Emerging Inflammasome Effector Mechanisms
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Molecular Markers of Serine Protease Evolution
The EMBO Journal Vol. 20 No. 12 pp. 3036±3045, 2001 Molecular markers of serine protease evolution Maxwell M.Krem and Enrico Di Cera1 ment and specialization of the catalytic architecture should correspond to signi®cant evolutionary transitions in the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St Louis, history of protease clans. Evolutionary markers encoun- MO 63110-1093, USA tered in the sequences contributing to the catalytic apparatus would thus give an account of the history of 1Corresponding author e-mail: [email protected] an enzyme family or clan and provide for comparative analysis with other families and clans. Therefore, the use The evolutionary history of serine proteases can be of sequence markers associated with active site structure accounted for by highly conserved amino acids that generates a model for protease evolution with broad form crucial structural and chemical elements of applicability and potential for extension to other classes of the catalytic apparatus. These residues display non- enzymes. random dichotomies in either amino acid choice or The ®rst report of a sequence marker associated with serine codon usage and serve as discrete markers for active site chemistry was the observation that both AGY tracking changes in the active site environment and and TCN codons were used to encode active site serines in supporting structures. These markers categorize a variety of enzyme families (Brenner, 1988). Since serine proteases of the chymotrypsin-like, subtilisin- AGY®TCN interconversion is an uncommon event, it like and a/b-hydrolase fold clans according to phylo- was reasoned that enzymes within the same family genetic lineages, and indicate the relative ages and utilizing different active site codons belonged to different order of appearance of those lineages. -
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants. -
Preclinical Characterization of Dostarlimab, a Therapeutic Anti-PD
MABS 2021, VOL. 13, NO. 1, e1954136 (12 pages) https://doi.org/10.1080/19420862.2021.1954136 REPORTS Preclinical characterization of dostarlimab, a therapeutic anti-PD-1 antibody with potent activity to enhance immune function in in vitro cellular assays and in vivo animal models Sujatha Kumara*, Srimoyee Ghoshb, Geeta Sharmac, Zebin Wangd, Marilyn R. Kehrye, Margaret H. Marinof, Tamlyn Y. Nebenf, Sharon Lug, Shouqi Luoh, Simon Robertsi, Sridhar Ramaswamyj, Hadi Danaeek, and David Jenkinsl aTranslational Research, Immuno-Oncology, Checkmate Pharmaceuticals, Cambridge, MA, USA; bOncology Experimental Medicine Unit, GlaxoSmithKline, Waltham, MA, USA; cSynthetic Lethal Research Unit, Oncolog, GlaxoSmithKline, Waltham, MA, USA; dTranslational Strategy & Research, GlaxoSmithKline,Waltham, MA, USA; eCell Biology, AnaptysBio, Inc,San Diego, CA, USA; fProgram Management, AnaptysBio, Inc, San Diego, CA, USA; gClinical Pharmacology, Scholar Rock, Cambridge, MA, USA; hToxicology, Atea Pharmaceuticals, Boston, MA, USA; iNonclinical Development, Research In Vivo/In Vitro Translation, GlaxoSmithKline, Waltham, MA, USA; jGoogle Ventures, Cambridge, MA, USA; kTranslational Medicine, Blue Print Medicines, Cambridge, MA, USA; lExternal Innovations, IPSEN, Cambridge, MA, USA ABSTRACT ARTICLE HISTORY Inhibitors of programmed cell death protein 1 (PD-1) and its ligand (PD-L1) have dramatically changed the Received 17 December 2020 treatment landscape for patients with cancer. Clinical activity of anti-PD-(L)1 antibodies has resulted in Revised 2 July 2021 increased median overall survival and durable responses in patients across selected tumor types. To date, Accepted 7 July 2021 6 PD-1 and PD-L1, here collectively referred to as PD-(L)1, pathway inhibitors are approved by the US Food KEYWORDS and Drug Administration for clinical use. -
Quantikine® ELISA
Quantikine® ELISA Human Granzyme B Immunoassay Catalog Number DGZB00 For the quantitative determination of human Granzyme B concentrations in culture supernates. This package insert must be read in its entirety before using this product. For research use only. Not for use in diagnostic procedures. TABLE OF CONTENTS SECTION PAGE INTRODUCTION .....................................................................................................................................................................1 PRINCIPLE OF THE ASSAY ...................................................................................................................................................2 LIMITATIONS OF THE PROCEDURE .................................................................................................................................2 TECHNICAL HINTS .................................................................................................................................................................2 MATERIALS PROVIDED & STORAGE CONDITIONS ...................................................................................................3 OTHER SUPPLIES REQUIRED .............................................................................................................................................3 PRECAUTIONS .........................................................................................................................................................................4 SAMPLE COLLECTION & STORAGE .................................................................................................................................4 -
Death by Granzyme B
RESEARCH HIGHLIGHTS APOPTOSIS Death by granzyme B DOI: 10.1038/nri1951 The death of effector T cells following pro-apoptotic ligands and effector lysosomal-associated membrane pro- Link activation is an important process molecules in AICD of T 1 cells and tein 1 (LAMP1; a marker of granules) Granzyme B H http://www.ncbi.nlm.nih.gov/ in the termination of an immune TH2 cells. Blocking the pro-apoptotic was observed in both resting TH1 entrez/viewer.fcgi?db=protein response. However, the mechanisms molecule CD95 ligand (also known cells and resting TH2 cells. However, &val=1247451 that are involved in this activation- as FAS ligand) with specific agents following TCR engagement, colocali- induced cell death (AICD) through inhibited AICD of TH1 cells, as previ- zation was observed only in TH1 cells, engagement of the T-cell receptor ously reported. However, these agents indicating that granzyme B is released (TCR) are not well understood. Now, had no effect on the death of TH2 from the granules on activation of TH2 new research published in Immunity cells. Similarly, blocking the activity of cells but not TH1 cells. Interestingly, shows that granzyme B has an impor- several caspases affected only TH1-cell the amount of SPI6, which is a tant role in AICD of T helper 2 (TH2) death, whereas inhibition of TRAIL protease inhibitor that specifically cells. (tumour-necrosis-factor-related inhibits the activity of granzyme B, Examination of the kinetics of apoptosis-inducing ligand) did not was found to be increased in activated AICD, by staining for annexin V affect either cell type. -
WO 2017/143026 Al 24 August 2017 (24.08.2017) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2017/143026 Al 24 August 2017 (24.08.2017) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12N 9/52 (2006.0 1) C12N 9/64 (2006.0 1) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, PCT/US2017/0181 16 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KH, KN, 16 February 2017 (16.02.2017) KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, (25) Filing Language: English NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, (26) Publication Language: English RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, (30) Priority Data: ZA, ZM, ZW. 62/295,636 16 February 2016 (16.02.2016) US (84) Designated States (unless otherwise indicated, for every (71) Applicant: RESEARCH DEVELOPMENT FOUNDA¬ kind of regional protection available): ARIPO (BW, GH, TION [US/US]; 402 North Division Street, Carson City, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, NV 89703 (US). -
Latest RPG Version Is Through Pip: Pip3 Install Rpg
RapidPeptidesGenerator Documentation Release 1.2.4 Nicolas Maillet May 25, 2021 Contents: 1 Overview 3 2 Installation 5 3 Usage 7 4 User and Developer Guides 9 4.1 User Guide................................................9 4.1.1 Overview............................................9 4.1.2 Installation...........................................9 4.1.2.1 From pip........................................9 4.1.2.2 From source code...................................9 4.1.2.3 Using without installation............................... 10 4.1.3 Classical use.......................................... 10 4.1.3.1 Getting help...................................... 10 4.1.3.2 Listing enzymes.................................... 10 4.1.3.3 Performing digestion................................. 10 4.1.3.4 Adding a new enzyme................................. 11 4.1.4 Options............................................. 11 4.1.5 Digestion modes........................................ 12 4.1.6 Miscleavage........................................... 13 4.1.7 Non-interactive mode...................................... 13 4.1.8 Output.............................................. 13 4.1.9 Random names......................................... 14 4.1.10 Verbosity............................................ 14 4.1.11 Creating a new enzyme..................................... 15 4.1.11.1 Definition of rules................................... 16 4.1.11.2 Definition of exceptions................................ 18 4.1.11.3 Easily writing complex enzymes.......................... -
The Serine Protease Domain of MASP-3: Enzymatic Properties and Crystal Structure in Complex with Ecotin
The serine protease domain of MASP-3: enzymatic properties and crystal structure in complex with ecotin. Christine Gaboriaud, Rajesh Kumar Gupta, Lydie Martin, Monique Lacroix, Laurence Serre, Florence Teillet, Gérard J Arlaud, Véronique Rossi, Nicole Thielens To cite this version: Christine Gaboriaud, Rajesh Kumar Gupta, Lydie Martin, Monique Lacroix, Laurence Serre, et al.. The serine protease domain of MASP-3: enzymatic properties and crystal structure in complex with ecotin.. PLoS ONE, Public Library of Science, 2013, 8 (7), pp.e67962. 10.1371/journal.pone.0067962. inserm-00868926 HAL Id: inserm-00868926 https://www.hal.inserm.fr/inserm-00868926 Submitted on 2 Oct 2013 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. The Serine Protease Domain of MASP-3: Enzymatic Properties and Crystal Structure in Complex with Ecotin Christine Gaboriaud1,2,3*, Rajesh Kumar Gupta1,2,3¤a, Lydie Martin1,2,3, Monique Lacroix1,2,3, Laurence Serre3,1¤b, Florence Teillet1,2,3,Ge´rard J. Arlaud1,2,3,Ve´ronique Rossi1,2,3, Nicole M. Thielens1,2,3 1 Institut de Biologie Structurale (IBS), Direction des Sciences du Vivant, Commissariat a` l’Energie Atomique et aux Energies Alternatives, Grenoble, France, 2 IBS, Centre National de la Recherche Scientifique, Grenoble, France, 3 IBS, Universite´ Grenoble Alpes, Grenoble, France Abstract Mannan-binding lectin (MBL), ficolins and collectin-11 are known to associate with three homologous modular proteases, the MBL-Associated Serine Proteases (MASPs). -
Molecular Mechanisms Underlying Toxicant Effects on Mast Cell Signaling and Mitochondria Juyoung Katherine Shim University of Maine, [email protected]
The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library Summer 8-17-2018 Molecular Mechanisms Underlying Toxicant Effects on Mast Cell Signaling and Mitochondria Juyoung Katherine Shim University of Maine, [email protected] Follow this and additional works at: https://digitalcommons.library.umaine.edu/etd Part of the Molecular Biology Commons, and the Toxicology Commons Recommended Citation Shim, Juyoung Katherine, "Molecular Mechanisms Underlying Toxicant Effects on Mast Cell Signaling and Mitochondria" (2018). Electronic Theses and Dissertations. 2909. https://digitalcommons.library.umaine.edu/etd/2909 This Open-Access Thesis is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. MOLECULAR MECHANISMS UNDERLYING TOXICANT EFFECTS ON MAST CELL SIGNALING AND MITOCHONDRIA By Juyoung K. Shim B.A. Hankook University of Foreign Studies, 1994 B.S. Bates College, 2005 A DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (in Biochemistry and Molecular Biology) The Graduate School The University of Maine August 2018 Advisory Committee: Julie A. Gosse, Associate Professor of Biochemistry; Advisor John T. Singer, Professor of Microbiology Paul J. Millard, Associate Professor of Chemical and Biological Engineering Rebecca J. Van Beneden, Professor of Biochemistry and Marine Sciences, Director for School of Marine Sciences Robert E. Gundersen, Chair of Molecular and Biomedical Sciences © 2018 Juyoung Katherine Shim All Rights Reserved ii MOLECULAR MECHANISMS UNDERLYING TOXICANT EFFECTS ON MAST CELL SIGNALING AND MITOCHONDRIA By Juyoung K. -
Proteolytic Cleavage—Mechanisms, Function
Review Cite This: Chem. Rev. 2018, 118, 1137−1168 pubs.acs.org/CR Proteolytic CleavageMechanisms, Function, and “Omic” Approaches for a Near-Ubiquitous Posttranslational Modification Theo Klein,†,⊥ Ulrich Eckhard,†,§ Antoine Dufour,†,¶ Nestor Solis,† and Christopher M. Overall*,†,‡ † ‡ Life Sciences Institute, Department of Oral Biological and Medical Sciences, and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada ABSTRACT: Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein’s structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissuefrom 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C- termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms -
Engineered Type 1 Regulatory T Cells Designed for Clinical Use Kill Primary
ARTICLE Acute Myeloid Leukemia Engineered type 1 regulatory T cells designed Ferrata Storti Foundation for clinical use kill primary pediatric acute myeloid leukemia cells Brandon Cieniewicz,1* Molly Javier Uyeda,1,2* Ping (Pauline) Chen,1 Ece Canan Sayitoglu,1 Jeffrey Mao-Hwa Liu,1 Grazia Andolfi,3 Katharine Greenthal,1 Alice Bertaina,1,4 Silvia Gregori,3 Rosa Bacchetta,1,4 Norman James Lacayo,1 Alma-Martina Cepika1,4# and Maria Grazia Roncarolo1,2,4# Haematologica 2021 Volume 106(10):2588-2597 1Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 2Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 3San Raffaele Telethon Institute for Gene Therapy, Milan, Italy and 4Center for Definitive and Curative Medicine, Stanford School of Medicine, Stanford, CA, USA *BC and MJU contributed equally as co-first authors #AMC and MGR contributed equally as co-senior authors ABSTRACT ype 1 regulatory (Tr1) T cells induced by enforced expression of interleukin-10 (LV-10) are being developed as a novel treatment for Tchemotherapy-resistant myeloid leukemias. In vivo, LV-10 cells do not cause graft-versus-host disease while mediating graft-versus-leukemia effect against adult acute myeloid leukemia (AML). Since pediatric AML (pAML) and adult AML are different on a genetic and epigenetic level, we investigate herein whether LV-10 cells also efficiently kill pAML cells. We show that the majority of primary pAML are killed by LV-10 cells, with different levels of sensitivity to killing. Transcriptionally, pAML sensitive to LV-10 killing expressed a myeloid maturation signature. -
Structure of Granzyme C Reveals an Unusual Mechanism of Protease Autoinhibition
Structure of granzyme C reveals an unusual mechanism of protease autoinhibition Dion Kaisermana,1, Ashley M. Bucklea,1, Petra Van Dammeb,c, James A. Irvinga, Ruby H. P. Lawa, Antony Y. Matthewsa, Tanya Bashtannyk-Puhalovicha, Chris Langendorfa, Philip Thompsond, Joe¨ l Vandekerckhoveb,c, Kris Gevaertb,c, James C. Whisstocka,e,2,3, and Phillip I. Birda,2,3 aDepartment of Biochemistry and Molecular Biology, and eAustralian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton 3800, Australia; bDepartment of Medical Protein Research, Flanders Institute for Biotechnology, B-9000 Ghent, Belgium; cDepartment of Biochemistry, Ghent University, B-9000 Ghent, Belgium; dMedicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia Edited by Brian W. Matthews, University of Oregon, Eugene, OR, and approved February 12, 2009 (received for review November 24, 2008) Proteases act in important homeostatic pathways and are tightly Many proteases incorporate a further level of control and are regulated. Here, we report an unusual structural mechanism of active only in the presence of small molecule cofactors [typically regulation observed by the 2.5-Å X-ray crystal structure of the metal ions (2)] or large ligands such as glycosaminoglycans (3) serine protease, granzyme C. Although the active-site triad resi- or other proteins (4). This results in a two-step active-site dues adopt canonical conformations, the oxyanion hole is improp- assembly pathway for activation, from the inactive zymogen to an erly formed, and access to the primary specificity (S1) pocket is intermediate with a partially formed active site, and finally the blocked through a reversible rearrangement involving Phe-191.