Sequence Similarity Function
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Biophysics 1
Biophysics 1 on interactions between proteins involved in Notch signaling using BIOPHYSICS modern biophysical methods. Thermodynamics of association and allosteric effects are determined by spectroscopic, ultracentrifugation, http://biophysics.jhu.edu/ and calorimetric methods. Atomic structure information is being obtained by NMR spectroscopy. The ultimate goal is to determine the The Department of Biophysics offers programs leading to the B.A., M.A., thermodynamic partition function for a signal transduction system and and Ph.D. degrees. Biophysics is appropriate for students who wish interpret it in terms of atomic structure. to develop and integrate their interests in the physical and biological sciences. NMR Spectroscopy (Dr. Lecomte) Research interests in the Department cover experimental and Many proteins require stable association with an organic compound computational, molecular and cellular structure, function, and biology, for proper functioning. One example of such “cofactor” is the heme membrane biology, and biomolecular energetics. The teaching and group, a versatile iron-containing molecule capable of catalyzing a research activities of the faculty bring its students in contact with broad range of chemical reactions. The reactivity of the heme group biophysical scientists throughout the university. Regardless of their choice is precisely controlled by interactions with contacting amino acids. of research area, students are exposed to a wide range of problems of Structural fluctuations within the protein are also essential to the fine- biological interest. For more information, and for the most up-to-date list tuning of the chemistry. We are studying how the primary structure of of course offerings and requirements, consult the department web page at cytochromes and hemoglobins codes for heme binding and the motions biophysics.jhu.edu (http://biophysics.jhu.edu/). -
Cpla2pathway in the Regulation of Platelet Apoptosis Induced by ABT
Citation: Cell Death and Disease (2013) 4, e931; doi:10.1038/cddis.2013.459 OPEN & 2013 Macmillan Publishers Limited All rights reserved 2041-4889/13 www.nature.com/cddis Dual role of the p38 MAPK/cPLA2 pathway in the regulation of platelet apoptosis induced by ABT-737 and strong platelet agonists N Rukoyatkina1,2, I Mindukshev2, U Walter3 and S Gambaryan*,1,2 p38 Mitogen-activated protein (MAP) kinase is involved in the apoptosis of nucleated cells. Although platelets are anucleated cells, apoptotic proteins have been shown to regulate platelet lifespan. However, the involvement of p38 MAP kinase in platelet apoptosis is not yet clearly defined. Therefore, we investigated the role of p38 MAP kinase in apoptosis induced by a mimetic of BH3-only proteins, ABT-737, and in apoptosis-like events induced by such strong platelet agonists as thrombin in combination with convulxin (Thr/Cvx), both of which result in p38 MAP kinase phosphorylation and activation. A p38 inhibitor (SB202190) inhibited the apoptotic events induced by ABT-737 but did not influence those induced by Thr/Cvx. The inhibitor also reduced the phosphorylation of cytosolic phospholipase A2 (cPLA2), an established p38 substrate, induced by ABT-737 or Thr/Cvx. ABT-737, but not Thr/Cvx, induced the caspase 3-dependent cleavage and inactivation of cPLA2. Thus, p38 MAPK promotes ABT-737- induced apoptosis by inhibiting the cPLA2/arachidonate pathway. We also show that arachidonic acid (AA) itself and in combination with Thr/Cvx or ABT-737 at low concentrations prevented apoptotic events, whereas at high concentrations it enhanced such events. -
Molecular Priming of Lyn by GPVI Enables an Immune Receptor to Adopt a Hemostatic Role
Molecular priming of Lyn by GPVI enables an immune receptor to adopt a hemostatic role Alec A. Schmaiera,b, Zhiying Zoua,b, Arunas Kazlauskasc, Lori Emert-Sedlakd, Karen P. Fonga,e, Keith B. Neevesf, Sean F. Maloneyg,h, Scott L. Diamondg,h, Satya P. Kunapulii, Jerry Warej, Lawrence F. Brassa,e, Thomas E. Smithgalld, Kalle Sakselac, and Mark L. Kahna,b,1 aDepartment of Medicine, bDivision of Cardiology, eDivision of Hematology, gDepartment of Chemical and Biomolecular Engineering, hInstitute for Medicine and Engineering, University of Pennsylvania School of Medicine, Philadelphia, PA 19104; cDepartment of Virology, Haartman Institute, University of Helsinki and Helsinki University Central Hospital, Finland; dMicrobiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261; iThe Sol Sherry Thrombosis Research Center, Temple University School of Medicine, Philadelphia, PA 19140; jDepartment of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR 72205; and fDepartment of Chemical Engineering, Colorado School of Mines, Golden, CO 80401 Edited by Shaun R. Coughlin, University of California, San Francisco, CA, and approved October 12, 2009 (received for review June 10, 2009) The immune receptor signaling pathway is used by nonimmune cells, (5, 6). This pathway, like the established G protein-coupled signaling but the molecular adaptations that underlie its functional diversifi- pathways that mediate platelet activation by thrombin and ADP, results cation are not known. Circulating platelets use the immune receptor in the elevation of intracellular calcium levels and platelet activation homologue glycoprotein VI (GPVI) to respond to collagen exposed at responses, including granule release and integrin conformational sites of vessel injury. -
Single Platelet Variability Governs Population Sensitivity and Initiates
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.22.915512; this version posted January 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Single platelet variability governs population sensitivity and 2 initiates intrinsic heterotypic behaviours 3 Maaike S. A. Jongen1, Ben D. MacArthur1,2,3, Nicola A. Englyst1,3 and Jonathan West1,3,* 4 1. Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK 5 2. Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK 6 3. Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK 7 *Correspondence to: [email protected] 8 9 Abstract 10 Droplet microfluidics combined with flow cytometry was used for high throughput single platelet function 11 analysis. A large-scale sensitivity continuum was shown to be a general feature of human platelets from 12 individual donors, with hypersensitive platelets coordinating significant sensitivity gains in bulk platelet 13 populations and shown to direct aggregation in droplet-confined minimal platelet systems. Sensitivity gains 14 scaled with agonist potency (convulxin>TRAP-14>ADP) and reduced the collagen and thrombin activation 15 threshold required for platelet population polarization into pro-aggregatory and pro-coagulant states. The 16 heterotypic platelet response results from an intrinsic behavioural program. The method and findings invite 17 future discoveries into the nature of hypersensitive platelets and how community effects produce population 18 level behaviours in health and disease. -
2020 Biomolecular Visualization Framework
2020 Biomolecular Visualization Framework Citation: Dries et al (2017) Biochemistry and Molecular Biology Education 45:69-75 https://iubmb.onlinelibrary.wiley.com/doi/full/10.1002/bmb.20991 However, please note that the Framework language below has been updated to standardize word choice as well as to rename some themes. Thus, the 2020 version is different from the 2017 Framework published in BAMBED. Major changes are the following: • Ligands and Modifications (LM) was formerly called Hetero Group Recognition (HG). • Macromolecular Building Blocks (MB) was formerly called Monomer Recognition (MR). Contact: [email protected] Funding Acknowledgement This material is based upon work supported by the National Science Foundation (NSF) under grants RCN- UBE #1920270 and NSF-IUSE #1712268. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. © 2020 BioMolViz.org Atomic Geometry (AG) - three-atom and four-atom dihedral/torsion angles, metal size and metal-ligand geometries, steric clashes. AG1. Students can describe the ideal geometry for a given atom within a molecule and deviations from the ideal geometry due to neighboring interactions. AG1.01 Students can identify atomic geometry/hybridization for a given atom. (Novice) AG1.02 Students can measure bond angles for a given atom. (Novice) AG1.03 Students can identify deviations from the ideal bond angles. (Amateur) AG1.04 Students can explain deviations from the ideal bond angles due to local effects. (Amateur, Expert) AG1.05 Students can predict the effect of deviations from ideal bond angles on the structure and function of a macromolecule. -
The Fact of Evolution? by David M
The Fact of Evolution? By David M. Kern http://sites.google.com/site/factofevolution/ May 7, 2011 Copyright © 2011 by David M. Kern – All Rights Reserved Important Copyright Notification In order to provide a thorough analysis of the so-called Fact of Evolution , this book includes many short quotations from a large number of experts in a wide variety of technical fields. These quotations are copyright protected by the sources documented in the endnotes (see the "Notes and References” section located at the end of each chapter). I believe that these quotations fall under the Fair Use limitation of US Copyright Law (http://www.copyright.gov/fls/fl102.html ). However, Fair Use has a very vague definition and copyright violations are subject to legal penalties. An About Copyright document with additional information on this topic is posted on the Fact of Evolution website . Where I am quoting a larger amount of copyrighted material, I have obtained permission to reproduce this material on my website. My use of this copyrighted material does not imply any endorsement of the views presented in this document. Any permission I have been granted to reproduce this copyrighted material applies only to my specific use. I gratefully acknowledge the various sources who have granted me permission to reproduce their copyrighted material. Each chapter of this book has an Acknowledgment section that lists any specific permission statements that I have received. The Acknowledgment section is located directly before the "Notes and References" section. My major goal in writing this book is to seek the truth about a very complex technical topic. -
Mouse Mutants As Models for Congenital Retinal Disorders
Experimental Eye Research 81 (2005) 503–512 www.elsevier.com/locate/yexer Review Mouse mutants as models for congenital retinal disorders Claudia Dalke*, Jochen Graw GSF-National Research Center for Environment and Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany Received 1 February 2005; accepted in revised form 1 June 2005 Available online 18 July 2005 Abstract Animal models provide a valuable tool for investigating the genetic basis and the pathophysiology of human diseases, and to evaluate therapeutic treatments. To study congenital retinal disorders, mouse mutants have become the most important model organism. Here we review some mouse models, which are related to hereditary disorders (mostly congenital) including retinitis pigmentosa, Leber’s congenital amaurosis, macular disorders and optic atrophy. q 2005 Elsevier Ltd. All rights reserved. Keywords: animal model; retina; mouse; gene mutation; retinal degeneration 1. Introduction Although mouse models are a good tool to investigate retinal disorders, one should keep in mind that the mouse Mice suffering from hereditary eye defects (and in retina is somehow different from a human retina, particular from retinal degenerations) have been collected particularly with respect to the number and distribution of since decades (Keeler, 1924). They allow the study of the photoreceptor cells. The mouse as a nocturnal animal molecular and histological development of retinal degener- has a retina dominated by rods; in contrast, cones are small ations and to characterize the genetic basis underlying in size and represent only 3–5% of the photoreceptors. Mice retinal dysfunction and degeneration. The recent progress of do not form cone-rich areas like the human fovea. -
Macromolecular Assemblies in Solution: Characterization by Light Scattering
#2009 The Society of Polymer Science, Japan AWARD ACCOUNTS SPSJ Award Accounts Macromolecular Assemblies in Solution: Characterization by Light Scattering By Takahiro SATO1;Ã and Yasuhiro MATSUDA2 This review article demonstrates that the light scattering technique provides important structural information of the following macromolecular assemblies, polymer living anions in a non-polar solvent, amphiphilic telechelic polymer and block copolymers in aqueous solution, and a thermally denatured double-helical polysaccharide aggregated during renaturation. To get accurate information from light scattering data, however, we have to analyze the data using proper theoretical tools, which are briefly explained in this article. The structural information of these macromolecular assemblies assists us in understanding, e.g., the kinetics of living anionic polymerization and gelation. KEY WORDS: Macromolecular Assembly / Light Scattering / Micellization / Aggregation / Telechelic Polymer / Block Copolymer / Helical Polymer / Associating polymers, bearing functional groups of strong have to formulate characteristic parameters using models attractive interactions, hydrophobic, solvophobic, electrostatic suitable for each architectures considering the dispersity effect interactions, or hydrogen-bonding, form macromolecular as- if necessary. semblies in solution.1 There are many types of architecture of The present article reviews recent light scattering studies on macromolecular assemblies (cf. Figure 1). For associating various macromolecular assemblies in dilute solution. Light polymers with a single attractive moiety per chain (e.g., scattering is one of the most suitable techniques to characterize diblock copolymers, polymer living anions, water-soluble macromolecular assemblies in solution. Its measurements are polymers hydrophobically modified at one end), the architec- made on assemblies in solution without any perturbations, and ture may be spherical (star-like), cylindrical, bilayer or nanometer to sub-micrometer structures can be investigated. -
MMA 2020 Brochure
Chang-Hui Shen (S): protein-nucleic acid, protein-protein interactions FACULTY TEAM LEADERS Chwen-Yang Shew (S): statistical mechanics of model biological systems Probal Banerjee (S): phosphatidylserine-membrane assemblies Ruth E. Stark (C): protein-ligand and plant biopolymer assem- and receptors blies; NMR methodology Lesley Davenport (B): lipid, protein and DNA interactions; Raymond Tu (C): peptide and biomacromolecule engineering, fluorescence spectroscopy interfacial assembly Ruel Desamero (Y) protein-small molecule interactions; Raman Eleanore Wurtzel (S): protein-mediated regulation of carotenoid and IR spectroscopy biosynthesis Ranajeet Ghose (C): structural biology of signal transduction, Yujia Xu (H): protein folding, macromolecular assembly protein dynamics; NMR methodology Zhou, Shuiqin (S): self-assembly of amphiphilic copolymers, M. Lane Gilchrist, Jr. (C): biomolecular materials; supramo- lipids and fullerene-based surfactants lecular assemblies Emeritus Faculty: Tom Haines, Maria Luisa Tasayco Dixie J. Goss (H): studies of protein-nucleic acid interactions Campus affiliation: B – Brooklyn College; H – Hunter College; Y – York Col- and regulation of transcription and translation. lege; C – City College; S – College of Staten Island; G – CUNY Graduate Center Paul Gottlieb (C): assembly, replication and structure of cysto- viruses; viral etiology of systemic autoimmune disease Nancy L. Greenbaum (H): RNA structure, interactions with REGIONAL PARTNERSHIPS ions and proteins; NMR and fluorescence spectroscopy Marilyn Gunner -
B-Mediated Induction of BAG3 Upon Inhibition of Constitutive Protein Degradation Pathways
Citation: Cell Death and Disease (2015) 6, e1692; doi:10.1038/cddis.2014.584 OPEN & 2015 Macmillan Publishers Limited All rights reserved 2041-4889/15 www.nature.com/cddis NIK is required for NF-κB-mediated induction of BAG3 upon inhibition of constitutive protein degradation pathways F Rapino1,5, BA Abhari1,5, M Jung2,3,4 and S Fulda*,1,3,4 Recently, we reported that induction of the co-chaperone Bcl-2-associated athanogene 3 (BAG3) is critical for recovery of rhabdomyosarcoma (RMS) cells after proteotoxic stress upon inhibition of the two constitutive protein degradation pathways, that is, the ubiquitin-proteasome system by Bortezomib and the aggresome-autophagy system by histone deacetylase 6 (HDAC6) inhibitor ST80. In the present study, we investigated the molecular mechanisms mediating BAG3 induction under these conditions. Here, we identify nuclear factor-kappa B (NF-κB)-inducing kinase (NIK) as a key mediator of ST80/Bortezomib-stimulated NF-κB activation and transcriptional upregulation of BAG3. ST80/Bortezomib cotreatment upregulates mRNA and protein expression of NIK, which is accompanied by an initial increase in histone H3 acetylation. Importantly, NIK silencing by siRNA abolishes NF-κB activation and BAG3 induction by ST80/Bortezomib. Furthermore, ST80/Bortezomib cotreatment stimulates NF-κB transcriptional activity and upregulates NF-κB target genes. Genetic inhibition of NF-κB by overexpression of dominant- negative IκBα superrepressor (IκBα-SR) or by knockdown of p65 blocks the ST80/Bortezomib-stimulated upregulation of BAG3 mRNA and protein expression. Interestingly, inhibition of lysosomal activity by Bafilomycin A1 inhibits ST80/Bortezomib- stimulated IκBα degradation, NF-κB activation and BAG3 upregulation, indicating that IκBα is degraded via the lysosome in the presence of Bortezomib. -
Automated Evaluation of Quaternary Structures from Protein Crystals
RESEARCH ARTICLE Automated evaluation of quaternary structures from protein crystals Spencer Bliven1,2, Aleix Lafita1,3, Althea Parker1,4, Guido Capitani1,5², Jose M. Duarte1,5,6* 1 Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland, 2 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America, 3 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland, 4 Scientific IT Services, ETH Zurich, Zurich, Switzerland, 5 Department of Biology, ETH Zurich, Zurich, Switzerland, 6 RCSB Protein Data Bank, SDSC, University of California San Diego, La Jolla, California, United States of America a1111111111 a1111111111 ² Deceased. a1111111111 * [email protected] a1111111111 a1111111111 Abstract A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with OPEN ACCESS other proteins. Currently about 90% of structures in the Protein Data Bank are crystal struc- Citation: Bliven S, Lafita A, Parker A, Capitani G, tures, in which the correct quaternary structure is embedded in the crystal lattice among a Duarte JM (2018) Automated evaluation of number of crystal contacts. Computational methods are required to 1) classify all protein- quaternary structures from protein crystals. PLoS Comput Biol 14(4): e1006104. https://doi.org/ protein contacts in crystal lattices as biologically relevant or crystal contacts and 2) provide 10.1371/journal.pcbi.1006104 an assessment of how the biologically relevant interfaces combine into a biological assem- Editor: Roland L. Dunbrack, Jr., Fox Chase Cancer bly. In our previous work we addressed the first problem with our EPPIC (Evolutionary Pro- Center, UNITED STATES tein Protein Interface Classifier) method. -
Absence of Sac2/INPP5F Enhances the Phenotype of a Parkinson's
Absence of Sac2/INPP5F enhances the phenotype of a Parkinson’s disease mutation of synaptojanin 1 Mian Caoa,b,c,d,1,2, Daehun Parka,b,c,d,1, Yumei Wua,b,c,d, and Pietro De Camillia,b,c,d,e,3 aDepartment of Neuroscience, Yale University School of Medicine, New Haven, CT 06510; bDepartment of Cell Biology, Yale University School of Medicine, New Haven, CT 06510; cHoward Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510; dProgram in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT 06510; and eKavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510 Contributed by Pietro De Camilli, April 9, 2020 (sent for review March 9, 2020; reviewed by Volker Haucke and David Sulzer) Numerous genes whose mutations cause, or increase the risk of, analysis of cultured neurons and brain tissue of these mice Parkinson’s disease (PD) have been identified. An inactivating mu- demonstrated defects in synaptic vesicle recycling and dystrophic tation (R258Q) in the Sac inositol phosphatase domain of synapto- changes selectively in nerve terminals of dopaminergic neurons janin 1 (SJ1/PARK20), a phosphoinositide phosphatase implicated in the striatum (17). Levels of auxilin (PARK19) and other in synaptic vesicle recycling, results in PD. The gene encoding Sac2/ endocytic factors were abnormally increased in the brains of such INPP5F, another Sac domain-containing protein, is located within a mice (17). In addition, levels of the PD gene parkin (PARK2) PD risk locus identified by genome-wide association studies. were strikingly elevated (17), strengthening the evidence for Knock-In mice carrying the SJ1 patient mutation (SJ1RQKI) exhibit a functional partnership among endophilin, SJ1, and parkin PD features, while Sac2 knockout mice (Sac2KO) do not have ob- reported by previous studies (18–20).