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Recent Development of Highly Sensitive Protease Assay Methods: Signal Amplification Through Enzyme Cascades
Biotechnology and Bioprocess Engineering 17: 1113-1119 (2012) DOI 10.1007/s12257-012-0545-9 REVIEW PAPER Recent Development of Highly Sensitive Protease Assay Methods: Signal Amplification through Enzyme Cascades Hyun Kyung Yoon, Sang Taek Jung, Jae-Ho Kim, and Tae Hyeon Yoo Received: 14 August 2012 / Revised: 29 August 2012 / Accepted: 5 September 2012 © The Korean Society for Biotechnology and Bioengineering and Springer 2012 Abstract Proteases are involved in almost all biological encode proteases or their homologs, and proteases are processes, and therefore, aberrant activity of many of these involved in various biological processes, such as develop- enzymes is an important indicator of disease. Various ment, immunity, blood clotting, and wound healing [1,2]. methods have been developed to analyze protease activity, Therefore, aberrant protease activity is associated with among which, protease assays based on resonance energy various diseases, including cancer, cardiovascular disease, transfer are currently used most widely. However, quanti- Alzheimer disease, inflammatory disease, and virus-related tative methods with relatively higher sensitivity are needed, diseases [3-7]. To treat diseases resulting from hyperactivity especially for disease diagnosis at early stages. One of the of proteases, small molecule inhibitors have been developed. strategies to achieve higher sensitivity is to implement Inhibitors against matrix metalloproteinase (MMP) and signal amplification of the protease activity. In this review, cathepsin, which play an important role in cancer metastasis, we briefly summarize the protease assay methods based on have been actively investigated [4,8,9]. Protease inhibitors resonance energy transfer, and then elaborate the efforts to against the HIV protease are one of the most successful develop sensitive protease assays through signal amplification approaches to controlling the disease [7]. -
Application of Plant Proteolytic Enzymes for Tenderization of Rabbit Meat
Biotechnology in Animal Husbandry 34 (2), p 229-238 , 2018 ISSN 1450-9156 Publisher: Institute for Animal Husbandry, Belgrade-Zemun UDC 637.5.039'637.55'712 https://doi.org/10.2298/BAH1802229D APPLICATION OF PLANT PROTEOLYTIC ENZYMES FOR TENDERIZATION OF RABBIT MEAT Maria Doneva, Iliana Nacheva, Svetla Dyankova, Petya Metodieva, Daniela Miteva Institute of Cryobiology and Food Technology, Cherni Vrah 53, 1407, Sofia, Bulgaria Corresponding author: Maria Doneva, e-mail: [email protected] Original scientific paper Abstract: The purpose of this study is to assess the tenderizing effect of plant proteolytic enzymes upon raw rabbit meat. Tests are performed on rabbit meat samples treated with papain and two vegetal sources of natural proteases (extracts of kiwifruit and ginger root). Two variants of marinade solutions are prepared from each vegetable raw materials– 50% (w/w) and 100 % (w/w), with a duration of processing 2h, 24h, and 48h. Changes in the following physico- chemical characteristics of meat have been observed: pH, water-holding capacity, cooking losses and quantity of free amino acids. Differences in values of these characteristics have been observed, both between control and test samples, as well as depending of treatment duration. For meat samples marinated with papain and ginger extracts, the water-holding capacity reached to 6.74 ± 0.04 % (papain), 5.58 ± 0.09 % (variant 1) and 6.80 ± 0.11 % (variant 2) after 48 hours treatment. In rabbit meat marinated with kiwifruit extracts, a significant increase in WHC was observed at 48 hours, 3.37 ± 0.07 (variant 3) and 6.84 ± 0.11 (variant 4). -
Activity of the Human Rhinovirus 3C Protease Studied in Various Buffers, Additives and Detergents Solutions for Recombinant Protein Production
RESEARCH ARTICLE Activity of the Human Rhinovirus 3C Protease Studied in Various Buffers, Additives and Detergents Solutions for Recombinant Protein Production Raheem Ullah1,2☯, Majid Ali Shah1,2☯, Soban Tufail1, Fouzia Ismat1, Muhammad Imran1¤, Mazhar Iqbal1,2, Osman Mirza3, Moazur Rhaman1,2* 1 Drug Discovery and Structural Biology group, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan, 2 Pakistan Institute of Engineering and Applied Sciences, P.O. Nilore, Islamabad, Pakistan, 3 Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark ☯ These authors contributed equally to this work. a11111 ¤ Current address: Forman Christian College (A Chartered University), Lahore, Pakistan * [email protected]; [email protected] Abstract Proteases are widely used to remove affinity and solubility tags from recombinant proteins OPEN ACCESS to avoid potential interference of these tags with the structure and function of the fusion part- Citation: Ullah R, Shah MA, Tufail S, Ismat F, Imran ner. In recent years, great interest has been seen in use of the human rhinovirus 3C prote- M, Iqbal M, et al. (2016) Activity of the Human ase owing to its stringent sequence specificity and enhanced activity. Like other proteases, Rhinovirus 3C Protease Studied in Various Buffers, activity of the human rhinovirus 3C protease can be affected in part by the buffer compo- Additives and Detergents Solutions for Recombinant Protein Production. PLoS ONE 11(4): e0153436. nents and additives that are generally employed for purification and stabilization of proteins, doi:10.1371/journal.pone.0153436 hence, necessitate their removal by tedious and time-consuming procedures before prote- Editor: Mark J van Raaij, Centro Nacional de olysis can occur. -
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. -
Current IUBMB Recommendations on Enzyme Nomenclature and Kinetics$
Perspectives in Science (2014) 1,74–87 Available online at www.sciencedirect.com www.elsevier.com/locate/pisc REVIEW Current IUBMB recommendations on enzyme nomenclature and kinetics$ Athel Cornish-Bowden CNRS-BIP, 31 chemin Joseph-Aiguier, B.P. 71, 13402 Marseille Cedex 20, France Received 9 July 2013; accepted 6 November 2013; Available online 27 March 2014 KEYWORDS Abstract Enzyme kinetics; The International Union of Biochemistry (IUB, now IUBMB) prepared recommendations for Rate of reaction; describing the kinetic behaviour of enzymes in 1981. Despite the more than 30 years that have Enzyme passed since these have not subsequently been revised, though in various respects they do not nomenclature; adequately cover current needs. The IUBMB is also responsible for recommendations on the Enzyme classification naming and classification of enzymes. In contrast to the case of kinetics, these recommenda- tions are kept continuously up to date. & 2014 The Author. Published by Elsevier GmbH. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/). Contents Introduction...................................................................75 Kinetics introduction...........................................................75 Introduction to enzyme nomenclature ................................................76 Basic definitions ................................................................76 Rates of consumption and formation .................................................76 Rate of reaction .............................................................76 -
Milligram Scale Expression, Refolding, and Purification of Bombyx Mori Cocoonase Using a Recombinant E
Protein Expression and Purification 186 (2021) 105919 Contents lists available at ScienceDirect Protein Expression and Purification journal homepage: www.elsevier.com/locate/yprep Milligram scale expression, refolding, and purification of Bombyx mori cocoonase using a recombinant E. coli system Chanrith Phoeurk a,b, Ameeq Ul Mushtaq a, Per Rogne a,*, Magnus Wolf-Watz a,* a Department of Chemistry, Umeå University, Umeå, Sweden b Department of Bio-Engineering, Royal University of Phnom Penh, Phnom Penh, Cambodia ARTICLE INFO ABSTRACT Keywords: Silk is one of the most versatile biomaterials with signature properties of outstanding mechanical strength and Silk moth (Bombyx mori) flexibility.A potential avenue for developing more environmentally friendly silk production is to make use of the Cocoonase silk moth (Bombyx mori) cocoonase, this will at the same time increase the possibility for using the byproduct, Serine protease sericin, as a raw material for other applications. Cocoonase is a serine protease utilized by the silk moth to soften Refolding the cocoon to enable its escape after completed metamorphosis. Cocoonase selectively degrades the glue protein Escherichia coli of the cocoon, sericin, without affecting the silk-fiber made of the protein fibroin. Cocoonase can be recombi nantly produced in E. coli, however, it is exclusively found as insoluble inclusion bodies. To solve this problem and to be able to utilize the benefits associated with an E. coli based expression system, we have developed a protocol that enables the production of soluble and functional protease in the milligram/liter scale. The core of the protocol is refolding of the protein in a buffer with a redox potential that is optimized for formation of native and intramolecular di-sulfidebridges. -
Molecular Insights Into Substrate Recognition and Discrimination By
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.17.423354; this version posted December 18, 2020. 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 Main Manuscript for 2 Molecular insights into substrate recognition and discrimination by the N- 3 terminal domain of Lon AAA+ protease 4 5 Authors: Shiou-Ru Tzeng1*, Yin-Chu Tseng1, Chien-Chu Lin2,5, Chia-Ying Hsu1, Shing-Jong Huang3, Yi- 6 Ting Kuo1, Chung-I Chang2,4* 7 8 Affiliations: 9 1. Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, 10 Taipei, Taiwan. 11 2. Institute of Biological Chemistry, Academia Sinica, Taipei 11529 12 3. Instrumentation Center, National Taiwan University 13 4. Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 10617 14 Taiwan 15 5. Present Address: Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan 16 17 *Corresponding authors 18 Shiou-Ru Tzeng: R907, No. 1 Jen- Ai Road Section 1, Taipei 10051, Taiwan.; TEL: (+886)-22312-3456 19 ext 88205; FAX: (+886)-2239-15295; E-mail: [email protected] 20 Chung-I Chang: 128, Section 2, Academia Road, Nankang 11529, Taipei, Taiwan.; TEL: (+886)-22785- 21 5696 ext 7110; E-mail: [email protected] 22 23 Keywords 24 Lon AAA+ protease; N-terminal domain; degrons; misfolded proteins; protein aggregates; Meiothermus 25 taiwanensis. 26 27 This PDF file includes: 28 Main Text 29 Table 1 30 Figures 1 to 7 31 32 Abstract 33 The Lon AAA+ proteases (LonA) is a ubiquitous ATP-dependent proteolytic machine, which selectively 34 degrades damaged proteins or native proteins carrying exposed motifs (degrons). -
SARS-Cov-2) Papain-Like Proteinase(Plpro
JOURNAL OF VIROLOGY, Oct. 2010, p. 10063–10073 Vol. 84, No. 19 0022-538X/10/$12.00 doi:10.1128/JVI.00898-10 Copyright © 2010, American Society for Microbiology. All Rights Reserved. Papain-Like Protease 1 from Transmissible Gastroenteritis Virus: Crystal Structure and Enzymatic Activity toward Viral and Cellular Substratesᰔ Justyna A. Wojdyla,1† Ioannis Manolaridis,1‡ Puck B. van Kasteren,2 Marjolein Kikkert,2 Eric J. Snijder,2 Alexander E. Gorbalenya,2 and Paul A. Tucker1* EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany,1 and Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, Netherlands2 Received 27 April 2010/Accepted 15 July 2010 Coronaviruses encode two classes of cysteine proteases, which have narrow substrate specificities and either a chymotrypsin- or papain-like fold. These enzymes mediate the processing of the two precursor polyproteins of the viral replicase and are also thought to modulate host cell functions to facilitate infection. The papain-like protease 1 (PL1pro) domain is present in nonstructural protein 3 (nsp3) of alphacoronaviruses and subgroup 2a betacoronaviruses. It participates in the proteolytic processing of the N-terminal region of the replicase polyproteins in a manner that varies among different coronaviruses and remains poorly understood. Here we report the first structural and biochemical characterization of a purified coronavirus PL1pro domain, that of transmissible gastroenteritis virus (TGEV). Its tertiary structure is compared with that of severe acute respiratory syndrome (SARS) coronavirus PL2pro, a downstream paralog that is conserved in the nsp3’s of all coronaviruses. -
Separase Protease Activity Is Required for Cytokinesis in Addition
bioRxiv preprint doi: https://doi.org/10.1101/069906; this version posted August 16, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Separase Protease Activity is Required for Cytokinesis in addition to Chromosome Segregation Xiaofei Bai1 and Joshua N. Bembenek1* 1Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, United States of America * Corresponding Author: Joshua N. Bembenek 1414 Cumberland Ave. C211 Walters Life Sciences Building Knoxville, TN 37996 (865)-974-4085 E-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/069906; this version posted August 16, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Chromosomal segregation and cytokinesis are tightly regulated processes required for successful cell division. The cysteine protease separase cleaves a subunit of the cohesin complex to allow chromosome segregation at anaphase onset. Separase also regulates meiotic cortical granule exocytosis and vesicle trafficking during cytokinesis, both of which involve RAB-11. Separase has non-proteolytic signaling functions in addition to its role in substrate cleavage, and its mechanism in exocytosis is unknown. We sought to determine whether separase regulates RAB-11 vesicle exocytosis through a proteolytic or non-proteolytic mechanism. -
Pub2019 Flipgfp.Pdf
Communication Cite This: J. Am. Chem. Soc. 2019, 141, 4526−4530 pubs.acs.org/JACS Designing a Green Fluorogenic Protease Reporter by Flipping a Beta Strand of GFP for Imaging Apoptosis in Animals ¶ § § ‡ § ‡ ¶ § ‡ ∥ ‡ ¶ § † Qiang Zhang, , Antonino Schepis, , Hai Huang, , Junjiao Yang, , , Wen Ma, , Joaquim Torra, , , ⊥ # ¶ § † # Shao-Qing Zhang, Lina Yang, Haifan Wu, , Santi Nonell, Zhiqiang Dong, § § ¶ § Thomas B. Kornberg, Shaun R. Coughlin, and Xiaokun Shu*, , ¶ Department of Pharmaceutical Chemistry, University of California−San Francisco, San Francisco, California 94158, United States § Cardiovascular Research Institute, University of California−San Francisco, San Francisco, California 94158, United States ∥ Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States † Institut Químic de Sarria,̀ Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain ⊥ Department of Neurology, Harvard Medical School and MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States # Bio-Medical Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China *S Supporting Information brightness (i.e., high quantum yield). Over the past few years, ABSTRACT: A family of proteases called caspases to overcome limitations of FRET-based executioner caspase − mediate apoptosis signaling in animals. We report a reporters,4 7 many different types of reporters have been − GFP-based fluorogenic protease reporter, dubbed developed.8 13 For example, the bipartite GFP was previously “FlipGFP”,byflipping a beta strand of the GFP. Upon engineered into a light-driven protease sensor.11 Here we protease activation and cleavage, the beta strand is report a new type of rationally designed fluorogenic protease restored, leading to reconstitution of the GFP and reporter based on GFP with both large dynamic range and high fl uorescence. -
Proteolytic Enzymes in Grass Pollen and Their Relationship to Allergenic Proteins
Proteolytic Enzymes in Grass Pollen and their Relationship to Allergenic Proteins By Rohit G. Saldanha A thesis submitted in fulfilment of the requirements for the degree of Masters by Research Faculty of Medicine The University of New South Wales March 2005 TABLE OF CONTENTS TABLE OF CONTENTS 1 LIST OF FIGURES 6 LIST OF TABLES 8 LIST OF TABLES 8 ABBREVIATIONS 8 ACKNOWLEDGEMENTS 11 PUBLISHED WORK FROM THIS THESIS 12 ABSTRACT 13 1. ASTHMA AND SENSITISATION IN ALLERGIC DISEASES 14 1.1 Defining Asthma and its Clinical Presentation 14 1.2 Inflammatory Responses in Asthma 15 1.2.1 The Early Phase Response 15 1.2.2 The Late Phase Reaction 16 1.3 Effects of Airway Inflammation 16 1.3.1 Respiratory Epithelium 16 1.3.2 Airway Remodelling 17 1.4 Classification of Asthma 18 1.4.1 Extrinsic Asthma 19 1.4.2 Intrinsic Asthma 19 1.5 Prevalence of Asthma 20 1.6 Immunological Sensitisation 22 1.7 Antigen Presentation and development of T cell Responses. 22 1.8 Factors Influencing T cell Activation Responses 25 1.8.1 Co-Stimulatory Interactions 25 1.8.2 Cognate Cellular Interactions 26 1.8.3 Soluble Pro-inflammatory Factors 26 1.9 Intracellular Signalling Mechanisms Regulating T cell Differentiation 30 2 POLLEN ALLERGENS AND THEIR RELATIONSHIP TO PROTEOLYTIC ENZYMES 33 1 2.1 The Role of Pollen Allergens in Asthma 33 2.2 Environmental Factors influencing Pollen Exposure 33 2.3 Classification of Pollen Sources 35 2.3.1 Taxonomy of Pollen Sources 35 2.3.2 Cross-Reactivity between different Pollen Allergens 40 2.4 Classification of Pollen Allergens 41 2.4.1 -
Engineering of TEV Protease for Manipulation of Biosystems
Engineering of TEV Protease for Manipulation of Biosystems by Xi Chen A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Institute of Biomaterials and Biomedical Engineering University of Toronto © Copyright by Xi Chen 2013 Engineering of TEV protease for Manipulation of Biosystems Xi Chen Doctor of Philosophy Institute of Biomaterials and Biomedical Engineering University of Toronto 2013 Abstract Synthetic biology is a nascent discipline that aims to design and construct new biological systems beyond those found in nature, ultimately using them to probe, control, or even replace existing biological systems. The success of synthetic biology depends on the assembly of a set of well-defined and modular tools. These tools should ideally be mutually compatible, reusable in different contexts, and have minimum crosstalk with endogenous proteins of the subject. The tobacco etch virus protease (TEV protease, TEVp) is a suitable candidate for such a tool due to its unique substrate specificity and high efficiency. Importantly, TEVp is capable of imitating proteolysis, a ubiquitous mechanism in nature for post-translational modifications and signal propagation. Here, TEVp is employed as a self-contained proteolytic device capable of executing biological tasks that are otherwise governed by endogenous proteins and processes. Consequently, the goal of using TEVp for synthetic manipulation of biosystems is achieved. First, a single-vector multiple gene expression strategy utilizing TEVp self-cleavage was created. This approach was used for the robust expression of up to three genes in both bacterial and mammalian cells with consistent stoichiometry. The products can then be individually purified or targeted to distinct subcellular compartments respectively.