p38-interacting protein, and the direct interaction between p38 and Imp7 was confirmed by in vitro and in vivo binding assays. Furthermore, silencing Imp7 inhibited CS-induced nuclear translocation of p38 and subsequent cytokine production. Notably, intratracheal administration of Imp7 siRNA nanoparticles attenuated lung inflammation and histological damage in the VILI mouse model. CONCLUSIONS Our findings uncover a key role for Imp7 in the process of p38 nuclear import after CS stimulation and highlight the potential of preventing p38 nuclear translocation in treatment of VILI.
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Affiliation(s)
- Ning Ding
- Department of Anesthesiology, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250031, China.
- Key Laboratory of Critical Rehabilitation Medicine of Shandong Province, Shandong Provincial Third Hospital, Jinan, 250031, China.
| | - Huiqing Li
- Department of Anesthesiology, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250031, China
- Key Laboratory of Critical Rehabilitation Medicine of Shandong Province, Shandong Provincial Third Hospital, Jinan, 250031, China
| | - Zengzhen Zhang
- Department of Anesthesiology, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250031, China
- Key Laboratory of Critical Rehabilitation Medicine of Shandong Province, Shandong Provincial Third Hospital, Jinan, 250031, China
| | - Haiyan Jia
- Department of Intensive Care Medicine, Shandong Provincial Third Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250031, China
- Key Laboratory of Critical Rehabilitation Medicine of Shandong Province, Shandong Provincial Third Hospital, Jinan, 250031, China
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8
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Spittler D, Indorato RL, Boeri Erba E, Delaforge E, Signor L, Harris SJ, Garcia-Saez I, Palencia A, Gabel F, Blackledge M, Noirclerc-Savoye M, Petosa C. Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex. Life Sci Alliance 2022; 5:5/10/e202201431. [PMID: 35995566 PMCID: PMC9396022 DOI: 10.26508/lsa.202201431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Rev mediates the nuclear export of intron-containing viral RNA transcripts and is essential for viral replication. Rev is imported into the nucleus by the host protein importin β (Impβ), but how Rev associates with Impβ is poorly understood. Here, we report biochemical, mutational, and biophysical studies of the Impβ/Rev complex. We show that Impβ binds two Rev monomers through independent binding sites, in contrast to the 1:1 binding stoichiometry observed for most Impβ cargos. Peptide scanning data and charge-reversal mutations identify the N-terminal tip of Rev helix α2 within Rev's arginine-rich motif (ARM) as a primary Impβ-binding epitope. Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos.
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Affiliation(s)
- Didier Spittler
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Rose-Laure Indorato
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elise Delaforge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Luca Signor
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Simon J Harris
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Isabel Garcia-Saez
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences, Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Marjolaine Noirclerc-Savoye
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
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9
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Structure of IMPORTIN-4 bound to the H3-H4-ASF1 histone-histone chaperone complex. Proc Natl Acad Sci U S A 2022; 119:e2207177119. [PMID: 36103578 PMCID: PMC9499513 DOI: 10.1073/pnas.2207177119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IMPORTIN-4, the primary nuclear import receptor of core histones H3 and H4, binds the H3-H4 dimer and histone chaperone ASF1 prior to nuclear import. However, how H3-H3-ASF1 is recognized for transport cannot be explained by available crystal structures of IMPORTIN-4-histone tail peptide complexes. Our 3.5-Å IMPORTIN-4-H3-H4-ASF1 cryoelectron microscopy structure reveals the full nuclear import complex and shows a binding mode different from suggested by previous structures. The N-terminal half of IMPORTIN-4 clamps the globular H3-H4 domain and H3 αN helix, while its C-terminal half binds the H3 N-terminal tail weakly; tail contribution to binding energy is negligible. ASF1 binds H3-H4 without contacting IMPORTIN-4. Together, ASF1 and IMPORTIN-4 shield nucleosomal H3-H4 surfaces to chaperone and import it into the nucleus where RanGTP binds IMPORTIN-4, causing large conformational changes to release H3-H4-ASF1. This work explains how full-length H3-H4 binds IMPORTIN-4 in the cytoplasm and how it is released in the nucleus.
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10
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Martinsen JH, Saar D, Fernandes CB, Schuler B, Bugge K, Kragelund BB. Structure, Dynamics and Stability of the Globular Domain of Human Linker Histone H1.0 and the Role of Positive Charges. Protein Sci 2022; 31:918-932. [PMID: 35066947 PMCID: PMC8927875 DOI: 10.1002/pro.4281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 11/25/2022]
Abstract
Linker histone H1 (H1) is an abundant chromatin‐binding protein that acts as an epigenetic regulator binding to nucleosomes and altering chromatin structures and dynamics. Nonetheless, the mechanistic details of its function remain poorly understood. Recent work suggest that the number and position of charged side chains on the globular domain (GD) of H1 influence chromatin structure and hence gene repression. Here, we solved the solution structure of the unbound GD of human H1.0, revealing that the structure is almost completely unperturbed by complex formation, except for a loop connecting two antiparallel β‐strands. We further quantified the role of the many positive charges of the GD for its structure and conformational stability through the analysis of 11 charge variants. We find that modulating the number of charges has little effect on the structure, but the stability is affected, resulting in a difference in melting temperature of 26 K between GD of net charge +5 versus +13. This result suggests that the large number of positive charges on H1‐GDs have evolved for function rather than structure and high stability. The stabilization of the GD upon binding to DNA can thus be expected to have a pronounced electrostatic component, a contribution that is amenable to modulation by posttranslational modifications, especially acetylation and phosphorylation. PDB Code(s): 6hq1;
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Affiliation(s)
- Jacob H Martinsen
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Daniel Saar
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Catarina B Fernandes
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.,Department of Physics, Winterthurerstrasse 190, 8057 University of Zurich, Zurich, Switzerland
| | - Katrine Bugge
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
| | - Birthe B Kragelund
- REPIN and the Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Ole Maaloes Vej 5, DK-.2200, Copenhagen N, Denmark
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11
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Wing CE, Fung HYJ, Chook YM. Karyopherin-mediated nucleocytoplasmic transport. Nat Rev Mol Cell Biol 2022; 23:307-328. [PMID: 35058649 PMCID: PMC10101760 DOI: 10.1038/s41580-021-00446-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 12/25/2022]
Abstract
Efficient and regulated nucleocytoplasmic trafficking of macromolecules to the correct subcellular compartment is critical for proper functions of the eukaryotic cell. The majority of the macromolecular traffic across the nuclear pores is mediated by the Karyopherin-β (or Kap) family of nuclear transport receptors. Work over more than two decades has shed considerable light on how the different Kap family members bring their respective cargoes into the nucleus or the cytoplasm in efficient and highly regulated manners. In this Review, we overview the main features and established functions of Kap family members, describe how Kaps recognize their cargoes and discuss the different ways in which these Kap-cargo interactions can be regulated, highlighting new findings and open questions. We also describe current knowledge of the import and export of the components of three large gene expression machines - the core replisome, RNA polymerase II and the ribosome - pointing out the questions that persist about how such large macromolecular complexes are trafficked to serve their function in a designated subcellular location.
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12
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Odeh HM, Fare CM, Shorter J. Nuclear-Import Receptors Counter Deleterious Phase Transitions in Neurodegenerative Disease. J Mol Biol 2022; 434:167220. [PMID: 34464655 PMCID: PMC8748273 DOI: 10.1016/j.jmb.2021.167220] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 01/17/2023]
Abstract
Nuclear-import receptors (NIRs) engage nuclear-localization signals (NLSs) of polypeptides in the cytoplasm and transport these cargo across the size-selective barrier of the nuclear-pore complex into the nucleoplasm. Beyond this canonical role in nuclear transport, NIRs operate in the cytoplasm to chaperone and disaggregate NLS-bearing clients. Indeed, NIRs can inhibit and reverse functional and deleterious phase transitions of their cargo, including several prominent neurodegenerative disease-linked RNA-binding proteins (RBPs) with prion-like domains (PrLDs), such as TDP-43, FUS, EWSR1, TAF15, hnRNPA1, and hnRNPA2. Importantly, elevated NIR expression can mitigate degenerative phenotypes connected to aberrant cytoplasmic aggregation of RBPs with PrLDs. Here, we review recent discoveries that NIRs can also antagonize aberrant interactions and toxicity of arginine-rich, dipeptide-repeat proteins that are associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) caused by G4C2 hexanucleotide repeat expansions in the first intron of C9ORF72. We also highlight recent findings that multiple NIR family members can prevent and reverse liquid-liquid phase separation of specific clients bearing RGG motifs in an NLS-independent manner. Finally, we discuss strategies to enhance NIR activity or expression, which could have therapeutic utility for several neurodegenerative disorders, including ALS, FTD, multisystem proteinopathy, limbic-predominant age-related TDP-43 encephalopathy, tauopathies, and related diseases.
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Affiliation(s)
- Hana M Odeh
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. https://twitter.com/CharlotteFare
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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13
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Nuclear import of histones. Biochem Soc Trans 2021; 48:2753-2767. [PMID: 33300986 PMCID: PMC7752055 DOI: 10.1042/bst20200572] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/30/2020] [Accepted: 11/13/2020] [Indexed: 12/14/2022]
Abstract
The transport of histones from the cytoplasm to the nucleus of the cell, through the nuclear membrane, is a cellular process that regulates the supply of new histones in the nucleus and is key for DNA replication and transcription. Nuclear import of histones is mediated by proteins of the karyopherin family of nuclear transport receptors. Karyopherins recognize their cargos through linear motifs known as nuclear localization/export sequences or through folded domains in the cargos. Karyopherins interact with nucleoporins, proteins that form the nuclear pore complex, to promote the translocation of their cargos into the nucleus. When binding to histones, karyopherins not only function as nuclear import receptors but also as chaperones, protecting histones from non-specific interactions in the cytoplasm, in the nuclear pore and possibly in the nucleus. Studies have also suggested that karyopherins might participate in histones deposition into nucleosomes. In this review we describe structural and biochemical studies from the last two decades on how karyopherins recognize and transport the core histone proteins H3, H4, H2A and H2B and the linker histone H1 from the cytoplasm to the nucleus, which karyopherin is the major nuclear import receptor for each of these histones, the oligomeric state of histones during nuclear import and the roles of post-translational modifications, histone-chaperones and RanGTP in regulating these nuclear import pathways.
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14
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Kimura M, Imai K, Morinaka Y, Hosono-Sakuma Y, Horton P, Imamoto N. Distinct mutations in importin-β family nucleocytoplasmic transport receptors transportin-SR and importin-13 affect specific cargo binding. Sci Rep 2021; 11:15649. [PMID: 34341383 PMCID: PMC8329185 DOI: 10.1038/s41598-021-94948-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 07/20/2021] [Indexed: 01/25/2023] Open
Abstract
Importin-(Imp)β family nucleocytoplasmic transport receptors (NTRs) are supposed to bind to their cargoes through interaction between a confined interface on an NTR and a nuclear localization or export signal (NLS/NES) on a cargo. Although consensus NLS/NES sequence motifs have been defined for cargoes of some NTRs, many experimentally identified cargoes of those NTRs lack those motifs, and consensus NLSs/NESs have been reported for only a few NTRs. Crystal structures of NTR-cargo complexes have exemplified 3D structure-dependent binding of cargoes lacking a consensus NLS/NES to different sites on an NTR. Since only a limited number of NTR-cargo interactions have been studied, whether most cargoes lacking a consensus NLS/NES bind to the same confined interface or to various sites on an NTR is still unclear. Addressing this issue, we generated four mutants of transportin-(Trn)SR, of which many cargoes lack a consensus NLS, and eight mutants of Imp13, where no consensus NLS has been defined, and we analyzed their binding to as many as 40 cargo candidates that we previously identified by a nuclear import reaction-based method. The cargoes bind differently to the NTR mutants, suggesting that positions on an NTR contribute differently to the binding of respective cargoes.
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Affiliation(s)
- Makoto Kimura
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
| | - Yuriko Morinaka
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Yoshiko Hosono-Sakuma
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Paul Horton
- Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
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15
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Peng Y, Li S, Landsman D, Panchenko AR. Histone tails as signaling antennas of chromatin. Curr Opin Struct Biol 2021; 67:153-160. [PMID: 33279866 PMCID: PMC8096652 DOI: 10.1016/j.sbi.2020.10.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/07/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022]
Abstract
Histone tails, representing the N-terminal or C-terminal regions flanking the histone core, play essential roles in chromatin signaling networks. Intrinsic disorder of histone tails and their propensity for post-translational modifications allow them to serve as hubs in coordination of epigenetic processes within the nucleosomal context. Deposition of histone variants with distinct histone tail properties further enriches histone tails' repertoire in epigenetic signaling. Given the advances in experimental techniques and in silico modelling, we review the most recent data on histone tails' effects on nucleosome stability and dynamics, their function in regulating chromatin accessibility and folding. Finally, we discuss different molecular mechanisms to understand how histone tails are involved in nucleosome recognition by binding partners and formation of higher-order chromatin structures.
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Affiliation(s)
- Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada.
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Banerjee A, Bhakta S, Sengupta J. Integrative approaches in cryogenic electron microscopy: Recent advances in structural biology and future perspectives. iScience 2021; 24:102044. [PMID: 33532719 PMCID: PMC7829201 DOI: 10.1016/j.isci.2021.102044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellular factories engage numerous highly complex "molecular machines" to perform pivotal biological functions. 3D structural visualization is an effective way to understand the functional mechanisms of these biomacromolecules. The "resolution revolution" has established cryogenic electron microscopy (cryo-EM) as a preferred structural biology tool. In parallel with the advances in cryo-EM methodologies aiming at atomic resolution, several innovative approaches have started emerging where other techniques are sensibly integrated with cryo-EM to obtain additional insights into the biological processes. For example, combining the time-resolved technique with high-resolution cryo-EM enables discerning structures of short-lived intermediates in the functional pathway of a biomolecule. Likewise, integrating mass spectrometry (MS) techniques with cryo-EM allows deciphering structural organizations of large molecular assemblies. Here, we discuss how the data generated upon combining either time resolve or MS techniques with cryo-EM supplement structural elucidations with in-depth understanding of the function of cellular macromolecules when they participate in fundamental biological processes.
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Affiliation(s)
- Aneek Banerjee
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sayan Bhakta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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17
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Linker histone defines structure and self-association behaviour of the 177 bp human chromatosome. Sci Rep 2021; 11:380. [PMID: 33432055 PMCID: PMC7801413 DOI: 10.1038/s41598-020-79654-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 12/08/2020] [Indexed: 01/02/2023] Open
Abstract
Linker histones play essential roles in the regulation and maintenance of the dynamic chromatin structure of higher eukaryotes. The influence of human histone H1.0 on the nucleosome structure and biophysical properties of the resulting chromatosome were investigated and compared with the 177-bp nucleosome using Cryo-EM and SAXS. The 4.5 Å Cryo-EM chromatosome structure showed that the linker histone binds at the nucleosome dyad interacting with both linker DNA arms but in a tilted manner leaning towards one of the linker sides. The chromatosome is laterally compacted and rigid in the dyad and linker DNA area, in comparison with the nucleosome where linker DNA region is more flexible and displays structural variability. In solution, the chromatosomes appear slightly larger than the nucleosomes, with the volume increase compared to the bound linker histone, according to solution SAXS measurements. SAXS X-ray diffraction characterisation of Mg-precipitated samples showed that the different shapes of the 177 chromatosome enabled the formation of a highly ordered lamello-columnar phase when precipitated by Mg2+, indicating the influence of linker histone on the nucleosome stacking. The biological significance of linker histone, therefore, may be affected by the change in the polyelectrolyte and DNA conformation properties of the chromatosomes, in comparison to nucleosomes.
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18
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Lacasse V, Beaudoin S, Jean S, Leyton JV. A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:99-119. [PMID: 33024794 PMCID: PMC7522293 DOI: 10.1016/j.omtm.2020.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 08/27/2020] [Indexed: 11/01/2022]
Abstract
The next breakthrough for protein therapeutics is effective intracellular delivery and accumulation within target cells. Nuclear localization signal (NLS)-tagged therapeutics have been hindered by the lack of efficient nuclear localization due to endosome entrapment. Although development of strategies for tagging therapeutics with technologies capable of increased membrane penetration has resulted in proportional increased potency, nonspecific membrane penetration limits target specificity and, hence, widespread clinical success. There is a long-standing idea that nuclear localization of NLS-tagged agents occurs exclusively via classical nuclear transport. In the present study, we modified the antibody-drug conjugate trastuzumab-emtansine (T-DM1) with a classical NLS linked to cholic acid (cell accumulator [Accum]) that enables modified antibodies to escape endosome entrapment and increase nuclear localization efficiency without abrogating receptor targeting. In parallel, we developed a proteomics-based method to evaluate nuclear transport. Accum-modified T-DM1 significantly enhanced cytotoxic efficacy in the human epidermal growth factor receptor 2 (HER2)-positive SKBR3 breast cancer system. We discovered that efficacy was dependent on the nonclassical importin-7. Our evaluation reveals that when multiple classical NLS tagging occurs, cationic charge build-up as opposed to sequence dominates and becomes a substrate for importin-7. This study results in an effective target cell-specific NLS therapeutic and a general approach to guide future NLS-based development initiatives.
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Affiliation(s)
- Vincent Lacasse
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Simon Beaudoin
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Steve Jean
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
| | - Jeffrey V Leyton
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada.,Sherbrooke Molecular Imaging Centre (CIMS), Centre de Recherche du CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
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19
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Weng J, Wang W. Dynamic multivalent interactions of intrinsically disordered proteins. Curr Opin Struct Biol 2020; 62:9-13. [DOI: 10.1016/j.sbi.2019.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022]
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20
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Young SG, Fong LG, Beigneux AP, Allan CM, He C, Jiang H, Nakajima K, Meiyappan M, Birrane G, Ploug M. GPIHBP1 and Lipoprotein Lipase, Partners in Plasma Triglyceride Metabolism. Cell Metab 2019; 30:51-65. [PMID: 31269429 PMCID: PMC6662658 DOI: 10.1016/j.cmet.2019.05.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lipoprotein lipase (LPL), identified in the 1950s, has been studied intensively by biochemists, physiologists, and clinical investigators. These efforts uncovered a central role for LPL in plasma triglyceride metabolism and identified LPL mutations as a cause of hypertriglyceridemia. By the 1990s, with an outline for plasma triglyceride metabolism established, interest in triglyceride metabolism waned. In recent years, however, interest in plasma triglyceride metabolism has awakened, in part because of the discovery of new molecules governing triglyceride metabolism. One such protein-and the focus of this review-is GPIHBP1, a protein of capillary endothelial cells. GPIHBP1 is LPL's essential partner: it binds LPL and transports it to the capillary lumen; it is essential for lipoprotein margination along capillaries, allowing lipolysis to proceed; and it preserves LPL's structure and activity. Recently, GPIHBP1 was the key to solving the structure of LPL. These developments have transformed the models for intravascular triglyceride metabolism.
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Affiliation(s)
- Stephen G Young
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Loren G Fong
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Anne P Beigneux
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher M Allan
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Cuiwen He
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Haibo Jiang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; School of Molecular Sciences, University of Western Australia, Crawley 6009, Australia
| | - Katsuyuki Nakajima
- Department of Clinical Laboratory Medicine, Gunma University Graduate School of Department of Medicine, Maebashi, Gunma 371-0805, Japan
| | - Muthuraman Meiyappan
- Discovery Therapeutics, Takeda Pharmaceutical Company Ltd., Cambridge, MA 02142, USA
| | - Gabriel Birrane
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Michael Ploug
- Finsen Laboratory, Rigshospitalet, Copenhagen DK-2200, Denmark; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.
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