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Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks DR, Pyles H, Yang A, Carter L, Lamb M, Li X, Levine PM, Stewart L, Garcia KC, Baker D. De novo design of buttressed loops for sculpting protein functions. Nat Chem Biol 2024; 20:974-980. [PMID: 38816644 PMCID: PMC11288887 DOI: 10.1038/s41589-024-01632-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/29/2024] [Indexed: 06/01/2024]
Abstract
In natural proteins, structured loops have central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that designs tandem repeat proteins with structured loops (9-14 residues) buttressed by extensive hydrogen bonding interactions. Experimental characterization shows that the designs are monodisperse, highly soluble, folded and thermally stable. Crystal structures are in close agreement with the design models, with the loops structured and buttressed as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute generally to efforts to design new protein functions.
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Affiliation(s)
- Hanlun Jiang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kejia Wu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
| | - Jorge Fallas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Harley Pyles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Aerin Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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2
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Tan WJ, Hawley HR, Wilson SJ, Fitzsimons HL. Deciphering the roles of subcellular distribution and interactions involving the MEF2 binding region, the ankyrin repeat binding motif and the catalytic site of HDAC4 in Drosophila neuronal morphogenesis. BMC Biol 2024; 22:2. [PMID: 38167120 PMCID: PMC10763444 DOI: 10.1186/s12915-023-01800-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Dysregulation of nucleocytoplasmic shuttling of histone deacetylase 4 (HDAC4) is associated with several neurodevelopmental and neurodegenerative disorders. Consequently, understanding the roles of nuclear and cytoplasmic HDAC4 along with the mechanisms that regulate nuclear entry and exit is an area of concerted effort. Efficient nuclear entry is dependent on binding of the transcription factor MEF2, as mutations in the MEF2 binding region result in cytoplasmic accumulation of HDAC4. It is well established that nuclear exit and cytoplasmic retention are dependent on 14-3-3-binding, and mutations that affect binding are widely used to induce nuclear accumulation of HDAC4. While regulation of HDAC4 shuttling is clearly important, there is a gap in understanding of how the nuclear and cytoplasmic distribution of HDAC4 impacts its function. Furthermore, it is unclear whether other features of the protein including the catalytic site, the MEF2-binding region and/or the ankyrin repeat binding motif influence the distribution and/or activity of HDAC4 in neurons. Since HDAC4 functions are conserved in Drosophila, and increased nuclear accumulation of HDAC4 also results in impaired neurodevelopment, we used Drosophila as a genetic model for investigation of HDAC4 function. RESULTS Here we have generated a series of mutants for functional dissection of HDAC4 via in-depth examination of the resulting subcellular distribution and nuclear aggregation, and correlate these with developmental phenotypes resulting from their expression in well-established models of neuronal morphogenesis of the Drosophila mushroom body and eye. We found that in the mushroom body, forced sequestration of HDAC4 in the nucleus or the cytoplasm resulted in defects in axon morphogenesis. The actions of HDAC4 that resulted in impaired development were dependent on the MEF2 binding region, modulated by the ankyrin repeat binding motif, and largely independent of an intact catalytic site. In contrast, disruption to eye development was largely independent of MEF2 binding but mutation of the catalytic site significantly reduced the phenotype, indicating that HDAC4 acts in a neuronal-subtype-specific manner. CONCLUSIONS We found that the impairments to mushroom body and eye development resulting from nuclear accumulation of HDAC4 were exacerbated by mutation of the ankyrin repeat binding motif, whereas there was a differing requirement for the MEF2 binding site and an intact catalytic site. It will be of importance to determine the binding partners of HDAC4 in nuclear aggregates and in the cytoplasm of these tissues to further understand its mechanisms of action.
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Affiliation(s)
- Wei Jun Tan
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Hannah R Hawley
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Sarah J Wilson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Helen L Fitzsimons
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
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3
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Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks D, Pyles H, Yang A, Carter L, Lamb M, Li X, Levine PM, Stewart L, Garcia KC, Baker D. De novo design of buttressed loops for sculpting protein functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554384. [PMID: 37662224 PMCID: PMC10473674 DOI: 10.1101/2023.08.22.554384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
In natural proteins, structured loops play central roles in molecular recognition, signal transduction and enzyme catalysis. However, because of the intrinsic flexibility and irregularity of loop regions, organizing multiple structured loops at protein functional sites has been very difficult to achieve by de novo protein design. Here we describe a solution to this problem that generates structured loops buttressed by extensive hydrogen bonding interactions with two neighboring loops and with secondary structure elements. We use this approach to design tandem repeat proteins with buttressed loops ranging from 9 to 14 residues in length. Experimental characterization shows the designs are folded and monodisperse, highly soluble, and thermally stable. Crystal structures are in close agreement with the computational design models, with the loops structured and buttressed by their neighbors as designed. We demonstrate the functionality afforded by loop buttressing by designing and characterizing binders for extended peptides in which the loops form one side of an extended binding pocket. The ability to design multiple structured loops should contribute quite generally to efforts to design new protein functions.
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Affiliation(s)
- Hanlun Jiang
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine
| | - Kejia Wu
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
- Biological Physics, Structure and Design Graduate Program, University of Washington
| | - Jorge Fallas
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - George Ueda
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - T J Brunette
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Derrick Hicks
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Harley Pyles
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Aerin Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine
| | - Lauren Carter
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Mila Lamb
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Xinting Li
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Paul M Levine
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - Lance Stewart
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine
- Department of Structural Biology, Stanford University School of Medicine
| | - David Baker
- Department of Biochemistry, University of Washington
- Institute for Protein Design, University of Washington
- Howard Hughes Medical Institute, Stanford University School of Medicine
- Howard Hughes Medical Institute, University of Washington
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Schwartz S, Wilson SJ, Hale TK, Fitzsimons HL. Ankyrin2 is essential for neuronal morphogenesis and long-term courtship memory in Drosophila. Mol Brain 2023; 16:42. [PMID: 37194019 DOI: 10.1186/s13041-023-01026-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 04/13/2023] [Indexed: 05/18/2023] Open
Abstract
Dysregulation of HDAC4 expression and/or nucleocytoplasmic shuttling results in impaired neuronal morphogenesis and long-term memory in Drosophila melanogaster. A recent genetic screen for genes that interact in the same molecular pathway as HDAC4 identified the cytoskeletal adapter Ankyrin2 (Ank2). Here we sought to investigate the role of Ank2 in neuronal morphogenesis, learning and memory. We found that Ank2 is expressed widely throughout the Drosophila brain where it localizes predominantly to axon tracts. Pan-neuronal knockdown of Ank2 in the mushroom body, a region critical for memory formation, resulted in defects in axon morphogenesis. Similarly, reduction of Ank2 in lobular plate tangential neurons of the optic lobe disrupted dendritic branching and arborization. Conditional knockdown of Ank2 in the mushroom body of adult Drosophila significantly impaired long-term memory (LTM) of courtship suppression, and its expression was essential in the γ neurons of the mushroom body for normal LTM. In summary, we provide the first characterization of the expression pattern of Ank2 in the adult Drosophila brain and demonstrate that Ank2 is critical for morphogenesis of the mushroom body and for the molecular processes required in the adult brain for the formation of long-term memories.
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Affiliation(s)
- Silvia Schwartz
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Current Address: Istituto Italiano di Tecnologia, Center for Life NanoScience, Rome, Italy
| | - Sarah J Wilson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Tracy K Hale
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Helen L Fitzsimons
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
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5
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Poxviral ANKR/F-box Proteins: Substrate Adapters for Ubiquitylation and More. Pathogens 2022; 11:pathogens11080875. [PMID: 36014996 PMCID: PMC9414399 DOI: 10.3390/pathogens11080875] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023] Open
Abstract
Poxviruses are double-stranded DNA viruses that infect insects and a variety of vertebrate species. The large genomes of poxviruses contain numerous genes that allow these viruses to successfully establish infection, including those that help evade the host immune response and prevent cell death. Ankyrin-repeat (ANKR)/F-box proteins are almost exclusively found in poxviruses, and they function as substrate adapters for Skp1-Cullin-1-F-box protein (SCF) multi-subunit E3 ubiquitin (Ub)-ligases. In this regard, they use their C-terminal F-box domain to bind Skp1, Cullin-1, and Roc1 to recruit cellular E2 enzymes to facilitate the ubiquitylation, and subsequent proteasomal degradation, of proteins bound to their N-terminal ANKRs. However, these proteins do not just function as substrate adapters as they also have Ub-independent activities. In this review, we examine both Ub-dependent and -independent activities of ANKR/F-box proteins and discuss how poxviruses use these proteins to counteract the host innate immune response, uncoat their genome, replicate, block cell death, and influence transcription. Finally, we consider important outstanding questions that need to be answered in order to better understand the function of this versatile protein family.
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6
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HDAC4 Inhibitors as Antivascular Senescence Therapeutics. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3087916. [PMID: 35814270 PMCID: PMC9259336 DOI: 10.1155/2022/3087916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/03/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022]
Abstract
Aging is an inevitable consequence of life, and during this process, the epigenetic landscape changes and reactive oxygen species (ROS) accumulation increases. Inevitably, these changes are common in many age-related diseases, including neurodegeneration, hypertension, and cardiovascular diseases. In the current research, histone deacetylation 4 (HDAC4) was studied as a potential therapeutic target in vascular senescence. HDAC4 is a specific class II histone deacetylation protein that participates in epigenetic modifications and deacetylation of heat shock proteins and various transcription factors. There is increasing evidence to support that HDAC4 is a potential therapeutic target, and developments in the synthesis and testing of HDAC4 inhibitors are now gaining interest from academia and the pharmaceutical industry.
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7
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Structural aspects of the MHC expression control system. Biophys Chem 2022; 284:106781. [PMID: 35228036 PMCID: PMC8941990 DOI: 10.1016/j.bpc.2022.106781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/04/2022] [Accepted: 02/13/2022] [Indexed: 12/11/2022]
Abstract
The major histocompatibility complex (MHC) spans innate and adaptive immunity by presenting antigenic peptides to CD4+ and CD8+ T cells. Multiple transcription factors form an enhanceosome complex on the MHC promoter and recruit transcriptional machinery to activate gene transcription. Immune signals such as interferon-γ (IFN-γ) control MHC level by up-regulating components of the enhanceosome complex. As MHC plays crucial roles in immune regulation, alterations in the MHC enhanceosome structure will alter the pace of rapid immune responses at the transcription level and lead to various diseases related to the immune system. In this review, we discuss the current understanding of the MHC enhanceosome, with a focus on the structures of MHC enhanceosome components and the molecular basis of MHC enhanceosome assembly.
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8
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Utgés JS, Tsenkov MI, Dietrich NJM, MacGowan SA, Barton GJ. Ankyrin repeats in context with human population variation. PLoS Comput Biol 2021; 17:e1009335. [PMID: 34428215 PMCID: PMC8415598 DOI: 10.1371/journal.pcbi.1009335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/03/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
Ankyrin protein repeats bind to a wide range of substrates and are one of the most common protein motifs in nature. Here, we collate a high-quality alignment of 7,407 ankyrin repeats and examine for the first time, the distribution of human population variants from large-scale sequencing of healthy individuals across this family. Population variants are not randomly distributed across the genome but are constrained by gene essentiality and function. Accordingly, we interpret the population variants in context with evolutionary constraint and structural features including secondary structure, accessibility and protein-protein interactions across 383 three-dimensional structures of ankyrin repeats. We find five positions that are highly conserved across homologues and also depleted in missense variants within the human population. These positions are significantly enriched in intra-domain contacts and so likely to be key for repeat packing. In contrast, a group of evolutionarily divergent positions are found to be depleted in missense variants in human and significantly enriched in protein-protein interactions. Our analysis also suggests the domain has three, not two surfaces, each with different patterns of enrichment in protein-substrate interactions and missense variants. Our findings will be of interest to those studying or engineering ankyrin-repeat containing proteins as well as those interpreting the significance of disease variants.
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Affiliation(s)
- Javier S. Utgés
- Division of Computational Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Maxim I. Tsenkov
- Division of Computational Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | - Noah J. M. Dietrich
- Division of Computational Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | - Stuart A. MacGowan
- Division of Computational Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | - Geoffrey J. Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
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9
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Chen X, Liao S, Makaros Y, Guo Q, Zhu Z, Krizelman R, Dahan K, Tu X, Yao X, Koren I, Xu C. Molecular basis for arginine C-terminal degron recognition by Cul2 FEM1 E3 ligase. Nat Chem Biol 2021; 17:254-262. [PMID: 33398168 DOI: 10.1038/s41589-020-00704-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/30/2020] [Indexed: 01/28/2023]
Abstract
Degrons are elements within protein substrates that mediate the interaction with specific degradation machineries to control proteolysis. Recently, a few classes of C-terminal degrons (C-degrons) that are recognized by dedicated cullin-RING ligases (CRLs) have been identified. Specifically, CRL2 using the related substrate adapters FEM1A/B/C was found to recognize C degrons ending with arginine (Arg/C-degron). Here, we uncover the molecular mechanism of Arg/C-degron recognition by solving a subset of structures of FEM1 proteins in complex with Arg/C-degron-bearing substrates. Our structural research, complemented by binding assays and global protein stability (GPS) analyses, demonstrates that FEM1A/C and FEM1B selectively target distinct classes of Arg/C-degrons. Overall, our study not only sheds light on the molecular mechanism underlying Arg/C-degron recognition for precise control of substrate turnover, but also provides valuable information for development of chemical probes for selectively regulating proteostasis.
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Affiliation(s)
- Xinyan Chen
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shanhui Liao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yaara Makaros
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Qiong Guo
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhongliang Zhu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Rina Krizelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Karin Dahan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Xiaoming Tu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Chao Xu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.
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10
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Li G, Tian Y, Zhu WG. The Roles of Histone Deacetylases and Their Inhibitors in Cancer Therapy. Front Cell Dev Biol 2020; 8:576946. [PMID: 33117804 PMCID: PMC7552186 DOI: 10.3389/fcell.2020.576946] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic mutations and abnormal gene regulation are key mechanisms underlying tumorigenesis. Nucleosomes, which consist of DNA wrapped around histone cores, represent the basic units of chromatin. The fifth amino group (Nε) of histone lysine residues is a common site for post-translational modifications (PTMs), and of these, acetylation is the second most common. Histone acetylation is modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), and is involved in the regulation of gene expression. Over the past two decades, numerous studies characterizing HDACs and HDAC inhibitors (HDACi) have provided novel and exciting insights concerning their underlying biological mechanisms and potential anti-cancer treatments. In this review, we detail the diverse structures of HDACs and their underlying biological functions, including transcriptional regulation, metabolism, angiogenesis, DNA damage response, cell cycle, apoptosis, protein degradation, immunity and other several physiological processes. We also highlight potential avenues to use HDACi as novel, precision cancer treatments.
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Affiliation(s)
- Guo Li
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Yuan Tian
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
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11
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Gao J, Xu C. Structural basis for the recognition of RFX7 by ANKRA2 and RFXANK. Biochem Biophys Res Commun 2020; 523:263-266. [DOI: 10.1016/j.bbrc.2019.12.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 10/25/2022]
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12
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Sonntag T, Moresco JJ, Yates JR, Montminy M. The KLDpT activation loop motif is critical for MARK kinase activity. PLoS One 2019; 14:e0225727. [PMID: 31794565 PMCID: PMC6890249 DOI: 10.1371/journal.pone.0225727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/11/2019] [Indexed: 11/19/2022] Open
Abstract
MAP/microtubule-affinity regulating kinases (MARK1-4) are members of the AMPK family of Ser/Thr-specific kinases, which phosphorylate substrates at consensus LXRXXSXXXL motifs. Within microtubule-associated proteins, MARKs also mediate phosphorylation of variant KXGS or ζXKXGSXXNΨ motifs, interfering with the ability of tau and MAP2/4 to bind to microtubules. Here we show that, although MARKs and the closely related salt-inducible kinases (SIKs) phosphorylate substrates with consensus AMPK motifs comparably, MARKs are more potent in recognizing variant ζXKXGSXXNΨ motifs on cellular tau. In studies to identify regions of MARKs that confer catalytic activity towards variant sites, we found that the C-terminal kinase associated-1 (KA1) domain in MARK1-3 mediates binding to microtubule-associated proteins CLASP1/2; but this interaction is dispensable for ζXKXGSXXNΨ phosphorylation. Mutational analysis of MARK2 revealed that the N-terminal kinase domain of MARK2 is sufficient for phosphorylation of both consensus and variant ζXKXGSXXNΨ sites. Within this domain, the KLDpT activation loop motif promotes MARK2 activity both intracellularly and in vitro, but has no effect on SIK2 activity. As KLDpT is conserved in all vertebrates MARKs, we conclude that this sequence is crucial for MARK-dependent regulation of cellular polarity.
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Affiliation(s)
- Tim Sonntag
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - James J. Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marc Montminy
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- * E-mail:
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13
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Koike R, Amemiya T, Horii T, Ota M. Structural changes of homodimers in the PDB. J Struct Biol 2017; 202:42-50. [PMID: 29233747 DOI: 10.1016/j.jsb.2017.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/30/2017] [Accepted: 12/08/2017] [Indexed: 01/25/2023]
Abstract
Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode. This approach was applied to all available homodimers in the Protein Data Bank (PDB). We defined two complex-specific motions: interface motion and subunit-spanning motion. In the former, each subunit of a complex constitutes a rigid body, and the relative movement between subunits occurs at the interface. In the latter, structural parts from distinct subunits constitute a rigid body, providing the relative movement spanning subunits. All structural changes were classified and examined. It was revealed that the complex-specific motions were common in the homodimers, detected in around 40% of families. The dimeric interfaces were likely to be small and flat for interface motion, while large and rugged for subunit-spanning motion. Interface motion was accompanied by a drastic change in contacts at the interface, while the change in the subunit-spanning motion was moderate. These results indicate that the interface properties of homodimers correlated with the type of complex-specific motion. The study demonstrates that the pipeline of SCPC and Motion Tree is useful for the massive analysis of structural change of protein complexes.
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Affiliation(s)
- Ryotaro Koike
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Takayuki Amemiya
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Tatsuya Horii
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Motonori Ota
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
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14
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Guo Q, Liao S, Zhu Z, Li Y, Li F, Xu C. Structural basis for the recognition of kinesin family member 21A (KIF21A) by the ankyrin domains of KANK1 and KANK2 proteins. J Biol Chem 2017; 293:557-566. [PMID: 29183992 DOI: 10.1074/jbc.m117.817494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/21/2017] [Indexed: 01/09/2023] Open
Abstract
A well-controlled microtubule organization is essential for intracellular transport, cytoskeleton maintenance, and cell development. KN motif and ankyrin repeat domain-containing protein 1 (KANK1), a member of KANK family, recruits kinesin family member 21A (KIF21A) to the cell cortex to control microtubule growth via its C-terminal ankyrin domain. However, how the KANK1 ankyrin domain recognizes KIF21A and whether other KANK proteins can also bind KIF21A remain unknown. Here, using a combination of structural, site-directed mutagenesis, and biochemical studies, we found that a stretch of ∼22 amino acids in KIF21A is sufficient for binding to KANK1 and its close homolog KANK2. We further solved the complex structure of the KIF21A peptide with either the KANK1 ankyrin domain or the KANK2 ankyrin domain. In each complex, KIF21A is recognized by two distinct pockets of the ankyrin domain and adopts helical conformations upon binding to the ankyrin domain. The elucidated KANK structures may advance our understanding of the role of KANK1 as a scaffolding molecule in controlling microtubule growth at the cell periphery.
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Affiliation(s)
- Qiong Guo
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China and.,the Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, Hefei 230027, China
| | - Shanhui Liao
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China and .,the Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, Hefei 230027, China
| | - Zhongliang Zhu
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China and.,the Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, Hefei 230027, China
| | - Yue Li
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China and.,the Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, Hefei 230027, China
| | - Fudong Li
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China and.,the Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, Hefei 230027, China
| | - Chao Xu
- From the Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China and .,the Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Sciences, Hefei 230027, China
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15
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Sluchanko NN. Association of Multiple Phosphorylated Proteins with the 14-3-3 Regulatory Hubs: Problems and Perspectives. J Mol Biol 2017; 430:20-26. [PMID: 29180038 DOI: 10.1016/j.jmb.2017.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/21/2017] [Accepted: 11/22/2017] [Indexed: 01/11/2023]
Abstract
14-3-3 proteins are well-known universal regulators binding a vast number of partners by recognizing their phosphorylated motifs, typically located within the intrinsically disordered regions. The abundance of such phosphomotifs ensures the involvement of 14-3-3 proteins in sophisticated protein-protein interaction networks that govern vital cellular processes. Thousands of 14-3-3 partners have been either experimentally identified or predicted, but the spatiotemporal hierarchy of the processes based on 14-3-3 interactions is not clearly understood. This is exacerbated by the lack of available structural information on full regulatory complexes involving 14-3-3, which resist high-resolution structural studies due to the presence of intrinsically disordered regions. Although deducing three-dimensional structures is of particular urgency, structural advances are lagging behind the rate at which novel 14-3-3 partners are discovered. Here I attempted to critically review the current state of the field and in particular to dissect the unknowns, focusing on questions that could help in moving the frontiers forward.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russian Federation; Department of Biophysics, School of Biology, Moscow State University, 119991 Moscow, Russian Federation.
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16
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Króliczewski J, Bartoszewski R, Króliczewska B. Chloroplast PetD protein: evidence for SRP/Alb3-dependent insertion into the thylakoid membrane. BMC PLANT BIOLOGY 2017; 17:213. [PMID: 29162052 PMCID: PMC5697057 DOI: 10.1186/s12870-017-1176-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/13/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND In thylakoid membrane, each monomer of the dimeric complex of cytochrome b 6 f is comprised of eight subunits that are both nucleus- and plastid-encoded. Proper cytochrome b 6 f complex integration into the thylakoid membrane requires numerous regulatory factors for coordinated transport, insertion and assembly of the subunits. Although, the chloroplast-encoded cytochrome b 6 f subunit IV (PetD) consists of three transmembrane helices, the signal and the mechanism of protein integration into the thylakoid membrane have not been identified. RESULTS Here, we demonstrate that the native PetD subunit cannot incorporate into the thylakoid membranes spontaneously, but that proper integration occurs through the post-translational signal recognition particle (SRP) pathway. Furthermore, we show that PetD insertion into thylakoid membrane involves the coordinated action of cpFTSY, cpSRP54 and ALB3 insertase. CONCLUSIONS PetD subunit integration into the thylakoid membrane is a post-translational and an SRP-dependent process that requires the formation of the cpSRP-cpFtsY-ALB3-PetD complex. This data provides a new insight into the molecular mechanisms by which membrane proteins integration into the thylakoid membrane is accomplished and is not limited to PetD.
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Affiliation(s)
- Jarosław Króliczewski
- Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany Medical University of Gdańsk, Hallera 107, 80-416 Gdansk, Poland
| | - Bożena Króliczewska
- Department of Animal Physiology and Biostructure, Faculty of Veterinary Medicine Wroclaw University of Environmental and Life Sciences, C.K Norwida 31, 50-375 Wrocław, Poland
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17
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Direct interaction with 14-3-3γ promotes surface expression of Best1 channel in astrocyte. Mol Brain 2017; 10:51. [PMID: 29121962 PMCID: PMC5679146 DOI: 10.1186/s13041-017-0331-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/28/2017] [Indexed: 01/01/2023] Open
Abstract
Background Bestrophin-1 (Best1) is a calcium-activated anion channel (CAAC) that is expressed broadly in mammalian tissues including the brain. We have previously reported that Best1 is expressed in hippocampal astrocytes at the distal peri-synaptic regions, called microdomains, right next to synaptic junctions, and that it disappears from the microdomains in Alzheimer’s disease mouse model. Although Best1 appears to be dynamically regulated, the mechanism of its regulation and modulation is poorly understood. It has been reported that a regulatory protein, 14-3-3 affects the surface expression of numerous membrane proteins in mammalian cells. Methods The protein-protein interaction between Best1 and 14-3-3γ was confirmed by yeast-two hybrid assay and BiFC method. The effect of 14-3-3γ on Best1-mediated current was measured by whole-cell patch clamp technique. Results We identified 14-3-3γ as novel binding partner of Best1 in astrocytes: among 7 isoforms of 14-3-3 protein, only 14-3-3γ was found to bind specifically. We determined a binding domain on the C-terminus of Best1 which is critical for an interaction with 14-3-3γ. We also revealed that interaction between Best1 and 14-3-3γ was mediated by phosphorylation of S358 in the C-terminus of Best1. We confirmed that surface expression of Best1 and Best1-mediated whole-cell current were significantly decreased after a gene-silencingof 14-3-3γ without a significant change in total Best1 expression in cultured astrocytes. Furthermore, we discovered that 14-3-3γ-shRNA reduced Best1-mediated glutamate release from hippocampal astrocyte by recording a PAR1 receptor-induced NMDA receptor-mediated current from CA1 pyramidal neurons in hippocampal slices injected with adenovirus carrying 14-3-3γ-shRNA. Finally, through a structural modeling, we found critical amino acid residues containing S358 of Best1 exhibiting binding affinities to 14-3-3γ. Conclusions 14-3-3γ promotes surface expression of Best1 channel in astrocytes through direct interaction.
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18
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Sluchanko NN, Tugaeva KV, Greive SJ, Antson AA. Chimeric 14-3-3 proteins for unraveling interactions with intrinsically disordered partners. Sci Rep 2017; 7:12014. [PMID: 28931924 PMCID: PMC5607241 DOI: 10.1038/s41598-017-12214-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023] Open
Abstract
In eukaryotes, several “hub” proteins integrate signals from different interacting partners that bind through intrinsically disordered regions. The 14-3-3 protein hub, which plays wide-ranging roles in cellular processes, has been linked to numerous human disorders and is a promising target for therapeutic intervention. Partner proteins usually bind via insertion of a phosphopeptide into an amphipathic groove of 14-3-3. Structural plasticity in the groove generates promiscuity allowing accommodation of hundreds of different partners. So far, accurate structural information has been derived for only a few 14-3-3 complexes with phosphopeptide-containing proteins and a variety of complexes with short synthetic peptides. To further advance structural studies, here we propose a novel approach based on fusing 14-3-3 proteins with the target partner peptide sequences. Such chimeric proteins are easy to design, express, purify and crystallize. Peptide attachment to the C terminus of 14-3-3 via an optimal linker allows its phosphorylation by protein kinase A during bacterial co-expression and subsequent binding at the amphipathic groove. Crystal structures of 14-3-3 chimeras with three different peptides provide detailed structural information on peptide-14-3-3 interactions. This simple but powerful approach, employing chimeric proteins, can reinvigorate studies of 14-3-3/phosphoprotein assemblies, including those with challenging low-affinity partners, and may facilitate the design of novel biosensors.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071, Moscow, Russian Federation. .,Department of biophysics, School of Biology, Moscow State University, 119991, Moscow, Russian Federation.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071, Moscow, Russian Federation.,Department of biochemistry, School of Biology, Moscow State University, 119991, Moscow, Russian Federation
| | - Sandra J Greive
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, United Kingdom
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19
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Lemonidis K, MacLeod R, Baillie GS, Chamberlain LH. Peptide array-based screening reveals a large number of proteins interacting with the ankyrin-repeat domain of the zDHHC17 S-acyltransferase. J Biol Chem 2017; 292:17190-17202. [PMID: 28882895 PMCID: PMC5655499 DOI: 10.1074/jbc.m117.799650] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/29/2017] [Indexed: 01/08/2023] Open
Abstract
zDHHC S-acyltransferases are enzymes catalyzing protein S-acylation, a common post-translational modification on proteins frequently affecting their membrane targeting and trafficking. The ankyrin repeat (AR) domain of zDHHC17 (HIP14) and zDHHC13 (HIP14L) S-acyltransferases, which is involved in both substrate recruitment and S-acylation-independent functions, was recently shown to bind at least six proteins, by specific recognition of a consensus sequence in them. To further refine the rules governing binding to the AR of zDHHC17, we employed peptide arrays based on zDHHC AR-binding motif (zDABM) sequences of synaptosomal-associated protein 25 (SNAP25) and cysteine string protein α (CSPα). Quantitative comparisons of the binding preferences of 400 peptides allowed us to construct a position-specific scoring matrix (PSSM) for zDHHC17 AR binding, with which we predicted and subsequently validated many putative zDHHC17 interactors. We identified 95 human zDABM sequences with unexpected versatility in amino acid usage; these sequences were distributed among 90 proteins, of which 62 have not been previously implicated in zDHHC17/13 binding. These zDABM-containing proteins included all family members of the SNAP25, sprouty, cornifelin, ankyrin, and SLAIN-motif containing families; seven endogenous Gag polyproteins sharing the same binding sequence; and several proteins involved in cytoskeletal organization, cell communication, and regulation of signaling. A dozen of the zDABM-containing proteins had more than one zDABM sequence, whereas isoform-specific binding to the AR of zDHHC17 was identified for the Ena/VASP-like protein. The large number of zDABM sequences within the human proteome suggests that zDHHC17 may be an interaction hub regulating many cellular processes.
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Affiliation(s)
- Kimon Lemonidis
- From The Strathclyde Institute of Pharmacy and Biomedical Sciences, 161 Cathedral Street, University of Strathclyde, Glasgow G4 0RE and
| | - Ruth MacLeod
- the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Wolfson Link Building, Glasgow G12 8QQ, Scotland, United Kingdom
| | - George S Baillie
- the Institute of Cardiovascular and Medical Sciences, University of Glasgow, Wolfson Link Building, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Luke H Chamberlain
- From The Strathclyde Institute of Pharmacy and Biomedical Sciences, 161 Cathedral Street, University of Strathclyde, Glasgow G4 0RE and
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20
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Substrate selectivity in the zDHHC family of S-acyltransferases. Biochem Soc Trans 2017; 45:751-758. [PMID: 28620036 DOI: 10.1042/bst20160309] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 02/07/2023]
Abstract
S-acylation is a reversible lipid modification occurring on cysteine residues mediated by a family of membrane-bound 'zDHHC' enzymes. S-acylation predominantly results in anchoring of soluble proteins to membrane compartments or in the trafficking of membrane proteins to different compartments. Recent work has shown that although S-acylation of some proteins may involve very weak interactions with zDHHC enzymes, a pool of zDHHC enzymes exhibit strong and specific interactions with substrates, thereby recruiting them for S-acylation. For example, the ankyrin-repeat domains of zDHHC17 and zDHHC13 interact specifically with unstructured consensus sequences present in some proteins, thus contributing to substrate specificity of these enzymes. In addition to this new information on zDHHC enzyme protein substrate specificity, recent work has also identified marked differences in selectivity of zDHHC enzymes for acyl-CoA substrates and has started to unravel the underlying molecular basis for this lipid selectivity. This review will focus on the protein and acyl-CoA selectivity of zDHHC enzymes.
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21
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Wong K, Perpich JD, Kozlov G, Cygler M, Abu Kwaik Y, Gehring K. Structural Mimicry by a Bacterial F Box Effector Hijacks the Host Ubiquitin-Proteasome System. Structure 2017; 25:376-383. [PMID: 28111017 DOI: 10.1016/j.str.2016.12.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/24/2016] [Accepted: 12/21/2016] [Indexed: 02/04/2023]
Abstract
Ankyrin B (AnkB/LegAU13) is a translocated F box effector essential for the intracellular replication of the pathogen Legionella pneumophila. AnkB co-opts a host ubiquitin ligase to decorate the pathogen-containing vacuole with K48-linked polyubiquitinated proteins and degrade host proteins as a source of energy. Here, we report that AnkB commandeers the host ubiquitin-proteasome system through mimicry of two eukaryotic protein domains. Using X-ray crystallography, we determined the 3D structure of AnkB in complex with Skp1, a component of the human SCF ubiquitination ligase. The structure confirms that AnkB contains an N-terminal F box similar to Skp2 and a C-terminal substrate-binding domain similar to eukaryotic ankyrin repeats. We identified crucial amino acids in the substrate-binding domain of AnkB and showed them to be essential for the function of AnkB in L. pneumophila intracellular proliferation. The study reveals how Legionella uses molecular mimicry to manipulate the host ubiquitination pathway and proliferate intracellularly.
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Affiliation(s)
- Kathy Wong
- Department of Biochemistry and Groupe de recherche axé sur la structure des protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - John D Perpich
- Department of Microbiology and Immunology, University of Louisville College of Medicine, Louisville, KY 40202, USA
| | - Guennadi Kozlov
- Department of Biochemistry and Groupe de recherche axé sur la structure des protéines, McGill University, Montreal, QC H3G 0B1, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville College of Medicine, Louisville, KY 40202, USA
| | - Kalle Gehring
- Department of Biochemistry and Groupe de recherche axé sur la structure des protéines, McGill University, Montreal, QC H3G 0B1, Canada.
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22
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Maolanon A, Madsen A, Olsen C. Innovative Strategies for Selective Inhibition of Histone Deacetylases. Cell Chem Biol 2016; 23:759-768. [DOI: 10.1016/j.chembiol.2016.06.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 05/24/2016] [Accepted: 06/22/2016] [Indexed: 01/22/2023]
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23
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Mullooly M, McGowan PM, Crown J, Duffy MJ. The ADAMs family of proteases as targets for the treatment of cancer. Cancer Biol Ther 2016; 17:870-80. [PMID: 27115328 DOI: 10.1080/15384047.2016.1177684] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The ADAMs (a disintegrin and metalloproteases) are transmembrane multidomain proteins implicated in multiple biological processes including proteolysis, cell adhesion, cell fusion, cell proliferation and cell migration. Of these varied activities, the best studied is their role in proteolysis. However, of the 22 ADAMs believed to be functional in humans, only approximately a half possess matrix metalloproteinase (MMP)-like protease activity. In contrast to MMPs which are mostly implicated in the degradation of extracellular matrix proteins, the main ADAM substrates are the ectodomains of type I and type II transmembrane proteins. These include growth factor/cytokine precursors, growth factor/cytokine receptors and adhesion proteins. Recently, several different ADAMs, especially ADAM17, have been shown to play a role in the development and progression of multiple cancer types. Consistent with this role in cancer, targeting ADAM17 with either low molecular weight inhibitors or monoclonal antibodies was shown to have anti-cancer activity in multiple preclinical systems. Although early phase clinical trials have shown no serious side effects with a dual ADAM10/17 low molecular weight inhibitor, the consequences of long-term treatment with these agents is unknown. Furthermore, efficacy in clinical trials remains to be shown.
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Affiliation(s)
- Maeve Mullooly
- a National Institutes of Health , Bethesda , MD , USA.,b UCD School of Medicine and Medical Science , Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Ireland
| | - Patricia M McGowan
- b UCD School of Medicine and Medical Science , Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Ireland.,c Education and Research Center , St. Vincent's University Hospital , Dublin , Ireland
| | - John Crown
- d Department of Medical Oncology , St. Vincent's University Hospital , Dublin , Ireland
| | - Michael J Duffy
- b UCD School of Medicine and Medical Science , Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Ireland.,e UCD Clinical Research Center , St. Vincent's University Hospital , Dublin , Ireland
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24
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Characterization and small-molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR. Proc Natl Acad Sci U S A 2016; 113:E1152-61. [PMID: 26888287 DOI: 10.1073/pnas.1516631113] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cystic fibrosis is a fatal genetic disease, most frequently caused by the retention of the CFTR (cystic fibrosis transmembrane conductance regulator) mutant protein in the endoplasmic reticulum (ER). The binding of the 14-3-3 protein to the CFTR regulatory (R) domain has been found to enhance CFTR trafficking to the plasma membrane. To define the mechanism of action of this protein-protein interaction, we have examined the interaction in vitro. The disordered multiphosphorylated R domain contains nine different 14-3-3 binding motifs. Furthermore, the 14-3-3 protein forms a dimer containing two amphipathic grooves that can potentially bind these phosphorylated motifs. This results in a number of possible binding mechanisms between these two proteins. Using multiple biochemical assays and crystal structures, we show that the interaction between them is governed by two binding sites: The key binding site of CFTR (pS768) occupies one groove of the 14-3-3 dimer, and a weaker, secondary binding site occupies the other binding groove. We show that fusicoccin-A, a natural-product tool compound used in studies of 14-3-3 biology, can stabilize the interaction between 14-3-3 and CFTR by selectively interacting with a secondary binding motif of CFTR (pS753). The stabilization of this interaction stimulates the trafficking of mutant CFTR to the plasma membrane. This definition of the druggability of the 14-3-3-CFTR interface might offer an approach for cystic fibrosis therapeutics.
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25
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Liu H, Li J, Raval MH, Yao N, Deng X, Lu Q, Nie S, Feng W, Wan J, Yengo CM, Liu W, Zhang M. Myosin III-mediated cross-linking and stimulation of actin bundling activity of Espin. eLife 2016; 5. [PMID: 26785147 PMCID: PMC4758956 DOI: 10.7554/elife.12856] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 01/18/2016] [Indexed: 11/13/2022] Open
Abstract
Class III myosins (Myo3) and actin-bundling protein Espin play critical roles in regulating the development and maintenance of stereocilia in vertebrate hair cells, and their defects cause hereditary hearing impairments. Myo3 interacts with Espin1 through its tail homology I motif (THDI), however it is not clear how Myo3 specifically acts through Espin1 to regulate the actin bundle assembly and stabilization. Here we discover that Myo3 THDI contains a pair of repeat sequences capable of independently and strongly binding to the ankyrin repeats of Espin1, revealing an unexpected Myo3-mediated cross-linking mechanism of Espin1. The structures of Myo3 in complex with Espin1 not only elucidate the mechanism of the binding, but also reveal a Myo3-induced release of Espin1 auto-inhibition mechanism. We also provide evidence that Myo3-mediated cross-linking can further promote actin fiber bundling activity of Espin1.
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Affiliation(s)
- Haiyang Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jianchao Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Manmeet H Raval
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, United States
| | - Ningning Yao
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Xiaoying Deng
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Qing Lu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Si Nie
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Feng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Christopher M Yengo
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, United States
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Mingjie Zhang
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
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26
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Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP. Biochem J 2015; 473:179-87. [PMID: 26527736 DOI: 10.1042/bj20150830] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 11/17/2022]
Abstract
TXNIP (thioredoxin-interacting protein) negatively regulates the antioxidative activity of thioredoxin and participates in pleiotropic cellular processes. Its deregulation is linked to various human diseases, including diabetes, acute myeloid leukaemia and cardiovascular diseases. The E3 ubiquitin ligase Itch (Itchy homologue) polyubiquitinates TXNIP to promote its degradation via the ubiquitin-proteasome pathway, and this Itch-mediated polyubiquitination of TXNIP is dependent on the interaction of the four WW domains of Itch with the two PPxY motifs of TXNIP. However, the molecular mechanism of this interaction of TXNIP with Itch remains elusive. In the present study, we found that each of the four WW domains of Itch exhibited different binding affinities for TXNIP, whereas multivalent engagement between the four WW domains of Itch and the two PPxY motifs of TXNIP resulted in their strong binding avidity. Our structural analyses demonstrated that the third and fourth WW domains of Itch were able to recognize both PPxY motifs of TXNIP simultaneously, supporting a multivalent binding mode between Itch and TXNIP. Interestingly, the phosphorylation status on the tyrosine residue of the PPxY motifs of TXNIP serves as a molecular switch in its choice of binding partners and thereby downstream biological signalling outcomes. Phosphorylation of this tyrosine residue of TXNIP diminished the binding capability of PPxY motifs of TXNIP to Itch, whereas this phosphorylation is a prerequisite to the binding activity of TXNIP to SHP2 [SH2 (Src homology 2) domain-containing protein tyrosine phosphatase 2] and their roles in stabilizing the phosphorylation and activation of CSK (c-Src tyrosine kinase).
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Babula JJ, Liu JY. Integrate Omics Data and Molecular Dynamics Simulations toward Better Understanding of Human 14-3-3 Interactomes and Better Drugs for Cancer Therapy. J Genet Genomics 2015; 42:531-547. [PMID: 26554908 DOI: 10.1016/j.jgg.2015.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/03/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022]
Abstract
The 14-3-3 protein family is among the most extensively studied, yet still largely mysterious protein families in mammals to date. As they are well recognized for their roles in apoptosis, cell cycle regulation, and proliferation in healthy cells, aberrant 14-3-3 expression has unsurprisingly emerged as instrumental in the development of many cancers and in prognosis. Interestingly, while the seven known 14-3-3 isoforms in humans have many similar functions across cell types, evidence of isoform-specific functions and localization has been observed in both healthy and diseased cells. The strikingly high similarity among 14-3-3 isoforms has made it difficult to delineate isoform-specific functions and for isoform-specific targeting. Here, we review our knowledge of 14-3-3 interactome(s) generated by high-throughput techniques, bioinformatics, structural genomics and chemical genomics and point out that integrating the information with molecular dynamics (MD) simulations may bring us new opportunity to the design of isoform-specific inhibitors, which can not only be used as powerful research tools for delineating distinct interactomes of individual 14-3-3 isoforms, but also can serve as potential new anti-cancer drugs that selectively target aberrant 14-3-3 isoform.
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Affiliation(s)
- JoAnne J Babula
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202, USA
| | - Jing-Yuan Liu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 980 W. Walnut Street, Indianapolis, IN 46202, USA; Department of Computer and Information Science, Indiana University Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, IN 46202, USA.
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Lemonidis K, Sanchez-Perez MC, Chamberlain LH. Identification of a Novel Sequence Motif Recognized by the Ankyrin Repeat Domain of zDHHC17/13 S-Acyltransferases. J Biol Chem 2015; 290:21939-50. [PMID: 26198635 PMCID: PMC4571948 DOI: 10.1074/jbc.m115.657668] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/20/2015] [Indexed: 11/06/2022] Open
Abstract
S-Acylation is a major post-translational modification affecting several cellular processes. It is particularly important for neuronal functions. This modification is catalyzed by a family of transmembrane S-acyltransferases that contain a conserved zinc finger DHHC (zDHHC) domain. Typically, eukaryote genomes encode for 7-24 distinct zDHHC enzymes, with two members also harboring an ankyrin repeat (AR) domain at their cytosolic N termini. The AR domain of zDHHC enzymes is predicted to engage in numerous interactions and facilitates both substrate recruitment and S-acylation-independent functions; however, the sequence/structural features recognized by this module remain unknown. The two mammalian AR-containing S-acyltransferases are the Golgi-localized zDHHC17 and zDHHC13, also known as Huntingtin-interacting proteins 14 and 14-like, respectively; they are highly expressed in brain, and their loss in mice leads to neuropathological deficits that are reminiscent of Huntington's disease. Here, we report that zDHHC17 and zDHHC13 recognize, via their AR domain, evolutionary conserved and closely related sequences of a [VIAP][VIT]XXQP consensus in SNAP25, SNAP23, cysteine string protein, Huntingtin, cytoplasmic linker protein 3, and microtubule-associated protein 6. This novel AR-binding sequence motif is found in regions predicted to be unstructured and is present in a number of zDHHC17 substrates and zDHHC17/13-interacting S-acylated proteins. This is the first study to identify a motif recognized by AR-containing zDHHCs.
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Affiliation(s)
- Kimon Lemonidis
- From the Strathclyde Institute of Pharmacy and Biomedical Sciences, Univesity of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Maria C Sanchez-Perez
- From the Strathclyde Institute of Pharmacy and Biomedical Sciences, Univesity of Strathclyde, Glasgow G4 0RE, United Kingdom
| | - Luke H Chamberlain
- From the Strathclyde Institute of Pharmacy and Biomedical Sciences, Univesity of Strathclyde, Glasgow G4 0RE, United Kingdom
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Secreted Frizzled-related protein 3 (sFRP3)-mediated suppression of interleukin-6 receptor release by A disintegrin and metalloprotease 17 (ADAM17) is abrogated in the osteoarthritis-associated rare double variant of sFRP3. Biochem J 2015; 468:507-18. [DOI: 10.1042/bj20141231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 04/07/2015] [Indexed: 11/17/2022]
Abstract
A disintegrin and metalloprotease 17 (ADAM17) activity and secreted Frizzled-related protein 3 (sFRP3) down-regulation or expression of its rare double variant is associated with arthritis. sFRP3 interacts with interleukin-6 receptor (IL-6R) and ADAM17 and suppresses ADAM17 activity, whereas the rare variant does not; these findings provide explanation for their opposing pathogenic associations.
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Nie J, Xu C, Jin J, Aka JA, Tempel W, Nguyen V, You L, Weist R, Min J, Pawson T, Yang XJ. Ankyrin repeats of ANKRA2 recognize a PxLPxL motif on the 3M syndrome protein CCDC8. Structure 2015; 23:700-12. [PMID: 25752541 DOI: 10.1016/j.str.2015.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 11/30/2022]
Abstract
Peptide motifs are often used for protein-protein interactions. We have recently demonstrated that ankyrin repeats of ANKRA2 and the paralogous bare lymphocyte syndrome transcription factor RFXANK recognize PxLPxL/I motifs shared by megalin, three histone deacetylases, and RFX5. We show here that that CCDC8 is a major partner of ANKRA2 but not RFXANK in cells. The CCDC8 gene is mutated in 3M syndrome, a short-stature disorder with additional facial and skeletal abnormalities. Two other genes mutated in this syndrome encode CUL7 and OBSL1. While CUL7 is a ubiquitin ligase and OBSL1 associates with the cytoskeleton, little is known about CCDC8. Binding and structural analyses reveal that the ankyrin repeats of ANKRA2 recognize a PxLPxL motif at the C-terminal region of CCDC8. The N-terminal part interacts with OBSL1 to form a CUL7 ligase complex. These results link ANKRA2 unexpectedly to 3M syndrome and suggest novel regulatory mechanisms for histone deacetylases and RFX7.
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Affiliation(s)
- Jianyun Nie
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada; Department of Breast Cancer, The Third Affiliated Hospital, Kunming Medical University, Yunnan 650118, China
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Jing Jin
- Lunenfeld-tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Juliette A Aka
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Vivian Nguyen
- Lunenfeld-tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Linya You
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Ryan Weist
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Tony Pawson
- Lunenfeld-tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Xiang-Jiao Yang
- The Rosalind & Morris Goodman Cancer Research Center, Department of Medicine, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada; McGill University Health Center, Montréal, QC H3A 1A3, Canada.
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Wang C, Wei Z, Chen K, Ye F, Yu C, Bennett V, Zhang M. Structural basis of diverse membrane target recognitions by ankyrins. eLife 2014; 3. [PMID: 25383926 PMCID: PMC4358367 DOI: 10.7554/elife.04353] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/07/2014] [Indexed: 12/24/2022] Open
Abstract
Ankyrin adaptors together with their spectrin partners coordinate diverse ion channels and cell adhesion molecules within plasma membrane domains and thereby promote physiological activities including fast signaling in the heart and nervous system. Ankyrins specifically bind to numerous membrane targets through their 24 ankyrin repeats (ANK repeats), although the mechanism for the facile and independent evolution of these interactions has not been resolved. Here we report the structures of ANK repeats in complex with an inhibitory segment from the C-terminal regulatory domain and with a sodium channel Nav1.2 peptide, respectively, showing that the extended, extremely conserved inner groove spanning the entire ANK repeat solenoid contains multiple target binding sites capable of accommodating target proteins with very diverse sequences via combinatorial usage of these sites. These structures establish a framework for understanding the evolution of ankyrins' membrane targets, with implications for other proteins containing extended ANK repeat domains. DOI:http://dx.doi.org/10.7554/eLife.04353.001 Proteins are made up of smaller building blocks called amino acids that are linked to form long chains that then fold into specific shapes. Each protein gets its unique identity from the number and order of the amino acids that it contains, but different proteins can contain similar arrangements of amino acids. These similar sequences, known as motifs, are usually short and typically mark the sites within proteins that bind to other molecules or proteins. A single protein can contain many motifs, including multiple repeats of the same motif. One common motif is called the ankyrin (or ANK) repeat, which is found in 100s of proteins in different species, including bacteria and humans. Ankyrin proteins perform a range of important functions, such as connecting proteins in the cell surface membrane to a scaffold-like structure underneath the membrane. Proteins containing ankyrin repeats are known to interact with a diverse range of other proteins (or targets) that are different in size and shape. The 24 repeats found in human ankyrin proteins appear to have essentially remained unchanged for the last 500 million years. As such, it remains unclear how the conserved ankyrin repeats can bind to such a wide variety of protein targets. Now, Wang, Wei et al. have uncovered the three-dimensional structure of ankyrin repeats from a human ankyrin protein while it was bound either to a regulatory fragment from another ankyrin protein or to a region of a target protein (which transports sodium ions in and out of cells). The ankyrin repeats were shown to form an extended ‘left-handed helix’: a structure that has also been seen in other proteins with different repeating motifs. Wang, Wei et al. found that the ankyrin protein fragment bound to the inner surface of the part of the helix formed by the first 14 ankyrin repeats. The target protein region also bound to the helix's inner surface. Wang, Wei et al. show that this surface contains many binding sites that can be used, in different combinations, to allow ankyrins to interact with diverse proteins. Other proteins with long sequences of repeats are widespread in nature, but uncovering the structures of these proteins is technically challenging. Wang, Wei et al.'s findings might reveal new insights into the functions of many of such proteins in a wide range of living species. Furthermore, the new structures could help explain why specific mutations in the genes that encode ankyrins (or their binding targets) can cause various diseases in humans—including heart diseases and psychiatric disorders. DOI:http://dx.doi.org/10.7554/eLife.04353.002
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Affiliation(s)
- Chao Wang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Zhiyi Wei
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Keyu Chen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Fei Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Cong Yu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Vann Bennett
- Department of Biochemistry, Howard Hughes Medical Institute, Duke University Medical Center, Durham, United States
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, Hong Kong
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Modular peptide binding: From a comparison of natural binders to designed armadillo repeat proteins. J Struct Biol 2014; 185:147-62. [DOI: 10.1016/j.jsb.2013.07.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 07/26/2013] [Accepted: 07/27/2013] [Indexed: 11/23/2022]
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Skjevik AA, Mileni M, Baumann A, Halskau O, Teigen K, Stevens RC, Martinez A. The N-terminal sequence of tyrosine hydroxylase is a conformationally versatile motif that binds 14-3-3 proteins and membranes. J Mol Biol 2013; 426:150-68. [PMID: 24055376 DOI: 10.1016/j.jmb.2013.09.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 01/17/2023]
Abstract
Tyrosine hydroxylase (TH) catalyzes the rate-limiting step in the synthesis of catecholamine neurotransmitters, and a reduction in TH activity is associated with several neurological diseases. Human TH is regulated, among other mechanisms, by Ser19-phosphorylation-dependent interaction with 14-3-3 proteins. The N-terminal sequence (residues 1-43), which corresponds to an extension to the TH regulatory domain, also interacts with negatively charged membranes. By using X-ray crystallography together with molecular dynamics simulations and structural bioinformatics analysis, we have probed the conformations of the Ser19-phosphorylated N-terminal peptide [THp-(1-43)] bound to 14-3-3γ, free in solution and bound to a phospholipid bilayer, and of the unphosphorylated peptide TH-(1-43) both free and bilayer bound. As seen in the crystal structure of THp-(1-43) complexed with 14-3-3γ, the region surrounding pSer19 adopts an extended conformation in the bound state, whereas THp-(1-43) adopts a bent conformation when free in solution, with higher content of secondary structure and higher number of internal hydrogen bonds. TH-(1-43) in solution presents the highest mobility and least defined structure of all forms studied, and it shows an energetically more favorable interaction with membranes relative to THp-(1-43). Cationic residues, notably Arg15 and Arg16, which are the recognition sites of the kinases phosphorylating at Ser19, are also contributing to the interaction with the membrane. Our results reveal the structural flexibility of this region of TH, in accordance with the functional versatility and conformational adaptation to different partners. Furthermore, this structural information has potential relevance for the development of therapeutics for neurodegenerative disorders, through modulation of TH-partner interactions.
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Affiliation(s)
| | - Mauro Mileni
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Oyvind Halskau
- Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5020 Bergen, Norway
| | - Knut Teigen
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Raymond C Stevens
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.
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Jin J, Pawson T. Modular evolution of phosphorylation-based signalling systems. Philos Trans R Soc Lond B Biol Sci 2012; 367:2540-55. [PMID: 22889906 DOI: 10.1098/rstb.2012.0106] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phosphorylation sites are formed by protein kinases ('writers'), frequently exert their effects following recognition by phospho-binding proteins ('readers') and are removed by protein phosphatases ('erasers'). This writer-reader-eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved.
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Affiliation(s)
- Jing Jin
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada.
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Tudor domains of the PRC2 components PHF1 and PHF19 selectively bind to histone H3K36me3. Biochem Biophys Res Commun 2012; 430:547-53. [PMID: 23228662 DOI: 10.1016/j.bbrc.2012.11.116] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 11/29/2012] [Indexed: 01/30/2023]
Abstract
PRC2 is the major H3K27 methyltransferase and is responsible for maintaining repressed gene expression patterns throughout development. It contains four core components: EZH2, EED, SUZ12 and RbAp46/48 and some cell-type specific components. In this study, we focused on characterizing the histone binding domains of PHF1 and PHF19, and found that the Tudor domains of PHF1 and PHF19 selectively bind to histone H3K36me3. Structural analysis of these Tudor domains also shed light on how these Tudor domains selectively bind to histone H3K36me3. The histone H3K36me3 binding by the Tudor domains of PHF1, PHF19 and likely MTF2 provide another recruitment and regulatory mechanism for the PRC2 complex. In addition, we found that the first PHD domains of PHF1 and PHF19 do not exhibit histone H3K4 binding ability, nor do they affect the Tudor domain binding to histones.
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