Receptor-Like Protein Tyrosine Phosphatase Homodimerizes On
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"Protein Quaternary Structure: Subunit&Ndash;Subunit
Protein Quaternary Secondary article Structure: Subunit–Subunit Article Contents . Introduction Interactions . Quaternary Structure Assembly . Folding and Function Susan Jones, University College, London, England . Protein–Protein Recognition Sites . Concluding Remarks Janet M Thornton, University College, London, England The quaternary structure of proteins is the highest level of structural organization observed in these macromolecules. The multimeric proteins that result from quaternary structure formation involve the association of protein subunits through hydrophobic and electrostatic interactions. Protein quaternary structure has important implications for protein folding and function. Introduction from, other components. Using these definitions, the Proteins are organized into a structural hierarchy. The haemoglobin tetramer (comprised of two a and two b polypeptide chain at the primary structural level comprises polypeptide chains) is defined as an oligomer consisting of a linear, noncovalently linked amino acid residue se- two protomers, each consisting of two monomers, i.e. one a quence. Secondary structure is the level at which the linear and one b polypeptide chain. The definition of a subunit sequences aggregate to form structural motifs such as allows the term to be used for either the a-orb-monomer, helices and sheets. The tertiary structure is formed by or for the ab-protomer. The term multimer is also widely packing of the secondary structural elements into one or used in the literature and is defined here as a protein with a more compact globular domains. In many cases proteins finite number of subunits that need not be identical. are composed of only a single polypeptide chain that has The quaternary nature of some proteins was first tertiary structure as its highest level of organization, e.g. -
RNA Isolation and Real-Time PCR Analysis
Pleiotrophin deletion alters glucose homeostasis, energy metabolism and brown fat thermogenic function. Sevillano, Julio1#; Sánchez-Alonso, María Gracia1#; Zapatería, Begoña1; Calderón, María1; Alcalá, Martín1, Limones, María1; Pita, Jimena1; Gramage, Esther2; Vicente- Rodríguez, Marta2; Horrillo, Daniel4; Medina-Gómez, Gema4; Obregón, María Jesús5; Viana, Marta1; Valladolid-Acebes, Ismael3, Herradón, Gonzalo2, Ramos, María del Pilar1*. Affiliations 1Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain. 2Department of Pharmaceutical and Health Sciences, Facultad de Farmacia, Universidad CEU San Pablo, Madrid, Spain. 3The Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76, Stockholm, Sweden 4Department of Basic Sciences of Health. Universidad Rey Juan Carlos. Alcorcón. Madrid. Spain. 5Department of Endocrine and Nervous System Pathophysiology, Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid (UAM), Madrid, Spain. Keywords: Glucose homeostasis; Metabolism; Adipose tissue; Insulin resistance, Thermogenesis. *To whom correspondence should be addressed: Mª del Pilar Ramos Álvarez, PhD. Department of Chemistry and Biochemistry Facultad de Farmacia, Universidad CEU San Pablo Ctra. Boadilla del Monte km 5,3 28668, Madrid 1 +34-91-3724760 [email protected] Additional Title Page Footnotes #Co-first authors This study was supported by Spanish Ministry of Economy and Competitiveness (SAF2010-19603 and SAF2014-56671-R, SAF2012-32491, BFU2013-47384-R and BFU2016-78951-R) and Community of Madrid (S2010/BMD-2423, S2017/BMD-3864). Running Title: PLEITROPHIN AND ENERGY METABOLISM Aims/hypothesis: Pleiotrophin, a developmentally regulated and highly conserved cytokine, exerts different functions including regulation of cell growth, migration and survival. -
Pleiotrophin Is a Neurotrophic Factor for Spinal Motor Neurons
Pleiotrophin is a neurotrophic factor for spinal motor neurons Ruifa Mi, Weiran Chen, and Ahmet Ho¨ ke* Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287 Edited by Thomas M. Jessell, Columbia University Medical Center, New York, NY, and approved January 18, 2007 (received for review April 21, 2006) Regeneration in the peripheral nervous system is poor after chronic facial motor neurons against cell death induced by deprivation from denervation. Denervated Schwann cells act as a ‘‘transient target’’ target-derived neurotrophic support. by secreting growth factors to promote regeneration of axons but lose this ability with chronic denervation. We discovered that the Results mRNA for pleiotrophin (PTN) was highly up-regulated in acutely PTN Is Up-Regulated in Denervated Schwann Cells and Muscle After denervated distal sciatic nerves, but high levels of PTN mRNA were Axotomy. To identify candidate neurotrophic factors underlying not maintained in chronically denervated nerves. PTN protected adaptive responses to chronic nerve degeneration, we used focused spinal motor neurons against chronic excitotoxic injury and caused cDNA microarrays to investigate the gene expression of neurotro- increased outgrowth of motor axons out of the spinal cord ex- phic factors in denervated Schwann cells. In microarray experi- plants and formation of ‘‘miniventral rootlets.’’ In neonatal mice, ments, 2 and 7 days after the sciatic nerve transection, PTN mRNA PTN protected the facial motor neurons against cell death induced was up-regulated in the distal denervated segments compared with by deprivation from target-derived growth factors. Similarly, PTN the contralateral side (data not shown). To confirm the up- significantly enhanced regeneration of myelinated axons across a regulation of the PTN mRNA observed in the microarray analysis graft in the transected sciatic nerve of adult rats. -
Gene Section Review
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Review XRCC2 (X-ray repair cross complementing 2) Paul R Andreassen, Helmut Hanenberg Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA; [email protected] (PRA); Department of Pediatrics III, University Children's Hospital Essen, University Duisburg- Essen, Essen Germany; [email protected] (HH) Published in Atlas Database: November 2017 Online updated version : http://AtlasGeneticsOncology.org/Genes/XRCC2ID334ch7q36.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/69759/11-2017-XRCC2ID334ch7q36.pdf DOI: 10.4267/2042/69759 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2019 Atlas of Genetics and Cytogenetics in Oncology and Haematology Clinically, the only known FA-U patient in the Abstract world exhibits severe congenital abnormalities, but XRCC2 is one of five somatic RAD51 paralogs, all had not developed, by seven years of age, the bone of which have Walker A and B ATPase motifs. marrow failure and cancer that are often seen in Each of the paralogs, including XRCC2, has a patients from other FA complementation groups. function in DNA double-strand break repair by Keywords homologous recombination (HR). However, their Fanconi anemia, Breast Cancer Susceptibility, individual roles are not as well understood as that Tumor Suppressor, Homologous Recombination, of RAD51 itself. DNA Repair, RAD51 Paralog The XRCC2 protein forms a complex (BCDX2) with three other RAD51 paralogs, RAD51B, RAD51C and RAD51D. It is believed that the Identity BCDX2 complex mediates HR downstream of Other names: FANCU BRCA2 but upstream of RAD51, as XRCC2 is HGNC (Hugo): XRCC2 involved in the assembly of RAD51 into DNA damage foci. -
Pleiotrophin Regulates the Ductular Reaction by Controlling the Migration
Gut Online First, published on March 10, 2015 as 10.1136/gutjnl-2014-308176 Hepatology ORIGINAL ARTICLE Gut: first published as 10.1136/gutjnl-2014-308176 on 16 January 2015. Downloaded from Pleiotrophin regulates the ductular reaction by controlling the migration of cells in liver progenitor niches Gregory A Michelotti,1 Anikia Tucker,1 Marzena Swiderska-Syn,1 Mariana Verdelho Machado,1 Steve S Choi,1,2 Leandi Kruger,1 Erik Soderblom,3 J Will Thompson,3 Meredith Mayer-Salman,3 Heather A Himburg,4 Cynthia A Moylan,1,2 Cynthia D Guy,5 Katherine S Garman,1,2 Richard T Premont,1 John P Chute,4 Anna Mae Diehl1 ▸ Additional material is ABSTRACT published online only. To view Objective The ductular reaction (DR) involves Significance of this study please visit the journal online (http://dx.doi.org/10.1136/ mobilisation of reactive-appearing duct-like cells (RDC) gutjnl-2014-308176). along canals of Hering, and myofibroblastic (MF) differentiation of hepatic stellate cells (HSC) in the space 1Division of Gastroenterology, What is already known about this subject? Duke University, Durham, of Disse. Perivascular cells in stem cell niches produce ▸ Various types of liver injury promote a ductular North Carolina, USA pleiotrophin (PTN) to inactivate the PTN receptor, protein reaction (DR) characterised by the periportal 2Section of Gastroenterology, tyrosine phosphatase receptor zeta-1 (PTPRZ1), thereby accumulation of small ductules, myofibroblasts Durham Veterans Affairs augmenting phosphoprotein-dependent signalling. We and collagen matrix. Medical Center, Durham, ▸ Pleiotrophin (PTN) is a heparin-binding growth North Carolina, USA hypothesised that the DR is regulated by PTN/PTPRZ1 3Proteomics Center, signalling. -
Genetic Drivers of Pancreatic Islet Function
| INVESTIGATION Genetic Drivers of Pancreatic Islet Function Mark P. Keller,*,1 Daniel M. Gatti,†,1 Kathryn L. Schueler,* Mary E. Rabaglia,* Donnie S. Stapleton,* Petr Simecek,† Matthew Vincent,† Sadie Allen,‡ Aimee Teo Broman,§ Rhonda Bacher,§ Christina Kendziorski,§ Karl W. Broman,§ Brian S. Yandell,** Gary A. Churchill,†,2 and Alan D. Attie*,2 *Department of Biochemistry, §Department of Biostatistics and Medical Informatics, and **Department of Horticulture, University of Wisconsin–Madison, Wisconsin 53706-1544, †The Jackson Laboratory, Bar Harbor, Maine 06409, and ‡Maine School of Science and Mathematics, Limestone, Maine 06409, ORCID IDs: 0000-0002-7405-5552 (M.P.K.); 0000-0002-4914-6671 (K.W.B.); 0000-0001-9190-9284 (G.A.C.); 0000-0002-0568-2261 (A.D.A.) ABSTRACT The majority of gene loci that have been associated with type 2 diabetes play a role in pancreatic islet function. To evaluate the role of islet gene expression in the etiology of diabetes, we sensitized a genetically diverse mouse population with a Western diet high in fat (45% kcal) and sucrose (34%) and carried out genome-wide association mapping of diabetes-related phenotypes. We quantified mRNA abundance in the islets and identified 18,820 expression QTL. We applied mediation analysis to identify candidate causal driver genes at loci that affect the abundance of numerous transcripts. These include two genes previously associated with monogenic diabetes (PDX1 and HNF4A), as well as three genes with nominal association with diabetes-related traits in humans (FAM83E, IL6ST, and SAT2). We grouped transcripts into gene modules and mapped regulatory loci for modules enriched with transcripts specific for a-cells, and another specific for d-cells. -
Hydrogel Mediated Delivery of Trophic Factors for Neural Repair Joshua S
Advanced Review Hydrogel mediated delivery of trophic factors for neural repair Joshua S. Katz1 and Jason A. Burdick∗ Neurotrophins have been implicated in a variety of diseases and their delivery to sites of disease and injury has therapeutic potential in applications including spinal cord injury, Alzheimer’s disease, and Parkinson’s disease. Biodegradable polymers, and specifically, biodegradable water-swollen hydrogels, may be advantageous as delivery vehicles for neurotrophins because of tissue-like properties, tailorability with respect to degradation and release behavior, and a history of biocompatibility. These materials may be designed to degrade via hydrolytic or enzymatic mechanisms and can be used for the sustained delivery of trophic factors in vivo. Hydrogels investigated to date include purely synthetic to purely natural, depending on the application and intended release profiles. Also, flexibility in material processing has allowed for the investigation of injectable materials, the development of scaffolding and porous conduits, and the use of composites for tailored molecule delivery profiles. It is the objective of this review to describe what has been accomplished in this area thus far and to remark on potential future directions in this field. Ultimately, the goal is to engineer optimal biomaterials to deliver molecules in a controlled and dictated manner that can promote regeneration and healing for numerous neural applications. 2008 John Wiley & Sons, Inc. Wiley Interdiscipl. Rev. Nanomed. Nanobiotechnol. 2009 1 128–139 -
Biochemistry-2018-Hartman.Pdf
Article Cite This: Biochemistry 2019, 58, 1527−1538 pubs.acs.org/biochemistry Experimental Evaluation of Coevolution in a Self-Assembling Particle Emily C. Hartman,† Marco J. Lobba,† Andrew H. Favor,† Stephanie A. Robinson,† Matthew B. Francis,*,†,‡ and Danielle Tullman-Ercek*,§ † Department of Chemistry, University of California, Berkeley, California 94720-1460, United States ‡ Materials Sciences Division, Lawrence Berkeley National Laboratories, Berkeley, California 94720-1460, United States § Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, Illinois 60208-3120, United States *S Supporting Information ABSTRACT: Protein evolution occurs via restricted evolutionary paths that are influenced by both previous and subsequent mutations. This effect, termed epistasis, is critical in population genetics, drug resistance, and immune escape; however, the effect of epistasis on the level of protein fitness is less well characterized. We generated and characterized a 6615-member library of all two-amino acid combinations in a highly mutable loop of a virus-like particle. This particle is a model of protein self- assembly and a promising vehicle for drug delivery and imaging. In addition to characterizing the effect of all double mutants on assembly, thermostability, and acid stability, we observed many instances of epistasis, in which combinations of mutations are either more deleterious or more beneficial than expected. These results were used to generate rules governing the effects of multiple mutations on the self-assembly of the virus-like particle. rotein evolution occurs through complex pathways, often have a significant impact on biotechnology in the coming involving nonintuitive leaps between functional var- decades.23,24 To maximize this potential, it is important to P − iants.1 3 These paths include local minima and maxima, in understand how non-native functions can be hindered by which the effect of a given mutation depends entirely on the unanticipated epistatic effects. -
Inhibition of Metastasis by HEXIM1 Through Effects on Cell Invasion and Angiogenesis
Oncogene (2013) 32, 3829–3839 & 2013 Macmillan Publishers Limited All rights reserved 0950-9232/13 www.nature.com/onc ORIGINAL ARTICLE Inhibition of metastasis by HEXIM1 through effects on cell invasion and angiogenesis W Ketchart1, KM Smith2, T Krupka3, BM Wittmann1,7,YHu1, PA Rayman4, YQ Doughman1, JM Albert5, X Bai6, JH Finke4,YXu2, AA Exner3 and MM Montano1 We report on the role of hexamethylene-bis-acetamide-inducible protein 1 (HEXIM1) as an inhibitor of metastasis. HEXIM1 expression is decreased in human metastatic breast cancers when compared with matched primary breast tumors. Similarly we observed decreased expression of HEXIM1 in lung metastasis when compared with primary mammary tumors in a mouse model of metastatic breast cancer, the polyoma middle T antigen (PyMT) transgenic mouse. Re-expression of HEXIM1 (through transgene expression or localized delivery of a small molecule inducer of HEXIM1 expression, hexamethylene-bis-acetamide) in PyMT mice resulted in inhibition of metastasis to the lung. Our present studies indicate that HEXIM1 downregulation of HIF-1a protein allows not only for inhibition of vascular endothelial growth factor-regulated angiogenesis, but also for inhibition of compensatory pro- angiogenic pathways and recruitment of bone marrow-derived cells (BMDCs). Another novel finding is that HEXIM1 inhibits cell migration and invasion that can be partly attributed to decreased membrane localization of the 67 kDa laminin receptor, 67LR, and inhibition of the functional interaction of 67LR with laminin. Thus, HEXIM1 re-expression in breast cancer has therapeutic advantages by simultaneously targeting more than one pathway involved in angiogenesis and metastasis. Our results also support the potential for HEXIM1 to indirectly act on multiple cell types to suppress metastatic cancer. -
Heparin/Heparan Sulfate Proteoglycans Glycomic Interactome in Angiogenesis: Biological Implications and Therapeutical Use
Molecules 2015, 20, 6342-6388; doi:10.3390/molecules20046342 OPEN ACCESS molecules ISSN 1420-3049 www.mdpi.com/journal/molecules Review Heparin/Heparan Sulfate Proteoglycans Glycomic Interactome in Angiogenesis: Biological Implications and Therapeutical Use Paola Chiodelli, Antonella Bugatti, Chiara Urbinati and Marco Rusnati * Section of Experimental Oncology and Immunology, Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy; E-Mails: [email protected] (P.C.); [email protected] (A.B.); [email protected] (C.U.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-030-371-7315; Fax: +39-030-371-7747. Academic Editor: Els Van Damme Received: 26 February 2015 / Accepted: 1 April 2015 / Published: 10 April 2015 Abstract: Angiogenesis, the process of formation of new blood vessel from pre-existing ones, is involved in various intertwined pathological processes including virus infection, inflammation and oncogenesis, making it a promising target for the development of novel strategies for various interventions. To induce angiogenesis, angiogenic growth factors (AGFs) must interact with pro-angiogenic receptors to induce proliferation, protease production and migration of endothelial cells (ECs). The action of AGFs is counteracted by antiangiogenic modulators whose main mechanism of action is to bind (thus sequestering or masking) AGFs or their receptors. Many sugars, either free or associated to proteins, are involved in these interactions, thus exerting a tight regulation of the neovascularization process. Heparin and heparan sulfate proteoglycans undoubtedly play a pivotal role in this context since they bind to almost all the known AGFs, to several pro-angiogenic receptors and even to angiogenic inhibitors, originating an intricate network of interaction, the so called “angiogenesis glycomic interactome”. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Role of Transglutaminase 2 in Cell Death, Survival, and Fibrosis
cells Review Role of Transglutaminase 2 in Cell Death, Survival, and Fibrosis Hideki Tatsukawa * and Kiyotaka Hitomi Cellular Biochemistry Laboratory, Graduate School of Pharmaceutical Sciences, Nagoya University, Tokai National Higher Education and Research System, Nagoya 464-8601, Aichi, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-52-747-6808 Abstract: Transglutaminase 2 (TG2) is a ubiquitously expressed enzyme catalyzing the crosslink- ing between Gln and Lys residues and involved in various pathophysiological events. Besides this crosslinking activity, TG2 functions as a deamidase, GTPase, isopeptidase, adapter/scaffold, protein disulfide isomerase, and kinase. It also plays a role in the regulation of hypusination and serotonylation. Through these activities, TG2 is involved in cell growth, differentiation, cell death, inflammation, tissue repair, and fibrosis. Depending on the cell type and stimulus, TG2 changes its subcellular localization and biological activity, leading to cell death or survival. In normal unstressed cells, intracellular TG2 exhibits a GTP-bound closed conformation, exerting prosurvival functions. However, upon cell stimulation with Ca2+ or other factors, TG2 adopts a Ca2+-bound open confor- mation, demonstrating a transamidase activity involved in cell death or survival. These functional discrepancies of TG2 open form might be caused by its multifunctional nature, the existence of splicing variants, the cell type and stimulus, and the genetic backgrounds and variations of the mouse models used. TG2 is also involved in the phagocytosis of dead cells by macrophages and in fibrosis during tissue repair. Here, we summarize and discuss the multifunctional and controversial Citation: Tatsukawa, H.; Hitomi, K. roles of TG2, focusing on cell death/survival and fibrosis.