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Teyssier V, Williamson CR, Shata E, Rosen SP, Jones N, Bisson N. Adapting to change: resolving the dynamic and dual roles of NCK1 and NCK2. Biochem J 2024; 481:1411-1435. [PMID: 39392452 DOI: 10.1042/bcj20230232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 09/12/2024] [Accepted: 09/16/2024] [Indexed: 10/12/2024]
Abstract
Adaptor proteins play central roles in the assembly of molecular complexes and co-ordinated activation of specific pathways. Through their modular domain structure, the NCK family of adaptor proteins (NCK1 and NCK2) link protein targets via their single SRC Homology (SH) 2 and three SH3 domains. Classically, their SH2 domain binds to phosphotyrosine motif-containing receptors (e.g. receptor tyrosine kinases), while their SH3 domains bind polyproline motif-containing cytoplasmic effectors. Due to these functions being established for both NCK1 and NCK2, their roles were inaccurately assumed to be redundant. However, in contrast with this previously held view, NCK1 and NCK2 now have a growing list of paralog-specific functions, which underscores the need to further explore their differences. Here we review current evidence detailing how these two paralogs are unique, including differences in their gene/protein regulation, binding partners and overall contributions to cellular functions. To help explain these contrasting characteristics, we then discuss SH2/SH3 structural features, disordered interdomain linker regions and post-translational modifications. Together, this review seeks to highlight the importance of distinguishing NCK1 and NCK2 in research and to pave the way for investigations into the origins of their interaction specificity.
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Affiliation(s)
- Valentine Teyssier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Division Oncologie, Québec, QC, Canada
- Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
- PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
| | - Casey R Williamson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Erka Shata
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Stephanie P Rosen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nina Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Division Oncologie, Québec, QC, Canada
- Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
- PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada
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2
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Paes de Faria J, Vale-Silva RS, Fässler R, Werner HB, Relvas JB. Pinch2 regulates myelination in the mouse central nervous system. Development 2022; 149:275524. [DOI: 10.1242/dev.200597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The extensive morphological changes of oligodendrocytes during axon ensheathment and myelination involve assembly of the Ilk-Parvin-Pinch (IPP) heterotrimeric complex of proteins to relay essential mechanical and biochemical signals between integrins and the actin cytoskeleton. Binding of Pinch1 and Pinch2 isoforms to Ilk is mutually exclusive and allows the formation of distinct IPP complexes with specific signaling properties. Using tissue-specific conditional gene ablation in mice, we reveal an essential role for Pinch2 during central nervous system myelination. Unlike Pinch1 gene ablation, loss of Pinch2 in oligodendrocytes results in hypermyelination and in the formation of pathological myelin outfoldings in white matter regions. These structural changes concur with inhibition of Rho GTPase RhoA and Cdc42 activities and phenocopy aspects of myelin pathology observed in corresponding mouse mutants. We propose a dual role for Pinch2 in preventing an excess of myelin wraps through RhoA-dependent control of membrane growth and in fostering myelin stability via Cdc42-dependent organization of cytoskeletal septins. Together, these findings indicate that IPP complexes containing Pinch2 act as a crucial cell-autonomous molecular hub ensuring synchronous control of key signaling networks during developmental myelination.
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Affiliation(s)
- Joana Paes de Faria
- Department of Neurobiology and Neurological Disease, Glial Cell Biology Laboratory, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto 1 , 4200-135 Porto , Portugal
- Department of Neurobiology and Neurological Disease, Glial Cell Biology Laboratory, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto 2 , 4200-135 Porto , Portugal
| | - Raquel S. Vale-Silva
- Department of Neurobiology and Neurological Disease, Glial Cell Biology Laboratory, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto 1 , 4200-135 Porto , Portugal
- Department of Neurobiology and Neurological Disease, Glial Cell Biology Laboratory, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto 2 , 4200-135 Porto , Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto 3 , 4050-313 Porto , Portugal
| | - Reinhard Fässler
- Department of Molecular Medicine, Max Planck Institute of Biochemistry 4 , 82152 Martinsried , Germany
| | - Hauke B. Werner
- Max Planck Institute of Experimental Medicine 5 Department of Neurogenetics , , D-37075 Gottingen , Germany
| | - João B. Relvas
- Department of Neurobiology and Neurological Disease, Glial Cell Biology Laboratory, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto 1 , 4200-135 Porto , Portugal
- Department of Neurobiology and Neurological Disease, Glial Cell Biology Laboratory, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto 2 , 4200-135 Porto , Portugal
- Faculty of Medicine, Universidade do Porto 6 Department of Biomedicine , , 4200-319 Porto , Portugal
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3
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ATP allosterically stabilizes integrin-linked kinase for efficient force generation. Proc Natl Acad Sci U S A 2022; 119:e2106098119. [PMID: 35259013 PMCID: PMC8933812 DOI: 10.1073/pnas.2106098119] [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] [Indexed: 12/15/2022] Open
Abstract
The pseudokinase integrin-linked kinase (ILK) is a central component of focal adhesions, cytoplasmic multiprotein complexes that integrate and transduce biochemical and mechanical signals from the extracellular environment into the cell and vice versa. However, the precise molecular functions, particularly the mechanosensory properties of ILK and the significance of retained adenosine triphosphate (ATP) binding, are still unclear. Combining molecular-dynamics simulations with cell biology, we establish a role for ATP binding to pseudokinases. We find that ATP promotes the structural stability of ILK, allosterically influences the interaction between ILK and its binding partner parvin at adhesions, and enhances the mechanoresistance of this complex. On the cellular level, ATP binding facilitates efficient traction force buildup, focal adhesion stabilization, and efficient cell migration. Focal adhesions link the actomyosin cytoskeleton to the extracellular matrix regulating cell adhesion, shape, and migration. Adhesions are dynamically assembled and disassembled in response to extrinsic and intrinsic forces, but how the essential adhesion component integrin-linked kinase (ILK) dynamically responds to mechanical force and what role adenosine triphosphate (ATP) bound to this pseudokinase plays remain elusive. Here, we apply force–probe molecular-dynamics simulations of human ILK:α-parvin coupled to traction force microscopy to explore ILK mechanotransducing functions. We identify two key salt-bridge–forming arginines within the allosteric, ATP-dependent force-propagation network of ILK. Disrupting this network by mutation impedes parvin binding, focal adhesion stabilization, force generation, and thus migration. Under tension, ATP shifts the balance from rupture of the complex to protein unfolding, indicating that ATP increases the force threshold required for focal adhesion disassembly. Our study proposes a role of ATP as an obligatory binding partner for structural and mechanical integrity of the pseudokinase ILK, ensuring efficient cellular force generation and migration.
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4
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Kadry YA, Huet-Calderwood C, Simon B, Calderwood DA. Kindlin-2 interacts with a highly conserved surface of ILK to regulate focal adhesion localization and cell spreading. J Cell Sci 2018; 131:jcs.221184. [PMID: 30254023 DOI: 10.1242/jcs.221184] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
The integrin-associated adaptor proteins integrin-linked kinase (ILK) and kindlin-2 play central roles in integrin signaling and control of cell morphology. A direct ILK-kindlin-2 interaction is conserved across species and involves the F2PH subdomain of kindlin-2 and the pseudokinase domain (pKD) of ILK. However, complete understanding of the ILK-kindlin-2 interaction and its role in integrin-mediated signaling has been impeded by difficulties identifying the binding site for kindlin-2 on ILK. We used conservation-guided mapping to dissect the interaction between ILK and kindlin-2 and identified a previously unknown binding site for kindlin-2 on the C-lobe of the pKD of ILK. Mutations at this site inhibit binding to kindlin-2 while maintaining structural integrity of the pKD. Importantly, kindlin-binding-defective ILK mutants exhibit impaired focal adhesion localization and fail to fully rescue the spreading defects seen in ILK knockdown cells. Furthermore, kindlin-2 mutants with impaired ILK binding are also unable to fully support cell spreading. Thus, the interaction between ILK and kindlin-2 is critical for cell spreading and focal adhesion localization, representing a key signaling axis downstream of integrins.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yasmin A Kadry
- From the Department of Pharmacology, Yale University, New Haven CT 06510, USA
| | | | - Bertrand Simon
- From the Department of Pharmacology, Yale University, New Haven CT 06510, USA
| | - David A Calderwood
- From the Department of Pharmacology, Yale University, New Haven CT 06510, USA .,Department of Cell Biology, Yale University, New Haven CT 06510, USA
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5
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Zhang K, Liu J, Truong T, Zukin E, Chen W, Saxon A. Blocking Allergic Reaction through Targeting Surface-Bound IgE with Low-Affinity Anti-IgE Antibodies. THE JOURNAL OF IMMUNOLOGY 2017; 198:3823-3834. [PMID: 28396318 DOI: 10.4049/jimmunol.1602022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/13/2017] [Indexed: 11/19/2022]
Abstract
Allergic disorders have now become a major worldwide public health issue, but the effective treatment options remain limited. We report a novel approach to block allergic reactivity by targeting the surface-bound IgE of the allergic effector cells via low-affinity anti-human IgE Abs with dissociation constants in the 10-6 to 10-8 M range. We demonstrated that these low-affinity anti-IgE mAbs bind to the cell surface-bound IgE without triggering anaphylactic degranulation even at high concentration, albeit they would weakly upregulate CD203c expression on basophils. This is in contrast to the high-affinity anti-IgE mAbs that trigger anaphylactic degranulation at low concentration. Instead, the low-affinity anti-IgE mAbs profoundly block human peanut- and cat-allergic IgE-mediated basophil CD63 induction indicative of anaphylactic degranulation; suppress peanut-, cat-, and dansyl-specific IgE-mediated passive cutaneous anaphylaxis; and attenuate dansyl IgE-mediated systemic anaphylaxis in human FcεRIα transgenic mouse model. Mechanistic studies reveal that the ability of allergic reaction blockade by the low-affinity anti-IgE mAbs was correlated with their capacity to downregulate the surface IgE and FcεRI level on human basophils and the human FcεRIα transgenic mouse bone marrow-derived mast cells via driving internalization of the IgE/FcεRI complex. Our studies demonstrate that targeting surface-bound IgE with low-affinity anti-IgE Abs is capable of suppressing allergic reactivity while displaying an excellent safety profile, indicating that use of low-affinity anti-IgE mAbs holds promise as a novel therapeutic approach for IgE-mediated allergic diseases.
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Affiliation(s)
- Ke Zhang
- Sixal Inc., Los Angeles, CA 90095; and .,Section of Clinical Immunology/Allergy, Division of Pulmonary, Critical Care, and Clinical Immunology/Allergy, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095
| | | | - Thao Truong
- Section of Clinical Immunology/Allergy, Division of Pulmonary, Critical Care, and Clinical Immunology/Allergy, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095
| | - Elyssa Zukin
- Section of Clinical Immunology/Allergy, Division of Pulmonary, Critical Care, and Clinical Immunology/Allergy, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095
| | - Wendy Chen
- Section of Clinical Immunology/Allergy, Division of Pulmonary, Critical Care, and Clinical Immunology/Allergy, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095
| | - Andrew Saxon
- Sixal Inc., Los Angeles, CA 90095; and.,Section of Clinical Immunology/Allergy, Division of Pulmonary, Critical Care, and Clinical Immunology/Allergy, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095
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6
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Balasopoulou A, Stanković B, Panagiotara A, Nikčevic G, Peters BA, John A, Mendrinou E, Stratopoulos A, Legaki AI, Stathakopoulou V, Tsolia A, Govaris N, Govari S, Zagoriti Z, Poulas K, Kanariou M, Constantinidou N, Krini M, Spanou K, Radlovic N, Ali BR, Borg J, Drmanac R, Chrousos G, Pavlovic S, Roma E, Zukic B, Patrinos GP, Katsila T. Novel genetic risk variants for pediatric celiac disease. Hum Genomics 2016; 10:34. [PMID: 27836013 PMCID: PMC5105295 DOI: 10.1186/s40246-016-0091-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/16/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic. METHODS Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition. RESULTS Analysis revealed six genomic variants of prime interest: SLC9A4 c.1919G>A, KIAA1109 c.2933T>C and c.4268_4269delCCinsTA, HoxB6 c.668C>A, HoxD12 c.418G>A, and NCK2 c.745_746delAAinsG, from which NCK2 c.745_746delAAinsG is novel. Data validation in pediatric celiac disease patients of Greek (n = 109) and Serbian (n = 73) descent and their healthy counterparts (n = 111 and n = 32, respectively) indicated that HoxD12 c.418G>A is more prevalent in celiac disease patients in the Serbian population (P < 0.01), while NCK2 c.745_746delAAinsG is less prevalent in celiac disease patients rather than healthy individuals of Greek descent (P = 0.03). SLC9A4 c.1919G>A and KIAA1109 c.2933T>C and c.4268_4269delCCinsTA were more abundant in patients; nevertheless, they failed to show statistical significance. CONCLUSIONS The next-generation sequencing-based family genomics approach described herein may serve as a paradigm towards the identification of novel functional variants with the aim of understanding complex disease pathobiology.
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Affiliation(s)
- Angeliki Balasopoulou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Biljana Stanković
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Angeliki Panagiotara
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Gordana Nikčevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Brock A Peters
- Complete Genomics Inc., Mountain View, CA, USA.,BGI Shenzhen, Shenzhen, 51803, China
| | - Anne John
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Effrosyni Mendrinou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Apostolos Stratopoulos
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Aigli Ioanna Legaki
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Vasiliki Stathakopoulou
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Aristoniki Tsolia
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Nikolaos Govaris
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Sofia Govari
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Zoi Zagoriti
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Konstantinos Poulas
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece
| | - Maria Kanariou
- Department of Immunology and Histocompatibility, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Nikki Constantinidou
- Department of Immunology and Histocompatibility, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Maro Krini
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Kleopatra Spanou
- Department of Immunology and Histocompatibility, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Nedeljko Radlovic
- Department of Gastroenterology and Nutrition, University Children's Hospital, Medical Faculty, University of Belgrade, Belgrade, Serbia
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Radoje Drmanac
- Complete Genomics Inc., Mountain View, CA, USA.,BGI Shenzhen, Shenzhen, 51803, China
| | - George Chrousos
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Eleftheria Roma
- First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Theodora Katsila
- Department of Pharmacy, School of Health Sciences, University of Patras, University Campus, Rion, 265 04, Patras, Greece.
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7
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Xu H, Cao H, Xiao G. Signaling via PINCH: Functions, binding partners and implications in human diseases. Gene 2016; 594:10-15. [PMID: 27590440 DOI: 10.1016/j.gene.2016.08.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/16/2022]
Abstract
Particularly interesting new cysteine-histidine-rich protein (PINCH) is a LIM-domain-only adaptor that plays important roles in cytoskeletal organization and extracellular matrix adhesion, migration, proliferation and survival. Mammalian cells have two functional PINCH proteins, PINCH1 and PINCH2. PINCH not only binds to Nck2 and engages in the signaling of growth factor receptors, but also forms a ternary complex with ILK and parvin (IPP complex). Normally, the IPP complex locates to focal adhesions participating in the signaling of integrins and mediating the interaction of cytoskeleton and extracellular matrix (ECM). Accumulative evidence indicates that abnormalities in PINCH signaling are involved in the pathogenesis of important diseases, such as cancers, renal diseases, cardiomyopathy, and HIV. Therefore, clarifying the functions of PINCH and its interactions with key factors is important for better understanding of signaling events both in health and disease.
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Affiliation(s)
- Huamin Xu
- Department of Physiology and Pathophysiology, Peking University Health Science Center, Beijing 100191, China; Department of Biology and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, China
| | - Huiling Cao
- Department of Biology and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guozhi Xiao
- Department of Biology and Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, China; Department of Biochemistry, Rush University Medical Center, Chicago, IL 60612, United States.
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8
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Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EGD, Sali A. Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data. Mol Cell Proteomics 2014; 13:2812-23. [PMID: 25139910 PMCID: PMC4223474 DOI: 10.1074/mcp.m114.040824] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 08/13/2014] [Indexed: 12/24/2022] Open
Abstract
The use of in vivo Förster resonance energy transfer (FRET) data to determine the molecular architecture of a protein complex in living cells is challenging due to data sparseness, sample heterogeneity, signal contributions from multiple donors and acceptors, unequal fluorophore brightness, photobleaching, flexibility of the linker connecting the fluorophore to the tagged protein, and spectral cross-talk. We addressed these challenges by using a Bayesian approach that produces the posterior probability of a model, given the input data. The posterior probability is defined as a function of the dependence of our FRET metric FRETR on a structure (forward model), a model of noise in the data, as well as prior information about the structure, relative populations of distinct states in the sample, forward model parameters, and data noise. The forward model was validated against kinetic Monte Carlo simulations and in vivo experimental data collected on nine systems of known structure. In addition, our Bayesian approach was validated by a benchmark of 16 protein complexes of known structure. Given the structures of each subunit of the complexes, models were computed from synthetic FRETR data with a distance root-mean-squared deviation error of 14 to 17 Å. The approach is implemented in the open-source Integrative Modeling Platform, allowing us to determine macromolecular structures through a combination of in vivo FRETR data and data from other sources, such as electron microscopy and chemical cross-linking.
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Affiliation(s)
- Massimiliano Bonomi
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158; §Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom;
| | - Riccardo Pellarin
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Seung Joong Kim
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Daniel Russel
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Bryan A Sundin
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Michael Riffle
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Daniel Jaschob
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Richard Ramsden
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Trisha N Davis
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Eric G D Muller
- ‖Department of Biochemistry, University of Washington, Seattle, Washington 98195
| | - Andrej Sali
- From the ‡Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158;
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9
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Kim YC, Gonzalez-Nieves R, Cutler ML. Rsu1 contributes to cell adhesion and spreading in MCF10A cells via effects on P38 map kinase signaling. Cell Adh Migr 2014; 9:227-32. [PMID: 25482629 PMCID: PMC4594256 DOI: 10.4161/19336918.2014.972775] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ILK, PINCH, Parvin (IPP) complex regulates adhesion and migration via binding of ILK to β1 integrin and α−parvin thus linking focal adhesions to actin cytoskeleton. ILK also binds the adaptor protein PINCH which connects signaling proteins including Rsu1 to the complex. A recent study of Rsu1 and PINCH1 in non-transformed MCF10A human mammary epithelial cells revealed that the siRNA-mediated depletion of either Rsu1 or PINCH1 decreased the number of focal adhesions (FAs) and altered the distribution and localization of FA proteins. This correlated with reduced adhesion, failure to spread or migrate in response to EGF and a loss of actin stress fibers and caveolae. The depletion of Rsu1 caused significant reduction in PINCH1 implying that Rsu1 may function in part by regulating levels of PINCH1. However, Rsu1, but not PINCH1, was required for EGF-induced activation of p38 Map kinase and ATF2 phosphorylation, suggesting a Rsu1 function independent from the IPP complex. Reconstitution of Rsu1-depleted cells with a Rsu1 mutant (N92D) that does not bind to PINCH1 failed to restore FAs or migration but did promote IPP-independent spreading and constitutive as well as EGF-induced p38 activation. In this commentary we discuss p38 activity in adhesion and how Rsu1 expression may be linked to Map kinase kinase (MKK) activation and detachment-induced stress kinase signaling.
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Affiliation(s)
- Yong-Chul Kim
- a Department of Pathology; F. Edward Hebert School of Medicine ; Uniformed Services University of the Health Sciences ; Bethesda , MD USA
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10
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Peng H, Talebzadeh-Farrooji M, Osborne MJ, Prokop JW, McDonald PC, Karar J, Hou Z, He M, Kebebew E, Orntoft T, Herlyn M, Caton AJ, Fredericks W, Malkowicz B, Paterno CS, Carolin AS, Speicher DW, Skordalakes E, Huang Q, Dedhar S, Borden KLB, Rauscher FJ. LIMD2 is a small LIM-only protein overexpressed in metastatic lesions that regulates cell motility and tumor progression by directly binding to and activating the integrin-linked kinase. Cancer Res 2014; 74:1390-1403. [PMID: 24590809 DOI: 10.1158/0008-5472.can-13-1275] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Proteins that communicate signals from the cytoskeleton to the nucleus are prime targets for effectors of metastasis as they often transduce signals regulating adhesion, motility, and invasiveness. LIM domain proteins shuttle between the cytoplasm and the nucleus, and bind to partners in both compartments, often coupling changes in gene expression to extracellular cues. In this work, we characterize LIMD2, a mechanistically undefined LIM-only protein originally found to be overexpressed in metastatic lesions but absent in the matched primary tumor. LIMD2 levels in fresh and archival tumors positively correlate with cell motility, metastatic potential, and grade, including bladder, melanoma, breast, and thyroid tumors. LIMD2 directly contributes to these cellular phenotypes as shown by overexpression, knockdown, and reconstitution experiments in cell culture models. The solution structure of LIMD2 that was determined using nuclear magnetic resonance revealed a classic LIM-domain structure that was highly related to LIM1 of PINCH1, a core component of the integrin-linked kinase-parvin-pinch complex. Structural and biochemical analyses revealed that LIMD2 bound directly to the kinase domain of integrin-linked kinase (ILK) near the active site and strongly activated ILK kinase activity. Cells that were null for ILK failed to respond to the induction of invasion by LIMD2. This strongly suggests that LIMD2 potentiates its biologic effects through direct interactions with ILK, a signal transduction pathway firmly linked to cell motility and invasion. In summary, LIMD2 is a new component of the signal transduction cascade that links integrin-mediated signaling to cell motility/metastatic behavior and may be a promising target for controlling tumor spread.
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Affiliation(s)
- Hongzhuang Peng
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Mehdi Talebzadeh-Farrooji
- Department of Pathology and Cell Biology, University of Montreal, Institute for Research in Immunology and Cancer
| | - Michael J Osborne
- Department of Pathology and Cell Biology, University of Montreal, Institute for Research in Immunology and Cancer
| | | | - Paul C McDonald
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jayashree Karar
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Zhaoyuan Hou
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Mei He
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Electron Kebebew
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | - Meenhard Herlyn
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Andrew J Caton
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - William Fredericks
- Department of Surgery, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Bruce Malkowicz
- Department of Surgery, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Christopher S Paterno
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Alexandra S Carolin
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - David W Speicher
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Emmanuel Skordalakes
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Qihong Huang
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Shoukat Dedhar
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Katherine L B Borden
- Department of Pathology and Cell Biology, University of Montreal, Institute for Research in Immunology and Cancer
| | - Frank J Rauscher
- The Wistar Institute, University of Pennsylvania and Veterans Affairs Medical Center, Philadelphia, Pennsylvania
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11
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Gonzalez-Nieves R, Desantis AI, Cutler ML. Rsu1 contributes to regulation of cell adhesion and spreading by PINCH1-dependent and - independent mechanisms. J Cell Commun Signal 2013; 7:279-93. [PMID: 23765260 PMCID: PMC3889256 DOI: 10.1007/s12079-013-0207-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 05/28/2013] [Indexed: 01/29/2023] Open
Abstract
Cell adhesion and migration are complex processes that require integrin activation, the formation and dissolution of focal adhesion (FAs), and linkage of actin cytoskeleton to the FAs. The IPP (ILK, PINCH, Parvin) complex regulates FA formation via binding of the adaptor protein ILK to β1 integrin, PINCH and parvin. The signaling protein Rsu1 is linked to the complex via binding PINCH1. The role of Rsu1 and PINCH1 in adhesion and migration was examined in non-transformed mammary epithelial cells. Confocal microscopy revealed that the depletion of either Rsu1 or PINCH1 by siRNA in MCF10A cells decreased the number of focal adhesions and altered the distribution and localization of β1 integrin, vinculin, talin and paxillin without affecting the levels of FA protein expression. This correlated with reduced adhesion, failure to spread or migrate in response to EGF and a loss of actin stress fibers and caveolae. In addition, constitutive phosphorylation of actin regulatory proteins occurred in the absence of PINCH1. The depletion of Rsu1 caused significant reduction in PINCH1 implying that Rsu1 may function by regulating levels of PINCH1. However, while both Rsu1- or PINCH1-depleted cells retained the ability to activate adhesion signaling in response to EGF stimulation, only Rsu1 was required for EGF-induced p38 Map Kinase phosphorylation and ATF2 activation, suggesting an Rsu1 function independent from the IPP complex. Reconstitution of Rsu1-depleted cells with an Rsu1 mutant that does not bind to PINCH1 failed to restore FAs or migration but did promote spreading and constitutive p38 activation. These data show that Rsu1-PINCH1 association with ILK and the IPP complex is required for regulation of adhesion and migration but that Rsu1 has a critical role in linking integrin-induced adhesion to activation of p38 Map kinase signaling and cell spreading. Moreover, it suggests that Rsu1 may regulate p38 signaling from the IPP complex affecting other functions including survival.
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Affiliation(s)
- Reyda Gonzalez-Nieves
- Department of Pathology, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
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12
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Santiveri CM, Sborgi L, de Alba E. Nuclear magnetic resonance study of protein-protein interactions involving apoptosis regulator Diva (Boo) and the BH3 domain of proapoptotic Bcl-2 members. J Mol Recognit 2013. [PMID: 23192964 DOI: 10.1002/jmr.2240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
According to biochemical assays, the Bcl-2 protein Diva from mouse regulates programmed cell death by heterodimerizing with other members of the family and by interacting with the apoptotic protease-activating factor Apaf-1. In typical Bcl-2 heterodimers, peptide fragments comprising the Bcl-2 homology domain 3 (BH3 domain) of proapoptotic members are capable of forming functional complexes with prosurvival proteins. High-resolution structural studies have revealed that the BH3 peptide forms an α-helix positioned in a canonical hydrophobic cleft of the antiapoptotic protein. Because Diva shows mutations in conserved residues within this area, it has been proposed to have a different interacting surface. However, we showed previously that Diva binds through the canonical groove the BH3 peptide of the human Bcl-2 killing member Harakiri. To further test Diva's binding capabilities, here we show Nuclear Magnetic Resonance (NMR) data, indicating that Diva binds peptides derived from the BH3 domain of several other proapoptotic Bcl-2 proteins, including mouse Harakiri, Bid, Bak and Bmf. We have measured the binding affinities of the heterodimers, which show significant variability. Structural models of the protein-peptide complexes based on NMR chemical shift perturbation data indicate that the binding surface is analogous. These models do not rely on NMR NOE (Nuclear Overhauser Effect) data, and thus our results can only suggest that the complexes share similar intermolecular interactions. However, the observed affinity differences correlate with the α-helical population of the BH3-peptides obtained from circular dichroism experiments, which highlights a role of conformational selection in the binding mechanism. Altogether, our results shed light on important factors governing Diva-BH3 peptide molecular recognition mode.
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Affiliation(s)
- Clara M Santiveri
- Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, Madrid, 28040, Spain
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13
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Ozdemir AY, Rom I, Kovalevich J, Yen W, Adiga R, Dave RS, Langford D. PINCH in the cellular stress response to tau-hyperphosphorylation. PLoS One 2013; 8:e58232. [PMID: 23554879 PMCID: PMC3595241 DOI: 10.1371/journal.pone.0058232] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 02/04/2013] [Indexed: 12/28/2022] Open
Abstract
Particularly interesting new cysteine- histidine- rich protein (PINCH) is an adaptor protein that our data have shown is required for neurite extension under stressful conditions. Our previous studies also report that PINCH is recalled by neurons showing decreased levels of synaptodendritic signaling proteins such as MAP2 or synaptophysin in the brains of human immunodeficiency virus (HIV) patients. The current study addressed potential role(s) for PINCH in neurodegenerative diseases. Mass spectrometry predicted the interaction of PINCH with Tau and with members of the heat shock response. Our in vitro data confirmed that PINCH binds to hyperphosphorylated (hp) Tau and to E3 ubiquitin ligase, carboxy-terminus of heat shock-70 interacting protein. Silencing PINCH prior to induction of hp-Tau resulted in more efficient clearance of accumulating hp-Tau, suggesting that PINCH may play a role in stabilizing hp-Tau. Accumulation of hp-Tau is implicated in more than 20 neuropathological diseases including Alzheimer's disease (AD), frontotemporal dementia (FTD), and human immunodeficiency virus encephalitis (HIVE). Analyses of brain tissues from HIVE, AD and FTD patients showed that PINCH is increased and binds to hp-Tau. These studies address a new mechanism by which AD and HIV may intersect and identify PINCH as a contributing factor to the accumulation of hyperphosphorylated Tau.
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Affiliation(s)
- Ahmet Yunus Ozdemir
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Inna Rom
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Jane Kovalevich
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - William Yen
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Radhika Adiga
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Rajnish S. Dave
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania, United States of America
| | - Dianne Langford
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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14
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Zhou L, Zhang Z, Zheng Y, Zhu Y, Wei Z, Xu H, Tang Q, Kong X, Hu L. SKAP2, a novel target of HSF4b, associates with NCK2/F-actin at membrane ruffles and regulates actin reorganization in lens cell. J Cell Mol Med 2011; 15:783-95. [PMID: 20219016 PMCID: PMC3922667 DOI: 10.1111/j.1582-4934.2010.01048.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In addition to roles in stress response, heat shock factors (HSFs) play crucial roles in differentiation and development. Heat shock transcription factor 4 (HSF4) deficiency leads to defect in lens epithelial cell (LEC) differentiation and cataract formation. However, the mechanism remains obscure. Here, we identified Src kinase-associated phosphoprotein 2 (SKAP2) as a downstream target of HSF4b and it was highly expressed at the anterior tip of lens elongating fibre cells in vivo. The HSF4-deficient lenses showed reduced SKAP2 expression and defects in actin reorganization. The disassembly of stress fibres and formation of cortical actin fibres are critical for the initiation of LEC differentiation. SKAP2 localized at actin-rich ruffles in human LECs (SRA01/04 cells) and knockdown SKAP2 using RNA interference impaired the disassembly of cellular stress fibres in response to fibroblast growth factor (FGF)-b. Overexpression of SKAP2, but not the N-terminal deletion mutant of SKAP2, induced the actin remodelling. We further found that SKAP2 interacted with the SH2 domain of non-catalytic region of tyrosine kinase adaptor protein 2 (NCK2) via its N-terminus. The complex of SKAP2-NCK2-F-actin accumulated at the leading edge of the lamellipodium, where FGF receptors and focal adhesion were also recruited. These results revealed an essential role for HSF4-mediated SKAP2 expression in the regulation of actin reorganization during lens differentiation, likely through a mechanism that SKAP2 anchors the complex of NCK2/focal adhesion to FGF receptors at the lamellipodium in lens epithelial cells.
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Affiliation(s)
- Li Zhou
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) & Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
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15
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Liang X, Sun Y, Chen J. Particularly interesting cysteine- and histidine-rich protein in cardiac development and remodeling. J Investig Med 2011; 57:842-8. [PMID: 19952891 DOI: 10.2310/jim.0b013e3181c5e31d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Integrin-mediated cell-extracellular matrix interaction plays key roles in tissue morphogenesis and integrity. The Lin11-Isl-1-Mec-3 (LIM) domain-only particularly interesting cysteine- and histidine-rich (PINCH) protein functions as an adaptor essential for the assembly and function of the focal adhesion complex that links integrin signaling to the cytoskeleton and other intracellular signaling pathways and regulates diverse cellular processes such as cell adhesion, migration, growth, differentiation, and survival. Recent biochemical and genetic studies have greatly advanced our knowledge surrounding the molecular interactions and functions of each component of the focal adhesion complex and revealed a requirement for PINCH in early embryogenesis, in morphogenesis of the neural crest and cardiac outflow, and in myocardial growth and remodeling. In this review article, we will provide an overview of the current knowledge of the molecular interactions of PINCH with other components of focal adhesions, highlighting recent discoveries of the in vivo role of PINCH and discuss its potential implication for human heart disease.
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Affiliation(s)
- Xingqun Liang
- Department of Medicine, University of California at San Diego (UCSD), La Jolla, CA 92093-0613C, USA
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16
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Rooney N, Streuli CH. How integrins control mammary epithelial differentiation: a possible role for the ILK-PINCH-Parvin complex. FEBS Lett 2011; 585:1663-72. [PMID: 21570968 DOI: 10.1016/j.febslet.2011.05.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/05/2011] [Accepted: 05/05/2011] [Indexed: 01/15/2023]
Abstract
Differentiation into tissue-specific cell types occurs in response to numerous external signals. Integrins impart signals from the extracellular matrix microenvironment that are required for cell differentiation. However, the precise cytoplasmic transducers of these signals are yet to be understood properly. In lactating mammary epithelial cells, integrin-linked kinase has been identified as an indispensable integrin-signalling adaptor that enables the activation of Rac1, which is necessary for prolactin-induced milk protein expression. Here we use examples from various tissues to summarise possible mechanisms by which ILK and its binding partners PINCH and Parvin (ILK-PINCH-Parvin complex) could be required for Rac activation and mammary epithelial differentiation.
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Affiliation(s)
- Nicholas Rooney
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences and Manchester Breast Centre, University of Manchester, Manchester, UK
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17
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Rowe AJ. Ultra-weak reversible protein–protein interactions. Methods 2011; 54:157-66. [DOI: 10.1016/j.ymeth.2011.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 01/15/2011] [Accepted: 02/07/2011] [Indexed: 10/18/2022] Open
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18
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Kovalevich J, Tracy B, Langford D. PINCH: More than just an adaptor protein in cellular response. J Cell Physiol 2011; 226:940-7. [PMID: 20945343 DOI: 10.1002/jcp.22437] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Particularly interesting new cysteine-histidine-rich protein (PINCH) is a LIM-domain-only adaptor protein involved in protein recruitment, subsequent assembly of multi-protein complexes, and subcellular localization of these complexes. PINCH is developmentally regulated and its expression is critical for proper cytoskeletal organization and extracellular matrix adhesion. Although PINCH has no catalytic abilities, the PIP (PINCH-ILK-parvin) complex serves as a link between integrins and components of growth factor receptor kinase and GTPase signaling pathways. Accordingly, PINCH-mediated signaling induces cell migration, spreading, and survival. Further research on the signaling cascades affected by PINCH is key to appreciating its biological significance in cell fate and systems maintenance, as the developmental functions of PINCH may extend to disease states and the cellular response to damage. PINCH is implicated in a diverse array of diseases including renal failure, cardiomyopathy, nervous system degeneration and demyelination, and tumorigenesis. This review presents evidence for PINCH's structural and functional importance in normal cellular processes and in pathogenesis. The current data for PINCH expression in nervous system disease is substantial, but due to the complex and ubiquitous nature of this protein, our understanding of its function in pathology remains unclear. In this review, an overview of studies identifying PINCH binding partners, their molecular interactions, and the potentially overlapping role(s) of PINCH in cancer and in nervous system diseases will be discussed. Many questions remain regarding PINCH's role in cells. What induces cell-specific PINCH expression? How does PINCH expression contribute to cell fate in the central nervous system? More broadly, is PINCH expression in disease a good thing? Clarifying the ambiguous functions of PINCH expression in the central nervous system and other systems is important to understand more clearly signaling events both in health and disease.
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Affiliation(s)
- Jane Kovalevich
- Temple University School of Medicine, Department of Neuroscience, Philadelphia, Pennsylvania 19140, USA
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19
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Bieri M, Kwan AH, Mobli M, King GF, Mackay JP, Gooley PR. Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination. FEBS J 2011; 278:704-15. [PMID: 21214861 DOI: 10.1111/j.1742-4658.2011.08005.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A strength of NMR spectroscopy is its ability to monitor, on an atomic level, molecular changes and interactions. In this review, which is intended for non-spectroscopist, we describe major uses of NMR in protein science beyond solution structure determination. After first touching on how NMR can be used to quickly determine whether a mutation induces structural perturbations in a protein, we describe the unparalleled ability of NMR to monitor binding interactions over a wide range of affinities, molecular masses and solution conditions. We discuss the use of NMR to measure the dynamics of proteins at the atomic level and over a wide range of timescales. Finally, we outline new and expanding areas such as macromolecular structure determination in multicomponent systems, as well as in the solid state and in vivo.
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Affiliation(s)
- Michael Bieri
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia
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20
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Vinogradova O, Qin J. NMR as a unique tool in assessment and complex determination of weak protein-protein interactions. Top Curr Chem (Cham) 2011; 326:35-45. [PMID: 21809187 DOI: 10.1007/128_2011_216] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-protein interactions are crucial for a wide variety of biological processes. These interactions range from high affinity (K (d)<nM) to very low affinity (K (d)>mM). While much is known about the nature of high affinity protein complexes, our knowledge about structural characteristics of weak protein-protein interactions (wPPIs) remains limited: in addition to the technical difficulties associated with their investigation, historically wPPIs used to be considered physiologically irrelevant. However, emerging evidence suggests that wPPIs, either in the form of intact protein complexes or as part of large molecular machineries, are fundamentally important for promoting rapid on/off switches of signal transduction, reversible cell-cell contacts, transient assembly/disassembly of signaling complexes, and enzyme-substrate recognition. Therefore an atomic-level elucidation of wPPIs is vital to understanding a cornucopia of diverse cellular events. Nuclear magnetic resonance (NMR) is famous for its unique abilities to study wPPIs and, by utilization of the new technical developments combined with sparse data based computational analysis, it now allows rapid identification and structural characterization of wPPIs. Here we present our perspective on the NMR methods employed.
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Affiliation(s)
- Olga Vinogradova
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA.
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21
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Kang S, Kwon H, Wen H, Song Y, Frueh D, Ahn HC, Yoo SH, Wagner G, Park S. Global dynamic conformational changes in the suppressor domain of IP3 receptor by stepwise binding of the two lobes of calmodulin. FASEB J 2010; 25:840-50. [PMID: 21084695 DOI: 10.1096/fj.10-160705] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The roles of calmodulin (CaM) have been key points of controversy in the regulation of inositol-1,4,5-trisphosphate receptor (IP(3)R). To address the issue, we studied the interaction between CaM and the suppressor domain of IP(3)R, a key allosteric regulatory domain. First, by means of a pulldown and a fluorescence titration experiment, we confirmed the interaction. Through subsequent NMR binding experiments, we observed dramatic peak disappearances of the suppressor domain on interaction with apo-CaM. The data indicated that apo-CaM induces large-scale dynamic conformational changes in the suppressor domain, involving partial unfolding and subdomain rearrangement. Analysis of the NMR data of CaM surprisingly revealed that its C lobe alone can cause such changes. Further binding experiments showed that calcium allows the free N lobe to bind to the suppressor domain, which induces extra conformational changes in both of the proteins. These results were also confirmed with CaM deletion mutants with either the N or C lobe. On the basis of this novel binding mechanism, we propose a model in which the partial unfolding of the suppressor domain by apo-CaM and the stepwise binding of the N lobe of CaM to the suppressor domain are important elements of calcium/CaM inhibition of IP(3)R. We believe that our working model encompasses previous regulation mechanisms of IP(3)R by calcium/CaM and provides new insights into the CaM-target interaction.
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Affiliation(s)
- Sunmi Kang
- Department of Biochemistry and Center for Advanced Medical Education by BK21 Project, School of Medicine, Inha University, Chungsuk Bldg., Rm. 505, Shinheung-dong, Chung-gu, Incheon, Korea, 400-712
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22
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Qi Y, Dhiman HK, Bhola N, Budyak I, Kar S, Man D, Dutta A, Tirupula K, Carr BI, Grandis J, Bar-Joseph Z, Klein-Seetharaman J. Systematic prediction of human membrane receptor interactions. Proteomics 2010; 9:5243-55. [PMID: 19798668 DOI: 10.1002/pmic.200900259] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Membrane receptor-activated signal transduction pathways are integral to cellular functions and disease mechanisms in humans. Identification of the full set of proteins interacting with membrane receptors by high-throughput experimental means is difficult because methods to directly identify protein interactions are largely not applicable to membrane proteins. Unlike prior approaches that attempted to predict the global human interactome, we used a computational strategy that only focused on discovering the interacting partners of human membrane receptors leading to improved results for these proteins. We predict specific interactions based on statistical integration of biological data containing highly informative direct and indirect evidences together with feedback from experts. The predicted membrane receptor interactome provides a system-wide view, and generates new biological hypotheses regarding interactions between membrane receptors and other proteins. We have experimentally validated a number of these interactions. The results suggest that a framework of systematically integrating computational predictions, global analyses, biological experimentation and expert feedback is a feasible strategy to study the human membrane receptor interactome.
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Affiliation(s)
- Yanjun Qi
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
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23
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Abstract
PURPOSE Integrin-Linked Kinase (ILK) is associated with integrin and growth factor receptor signalling. As both signalling pathways contribute to cancer cell resistance, ILK seems well suited as a promising tumour target. MATERIAL AND METHODS Data were obtained by performing a PubMed database search and summarised with a focus on the function of ILK in cancer biology. RESULTS The findings on the catalytic function of ILK, on the putative substrates of ILK and on the expression of ILK in tumour and normal tissues are heterogeneous. In the context of cancer, two of these issues might be of importance. First, a variety of reports indicate a lack of ILK overexpression in tumours. Second, wild-type or overexpression of ILK has been found to considerably sensitise tumour cells to ionising irradiation as compared to ILK knockout or ILK knockdown conditions. In contrast, wild-type or overexpression of ILK has been shown to protect tumour cells from chemotherapy-induced cell death. CONCLUSIONS Due to these conflicting data, it is difficult to evaluate if therapeutic targeting of ILK is a reasonable strategy in cancer therapy. A more comprehensive understanding of the molecular mechanisms controlled by ILK may help to answer this question.
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Affiliation(s)
- Iris Eke
- OncoRay-Center for Radiation Research in Oncology, Medical Faculty Carl-Gustav Carus, Dresden University of Technology, Dresden, Germany
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24
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Ivanova VP, Kovaleva ZV, Krivchenko AI. Collagen fragment accelerates adhesion and spreading of mouse embryonic fibroblasts. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2009; 426:302-305. [PMID: 19650346 DOI: 10.1134/s0012496609030338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- V P Ivanova
- a Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr Morisa Toreza 44, St. Petersburg, 194223 Russia
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25
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Abstract
Integrins are cell surface transmembrane receptors that recognize and bind to extracellular matrix proteins and counter receptors. Binding of activated integrins to their ligands induces a vast number of structural and signaling changes within the cell. Large, multimolecular complexes assemble onto the cytoplasmic tails of activated integrins to engage and organize the cytoskeleton, and activate signaling pathways that ultimately lead to changes in gene expression. Additionally, integrin-mediated signaling intersects with growth factor-mediated signaling through various levels of cross-talk. This review discusses recent work that has tremendously broadened our understanding of the complexity of integrin-mediated signaling.
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26
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The structural basis of integrin-linked kinase-PINCH interactions. Proc Natl Acad Sci U S A 2008; 105:20677-82. [PMID: 19074270 DOI: 10.1073/pnas.0811415106] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The heterotrimeric complex between integrin-linked kinase (ILK), PINCH, and parvin is an essential signaling platform, serving as a convergence point for integrin and growth-factor signaling and regulating cell adhesion, spreading, and migration. We report a 1.6-A crystal structure of the ILK ankyrin repeat domain bound to the PINCH1 LIM1 domain, revealing the molecular basis of ILK-PINCH interactions and providing a structural description of this region of ILK. This structure identifies 5 ankyrin repeats in ILK, explains previous deletion mutagenesis data, permits identification of ILK and PINCH1 point mutations that disrupt the interaction, shows how zincs are coordinated by PINCH1 LIM1, and suggests that conformational flexibility and twisting between the 2 zinc fingers within the LIM1 domain may be important for ILK binding. These data provide an atomic-resolution description of a key interaction in the ILK-PINCH-parvin scaffolding complex.
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27
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Wang X, Fukuda K, Byeon IJ, Velyvis A, Wu C, Gronenborn A, Qin J. The structure of alpha-parvin CH2-paxillin LD1 complex reveals a novel modular recognition for focal adhesion assembly. J Biol Chem 2008; 283:21113-9. [PMID: 18508764 PMCID: PMC2475713 DOI: 10.1074/jbc.m801270200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 05/14/2008] [Indexed: 01/15/2023] Open
Abstract
Alpha-parvin is an essential component of focal adhesions (FAs), which are large multiprotein complexes that link the plasma membrane and actin cytoskeleton. Alpha-parvin contains two calponin homology (CH) domains and its C-terminal CH2 domain binds multiple targets including paxillin LD motifs for regulating the FA network and signaling. Here we describe the solution structure of alpha-parvin CH2 bound to paxillin LD1. We show that although CH2 contains the canonical CH-fold, a previously defined N-terminal linker forms an alpha-helix that packs unexpectedly with the C-terminal helix of CH2, resulting in a novel variant of the CH domain. Importantly, such packing generates a hydrophobic surface that recognizes the Leu-rich face of paxillin-LD1, and the binding pattern differs drastically from the classical paxillin-LD binding to four-helix bundle proteins such as focal adhesion kinase. These results define a novel modular recognition mode and reveal how alpha-parvin associates with paxillin to mediate the FA assembly and signaling.
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Affiliation(s)
- Xiaoxia Wang
- Structural Biology Program,
Lerner Research Institute, Cleveland Clinic, the Department of
Chemistry, Cleveland State
University, Cleveland, Ohio 44195 and the Departments of
Structural Biology and
Pathology, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261
| | - Koichi Fukuda
- Structural Biology Program,
Lerner Research Institute, Cleveland Clinic, the Department of
Chemistry, Cleveland State
University, Cleveland, Ohio 44195 and the Departments of
Structural Biology and
Pathology, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261
| | - In-Ja Byeon
- Structural Biology Program,
Lerner Research Institute, Cleveland Clinic, the Department of
Chemistry, Cleveland State
University, Cleveland, Ohio 44195 and the Departments of
Structural Biology and
Pathology, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261
| | - Algirdas Velyvis
- Structural Biology Program,
Lerner Research Institute, Cleveland Clinic, the Department of
Chemistry, Cleveland State
University, Cleveland, Ohio 44195 and the Departments of
Structural Biology and
Pathology, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261
| | - Chuanyue Wu
- Structural Biology Program,
Lerner Research Institute, Cleveland Clinic, the Department of
Chemistry, Cleveland State
University, Cleveland, Ohio 44195 and the Departments of
Structural Biology and
Pathology, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261
| | - Angela Gronenborn
- Structural Biology Program,
Lerner Research Institute, Cleveland Clinic, the Department of
Chemistry, Cleveland State
University, Cleveland, Ohio 44195 and the Departments of
Structural Biology and
Pathology, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261
| | - Jun Qin
- Structural Biology Program,
Lerner Research Institute, Cleveland Clinic, the Department of
Chemistry, Cleveland State
University, Cleveland, Ohio 44195 and the Departments of
Structural Biology and
Pathology, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261
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28
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Ababou A, Gautel M, Pfuhl M. Dissecting the N-terminal Myosin Binding Site of Human Cardiac Myosin-binding Protein C. J Biol Chem 2007; 282:9204-15. [PMID: 17192269 DOI: 10.1074/jbc.m610899200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myosin-binding protein C (MyBP-C) binds to myosin with two binding sites, one close to the N terminus and the other at the C terminus. Here we present the solution structure of one part of the N-terminal binding site, the third immunoglobulin domain of the cardiac isoform of human MyBP-C (cC2) together with a model of its interaction with myosin. Domain cC2 has the beta-sandwich structure expected from a member of the immunoglobulin fold. The C-terminal part of the structure of cC2 is very closely related to telokin, the myosin binding fragment of myosin light chain kinase. Domain cC2 also contains two cysteines on neighboring strands F and G, which would be able to form a disulfide bridge in a similar position as in telokin. Using NMR spectroscopy and isothermal titration calorimetry we demonstrate that cC2 alone binds to a fragment of myosin, S2Delta, with low affinity (kD = 1.1 mM) but exhibits a highly specific binding site. This consists of the C-terminal surface of the C'CFGA' beta-sheet, which includes Glu(301), a residue mutated to Gln in the disease familial hypertrophic cardiomyopathy. The binding site on S2 was identified by a combination of NMR binding experiments of cC2 with S2Delta containing the cardiomyopathy-linked mutation R870H and molecular modeling. This mutation lowers the binding affinity and changes the arrangement of side chains at the interface. Our model of the cC2-S2Delta complex gives a first glimpse of details of the MyBP-C-myosin interaction. Using this model we suggest that most key interactions are between polar amino acids, explaining why the mutations E301Q in cC2 and R870H in S2Delta could be involved in cardiomyopathy. We expect that this model will stimulate future research to further refine the details of this interaction and their importance for cardiomyopathy.
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Affiliation(s)
- Abdessamad Ababou
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH
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29
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Hehlgans S, Haase M, Cordes N. Signalling via integrins: implications for cell survival and anticancer strategies. Biochim Biophys Acta Rev Cancer 2006; 1775:163-80. [PMID: 17084981 DOI: 10.1016/j.bbcan.2006.09.001] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 09/26/2006] [Accepted: 09/28/2006] [Indexed: 01/13/2023]
Abstract
Integrin-associated signalling renders cells more resistant to genotoxic anti-cancer agents like ionizing radiation and chemotherapeutic substances, a phenomenon termed cell adhesion-mediated radioresistance/drug resistance (CAM-RR, CAM-DR). Integrins are heterodimeric cell-surface molecules that on one side link the actin cytoskeleton to the cell membrane and on the other side mediate cell-matrix interactions. In addition to their structural functions, integrins mediate signalling from the extracellular space into the cell through integrin-associated signalling and adaptor molecules such as FAK (focal adhesion kinase), ILK (integrin-linked kinase), PINCH (particularly interesting new cysteine-histidine rich protein) and Nck2 (non-catalytic (region of) tyrosine kinase adaptor protein 2). Via these molecules, integrin signalling tightly and cooperatively interacts with receptor tyrosine kinase signalling to regulate survival, proliferation and cell shape as well as polarity, adhesion, migration and differentiation. In tumour cells of diverse origin like breast, colon or skin, the function and regulation of these molecules is partly disturbed and thus might contribute to the malignant phenotype and pre-existent and acquired multidrug resistance. These issues as well as a variety of therapeutic options envisioned to influence tumour cell growth, metastasis and resistance, including kinase inhibitors, anti-integrin antibodies or RNA interference, will be summarized and discussed in this review.
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Affiliation(s)
- Stephanie Hehlgans
- OncoRay, Center for Radiation Research in Oncology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Fetscherstrasse 74/PF 86, 01307 Dresden, Germany
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30
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Liew CW, Rand KD, Simpson RJY, Yung WW, Mansfield RE, Crossley M, Proetorius-Ibba M, Nerlov C, Poulsen FM, Mackay JP. Molecular Analysis of the Interaction between the Hematopoietic Master Transcription Factors GATA-1 and PU.1. J Biol Chem 2006; 281:28296-306. [PMID: 16861236 DOI: 10.1074/jbc.m602830200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GATA-1 and PU.1 are transcription factors that control erythroid and myeloid development, respectively. The two proteins have been shown to function in an antagonistic fashion, with GATA-1 repressing PU.1 activity during erythropoiesis and PU.1 repressing GATA-1 function during myelopoiesis. It has also become clear that this functional antagonism involves direct interactions between the two proteins. However, the molecular basis for these interactions is not known, and a number of inconsistencies exist in the literature. We have used a range of biophysical methods to define the molecular details of the GATA-1-PU.1 interaction. A combination of NMR titration data and extensive mutagenesis revealed that the PU.1-Ets domain and the GATA-1 C-terminal zinc finger (CF) form a low affinity interaction in which specific regions of each protein are implicated. Surprisingly, the interaction cannot be disrupted by single alanine substitution mutations, suggesting that binding is distributed over an extended interface. The C-terminal basic tail region of CF appears to be sufficient to mediate an interaction with PU.1-Ets, and neither acetylation nor phosphorylation of a peptide corresponding to this region disrupts binding, indicating that the interaction is not dominated by electrostatic interactions. The CF basic tail shares significant sequence homology with the PU.1 interacting motif from c-Jun, suggesting that GATA-1 and c-Jun might compete to bind PU.1. Taken together, our data provide a molecular perspective on the GATA-1-PU.1 interaction, resolving several issues in the existing data and providing insight into the mechanisms through which these two proteins combine to regulate blood development.
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Affiliation(s)
- Chu Wai Liew
- School of Molecular and Microbial Biosciences, G08, University of Sydney, New South Wales 2006, Australia
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31
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Bhattacharjya S, Gingras R, Xu P. An NMR-based identification of a peptide fragment from the beta-subunit of a G-protein showing specific interactions with the GBB domain of the Ste20 kinase in budding yeast. Biochem Biophys Res Commun 2006; 347:1145-50. [PMID: 16870141 DOI: 10.1016/j.bbrc.2006.07.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Accepted: 07/09/2006] [Indexed: 11/28/2022]
Abstract
In mitogen-activated protein kinase (MAPK) cascades of budding yeast, pheromone-induced mating signal is transmitted by interactions between the beta-subunit of a G-protein (G-beta) and the G-beta binding (GBB) domain of Ste20 kinase. Previously, mutational analyses of the beta-subunit of G-protein had identified two critical mutations which abrogate binding of the GBB domain of Ste20. In this work, we have identified, by use of NMR spectroscopy, a peptide fragment from the G-beta that shows specific interactions with the isolated GBB domain of Ste20. A model structure of the Ste20/G-beta complex reveals that the interface of the hetero-complex may be sustained by parallel orientation of two potentially interacting helical segments that are further stabilized by ionic, hydrogen bond, and helix macro-dipole interactions.
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Affiliation(s)
- Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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32
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Li S, Peters GA, Ding K, Zhang X, Qin J, Sen GC. Molecular basis for PKR activation by PACT or dsRNA. Proc Natl Acad Sci U S A 2006; 103:10005-10. [PMID: 16785445 PMCID: PMC1502496 DOI: 10.1073/pnas.0602317103] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The mammalian protein kinase PKR is a critical component of the innate immune response against virus infection. Its cellular actions are mediated by modulating cell signaling and translational regulation. To be enzymatically active, latent PKR needs to be activated by binding to one of its activators, dsRNA or PACT protein. Although the structures of the N-terminal dsRNA-binding domain and the C-terminal kinase domain of PKR have been separately determined, the mode of activation of the enzyme remains unknown. To address this problem, we used biochemical, genetic, and NMR analyses to identify the PACT-binding motif (PBM) located in the kinase domain and demonstrated an intramolecular interaction between PBM and dsRNA-binding domain. This interaction is responsible for keeping PKR in an inactive conformation, because its disruption by point mutations of appropriate residues produced constitutively active PKR. Furthermore, a short decoy peptide, representing PBM, was able to activate PKR by interfering with the intramolecular interaction. These observations suggest a model for PKR activation upon binding of dsRNA or PACT.
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Affiliation(s)
- Shoudong Li
- *Department of Molecular Genetics and
- Graduate Program in Molecular Virology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | | | - Keyang Ding
- Structural Biology Program and Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195; and
| | - Xiaolun Zhang
- Structural Biology Program and Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195; and
| | - Jun Qin
- Structural Biology Program and Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195; and
| | - Ganes C. Sen
- *Department of Molecular Genetics and
- Graduate Program in Molecular Virology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
- To whom correspondence should be addressed at:
Department of Molecular Genetics/NE20, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195. E-mail:
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33
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Martinsen BJ, Neumann AN, Frasier AJ, Baker CVH, Krull CE, Lohr JL. PINCH-1 expression during early avian embryogenesis: implications for neural crest and heart development. Dev Dyn 2006; 235:152-62. [PMID: 16258920 DOI: 10.1002/dvdy.20616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The invasion of the cardiac neural crest (CNC) into the outflow tract (OFT) and subsequent OFT septation are critical events during vertebrate heart development. We previously had performed four modified differential display (DD) screens in the chick embryo to identify genes that may be involved in CNC and heart development. Full-length sequence of one of the DD clones has been obtained and identified as chick PINCH-1. This particularly interesting new cysteine-histidine-rich protein contains five protein-binding LIM domains (five double zinc fingers), a nuclear localization signal, and a nuclear export signal, allowing it to participate in integrin and growth factor signaling and possibly act as a transcription factor. We show here for the first time that chick PINCH-1 is expressed in neural crest cells, both in the neural fold and cardiac OFT, and is also expressed in mesoderm derived-structures, including the myocardium, during avian embryogenesis. The normal expression pattern and overexpression in neural crest cell explants suggest that PINCH-1 may be a regulator of neural crest cell adhesion and migration.
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Affiliation(s)
- Brad J Martinsen
- Division of Pediatric Cardiology, Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, Minnesota 55455, USA.
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34
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Legate KR, Montañez E, Kudlacek O, Fässler R. ILK, PINCH and parvin: the tIPP of integrin signalling. Nat Rev Mol Cell Biol 2006; 7:20-31. [PMID: 16493410 DOI: 10.1038/nrm1789] [Citation(s) in RCA: 528] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The ternary complex of integrin-linked kinase (ILK), PINCH and parvin functions as a signalling platform for integrins by interfacing with the actin cytoskeleton and many diverse signalling pathways. All these proteins have synergistic functions at focal adhesions, but recent work has indicated that these proteins might also have separate roles within a cell. They function as regulators of gene transcription or cell-cell adhesion.
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Affiliation(s)
- Kyle R Legate
- Department of Molecular Medicine, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsreid, Germany.
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35
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Chen Y, Lai M, Maeno-Hikichi Y, Zhang JF. Essential role of the LIM domain in the formation of the PKCɛ–ENH–N-type Ca2+ channel complex. Cell Signal 2006; 18:215-24. [PMID: 15979848 DOI: 10.1016/j.cellsig.2005.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 04/14/2005] [Accepted: 04/19/2005] [Indexed: 01/21/2023]
Abstract
A LIM domain is a specialized double-zinc finger motif found in a variety of proteins. LIM domains are thought to function as molecular modules, mediating specific protein-protein interactions in cellular signaling. In a recent study, we have demonstrated that ENH, which has three consecutive LIM domains, acts as an adaptor protein for the formation of a functional PKCepsilon-ENH-N-type Ca2+ channel complex in neurons. Formation of this complex selectively recruits PKCepsilon to its specific substrate, N-type Ca2+ channels, and is critical for rapid and efficient potentiation of the Ca2+ channel activity by PKC in neurons. However, it is not clear whether changes in the local Ca2+ concentrations near the channel mouth may affect the formation of the triprotein complex. Furthermore, the molecular determinants for the interactions among these three proteins remain unknown. Biochemical studies were performed to address these questions. Within the physiological Ca2+ concentration range (0-300 microM), binding of ENH to the channel C-terminus was significantly increased by Ca2+, whereas increased Ca2+ levels led to dissociation of PKCepsilon from ENH. Mutagenesis studies revealed that the second LIM domain in ENH was primarily responsible for Ca2+-dependent binding of ENH to both the Ca2+ channel C-terminus and PKCepsilon. ENH existed as a dimer in vivo. PKCepsilon translocation inhibition peptide, which blocks the translocation of PKCepsilon from the cytosol to the membrane, inhibited the interaction between PKCepsilon and ENH. These results provide a molecular mechanism for how the PKCepsilon-ENH-N-type Ca2+ channel complex is formed and regulated, as well as potential drug targets to selectively disrupt the PKC signaling complex.
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Affiliation(s)
- Yuan Chen
- Department of Physiology, Jefferson Medical College, 1020 Locust Street, Philadelphia, PA 19107, USA
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36
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Xu Y, Wang X, Yang J, Vaynberg J, Qin J. PASA--a program for automated protein NMR backbone signal assignment by pattern-filtering approach. JOURNAL OF BIOMOLECULAR NMR 2006; 34:41-56. [PMID: 16505963 DOI: 10.1007/s10858-005-5358-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 11/09/2005] [Indexed: 05/05/2023]
Abstract
We present a new program, PASA (Program for Automated Sequential Assignment), for assigning protein backbone resonances based on multidimensional heteronuclear NMR data. Distinct from existing programs, PASA emphasizes a per-residue-based pattern-filtering approach during the initial stage of the automated 13Calpha and/or 13Cbeta chemical shift matching. The pattern filter employs one or multiple constraints such as 13Calpha/Cbeta chemical shift ranges for different amino acid types and side-chain spin systems, which helps to rule out, in a stepwise fashion, improbable assignments as resulted from resonance degeneracy or missing signals. Such stepwise filtering approach substantially minimizes early false linkage problems that often propagate, amplify, and ultimately cause complication or combinatorial explosion of the automation process. Our program (http://www.lerner.ccf.org/moleccard/qin/) was tested on four representative small-large sized proteins with various degrees of resonance degeneracy and missing signals, and we show that PASA achieved the assignments efficiently and rapidly that are fully consistent with those obtained by laborious manual protocols. The results demonstrate that PASA may be a valuable tool for NMR-based structural analyses, genomics, and proteomics.
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Affiliation(s)
- Yizhuang Xu
- Structural Biology Program, NB20, The Lerner Research Institute, The Cleveland Clinic Foundation, 9500 Euclid Ave., Cleveland, OH 44195, USA
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37
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Vaynberg J, Qin J. Weak protein-protein interactions as probed by NMR spectroscopy. Trends Biotechnol 2005; 24:22-7. [PMID: 16216358 DOI: 10.1016/j.tibtech.2005.09.006] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Revised: 08/12/2005] [Accepted: 09/23/2005] [Indexed: 11/29/2022]
Abstract
Weak protein-protein interactions (PPIs) are fundamental to many cellular processes, such as reversible cell-cell contact, rapid enzyme turnover and transient assembly and/or reassembly of large signaling complexes. However, structural and functional characterizations of weak PPIs have been technically challenging and lagged behind those for strong PPIs. Here, we describe nuclear magnetic resonance (NMR) spectroscopy as a highly effective tool for unraveling the atomic details of weak PPIs. We highlight the recent advances of how NMR can be used to rapidly detect and structurally determine extremely weak PPIs (K(d)>10(-4)M). Coupled with functional approaches, NMR has the potential to look into a wide variety of biologically important weak PPIs at the detailed molecular level, thereby facilitating a thorough view of how proteins function in living cells.
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Affiliation(s)
- Julia Vaynberg
- Structural Biology Program, Lerner Research Institute, The Cleveland Clinic Foundation, 9500 Euclid Ave., Cleveland, OH 44195, USA
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38
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Xu Z, Fukuda T, Li Y, Zha X, Qin J, Wu C. Molecular Dissection of PINCH-1 Reveals a Mechanism of Coupling and Uncoupling of Cell Shape Modulation and Survival. J Biol Chem 2005; 280:27631-7. [PMID: 15941716 DOI: 10.1074/jbc.m504189200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
How cells couple and uncouple regulation of cellular processes such as shape change and survival is an important question in molecular cell biology. PINCH-1, a widely expressed protein consisting of five LIM domains and a C-terminal tail, is an essential focal adhesion protein with multiple functions including regulation of the integrin-linked kinase (ILK) level, cell shape, and survival signaling. We show here that the LIM1-mediated interaction with ILK regulates all these three processes. By contrast, the LIM4-mediated interaction with Nck-2, which regulates cell morphology and migration, is not required for the control of the ILK level and survival. Remarkably, a short 15-residue tail C-terminal to LIM5 is required for both cell shape modulation and survival, albeit it is not required for the control of the ILK level. The C-terminal tail not only regulates PINCH-1 localization to focal adhesions but also functions after it localizes there. These findings suggest that PINCH-1 functions as a molecular platform for coupling and uncoupling diverse cellular processes via overlapping but yet distinct domain interactions.
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Affiliation(s)
- Zhen Xu
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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39
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Dougherty GW, Chopp T, Qi SM, Cutler ML. The Ras suppressor Rsu-1 binds to the LIM 5 domain of the adaptor protein PINCH1 and participates in adhesion-related functions. Exp Cell Res 2005; 306:168-79. [PMID: 15878342 DOI: 10.1016/j.yexcr.2005.01.025] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2004] [Revised: 01/20/2005] [Accepted: 01/25/2005] [Indexed: 01/29/2023]
Abstract
Rsu-1 is a highly conserved leucine rich repeat (LRR) protein that is expressed ubiquitously in mammalian cells. Rsu-1 was identified based on its ability to inhibit transformation by Ras, and previous studies demonstrated that ectopic expression of Rsu-1 inhibited anchorage-independent growth of Ras-transformed cells and human tumor cell lines. Using GAL4-based yeast two-hybrid screening, the LIM domain protein, PINCH1, was identified as the binding partner of Rsu-1. PINCH1 is an adaptor protein that localizes to focal adhesions and it has been implicated in the regulation of adhesion functions. Subdomain mapping in yeast revealed that Rsu-1 binds to the LIM 5 domain of PINCH1, a region not previously identified as a specific binding domain for any other protein. Additional testing demonstrated that PINCH2, which is highly homologous to PINCH1, except in the LIM 5 domain, does not interact with Rsu-1. Glutathione transferase fusion protein binding studies determined that the LRR region of Rsu-1 interacts with PINCH1. Transient expression studies using epitope-tagged Rsu-1 and PINCH1 revealed that Rsu-1 co-immunoprecipitated with PINCH1 and colocalized with vinculin at sites of focal adhesions in mammalian cells. In addition, endogenous P33 Rsu-1 from 293T cells co-immunoprecipitated with transiently expressed myc-tagged PINCH1. Furthermore, RNAi-induced reduction in Rsu-1 RNA and protein inhibited cell attachment, and while previous studies demonstrated that ectopic expression of Rsu-1 inhibited Jun kinase activation, the depletion of Rsu-1 resulted in activation of Jun and p38 stress kinases. These studies demonstrate that Rsu-1 interacts with PINCH1 in mammalian cells and functions, in part, by altering cell adhesion.
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Affiliation(s)
- Gerard W Dougherty
- Department of Pathology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, B3122, Bethesda, MD 20814, USA
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40
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Grashoff C, Thievessen I, Lorenz K, Ussar S, Fässler R. Integrin-linked kinase: integrin's mysterious partner. Curr Opin Cell Biol 2005; 16:565-71. [PMID: 15363808 DOI: 10.1016/j.ceb.2004.07.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Integrin-mediated cell adhesion regulates a vast number of biological processes including migration, survival and proliferation of cells. It is therefore not surprising that defects in integrin function are often rate-limiting for development and profoundly affect the progression of several diseases. The functions of integrins are mediated through the recruitment of cytoplasmic plaque proteins. One of these is integrin-linked kinase, which connects integrins to the actin cytoskeleton and transduces signals through integrins to the extracellular matrix and from integrins to various subcellular compartments.
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Affiliation(s)
- Carsten Grashoff
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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41
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Vaynberg J, Fukuda T, Chen K, Vinogradova O, Velyvis A, Tu Y, Ng L, Wu C, Qin J. Structure of an Ultraweak Protein-Protein Complex and Its Crucial Role in Regulation of Cell Morphology and Motility. Mol Cell 2005; 17:513-23. [PMID: 15721255 DOI: 10.1016/j.molcel.2004.12.031] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Revised: 08/13/2004] [Accepted: 12/29/2004] [Indexed: 10/25/2022]
Abstract
Weak protein-protein interactions (PPIs) (K(D) > 10(-6) M) are critical determinants of many biological processes. However, in contrast to a large growing number of well-characterized, strong PPIs, the weak PPIs, especially those with K(D) > 10(-4) M, are poorly explored. Genome wide, there exist few 3D structures of weak PPIs with K(D) > 10(-4) M, and none with K(D) > 10(-3) M. Here, we report the NMR structure of an extremely weak focal adhesion complex (K(D) approximately 3 x 10(-3) M) between Nck-2 SH3 domain and PINCH-1 LIM4 domain. The structure exhibits a remarkably small and polar interface with distinct binding modes for both SH3 and LIM domains. Such an interface suggests a transient Nck-2/PINCH-1 association process that may trigger rapid focal adhesion turnover during integrin signaling. Genetic rescue experiments demonstrate that this interface is indeed involved in mediating cell shape change and migration. Together, the data provide a molecular basis for an ultraweak PPI in regulating focal adhesion dynamics during integrin signaling.
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Affiliation(s)
- Julia Vaynberg
- Structural Biology Program, Lerner Research Institute, The Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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42
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Abstract
Cell-extracellular matrix (ECM) adhesion is crucial for control of cell behavior. It connects the ECM to the intracellular cytoskeleton and transduces bidirectional signals between the extracellular and intracellular compartments. The subcellular machinery that mediates cell-ECM adhesion and signaling is complex. It consists of transmembrane proteins (e.g., integrins) and at least several dozens of membrane-proximal proteins that assemble into a network through multiple protein interactions. Furthermore, despite sharing certain common components, cell-ECM adhesions exhibit considerable heterogeneity in different types of cells (e.g., the cell-ECM adhesions in cardiac myocytes are considerably different from those in fibroblasts). Here, we will first briefly describe the general properties of the integrin-mediated cell-ECM adhesion and signal transduction. Next, we will focus on one of the recently discovered cell-ECM adhesion protein complexes consisting of PINCH, integrin-linked kinase (ILK), and Parvin and use it as an example to illustrate the molecular basis underlying the assembly and functions of cell-ECM adhesions. Finally, we will discuss in detail the structure and regulation of cell-ECM adhesion complexes in cardiac myocytes, which illustrate the importance and complexity of the cell-ECM adhesion structures in organogenesis and diseases.
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Affiliation(s)
- Jorge L Sepulveda
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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43
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Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004; 14:313-24. [PMID: 15193311 DOI: 10.1016/j.sbi.2004.04.006] [Citation(s) in RCA: 189] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structures of macromolecular complexes are necessary for a mechanistic description of biochemical and cellular processes. They can be solved by experimental methods, such as X-ray crystallography, NMR spectroscopy and electron microscopy, as well as by computational protein structure prediction, docking and bioinformatics. Recent advances and applications of these methods emphasize the need for hybrid approaches that combine a variety of data to achieve better efficiency, accuracy, resolution and completeness.
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44
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Kadrmas JL, Beckerle MC. The LIM domain: from the cytoskeleton to the nucleus. Nat Rev Mol Cell Biol 2004; 5:920-31. [PMID: 15520811 DOI: 10.1038/nrm1499] [Citation(s) in RCA: 569] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
First described 15 years ago as a cysteine-rich sequence that was common to a small group of homeodomain transcription factors, the LIM domain is now recognized as a tandem zinc-finger structure that functions as a modular protein-binding interface. LIM domains are present in many proteins that have diverse cellular roles as regulators of gene expression, cytoarchitecture, cell adhesion, cell motility and signal transduction. An emerging theme is that LIM proteins might function as biosensors that mediate communication between the cytosolic and the nuclear compartments.
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Affiliation(s)
- Julie L Kadrmas
- Huntsman Cancer Institute and the Department of Biology, University of Utah, 2000 East, Circle of Hope, Salt Lake City, Utah 84112, USA
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45
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Wu C. The PINCH-ILK-parvin complexes: assembly, functions and regulation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2004; 1692:55-62. [PMID: 15246679 DOI: 10.1016/j.bbamcr.2004.01.006] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Accepted: 01/23/2004] [Indexed: 01/18/2023]
Abstract
Cell-extracellular matrix (ECM) adhesion is mediated by transmembrane cell adhesion receptors (e.g., integrins) and receptor proximal cytoplasmic proteins. Over the past several years, studies using biochemical, structural, cell biological and genetic approaches have provided important evidence suggesting crucial roles of integrin-linked kinase (ILK), PINCH and CH-ILKBP/actopaxin/affixin/parvin (abbreviated as parvin herein) in ECM control of cell behavior. One general theme emerging from these studies is that the formation of ternary protein complexes consisting of ILK, PINCH and parvin is pivotal to the functions of PINCH, ILK and parvin proteins. In addition, recent studies have begun to uncover the molecular mechanisms underlying the assembly, functions and regulation of the PINCH-ILK-parvin (PIP) complexes. The PIP complexes provide crucial physical linkages between integrins and the actin cytoskeleton and transduce diverse signals from ECM to intracellular effectors. Among the challenges of future studies are to define the functions of different PIP complexes in various cellular processes, identify additional partners of the PIP complexes that regulate and/or mediate the functions of the PIP complexes, and determine the roles of the PIP complexes in the pathogenesis of human diseases involving abnormal cell-ECM adhesion and signaling.
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Affiliation(s)
- Chuanyue Wu
- Department of Pathology, University of Pittsburgh, 707B Scaife Hall, 3550 Terrace Street, PA 15261, USA.
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46
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Cereijido M, Contreras RG, Shoshani L. Cell Adhesion, Polarity, and Epithelia in the Dawn of Metazoans. Physiol Rev 2004; 84:1229-62. [PMID: 15383651 DOI: 10.1152/physrev.00001.2004] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Transporting epithelia posed formidable conundrums right from the moment that Du Bois Raymond discovered their asymmetric behavior, a century and a half ago. It took a century and a half to start unraveling the mechanisms of occluding junctions and polarity, but we now face another puzzle: lest its cells died in minutes, the first high metazoa (i.e., higher than a sponge) needed a transporting epithelium, but a transporting epithelium is an incredibly improbable combination of occluding junctions and cell polarity. How could these coincide in the same individual organism and within minutes? We review occluding junctions (tight and septate) as well as the polarized distribution of Na+-K+-ATPase both at the molecular and the cell level. Junctions and polarity depend on hosts of molecular species and cellular processes, which are briefly reviewed whenever they are suspected to have played a role in the dawn of epithelia and metazoan. We come to the conclusion that most of the molecules needed were already present in early protozoan and discuss a few plausible alternatives to solve the riddle described above.
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Affiliation(s)
- M Cereijido
- Center For Research and Advanced Studies, Dept. of Physiology, Biophysics, and Neurosciences, Avenida Instituto Politécnico Nacional 2508, Código Postal 07360, México D.F., Mexico.
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47
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Jiang H, Van De Ven C, Satwani P, Baxi LV, Cairo MS. Differential gene expression patterns by oligonucleotide microarray of basal versus lipopolysaccharide-activated monocytes from cord blood versus adult peripheral blood. THE JOURNAL OF IMMUNOLOGY 2004; 172:5870-9. [PMID: 15128766 DOI: 10.4049/jimmunol.172.10.5870] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Monocytes (Mo) are critically important in the generation of inflammatory mediators, cytokines/chemokines, and regulation of innate and adaptive immune responses. We and others have previously demonstrated significant dysregulated cytokine gene expression and protein production and in vitro functional activities of activated cord blood (CB) vs adult peripheral blood (APB) mononuclear cells (MNC). In this study, we compared, by oligonucleotide microarray, the differential gene expression profiles of basal and LPS-activated APB vs CB Mo. We demonstrated a significant increase in the gene expression of several important functional groups of CB genes compared with basal levels including cytokine (IL-12p40, 5-fold), immunoregulatory (signaling lymphocytic activation molecule, 4-fold), signal transduction (Pim-2, 3-fold), and cell structure (Rho7, 4-fold) among others. Furthermore, there was significantly differentially amplified gene expression in LPS-activated APB vs LPS-activated CB Mo, including cytokine (G-CSF, 14-fold), chemokine (macrophage-inflammatory protein 1alpha, 5-fold), immunoregulatory (MHC DRB1, 5-fold), transcription factor (JunB, 4-fold), signal transduction (STAT4, 5-fold), apoptotic regulation (BAX, 5-fold), and cell structure (ladinin 1, 6-fold) among others. These results provide insight into the molecular basis for normal genetic regulation of Mo development and cellular function and differential inflammatory and innate and adaptive immune responses between activated CB and APB Mo.
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Affiliation(s)
- Hong Jiang
- Department of Pediatrics, Children's Hospital of New York-Presbyterian, Columbia University, New York, NY 10032, USA
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48
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Deane JE, Ryan DP, Sunde M, Maher MJ, Guss JM, Visvader JE, Matthews JM. Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex. EMBO J 2004; 23:3589-98. [PMID: 15343268 PMCID: PMC517615 DOI: 10.1038/sj.emboj.7600376] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Accepted: 07/27/2004] [Indexed: 11/09/2022] Open
Abstract
Nuclear LIM-only (LMO) and LIM-homeodomain (LIM-HD) proteins have important roles in cell fate determination, organ development and oncogenesis. These proteins contain tandemly arrayed LIM domains that bind the LIM interaction domain (LID) of the nuclear adaptor protein LIM domain-binding protein-1 (Ldb1). We have determined a high-resolution X-ray crystal structure of LMO4, a putative breast oncoprotein, in complex with Ldb1-LID, providing the first example of a tandem LIM:Ldb1-LID complex and the first structure of a type-B LIM domain. The complex possesses a highly modular structure with Ldb1-LID binding in an extended manner across both LIM domains of LMO4. The interface contains extensive hydrophobic and electrostatic interactions and multiple backbone-backbone hydrogen bonds. A mutagenic screen of Ldb1-LID, assessed by yeast two-hybrid and competition ELISA analysis, identified key features at the interface and revealed that the interaction is tolerant to mutation. These combined properties provide a mechanism for the binding of Ldb1 to numerous LMO and LIM-HD proteins. Furthermore, the modular extended interface may form a general mode of binding to tandem LIM domains.
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Affiliation(s)
- Janet E Deane
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
| | - Daniel P Ryan
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
| | - Margaret Sunde
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
| | - Megan J Maher
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
| | - J Mitchell Guss
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
| | - Jane E Visvader
- Walter and Eliza Hall Institute for Medical Research, Parkville, Australia
| | - Jacqueline M Matthews
- School of Molecular and Microbial Biosciences, University of Sydney, Australia
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney NSW 2006, Australia. Tel.: +61 2 9351 6025; Fax: +61 2 9351 4726; E-mail:
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49
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Zhang Y, Chen K, Tu Y, Wu C. Distinct roles of two structurally closely related focal adhesion proteins, alpha-parvins and beta-parvins, in regulation of cell morphology and survival. J Biol Chem 2004; 279:41695-705. [PMID: 15284246 DOI: 10.1074/jbc.m401563200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Proteins at cell-extracellular matrix adhesions (e.g. focal adhesions) are crucially involved in regulation of cell morphology and survival. We show here that CH-ILKBP/actopaxin/alpha-parvin and affixin/beta-parvin (abbreviated as alpha- and beta-parvin, respectively), two structurally closely related integrin-linked kinase (ILK)-binding focal adhesion proteins, are co-expressed in human cells. Depletion of alpha-parvin dramatically increased the level of beta-parvin, suggesting that beta-parvin is negatively regulated by alpha-parvin in human cells. Loss of PINCH-1 or ILK, to which alpha- and beta-parvin bind, significantly reduced the activation of Rac, a key signaling event that controls lamellipodium formation and cell spreading. We were surprised to find that loss of alpha-parvin, but not that of beta-parvin, markedly stimulated Rac activation and enhanced lamellipodium formation. Overexpression of beta-parvin, however, was insufficient for stimulation of Rac activation or lamellipodium formation, although it was sufficient for promotion of apoptosis, another important cellular process that is regulated by PINCH-1, ILK, and alpha-parvin. In addition, we show that the interactions of ILK with alpha- and beta-parvin are mutually exclusive. Overexpression of beta-parvin or its CH(2) fragment, but not a CH(2) deletion mutant, inhibited the ILK-alpha-parvin complex formation. Finally, we provide evidence suggesting that inhibition of the ILK-alpha-parvin complex is sufficient, although not necessary, for promotion of apoptosis. These results identify Rac as a downstream target of PINCH-1, ILK, and parvin. Furthermore, they demonstrate that alpha- and beta-parvins play distinct roles in mammalian cells and suggest that the formation of the ILK-alpha-parvin complex is crucial for protection of cells from apoptosis.
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Affiliation(s)
- Yongjun Zhang
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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