DOCSLIB.ORG

Ping-Hsin Lin, M.S

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Ping-Hsin Lin, M.S Angiogenin Inhibits Human Immunodeficiency Virus type 1 (HIV-1) Replication in Peripheral Blood Mononuclear Cells by a Complex Mechanism that Includes an Intracellular Component Authors Lin, Ping-Hsin Publication Date 2012 Abstract Angiogenin (ANG, also known as ribonuclease 5) is a 14.1kDa polypeptide secreted by T lymphocytes and epithelial cells. Other than its well-characterized function of promoting development of vasculature, ANG also possesses anti- Human Immunodeficienc... Keywords angiogenin; p24; PBMC; HIV-1 Download date 02/10/2021 11:30:10 Link to Item http://hdl.handle.net/10713/2163 Ping-Hsin Lin, M.S. [email protected] Education Master of Science in Medical Research July 2012 University of Maryland, Baltimore MD. Bachelor of Science in Medical Technology June 2004 Chang Gung University, Taoyuan, Taiwan Experience Institute of Human Virology, University of Maryland 09/2010-02/2012 Graduate Research Assistant • Studied the mechanism of human immunodeficiency virus type 1 (HIV-1) inhibition by angiogenin. Department of Medical & Research Technology, University of Maryland 01/2011-05/2011 Graduate Teaching Assistant • Assisted the teaching faculty by preparing lessons and lab experiments by photocopying class materials, and setting up equipment. • Graded students’ tests and homework. • Prepared and delivered lectures on various topics to undergraduate students. Department of Biochemistry and Molecular Biology, University of 03/2010-09/2010 Maryland Laboratory Assistant • Made aseptic buffer solutions and growth media, and autoclave glassware and instruments . Chang Gung University, Taoyuan, Taiwan 09/2006-06/2007 Research Assistant • Supported clinical research by using quantitative and qualitative techniques at the Liver Research Unit, Chang Gung Memorial Hospital, Taoyuan, Taiwan Licensure and Qualification • License for Medical Technician, the Ministry of Health Taiwan. Presentation • Poster, “: Angiogenin Inhibits Human Immunodeficiency Virus type 1 (HIV-1) Replication in Peripheral Blood Mononuclear Cells by a Complex Mechanism that Includes an Intracellular Component.” , Graduate Research Conference 2012 University of Maryland Baltimore Activity • 13th Annual International Meeting of the Institute of Human Virology Abstract Title of Thesis: Angiogenin Inhibits Human Immunodeficiency Virus type 1 (HIV-1) Replication in Peripheral Blood Mononuclear Cells by a Complex Mechanism that Includes an Intracellular Component Ping-Hsin Lin, Master of Science, 2012 Thesis Directed By: Alfredo Garzino-Demo, Ph.D. Associate Professor, Department of Microbiology and Immunology, Institute of Human Virology Angiogenin (ANG, also known as ribonuclease 5) is a 14.1kDa polypeptide secreted by T lymphocytes and epithelial cells. Other than its well-characterized function of promoting development of vasculature, ANG also possesses anti- Human Immunodeficiency Virus- 1 (HIV-1) properties. Previous findings show that ANG inhibits X4 tropic HIV-1 replication in peripheral blood mononuclear cells (PBMCs). Our studies show that ANG also inhibits R5 tropic virus, the most commonly transmitted HIV-1 strain. Inhibition was detected treating cells prior to or after infection by p24 ELISA, and is not mediated by CD4, CXCR4, or CCR5 as determined by flow cytometry assays. Furthermore, we demonstrated that ANG binds to tRNA-Lys, which serves as primer for HIV-1 reverse transcription. These results indicate that ANG inhibits HIV-1 replication by a post-entry mechanism, which might be exploited to develop new antiretroviral strategies. Angiogenin Inhibits Human Immunodeficiency Virus type 1 (HIV-1) Replication in Peripheral Blood Mononuclear Cells by a Complex Mechanism that Includes an Intracellular Component By Ping-Hsin Lin Thesis submitted to the faculty of the Graduate School of the University of Maryland Baltimore in partial fulfillment of the requirements for the degree of Master of Science 2012 © Copyright 2012 by Ping-Hsin Lin All Rights Reserved Acknowledgements It would not have been possible to write this thesis without the help and support of the kind people around me. Since it would be too many to list them all, I would only address some here. First and foremost, I would like to show my deepest gratitude to my mentor, Dr. Alfredo Garzino-Demo, for his constant support, guidance, encouragement, and patience. Professor Garzino-Demo undertook the responsibility as my supervisor in spite of his many academic and professional commitments. His wisdom, knowledge and passion for science has inspired and motivated me. I would also like to thank the members of my dissertation committee: Dr. Jianyuan Luo, Dr. Anthony DeVico, and Dr. Olga Latinovic. Their insightful advice and wonderful support have been invaluable to me both professionally and personally. I also appreciate Dr. Robert Gallo for providing the opportunity to pursue my research at the Institute of Human Virology. I am fortunate not only to meet and but also to work with many wonderful people throughout my time in graduate school. I am truly indebted and thankful all of the members of our lab, Dr. Lingling Sun, Dr. Mark Lafferty, Dr. Mohammad Khan, Dr. Jennifer Bharucha, Aaron Christensen-Quick, and Khrystal McGrant, for their helpful discussions on my project. I would especially like to thank Dr. Mark Lafferty who has generously shared his academic and experimental experiences, and Dr. LingLing Sun who has served as a tremendous source of technical expertise. Appreciation to my dear friends, Rebecca Hu, Yunting Fu, Vogtle Nanh, and Jane Huang for providing good company to make my memory at University of Maryland at Baltimore enjoyable. iii Table of Contents Acknowledgements ........................................................................................................... iii List of Figures .................................................................................................................. vii List of Abbreviations ........................................................................................................ ix Chapter1: Background and hypothesis ........................................................................... 1 Introduction ............................................................................................................. 1 Human Immunodeficiency Virus (HIV) ................................................................. 3 HIV Replication Cycle ............................................................................................ 9 HIV Pathogenesis .................................................................................................. 12 HIV Reverse Transcription ................................................................................... 16 Reverse Transcription ............................................................................... 16 tRNA-Lys3 ................................................................................................ 17 Angiogenin ............................................................................................................ 22 Angiogenin Molecular Structure and Domains ..................................................... 22 Angiogenin Receptor and Binding Protein ........................................................... 25 Angiogenesis ......................................................................................................... 26 Angiogenin RNase activity ................................................................................... 28 Angiogenin Anti-HIV Activity ............................................................................. 30 Specific Aims ........................................................................................................ 31 Chapter 2: Materials and Methods................................................................................ 32 Isolation and culture of primary cells and cell lines.............................................. 32 Virus production .................................................................................................... 32 Angiogenin antiviral assay .................................................................................... 32 Infectivity assays – p24 ......................................................................................... 33 Detecting CD4, CXCR4, and CCR5 by flow cytometry assay ............................. 34 iv Cell metabolism assay ........................................................................................... 34 AMLV pseudo type virus production.................................................................... 35 Virus concentration ............................................................................................... 36 Sucrose Gradient assay.............................................................................. 36 PEG 6000 assay ......................................................................................... 36 Chapter 3: To determine if ANG inhibits X4 and R5 tropic HIV-1 replication by an intracellular mechanism ................................................................................................. 37 3.1 Angiogenin inhibits both X4 and R5 tropic virus in PBMCs ........................ 37 Introduction ........................................................................................................... 37 Experimental Design ............................................................................................. 39 Results ..................................................................................................................
Load more

Recommended publications
  • 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.
    [Show full text]
  • Current Status and Perspectives of Protease Inhibitors and Their
    Current Status and Perspectives of Protease Inhibitors and Their Combination with Nanosized Drug Delivery Systems for Targeted Cancer Therapy Magdalena Rudzińska, Cenk Daglioglu, Lyudmila Savvateeva, Fatma Necmiye Kaci, Rodolphe Antoine, Andrey Zamyatnin Jr To cite this version: Magdalena Rudzińska, Cenk Daglioglu, Lyudmila Savvateeva, Fatma Necmiye Kaci, Rodolphe An- toine, et al.. Current Status and Perspectives of Protease Inhibitors and Their Combination with Nanosized Drug Delivery Systems for Targeted Cancer Therapy. Drug Design, Development and Therapy, Dove Medical Press, 2021, 15, pp.9-20. 10.2147/DDDT.S285852. hal-03128092 HAL Id: hal-03128092 https://hal.archives-ouvertes.fr/hal-03128092 Submitted on 26 May 2021 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. Drug Design, Development and Therapy Dovepress open access to scientific and medical research Open Access Full Text Article PERSPECTIVES Current Status and Perspectives of Protease Inhibitors and Their Combination with Nanosized Drug Delivery Systems for Targeted Cancer Therapy This article was published in the following Dove Press journal: Drug Design, Development and Therapy Magdalena Rudzińska 1 Abstract: In cancer treatments, many natural and synthetic products have been examined; Cenk Daglioglu 2 among them, protease inhibitors are promising candidates for anti-cancer agents.
    [Show full text]
  • The Herpesvirus Proteases As Targets for Antiviral Chemotherapy
    Antiviral Chemistry & Chemotherapy 11:1–22 Review The herpesvirus proteases as targets for antiviral chemotherapy Lloyd Waxman and Paul L Darke* Department of Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA Corresponding author: Tel: +1 215 652 7533 ; Fax: +1 215 652 6452; E-mail: [email protected] Viruses of the family Herpesviridae are respon- and catalytic properties of the herpesvirus pro- sible for a diverse set of human diseases. The teases lead to common considerations for this available treatments are largely ineffective, group of proteases in the early phases of with the exception of a few drugs for treatment inhibitor discovery. In general, classical serine of herpes simplex virus (HSV) infections. For protease inhibitors that react with active site several members of this DNA virus family, residues do not readily inactivate the her- advances have been made recently in the bio- pesvirus proteases. There has been progress chemistry and structural biology of the essen- however, with activated carbonyls that exploit tial viral protease, revealing common features the selective nucleophilicity of the active site that may be possible to exploit in the develop- serine. In addition, screening of chemical ment of a new class of anti-herpesvirus agents. libraries has yielded novel structures as starting The herpesvirus proteases have been identified points for drug development. Recent crystal as belonging to a unique class of serine pro- structures of the herpesvirus proteases now tease, with a Ser-His-His catalytic triad. A new, allow more direct interpretation of ligand struc- single domain protein fold has been deter- ture–activity relationships.
    [Show full text]
  • Crystal Structure of Varicella-Zoster Virus Protease
    Proc. Natl. Acad. Sci. USA Vol. 94, pp. 2874–2879, April 1997 Biochemistry Crystal structure of varicella-zoster virus protease XIAYANG QIU*, CHERYL A. JANSON†,JEFFREY S. CULP†,SUSAN B. RICHARDSON‡,CHRISTINE DEBOUCK‡, WARD W. SMITH*, AND SHERIN S. ABDEL-MEGUID*§ Departments of *Macromolecular Sciences, †Protein Biochemistry, and ‡Molecular Genetics, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406 Communicated by William N. Lipscomb, Harvard University, Cambridge, MA, January 27, 1997 (received for review October 28, 1996) ABSTRACT Varicella-zoster virus (VZV), an a-herpes vi- quence for chymotrypsin-like and G-T-S-MyA for subtilisin- rus, is the causative agent of chickenpox, shingles, and posther- like proteases. All human herpes virus proteases cleave a petic neuralgia. The three-dimensional crystal structure of the peptide bond between an alanine and a serine (6). Differences serine protease from VZV has been determined at 3.0-Å resolu- in substrate specificity exist. For example, HSV-1 protease tion. The VZV protease is essential for the life cycle of the virus cannot cleave the protein substrate of CMV protease, but the and is a potential target for therapeutic intervention. The CMV protease can cleave that of HSV-1 protease (7). structure reveals an overall fold that is similar to that recently Recently the crystal structure of CMV protease has been reported for the serine protease from cytomegalovirus (CMV), a reported (8–11). The structure reveals a new fold that has not herpes virus of the b subfamily. The VZV protease structure been reported for any other serine protease, and an active site provides further evidence to support the finding that herpes virus consisting of a novel catalytic triad in which the third member proteases have a fold and active site distinct from other serine of the triad is a histidine instead of an aspartic acid.
    [Show full text]
  • Arxiv:1212.4161V1 [Q-Bio.BM] 17 Dec 2012
    Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments Cristian Micheletti Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, Italy; e-mail: [email protected] (Dated: October 30, 2018) The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexi- bility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an ac- count of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship. Link to published article in Physics of Live Reviews: http://dx.doi.org/10.1016/j.plrev.2012.10.009 PACS numbers: I. INTRODUCTION tend to conserve very precisely functional structural el- ements and the location of the active site where differ- Over the past decades enormous efforts have been ent amino acids can be recruited for different function[10, made to clarify the sequence ! structure ! function 28, 115, 123, 169]. More recently it has also emerged that relationships for proteins and enzymes. In particular specific features of protein internal dynamics that impact the sequence ! structure connection has been exten- biological activity and functionality can also be subject sively probed by dissecting the detailed physico-chemical to evolutionary conservation[21, 87, 137, 181, 182].
    [Show full text]
  • 12) United States Patent (10
    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,561,811 B2 Bluchel Et Al
    USOO8561811 B2 (12) United States Patent (10) Patent No.: US 8,561,811 B2 Bluchel et al. (45) Date of Patent: Oct. 22, 2013 (54) SUBSTRATE FOR IMMOBILIZING (56) References Cited FUNCTIONAL SUBSTANCES AND METHOD FOR PREPARING THE SAME U.S. PATENT DOCUMENTS 3,952,053 A 4, 1976 Brown, Jr. et al. (71) Applicants: Christian Gert Bluchel, Singapore 4.415,663 A 1 1/1983 Symon et al. (SG); Yanmei Wang, Singapore (SG) 4,576,928 A 3, 1986 Tani et al. 4.915,839 A 4, 1990 Marinaccio et al. (72) Inventors: Christian Gert Bluchel, Singapore 6,946,527 B2 9, 2005 Lemke et al. (SG); Yanmei Wang, Singapore (SG) FOREIGN PATENT DOCUMENTS (73) Assignee: Temasek Polytechnic, Singapore (SG) CN 101596422 A 12/2009 JP 2253813 A 10, 1990 (*) Notice: Subject to any disclaimer, the term of this JP 2258006 A 10, 1990 patent is extended or adjusted under 35 WO O2O2585 A2 1, 2002 U.S.C. 154(b) by 0 days. OTHER PUBLICATIONS (21) Appl. No.: 13/837,254 Inaternational Search Report for PCT/SG2011/000069 mailing date (22) Filed: Mar 15, 2013 of Apr. 12, 2011. Suen, Shing-Yi, et al. “Comparison of Ligand Density and Protein (65) Prior Publication Data Adsorption on Dye Affinity Membranes Using Difference Spacer Arms'. Separation Science and Technology, 35:1 (2000), pp. 69-87. US 2013/0210111A1 Aug. 15, 2013 Related U.S. Application Data Primary Examiner — Chester Barry (62) Division of application No. 13/580,055, filed as (74) Attorney, Agent, or Firm — Cantor Colburn LLP application No.
    [Show full text]
  • Peptide Sequence
    Peptide Sequence Annotation AADHDG CAS-L1 AAEAISDA M10.005-stromelysin 1 (MMP-3) AAEHDG CAS-L2 AAEYGAEA A01.009-cathepsin D AAGAMFLE M10.007-stromelysin 3 (MMP-11) AAQNASMW A06.001-nodavirus endopeptidase AASGFASP M04.003-vibriolysin ADAHDG CAS-L3 ADAPKGGG M02.006-angiotensin-converting enzyme 2 ADATDG CAS-L5 ADAVMDNP A01.009-cathepsin D ADDPDG CAS-21 ADEPDG CAS-L11 ADETDG CAS-22 ADEVDG CAS-23 ADGKKPSS S01.233-plasmin AEALERMF A01.009-cathepsin D AEEQGVTD C03.007-rhinovirus picornain 3C AETFYVDG A02.001-HIV-1 retropepsin AETWYIDG A02.007-feline immunodeficiency virus retropepsin AFAHDG CAS-L24 AFATDG CAS-25 AFDHDG CAS-L26 AFDTDG CAS-27 AFEHDG CAS-28 AFETDG CAS-29 AFGHDG CAS-30 AFGTDG CAS-31 AFQHDG CAS-32 AFQTDG CAS-33 AFSHDG CAS-L34 AFSTDG CAS-35 AFTHDG CAS-L36 AGERGFFY Insulin B-chain AGLQRGGG M14.004-carboxypeptidase N AGSHLVEA Insulin B-chain AIDIDG CAS-L37 AIDPDG CAS-38 AIDTDG CAS-39 AIDVDG CAS-L40 AIEHDG CAS-L41 AIEIDG CAS-L42 AIENDG CAS-43 AIEPDG CAS-44 AIEQDG CAS-45 AIESDG CAS-46 AIETDG CAS-47 AIEVDG CAS-48 AIFQGPID C03.007-rhinovirus picornain 3C AIGHDG CAS-49 AIGNDG CAS-L50 AIGPDG CAS-L51 AIGQDG CAS-52 AIGSDG CAS-53 AIGTDG CAS-54 AIPMSIPP M10.051-serralysin AISHDG CAS-L55 AISNDG CAS-L56 AISPDG CAS-57 AISQDG CAS-58 AISSDG CAS-59 AISTDG CAS-L60 AKQRAKRD S08.071-furin AKRQGLPV C03.007-rhinovirus picornain 3C AKRRAKRD S08.071-furin AKRRTKRD S08.071-furin ALAALAKK M11.001-gametolysin ALDIDG CAS-L61 ALDPDG CAS-62 ALDTDG CAS-63 ALDVDG CAS-L64 ALEIDG CAS-L65 ALEPDG CAS-L66 ALETDG CAS-67 ALEVDG CAS-68 ALFQGPLQ C03.001-poliovirus-type picornain
    [Show full text]
  • The Effect of N-Terminal Mutations on the Thermostability of Vpr, a Cold Active Subtilisin-Like Serine Protease
    The effect of N-terminal mutations on the thermostability of VPR, a cold active subtilisin-like serine protease Árni Thorlacius FacultyFaculty of of Physical Physical Sciences Sciences UniversityUniversity of of Iceland Iceland 20192019 THE EFFECT OF N-TERMINAL MUTATIONS ON THE THERMOSTABILITY OF VPR, A COLD ACTIVE SUBTILISIN-LIKE SERINE PROTEASE Árni Thorlacius 15 ECTS thesis submitted in partial fulfillment of a Baccalaureus Scientiarum degree in Biochemistry Advisor Prof. Magnús Már Kristjánsson Co-advisor Kristinn Ragnar Óskarsson, M.Sc. Faculty of Physical Sciences School of Engineering and Natural Sciences University of Iceland Reykjavik, May 2019 The effect of N-terminal mutations on the thermostability of VPR, a cold active subtilisin- like serine protease 15 ECTS thesis submitted in partial fulfillment of a B.Sc. degree in Biochemistry Copyright © 2019 Árni Thorlacius All rights reserved Faculty of Physical Sciences School of Engineering and Natural Sciences University of Iceland Dunhagi 5 107, Reykjavik, Reykjavik Iceland Telephone: 525 4000 Bibliographic information: Árni Thorlacius, 2019, The effect of N-terminal mutations on the thermostability of VPR, a cold active subtilisin-like serine protease, B.Sc. thesis, Faculty of Physical Sciences, University of Iceland. Printing: Háskólaprent, Fálkagata 2, 107 Reykjavík Reykjavik, Iceland, May 2019 Útdráttur Rannsóknarverkefnið byggir á fyrri rannsóknum varðandi byggingareinkenni sem ákvarða hitastigsaðlögun í mismunandi próteinum, þar sem borin voru saman tvö samstofna ensím: C-enda stytt afbrigði af kuldaaðlöguðu VPR (VPR∆C) úr kuldakærri Vibrio örveru, og hitastöðugt aqualysin I (AQUI) úr hitakæru örverunni Thermus aquaticus. Stökkbreytingar við N-endann hafa áhrif á víxlverkanir milli N-enda lykkjunnar og megin- byggingar þessara ensíma og þ.a.l.
    [Show full text]
  • Serine Proteases Enrico Di Cera Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St
    IUBMB Life, 61(5): 510–515, May 2009 Critical Review Serine Proteases Enrico Di Cera Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO, USA the serine protease fold especially evident in the trypsins. This Summary new dimension changes our understanding of serine protease Over one third of all known proteolytic enzymes are serine function, regulation, and specificity. proteases. Among these, the trypsins underwent the most pre- dominant genetic expansion yielding the enzymes responsible for digestion, blood coagulation, fibrinolysis, development, fer- tilization, apoptosis, and immunity. The success of this expan- GENERAL PROPERTIES OF SERINE PROTEASES sion resides in a highly efficient fold that couples catalysis and Barrett and coworkers have devised a classification scheme regulatory interactions. Added complexity comes from the recent observation of a significant conformational plasticity of based on statistically significant similarities in sequence and the trypsin fold. A new paradigm emerges where two forms of structure of all known proteolytic enzymes and term this data- the protease, E* and E, are in allosteric equilibrium and deter- base MEROPS (8). The classification system divides proteases mine biological activity and specificity. Ó 2009 IUBMB into clans based on catalytic mechanism and families on the ba- IUBMB Life, 61(5): 510–515, 2009 sis of common ancestry. Over one third of all known proteolytic enzymes are serine proteases grouped into 13 clans and 40 fam- Keywords serine proteases; enzyme catalysis; thrombin; allostery. ilies. The family name stems from the nucleophilic Ser in the enzyme active site, which attacks the carbonyl moiety of the substrate peptide bond to form an acyl-enzyme intermediate (4).
    [Show full text]
  • Understanding the Relationship Between Enzyme Structure and Catalysis
    Understanding the Relationship Between Enzyme Structure and Catalysis Alex Gutteridge∗ Darwin College, Cambridge This dissertation is submitted for the degree of Doctor of Philosophy October 15, 2005 ∗EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD. Preface This dissertation is the result of my own work, and includes nothing which is the outcome of work done in collaboration, except where specifically indicated in the text. The length of this dissertation does not exceed the word limit specified by the Graduate School of Biological, Medical and Veterinary Sciences. i Abstract The three dimensional structure of an enzyme is of fundamental importance to almost every function it performs. In this thesis, we aim to analyse the structures of many enzymes in order to gain insights into how they perform catalysis, and the role of structure in enzyme function. As well as improving our understanding of these important biological molecules, these insights will help in developing new tools for annotating enzyme structures of unknown function and for designing novel enzymes. Predicting the location of the active site, and the identity of the catalytic residues, is an important first step for annotating an enzyme of unknown function. We have developed a neural network trained to distinguish catalytic and non-catalytic residues based on a mixture of sequence and structural parameters. We find that the correct location of the active site can be predicted in ∼70% of cases. We also find that the most important factor in making a prediction is the conservation score of each residue. However, including structural data does improve the predictions that are made over those made on the basis of conservation alone.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8.445,533 B2 Liu Et Al
    USOO8445533B2 (12) United States Patent (10) Patent No.: US 8.445,533 B2 Liu et al. (45) Date of Patent: May 21, 2013 (54) ANDROGRAPHOLIDE DERIVATIVESTO FOREIGN PATENT DOCUMENTS TREATVIRAL INFECTIONS CN 1293955 A 5, 2001 CN 1433756 A * 8, 2003 (75) Inventors: Rui Hai Liu, Ithaca, NY (US); James R. CN 1433,757 A 8, 2003 CN 1433758 A 8, 2003 Jacob, Cortland, NY (US); Bud CN 1437939. A 8, 2003 Tennant, Ithaca, NY (US) CN 145.0059 A 10, 2003 CN 1478774 A 3, 2004 (73) Assignee: Cornell Research Foundation, Inc., CN 1554337 A 12, 2004 Ithaca, NY (US) WO WO96, 17605 A1 * 6, 1996 WO O1,57026 A1 8, 2001 (*) Notice: Subject to any disclaimer, the term of this WO 01f85710 A1 11, 2001 patent is extended or adjusted under 35 OTHER PUBLICATIONS U.S.C. 154(b) by 922 days. Puri et al. “Immunostimulantagents from Andrographis paniculata.” (21) Appl. No.: 11/269,942 J. Nat. Prod. 1993, vol. 56, No. 7, pp. 995-999.* Rice, Fields Virology, Third Eddition, 1995, pp. 931-933.* (22) Filed: Nov. 8, 2005 Ding et al. CN 1433756 abstract, CAPLUS Accession No. 2005:327819.* (65) Prior Publication Data Machine translation of CN 1433756A. Basaket al., “Inhibition of Proprotein Convertases-1, -7 and Furin by US 2006/0223 785 A1 Oct. 5, 2006 Diterpines of Andrographis Paniculata andTheir Succinoyl Esters.” Biochem. J.338: 107-13 (1999). Related U.S. Application Data Supplementary European Search Report for European Patent Appli (60) Provisional application No. 60/626.253, filed on Nov. cation No. EP05857736 (Dec.
    [Show full text]