DOCSLIB.ORG

University of Alberta Structural Studies Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Alberta Structural Studies Of UNIVERSITY OF ALBERTA STRUCTURAL STUDIES OF MALARIAL ASPARTIC PROTEINASE ACTIVATION NINA KHAZANOVICH BERNSTEIN O A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDES AND RESEARCH IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOCHEMISTRY EDMONTON, ALBERTA SPFüNG, 2000 National tibraiy Bibliothbque nationale 141 dc-da du Canada A uisitionsarid Acquisitions et B8o9raphic Services services bibliographiques 385 ~eüingbmçtreet 395, rue WeUingtori Ottawa ON KIA ON4 OttawaON KIAW Canada Canada The author has granted a non- L'auteur a accordé une licence non exclusive licence allowing the exclusive permettant à la Natioaal Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, distriiute or sell reproduire, prêter, distri'buer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/nlm, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts fiom it Ni la thèse ni des extraits substantiels may be printed or otherwise de celle-ci ne doivent être imprimes reproduced without the author's ou autrement reproduits sans son permission. autorisation. Dedicated to my parents. Abstract Malaria is a complex and devastating disease that is a major public heaith problem in many areas of the world During the blood stage of the malaria infection, the malaria parasite, Plasmodium, lives in the human host's erythrocytes, where it digests large quantities of hernoglobin as a source of nutrients. Hemoglobin digestion is an ordered and highly efficient process that is cdedout in a specialized acidic cornpartment by several of the parasite's proteolytic enzymes. These enzymes, the hemoglobinases. include a cysteine proteinase, a metalloproteinase and at least two aspartic proteinases. The aspartic proteinases, plasmepsins, are the subject of this thesis. Like al1 known eukaryotic aspartic proteinases, the plasmepsins are produced as inactive precursors, or zymogens, called proplasrnepsins. Proteolytic removal of the amino-terminal extension, or prosegment, at acidic pH converts the inactive zymogen into the active proteinase. We detemined the X-ray crystal structure of pmplasmepsin II frorn the most dangerous human malaria parasite Plasmodium falciparum. Comparison of the structure of this zymogen to the swcture of the corresponding mature enzyme, plasmepsin LI, reveaied the basis of inactivity of proplasmepsin II. The prosegment and the first 15 amino acids of the mamsequence enforce a major domain rotation in the zymogen relative to the mature enzyme. This domain shift severely distorts the active site in proplasmepsin II relative to plasmepsin II. At this "immature" active site, the catalytic machinery is in the wrong orientation to carry out proteolysis. The crystal structure of proplasmepsin II was used to propose a possible pathway of autocatalytic activation that occurs at low pH in vitro, and to rationalize the need for acidic pH for maturase-assisted activation in vivo. Until recently, our understanding of aspartic proteinase activation had ken Limited, on a structural level, to the gastric aspartic proteinase zymogens, human and porcine pepsinogen and human progasnicsin. In all of these zymogens, the prosegrnent prevents activity at neutral pH by blocking a pre-assembled active site. Disruption of severai salt bridges at acidic pH clears the prosegrnent out of the proteinase's active site, leading to autaiatalyzed activation. In proplasmepsin II, the method of inactivation is fundamentally different. In this case, the active site is accessible, but incornpletely formed, and therefore unable to catalyze peptide bond hydrolysis. We also investigated the activation of plasmepsin in another human malaria parasite, P. vivax, by determining the crystal structures of plasmepsin and proplasmepsin. P. vivcur plasmepsin has the structure of a typical aspartic proteinase. P. vivar proplasmepsin possesses many of the structural feanires that were observed in P. faicipartrm proplasmepsin II, including the same method of inactivation. Thus, the domain shift that prevents the formation of a functional active site in the zymogen is established as a common mode of inactivation for the propiasmepsins. The hemoglobinases of Plasmodium have been recognized as targets for anti- malarial dmg design, since inhibition of these enzymes kills the parasites in culture. Crystal structures of the proplasmepsins suggest that their unusual active site architecture may also render these zyrnogens potential dnig design targets. Acknowledgements 1 would like to thank my supervisor, Michael James, for his guidance and support during my graduate studies. It was wondemil to have him share his extensive knowledge of protein structure and function, and it has ken a pleasure to leam from him. 1would like to acknowledge the generous contributions of our collaboraton, Hansrnedi Loetscher and Robert Eüdley at Hoffmann La Roche who provided P. falciparzcm proplasmepsin II, and Charles Yowell and John Dame at the University of monda, Gainesville, who provided P. vivar proplasmepsin. 1 also appreciate the many helpful discussions that 1 have had with John Darne and Daniel Bur (Hoffmann La Roche). A very specid note of thanks io Maia Chemey, not only for al1 her hard work in growing the crystals that 1 used in my experiments, but also for always sharing great enthusiasm for the projects. 1 appreciate a11 the help that 1 received from the members of our group and from Randy Read's group. Marie, Masao, Jens, Katherine, Ernst, Steve, Craig, Ken, Natalie, Stan, Marc, Hong, Bart and Jonathan have helped me lem various aspects of protein crystallography and biochemistry. 1 would also like to rhank Mae Wylie for help with various administrative tasks (which were usually sprung on her with little or no waming), and Janet Wright for ail her help in organizing my parental leave and de fense. I would like to thank my supervisory and examination comrnittee, Dr. Bleackley, Dr. Sykes and Dr. Ryan, as well as the extemal examines Dr. Hindsgaul and Dr. Dunn. 1thank my friends, especially Kathy, JOand Gregory who have been able to make grad school ever so much more interesting. I am grateful to the University of Alberta, NSERC and AHFMR for financial support, and I especially appreciate AHFMFCs wonderfully progressive policy of paid parental leaves. Finally, and very importantly, 1would like to thank my family: Alex for ail his support, Nathan for never failing to make me smile, and my parents for dl their hard work and patience. Table of Contents CHAPTER 1: GENEML INTRODUCTION .................................................................................... 1 1. I MALARIA .PAST AND PRESENT.............................................................................................................. t 1.2 BIOLOGY OF MALARIA .............................................................................................................................. 6 1.2.1 LEE CYCLE OF THE PLAS~~OD~U~IPARASITE ........................................................................................ 7 13.2 HE~~OGLOBINDEGRADATION 8Y PLAShI0DIUh.f ....................................................................................... 9 1.2.3 PRO~ASESOF PWSMODIUM .................... .... ................................................................................ 10 1.3 REFERENCES ........................... ,.. ........................................................................................................... 14 CHAPTER 2: CRYSTAL STRUCTURE OF P . VIV'PLASMEPSIN ............................................... 20 2.1.1 Bro~ffirc$,.~ROLE OFASPARTIC PROTEINASES ...................................................................................... 20 2.1.2 STRUCIVRE AND biECHANIShl OF ASPARTiC PROTEINASES .................................................................... 21 2.1.3 FLEXIBILITYIN ASPARTIC PROTEINASES .................................*....,. .......*.............*................................31 2.1.4 MURIAL PUSMEPSINS ........................................................................................................................ 35 2.3. f ACI~VAT~ONAND CRYSTUIWTION ..................................................................................................... 39 2.2.2 DATAcou~crro~ .................................................................................................................................. 40 2.2.3 STRUCTUREDETERMINATION AND REFINEMENT ................................................................................... 40 2.2.3 MODELLINGOF P . OVALEAND P .MAURIAE PLASXIEPSINS ................................................*..................45 23 RESULTS AND DISCUSSION .................................................................................................................... 45 2.3.1 DESCRIP~ONOF STRUCTURE.................................................................................................................. 45 2.3.2 COMPARISONOF THE NCS-REWTEDMOEC~LES ................................................................................. 49 2.3.3 RPSTATIN A BINDING ............................................................................................................................ 53 .. 2.3.4 COMPARISONTO PFP~III .........................................................................................................................
Load more

Recommended publications
  • Data-Mining Approaches Reveal Hidden Families of Proteases in The
    Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite Yimin Wu,1,4 Xiangyun Wang,2 Xia Liu,1 and Yufeng Wang3,5 1Department of Protistology, American Type Culture Collection, Manassas, Virginia 20110, USA; 2EST Informatics, Astrazeneca Pharmaceuticals, Wilmington, Delaware 19810, USA; 3Department of Bioinformatics, American Type Culture Collection, Manassas, Virginia 20110, USA The search for novel antimalarial drug targets is urgent due to the growing resistance of Plasmodium falciparum parasites to available drugs. Proteases are attractive antimalarial targets because of their indispensable roles in parasite infection and development,especially in the processes of host e rythrocyte rupture/invasion and hemoglobin degradation. However,to date,only a small number of protease s have been identified and characterized in Plasmodium species. Using an extensive sequence similarity search,we have identifi ed 92 putative proteases in the P. falciparum genome. A set of putative proteases including calpain,metacaspase,and s ignal peptidase I have been implicated to be central mediators for essential parasitic activity and distantly related to the vertebrate host. Moreover,of the 92,at least 88 have been demonstrate d to code for gene products at the transcriptional levels,based upon the microarray and RT-PCR results,an d the publicly available microarray and proteomics data. The present study represents an initial effort to identify a set of expressed,active,and essential proteases as targets for inhibitor-based drug design. [Supplemental material is available online at www.genome.org.] Malaria remains one of the most dangerous infectious diseases metalloprotease (falcilysin; Eggleson et al.
    [Show full text]
  • Handbook of Proteolytic Enzymes Second Edition Volume 1 Aspartic and Metallo Peptidases
    Handbook of Proteolytic Enzymes Second Edition Volume 1 Aspartic and Metallo Peptidases Alan J. Barrett Neil D. Rawlings J. Fred Woessner Editor biographies xxi Contributors xxiii Preface xxxi Introduction ' Abbreviations xxxvii ASPARTIC PEPTIDASES Introduction 1 Aspartic peptidases and their clans 3 2 Catalytic pathway of aspartic peptidases 12 Clan AA Family Al 3 Pepsin A 19 4 Pepsin B 28 5 Chymosin 29 6 Cathepsin E 33 7 Gastricsin 38 8 Cathepsin D 43 9 Napsin A 52 10 Renin 54 11 Mouse submandibular renin 62 12 Memapsin 1 64 13 Memapsin 2 66 14 Plasmepsins 70 15 Plasmepsin II 73 16 Tick heme-binding aspartic proteinase 76 17 Phytepsin 77 18 Nepenthesin 85 19 Saccharopepsin 87 20 Neurosporapepsin 90 21 Acrocylindropepsin 9 1 22 Aspergillopepsin I 92 23 Penicillopepsin 99 24 Endothiapepsin 104 25 Rhizopuspepsin 108 26 Mucorpepsin 11 1 27 Polyporopepsin 113 28 Candidapepsin 115 29 Candiparapsin 120 30 Canditropsin 123 31 Syncephapepsin 125 32 Barrierpepsin 126 33 Yapsin 1 128 34 Yapsin 2 132 35 Yapsin A 133 36 Pregnancy-associated glycoproteins 135 37 Pepsin F 137 38 Rhodotorulapepsin 139 39 Cladosporopepsin 140 40 Pycnoporopepsin 141 Family A2 and others 41 Human immunodeficiency virus 1 retropepsin 144 42 Human immunodeficiency virus 2 retropepsin 154 43 Simian immunodeficiency virus retropepsin 158 44 Equine infectious anemia virus retropepsin 160 45 Rous sarcoma virus retropepsin and avian myeloblastosis virus retropepsin 163 46 Human T-cell leukemia virus type I (HTLV-I) retropepsin 166 47 Bovine leukemia virus retropepsin 169 48
    [Show full text]
  • Overexpression of Plasmepsin II and Plasmepsin III Does Not Directly Cause Reduction in Plasmodium Falciparum Sensitivity to Artesunate, Chloroquine T and Piperaquine
    IJP: Drugs and Drug Resistance 9 (2019) 16–22 Contents lists available at ScienceDirect IJP: Drugs and Drug Resistance journal homepage: www.elsevier.com/locate/ijpddr Overexpression of plasmepsin II and plasmepsin III does not directly cause reduction in Plasmodium falciparum sensitivity to artesunate, chloroquine T and piperaquine Duangkamon Loesbanluechaia,b, Namfon Kotanana, Cristina de Cozarc, Theerarat Kochakarna, Megan R. Ansbrod,e, Kesinee Chotivanichf,g, Nicholas J. Whiteg,h, Prapon Wilairati, ∗∗ Marcus C.S. Leee, Francisco Javier Gamoc, Laura Maria Sanzc, Thanat Chookajorna, , ∗ Krittikorn Kümpornsine, a Genomics and Evolutionary Medicine Unit (GEM), Centre of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand b Molecular Medicine Program, Multidisciplinary Unit, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand c Tres Cantos Medicine Development Campus, GlaxoSmithKline, Parque Tecnológico de Madrid, Tres Cantos, 28760, Spain d Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA e Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom f Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand g Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand h Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Churchill Hospital, Oxford, OX3 7LJ, United Kingdom i Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand ARTICLE INFO ABSTRACT Keywords: Artemisinin derivatives and their partner drugs in artemisinin combination therapies (ACTs) have played a Artemisinin pivotal role in global malaria mortality reduction during the last two decades.
    [Show full text]
  • Hemoglobin-Degrading, Aspartic Proteases of Blood-Feeding Parasites SUBSTRATE SPECIFICITY REVEALED by HOMOLOGY MODELS*
    THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 276, No. 42, Issue of October 19, pp. 38844–38851, 2001 © 2001 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Hemoglobin-degrading, Aspartic Proteases of Blood-feeding Parasites SUBSTRATE SPECIFICITY REVEALED BY HOMOLOGY MODELS* Received for publication, March 2, 2001, and in revised form, August 6, 2001 Published, JBC Papers in Press, August 8, 2001, DOI 10.1074/jbc.M101934200 Ross I. Brinkworth‡, Paul Prociv§, Alex Loukas¶, and Paul J. Brindleyʈ** From the ‡Institute of Molecular Biosciences and §Department of Microbiology and Parasitology, University of Queensland, Brisbane, Queensland 4072, Australia, ¶Division of Infectious Diseases and Immunology, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia, and ʈDepartment of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana 70112 Blood-feeding parasites, including schistosomes, hook- and mortality (1). Although phylogenetically unrelated, these worms, and malaria parasites, employ aspartic pro- parasites all share the same food source; they are obligate blood teases to make initial or early cleavages in ingested host feeders, or hematophages. Hb from ingested or parasitized hemoglobin. To better understand the substrate affinity erythrocytes is their major source of exogenous amino acids for Downloaded from of these aspartic proteases, sequences were aligned with growth, development, and reproduction; the Hb, a ϳ64-kDa and/or three-dimensional, molecular models were con- tetrameric polypeptide, is comprehensively catabolized by par- structed of the cathepsin D-like aspartic proteases of asite enzymes to free amino acids or small peptides. Intrigu- schistosomes and hookworms and of plasmepsins of ingly, all these parasites appear to employ cathepsin D-like Plasmodium falciparum and Plasmodium vivax, using aspartic proteases to make initial or early cleavages in the Hb the structure of human cathepsin D bound to the inhib- substrate (2–4).
    [Show full text]
  • Downloaded 10/1/2021 8:14:38 AM
    RSC Advances View Article Online REVIEW View Journal | View Issue Pepsin-like aspartic proteases (PAPs) as model systems for combining biomolecular simulation Cite this: RSC Adv.,2021,11,11026 with biophysical experiments† Soumendranath Bhakat Pepsin-like aspartic proteases (PAPs) are a class of aspartic proteases which shares tremendous structural similarity with human pepsin. One of the key structural features of PAPs is the presence of a b-hairpin motif otherwise known as flap. The biological function of the PAPs is highly dependent on the conformational dynamics of the flap region. In apo PAPs, the conformational dynamics of the flap is dominated by the rotational degrees of freedom associated with c1andc2 angles of conserved Tyr (or Phe in some cases). However it is plausible that dihedral order parameters associated with several other residues might play crucial roles in the conformational dynamics of apo PAPs. Due to their size, complexities associated with conformational dynamics and clinical significance (drug targets for Creative Commons Attribution-NonCommercial 3.0 Unported Licence. malaria, Alzheimer's disease etc.), PAPs provide a challenging testing ground for computational and experimental methods focusing on understanding conformational dynamics and molecular recognition in biomolecules. The opening of the flap region is necessary to accommodate substrate/ ligand in the active site of the PAPs. The BIG challenge is to gain atomistic details into how reversible ligand binding/unbinding (molecular recognition) affects the conformational dynamics. Recent reports of kinetics (Ki, Kd) and thermodynamic parameters (DH, TDS,andDG) associated with macro-cyclic ligands bound to BACE1 (belongs to PAP family) provide a perfect challenge (how to deal with big ligands with multiple torsional angles and select optimum order parameters to study reversible ligand binding/unbinding) for computational methods to predict binding free energies and kinetics beyond This article is licensed under a typical test systems e.g.
    [Show full text]
  • Structure-Assisted Design of Drugs Towards HIV-1 and Malaria Targets
    Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1040 Structure-Assisted Design of Drugs Towards HIV-1 and Malaria Targets Applied on Reverse Transcriptase and Protease from HIV-1 and Plasmepsin II from Plasmodium falciparum BY JIMMY LINDBERG ACTA UNIVERSITATIS UPSALIENSIS UPPSALA 2004 !" # $ % # # &$ $' ($ ) * %$' + % ,' ' - ./ % # % ( ) 012. ( % ' / 3 ( & # 012. & 11 # ' / ' ' 62 p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ill min Annika List of Papers My thesis consists of a comprehensive summary based on the following papers, in which they will be referred to by their numbers. I Lindberg,
    [Show full text]
  • Plasmepsin II As a Potential Drug Target for Resistant Malaria
    DU Journal of Undergraduate Research and Innovation Volume 1, Issue 3 pp 85-95, 2015 Plasmepsin II as a Potential Drug Target for Resistant Malaria Megha Gulati*1, Aruna Narula2, Raj Vishnu3, Gunjan Katyal4, Arti Negi5, Isbah Ajaz6, Kritika Narula7, Gunjan Chauhan8, Ravi Kanta, Vanshika Lumb9, Smriti Babbar10, Neena R. Wadehra11, Deepika Bhaskarb *[email protected], 1-11Department of Biochemistry, Shivaji College, University of Delhi 110027, a University of Delhi South Campus, b Research Council, University of Delhi ABSTRACT With drug resistance becoming extensively pervasive in Plasmodium falciparum infections, research for alternative drugs is becoming mandatory for prevention and cure of malaria. Increased resistance against anti malarials such as chloroquine and sulfadoxin/pyrimethamine, has resulted in developing new drug therapies . Aspartic proteases called plasmepsin are present in different species of Plasmodium. With the use of in silico structure-based drug design approach, the differences in binding energies of the substrate and inhibitor were exploited between target sites of parasite and human. The docking studies show several promising molecules from GSK library with more effective binding as compared to the already known inhibitors for the drug targets. Stronger interactions are shown by several molecules as compared to the reference molecules which have shown to be the potential as drug candidates. Key Words Aspartic protease, Drug resistance, Drug targets, Inhibitors, in silico studies, Plasmepsin, Plasmodium falciparum INTRODUCTION Malaria, a global contagious disease, causes over one million deaths per year. Malaria is caused by a protozoan called Plasmodium which has four species namely P. falciparum, P. ovale, P. malariae and P. vivax. Out of these four species, P.
    [Show full text]
  • High Level Expression and Characterisation of Plasmepsin II, an Aspartic Proteinase from Plasmodium Falciparum
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector FEBS Letters 352 (1994) 155-158 FEBS 14553 High level expression and characterisation of Plasmepsin II, an aspartic proteinase from Plasmodium falciparum Jeffrey Hill”, Lorraine Tyasa, Lowri H. Phylip”, John Kay”, Ben M. Dunnb, Colin Berrya “Department of Biochemistry, University of Wales College of Cardijjf PO Box 903, Cardiff CFI 1Sr Wales, UK bDepartment of Biochemistry and Molecular Biology, J. Hillis Miller Health Center, University of Florida, Gainesville, FL 32610, USA Received 22 July 1994 Abstract DNA encoding the last 48 residues of the propart and the whole mature sequence of Plasmepsin II was inserted into the T7 dependent vector PET 3a for expression in E. coli. The resultant product was insoluble but accumulated at -20 mg/l of cell culture. Following solubilisation with urea, the zymogen was refolded and, after purification by ion-exchange chromatography, was autoactivated to generate mature Plasmepsin II. The ability of this enzyme to hydrolyse several chromogenic peptide substrates was examined; despite an overall identity of -35% to human renin, Plasmepsin II was not inhibited significantly by renin inhibitors. Key words: Aspartic proteinase; Plasmepsin II; Plasmodium falciparum 1. Introduction high levels of expression of recombinant proteins as fusions with a 13 amino acid leader sequence derived from the N-terminus of the T7 gene 10 protein [5]. The sequence of a positive clone containing the Plasmep- During the blood borne stages of human infection by the sin II insert in the correct orientation was determined in its entirety to malarial parasite Plasmodium falciparum, haemoglobin is di- ensure that no mutations had been introduced during the polymerase gested in huge amounts as a source of nutrients to support chain reaction.
    [Show full text]
  • Protease-Associated Cellular Networks in Malaria Parasite Plasmodium Falciparum Timothy G Lilburn1, Hong Cai2, Zhan Zhou2,3, Yufeng Wang2,4* from BIOCOMP 2010
    Lilburn et al. BMC Genomics 2011, 12(Suppl 5):S9 http://www.biomedcentral.com/1471-2164/12/S5/S9 RESEARCH Open Access Protease-associated cellular networks in malaria parasite Plasmodium falciparum Timothy G Lilburn1, Hong Cai2, Zhan Zhou2,3, Yufeng Wang2,4* From BIOCOMP 2010. The 2010 International Conference on Bioinformatics and Computational Biology Las Vegas, NV, USA. 12-15 July 2010 Abstract Background: Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need for the development of novel antimalarial targets. Proteases are a group of enzymes that play essential roles in parasite growth and invasion. The possibility of designing specific inhibitors for proteases makes them promising drug targets. Previously, combining a comparative genomics approach and a machine learning approach, we identified the complement of proteases (degradome) in the malaria parasite Plasmodium falciparum and its sibling species [1-3], providing a catalog of targets for functional characterization and rational inhibitor design. Network analysis represents another route to revealing the role of proteins in the biology of parasites and we use this approach here to expand our understanding of the systems involving the proteases of P. falciparum. Results: We investigated the roles of proteases in the parasite life cycle by constructing a network using protein- protein association data from the STRING database [4], and analyzing these data, in conjunction with the data from protein-protein interaction assays using the yeast 2-hybrid (Y2H) system [5], blood stage microarray experiments [6-8], proteomics [9-12], literature text mining, and sequence homology analysis.
    [Show full text]
  • Antimalarial Activity of Human Immunodeficiency Virus Type 1 Protease Inhibitors Sunil Parikh University of California - San Francisco
    Washington University School of Medicine Digital Commons@Becker Open Access Publications 2005 Antimalarial activity of human immunodeficiency virus type 1 protease inhibitors Sunil Parikh University of California - San Francisco Jiri Gut University of California - San Francisco Eva Istvan Washington University School of Medicine in St. Louis Daniel E. Goldberg Washington University School of Medicine in St. Louis Diane V. Havlir University of California - San Francisco See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Parikh, Sunil; Gut, Jiri; Istvan, Eva; Goldberg, Daniel E.; Havlir, Diane V.; and Rosenthal, Philip J., ,"Antimalarial activity of human immunodeficiency virus type 1 protease inhibitors." Antimicrobial Agents and Chemotherapy.49,7. 2983. (2005). https://digitalcommons.wustl.edu/open_access_pubs/2360 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Sunil Parikh, Jiri Gut, Eva Istvan, Daniel E. Goldberg, Diane V. Havlir, and Philip J. Rosenthal This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/2360 Antimalarial Activity of Human Immunodeficiency Virus Type 1 Protease Inhibitors Sunil Parikh, Jiri Gut, Eva Istvan, Daniel E. Goldberg, Diane V. Havlir and Philip J. Rosenthal Antimicrob. Agents Chemother. 2005, 49(7):2983. DOI: Downloaded from 10.1128/AAC.49.7.2983-2985.2005. Updated information and services can be found at: http://aac.asm.org/content/49/7/2983 http://aac.asm.org/ These include: REFERENCES This article cites 14 articles, 6 of which can be accessed free at: http://aac.asm.org/content/49/7/2983#ref-list-1 CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new on March 8, 2014 by Washington University in St.
    [Show full text]
  • Identification and Characterization of Falcilysin, a Metallopeptidase Involved in Hemoglobin Catabolism Within the Malaria Parasite Plasmodium Falciparum*
    THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 274, No. 45, Issue of November 5, pp. 32411–32417, 1999 © 1999 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Identification and Characterization of Falcilysin, a Metallopeptidase Involved in Hemoglobin Catabolism within the Malaria Parasite Plasmodium falciparum* (Received for publication, May 25, 1999, and in revised form, August 24, 1999) Kathleen Kolakovich Eggleson, Kevin L. Duffin‡, and Daniel E. Goldberg§ From the Howard Hughes Medical Institute, Washington University, Departments of Molecular Microbiology and Medicine, St. Louis, Missouri 63110 and ‡Monsanto Corporate Research, Monsanto Company, St. Louis, Missouri 63198 The malaria parasite Plasmodium falciparum de- organelle, the food vacuole. This compartment has a pH esti- grades hemoglobin in its acidic food vacuole for use as a mated at 5.0–5.4 (3, 4). major nutrient source. A novel metallopeptidase activ- Nonproteolytic acid hydrolases could not be detected in food ity, falcilysin, was purified from food vacuoles and char- vacuoles isolated from P. falciparum (5). Thus, it appears that acterized. Falcilysin appears to function downstream of the food vacuole of P. falciparum does not function in degrada- the aspartic proteases plasmepsins I and II and the cys- tion and recycling of macromolecules in general. The catabolic Downloaded from teine protease falcipain in the hemoglobin proteolytic capability of this organelle is focused on hemoglobin. Disrup- pathway. It is unable to cleave hemoglobin or denatured tion of hemoglobin catabolism causes parasite death in an globin but readily destroys peptide fragments of hemo- globin. Falcilysin cleavage sites along the a and b chains animal model and in culture (2, 6, 7).
    [Show full text]
  • Chemical Genetic Approaches for Elucidating Protease Function and Drug-Target Potential in Plasmodium Falciparum
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2012 Chemical Genetic Approaches for Elucidating Protease Function and Drug-Target Potential in Plasmodium Falciparum Michael Harbut University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Chemistry Commons, Parasitology Commons, and the Pharmacology Commons Recommended Citation Harbut, Michael, "Chemical Genetic Approaches for Elucidating Protease Function and Drug-Target Potential in Plasmodium Falciparum" (2012). Publicly Accessible Penn Dissertations. 518. https://repository.upenn.edu/edissertations/518 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/518 For more information, please contact [email protected]. Chemical Genetic Approaches for Elucidating Protease Function and Drug-Target Potential in Plasmodium Falciparum Abstract Plasmodium falciparum is a protozoan parasite and the causative agent of malaria, which kills upwards of 1 million people annually. With the increasing prevalence of drug-resistant parasites, considerable interest now exists in the identification of new biological targets for the development of new malaria chemotherapeutics. However, given the genetic intractability inherent in studying P. falciparum, it is imperative that novel approaches be developed if we are to understand the role of essential enzymes. My work presented here focuses on the development and use of chemical tools to study malarial proteases, a class of enzymes that have been shown to play essential roles throughout the parasite lifecycle, but the majority of which though are still uncharacterized. In Chapter 2 I develop a novel set of activity-based probes (ABPs) based on the natural product metallo-aminopeptidase (MAP) inhibitor bestatin. I show the bestatin-based ABP allows the functional characterization of MAP activity within a complex proteome.
    [Show full text]