Structure-Based Optimization of Inhibitors of the Aspartic Protease Endothiapepsin
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In Vitro Inhibition of HIV-1 Proteinase by Cerulenin
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Volume 261, number 2, 373-377 FEBS 08165 February 1990 In vitro inhibition of HIV-1 proteinase by cerulenin Karin Moelling, Thomas Schulze, Marie-Theres Knoop, John Kay +, Raymond Jupp +, George Nicolaou* and Laurence H. Pearl* Max-Planck lnstitut fiir Molekular Genetik, lhnestrasse 73, D-IO00 Berlin 33, FRG, +Department of Biochemistry, University College of Wales, PO Box 903, Cardiff CFl 1ST, UK and *Department of Biochemistry, University College London, Gower Street, London WCIE 6BT, UK Received 13 October 1989; revised version received 18 December 1989 Retroviruses encode proteinases necessary for the proteolytic processing of the viral gag and gag-pol precursor proteins. These enzymes have been shown to be structurally and functionally related to aspartyl proteinases such as pepsin and renin. Cerulenin is a naturally occurring antibiotic, commonly used as an inhibitor of fatty acid synthesis. Cerulenin has been observed to inhibit production of Rous sarcoma virus and murine leukae- mia virus by infected cells, possibly by interfering with proteolytic processing of viral precursor proteins. We show here that cerulenin inhibits the action of the HIV-1 proteinase in vitro, using 3 substrates: a synthetic heptapeptide (SQNYPIV) which corresponds to the sequence at the HIV-I gag p17/p24 junction, a bacterially expressed gag precursor, and purified 66 kDa reverse transcriptase. Inhibition of cleavage by HIV-1 proteinase required preincubation with cerulenin. Cerulenin also inactivates endothiapepsin, a well-characterised fungal aspartyl proteinase, sug- gesting that the action of cerulenin is a function of the common active site structure of the retroviral and aspartic proteinases. -
Membrane Proteins • Cofactors – Plimstex • Membranes • Dna • Small Molecules/Gas • Large Complexes
Structural mass spectrometry hydrogen/deuterium exchange Petr Man Structural Biology and Cell Signalling Institute of Microbiology, Czech Academy of Sciences Structural biology methods Low-resolution methods High-resolution methods Rigid SAXS IR Raman CD ITC MST Cryo-EM AUC SPR MS X-ray crystallography Chemical cross-linking H/D exchange Native ESI + ion mobility Oxidative labelling Small Large NMR Dynamic Structural biology approaches Simple MS, quantitative MS Cross-linking, top-down, native MS+dissociation native MS+ion mobility Cross-linking Structural MS What can we get using mass spectrometry IM – ion mobility CXL – chemical cross-linking AP – afinity purification OFP – oxidative footprinting HDX – hydrogen/deuterium exchange ISOTOPE EXCHANGE IN PROTEINS 1H 2H 3H occurence [%] 99.988 0.0115 trace 5 …Kaj Ulrik Linderstrøm-Lang „Cartesian diver“ Proteins are migrating in tubes with density gradient until they stop at the point where the densities are equal 1H 2H 3H % 99.9885 0.0115 trace density [g/cm3] 1.000 1.106 1.215 Methods of detection IR: β-: NMR: 1 n = 1.6749 × 10-27 kg MS: 1H 2H 3H výskyt% [%] 99.9885 0.0115 trace hustotadensity vody [g/cm [g/cm3] 3] 1.000 1.106 1.215 jadernýspinspin ½+ 1+ ½+ mass [u] 1.00783 2.01410 3.01605 Factors affecting H/D exchange hydrogen bonding solvent accessibility Factors affecting H/D exchange Side chains (acidity, steric shielding) Bai et al.: Proteins (1993) Glasoe, Long: J. Phys. Chem. (1960) Factors affecting H/D exchange – side chain effects Inductive effect – electron density is Downward shift due to withdrawn from peptide steric hindrance effect of bond (S, O). -
Progress in the Field of Aspartic Proteinases in Cheese Manufacturing
Progress in the field of aspartic proteinases in cheese manufacturing: structures, functions, catalytic mechanism, inhibition, and engineering Sirma Yegin, Peter Dekker To cite this version: Sirma Yegin, Peter Dekker. Progress in the field of aspartic proteinases in cheese manufacturing: structures, functions, catalytic mechanism, inhibition, and engineering. Dairy Science & Technology, EDP sciences/Springer, 2013, 93 (6), pp.565-594. 10.1007/s13594-013-0137-2. hal-01201447 HAL Id: hal-01201447 https://hal.archives-ouvertes.fr/hal-01201447 Submitted on 17 Sep 2015 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. Dairy Sci. & Technol. (2013) 93:565–594 DOI 10.1007/s13594-013-0137-2 REVIEW PAPER Progress in the field of aspartic proteinases in cheese manufacturing: structures, functions, catalytic mechanism, inhibition, and engineering Sirma Yegin & Peter Dekker Received: 25 February 2013 /Revised: 16 May 2013 /Accepted: 21 May 2013 / Published online: 27 June 2013 # INRA and Springer-Verlag France 2013 Abstract Aspartic proteinases are an important class of proteinases which are widely used as milk-coagulating agents in industrial cheese production. They are available from a wide range of sources including mammals, plants, and microorganisms. -
Crystal Structures of Native and Inhibitedforms of Human Cathepsin
Proc. Natl. Acad. Sci. USA Vol. 90, pp. 6796-6800, July 1993 Biochemustry Crystal structures of native and inhibited forms of human cathepsin D: Implications for lysosomal targeting and drug design (aspartic protcase/N-linked oligosaccharide/pepstatin A) ERic T. BALDWIN*, T. NARAYANA BHAT*, SERGEI GULNIK*, MADHUSOODAN V. HOSUR*t, RAYMOND C. SOWDER Il, RAUL E. CACHAU*, JACK COLLINS*, ABELARDO M. SILVA*, AND JOHN W. ERICKSON*§ *Structural Biochemistry Program, Frederick Biomedical Supercomputing Center and tAIDS Vaccine Program, Program Resources Inc./DynCorp, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, MD 21702 Communicated by David R. Davies, March 24, 1993 (receivedfor review February 4, 1993) ABSTRACT Cathepsin D (EC 3.4.23.5) is a lysosomal duced in the vicinity of the growing tumor, may degrade the protease suspected to play important roles in protein catabo- extracellular matrix and thereby promote the escape of lism, antigen processing, degenerative diseases, and breast cancer cells to the lymphatic and circulatory systems and cancer progresson. Determination of the crystal structures of enhance the invasion of new tissues (17, 18). The design of cathepsin D and a complex with pepstatin at 2.5 A resolution potent and specific inhibitors of cathepsin D will aid the provides insights into inhibitor binding and lysosomal targeting further elucidation of the roles of this enzyme in human for this two-chain, N-glycosylated aspartic protease. Compar- disease. We previously described the purification and crys- ison with the structures of a complex of pepstatin bound to tallization ofhuman cathepsin D from liver (3); similar studies rhizopuspepsin and with a human renin-bihbitor complex have been reported recently for cathepsin D isolated from revealed differences in subsite structures and inhibitor-enzyme bovine liver (19) and human spleen (20). -
Structure of the Human Renin Gene
Proc. Nati. Acad. Sci. USA Vol. 81, pp. 5999-6003, October 1984 Biochemistry Structure of the human renin gene (hypertension/aspartyl proteinase/nucleotide sequence/splice junction) HITOSHI MIYAZAKI*, AKIYOSHI FUKAMIZU*, SHIGEHISA HIROSE*, TAKASHI HAYASHI*, HITOSHI HORI*, HIROAKI OHKUBOt, SHIGETADA NAKANISHIt, AND KAZUO MURAKAMI** *Institute of Applied Biochemistry, University of Tsukuba, Ibaraki 305, Japan; and tInstitute for Immunology, Kyoto University Faculty of Medicine, Kyoto 606, Japan Communicated by Leroy Hood, June 27, 1984 ABSTRACT The human renin gene was isolated from a between the intron-exon organization of the gene and the Charon 4A human genomic library and characterized. The tertiary structure of the protein. gene spans about 11.7 kilobases and consists of 10 exons and 9 introns that map at points that could be variable surface loops MATERIALS AND METHODS of the enzyme. The complete coding regions, the 5'- and 3'- Materials. All restriction enzymes were obtained from flanking regions, and the exon-intron boundaries were se- either New England Biolabs or Takara Shuzo (Kyoto, Ja- quenced. The active site aspartyl residues Asp-38 and Asp-226 pan). Escherichia coli alkaline phosphatase and T4 DNA li- are encoded by the third and eighth exons, respectively. The gase were from Takara Shuzo. [_y-32P]ATP (>5000 Ci/mmol; extra three amino acids (Asp-165, Ser-166, Glu-167) that are 1 Ci = 37 GBq) and [a-32P]dCTP (=3000 Ci/mmol) were not present in mouse renin are encoded by the separate sixth from Amersham. exon, an exon as small as 9 nucleotides. The positions of the Screening. A human genomic library, prepared from partial introns are in remarkable agreement with those in the human Alu I and Hae III digestion and ligated into the EcoRI arms pepsin gene, supporting the view that the genes coding for of the X vector Charon 4A, was kindly provided by T. -
Arabidopsis Thaliana Atypical Aspartic Proteases Involved in Primary Root Development and Lateral Root Formation
André Filipe Marques Soares RLR1 and RLR2, two novel Arabidopsis thaliana atypical aspartic proteases involved in primary root development and lateral root formation 2016 Thesis submitted to the Institute for Interdisciplinary Research of the University of Coimbra to apply for the degree of Doctor in Philosophy in the area of Experimental Biology and Biomedicine, specialization in Molecular, Cell and Developmental Biology This work was conducted at the Center for Neuroscience and Cell Biology (CNC) of University of Coimbra and at Biocant - Technology Transfer Association, under the scientific supervision of Doctor Isaura Simões and at the Department of Biochemistry of University of Massachusetts, Amherst, under the scientific supervision of Doctor Alice Y. Cheung. Part of this work was also performed at the Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, under the scientific supervision of Doctor Herta Steinkellner and also at the Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, under the schientific supervision of Doctor Pitter F. Huesgen. André Filipe Marques Soares was a student of the Doctoral Programme in Experimental Biology and Biomedicine coordinated by the Center for Neuroscience and Cell Biology (CNC) of the University of Coimbra and a recipient of the fellowship SFRH/BD/51676/2011 from the Portuguese Foundation for Science and Technology (FCT). The execution of this work was supported by a PPP grant of the German Academic Exchange Service with funding from the Federal Ministry of Education and Research (Project-ID 57128819 to PFH) and the Fundação para a Ciência e a Tecnologia (FCT) (grant: Scientific and Technological Bilateral Agreement 2015/2016 to IS) Agradecimentos/Acknowledgments Esta tese e todo o percurso que culminou na sua escrita não teriam sido possíveis sem o apoio, o carinho e a amizade de várias pessoas que ainda estão ou estiveram presentes na minha vida. -
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 -
Hemoglobin Degradation in the Human Malaria Pathogen Plasmodium Falciparum : a Catabolic Pathway Initiated by a Specific Aspartic Protease by Daniel E
Hemoglobin Degradation in the Human Malaria Pathogen Plasmodium falciparum : A Catabolic Pathway Initiated by a Specific Aspartic Protease By Daniel E. Goldberg,* Andrew F. G. Slater,* Ronald Beavis,$ Brian Chait, $ Anthony Cerami," and Graeme B. Henderson" II From the 'Laboratory of Medical Biochemistry and the LLaboratory ofMass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10021 Summary Hemoglobin is an important nutrient source for intraerythrocytic malaria organisms. Its catabolism occurs in an acidic digestive vacuole . Our previous studies suggested that an aspartic protease plays a key role in the degradative process. We have now isolated this enzyme and defined its role in the hemoglobinolysic pathway. Laser desorption mass spectrometry was used to analyze the proteolytic action of the purified protease. The enzyme has a remarkably stringent specificity Downloaded from towards native hemoglobin, making a single cleavage between tx33Phe and 34Leu. This scission is in the hemoglobin hinge region, unraveling the molecule and exposing other sites for proteolysis. The protease is inhibited by pepstatin and has NH2-terminal homology to mammalian aspartic proteases . Isolated digestive vacuoles make a pepstatin-inhibitable cleavage identical to that of the purified enzyme. The pivotal role of this aspartic hemoglobinase in initiating hemoglobin degradation in the malaria parasite digestive vacuoles is demonstrated. www.jem.org he intraerythrocytic malaria parasite develops within a Materials and Methods on January 24, 2005 cell that contains a single major cytosolic protein, he- Materials. Saponin, Triton X-100, and bovine spleen cathepsin moglobinT . The organism avidly ingests host hemoglobin and D were from Sigma Chemical Co. (St. -
EUROPEAN COMMISSION Brussels, 28 April 2020 REGISTER of FOOD
EUROPEAN COMMISSION DIRECTORATE-GENERAL FOR HEALTH AND FOOD SAFETY Food and feed safety, innovation Food processing technologies and novel foods Brussels, 28 April 2020 REGISTER OF FOOD ENZYMES TO BE CONSIDERED FOR INCLUSION IN THE UNION LIST Article 17 of Regulation (EC) No 1332/20081 provides for the establishment of a Register of all food enzymes to be considered for inclusion in the Union list. In accordance with that Article, the Register includes all applications which were submitted within the initial period fixed by that Regulation and which comply with the validity criteria laid down in accordance with Article 9(1) of (EC) No 1331/2008 establishing a common authorisation procedure for food additives, food enzymes and food flavourings2. The Register therefore lists all valid food enzyme applications submitted until 11 March 2015 except those withdrawn by the applicant before that date. Applications submitted after that date are not included in the Register but will be processed in accordance with the Common Authorisation Procedure. The entry of a food enzyme in the Register specifies the identification, the name, the source of the food enzyme as provided by the applicant and the EFSA question number under which the status of the Authority’s assessment can be followed3. As defined by Article 3 of Regulation (EC) No 1332/2008, ‘food enzyme’ subject to an entry in the Register, refers to a product that may contain more than one enzyme capable of catalysing a specific biochemical reaction. In the assessment process, such a food enzyme may be linked with several EFSA question numbers. -
Proteases in Fish and Shellfish: Role on Muscle Softening and Prevention *Sriket, C
International Food Research Journal 21(1): 433-445 (2014) Journal homepage: http://www.ifrj.upm.edu.my Mini Review Proteases in fish and shellfish: Role on muscle softening and prevention *Sriket, C. Program in Food Science and Technology, Faculty of Agriculture, Ubon Ratchathani Rajabhat University, Ubon Ratchathani, 34000, Thailand Article history Abstract Received: 10 January 2013 Textural quality of fish and shellfish is the most important factor because it limits consumer Received in revised form: acceptance as well as market price. The muscle softening or mushiness of fish and shellfish 17 October 2013 during storage or distribution in ice is generally occurred. This phenomenon is considered as the Accepted: 19 October 2013 muscle protein degradation due to the proteolytic activity. The presence of active proteases in Keywords muscle and digestive organ makes the flesh fish and shellfish prone to degrade especially during iced storage, since the digestive organ is not practically removed prior to storage. The digestive Protease Softening tracts have been known to have high proteolytic or collagenolytic enzymes. During storage of Mushiness fish and shellfish, the intensive hydrolysis of myofibrillar and collagenous proteins by proteases Muscle degradation can be observed. To lower the muscle degradation, different pre-treatment methods as well Protease inhibitor as protease inhibitors have been applied in the stored fish and shellfish. Thus, the knowledge Prevention gained can be then transferred to the seafood processors for the quality improvement of fish and Postmortem shellfish, especially those with iced storage, leading to a full market value of fish species. Digestive enzyme © All Rights Reserved Introduction and collagenolytic proteases (Cao et al., 2000b; Aoki et al., 2003; Sriket et al., 2011a). -
Homology Modeling and SAR Analysis of Schistosoma Japonicum
Article in press - uncorrected proof Biol. Chem., Vol. 386, pp. 339–349, April 2005 • Copyright ᮊ by Walter de Gruyter • Berlin • New York. DOI 10.1515/BC.2005.041 Homology modeling and SAR analysis of Schistosoma japonicum cathepsin D (SjCD) with statin inhibitors identify a unique active site steric barrier with potential for the design of specific inhibitors Conor R. Caffrey1, Lenka Placha2, Cyril Introduction Barinka2, Martin Hradilek2, Jirˇı´ Dosta´l2, Mohammed Sajid1, James H. McKerrow1, Pavel Schistosomiasis, caused by parasitic bloodflukes of the Majer3, Jan Konvalinka2 and Jirˇı´ Vondra´sˇek2,4,* genus Schistosoma, is of serious public health concern in 74 tropical and sub-tropical countries. More than 200 1 Sandler Center for Basic Research in Parasitic million people are infected, with 20 million suffering from Diseases, University of California at San Francisco, Box serious disease (Chitsulo et al., 2004). Adult worms 0511, San Francisco, CA 94143, USA reside within the blood vessels of the intestine and blad- 2 Institute of Organic Chemistry and Biochemistry, der, and their eggs cause morbidity associated with a Academy of Sciences of the Czech Republic, progressive, immunopathological reaction in various tis- Flemingovo n. 2, 166 10 Praha 6, Czech Republic sues including the liver and intestine (Pearce and Mac- 3 Guilford Pharmaceuticals Inc., 6611 Tributary Street, Donald, 2002). Baltimore, MD 21224, USA Schistosomes feed on blood proteins, including hemo- 4 Center for Biomolecules and Complex Molecular globin, and express a range of gut-associated proteases Systems, Institute of Organic Chemistry and to facilitate digestion. The proteases thought to be direct- Biochemistry, Academy of Sciences of the Czech ly involved in this process include orthologs of the mam- Republic, Flemingovo n. -
A Novel Thermostable Aspartic Protease from Talaromyces Leycettanus and Its Specific
bioRxiv preprint doi: https://doi.org/10.1101/528265; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 1 RESEARCH ARTICLE 2 3 A novel thermostable aspartic protease from Talaromyces leycettanus and its specific 4 autocatalytic activation through an intermediate transition state 5 6 Yujie Guo1, Tao Tu1, Yaxin Ren1, Yaru Wang1, Yingguo Bai1, Xiaoyun Su1, Yuan 7 Wang1, Bin Yao1, Huoqing Huang1*, Huiying Luo1* 8 9 1Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research 10 Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China 11 Running title: Insights into a specific auto-activation of proTlAPA1 12 * Corresponding authors. 13 E-mail addresses: [email protected] (H. Luo), [email protected] (H. Huang). 2 bioRxiv preprint doi: https://doi.org/10.1101/528265; this version posted January 23, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 14 ABSTRACT 15 Aspartic proteases exhibit optimum enzyme activity under acidic condition and 16 have been extensively used in food, fermentation and leather industries. In this study, 17 a novel aspartic protease precursor (proTlAPA1) from Talaromyces leycettanus was 18 identified and successfully expressed in Pichia pastoris. Subsequently, the 19 auto-activation processing of the zymogen proTlAPA1 was studied by SDS-PAGE 20 and N-terminal sequencing, under different processing conditions. TlAPA1 shared the 21 highest identity of 70.3 % with the aspartic endopeptidase from Byssochlamys 22 spectabilis (GAD91729) and was classified into a new subgroup of the aspartic 23 protease A1 family, based on evolutionary analysis.