Design and Applications of a Clamp for Green Fluorescent Protein with Picomolar Afnity Received: 22 August 2017 Simon Hansen1,2, Jakob C
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Structural Analysis of 3′Utrs in Insect Flaviviruses
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.23.449515; this version posted June 24, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Structural analysis of 3’UTRs in insect flaviviruses reveals novel determinant of sfRNA biogenesis and provides new insights into flavivirus evolution Andrii Slonchak1,#, Rhys Parry1, Brody Pullinger1, Julian D.J. Sng1, Xiaohui Wang1, Teresa F Buck1,2, Francisco J Torres1, Jessica J Harrison1, Agathe M G Colmant1, Jody Hobson- Peters1,3, Roy A Hall1,3, Andrew Tuplin4, Alexander A Khromykh1,3,# 1 School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia 2Current affiliation: Institute for Medical and Marine Biotechnology, University of Lübeck, Lübeck, Germany 3Australian Infectious Diseases Research Centre, Global Virus Network Centre of Excellence, Brisbane, QLD, Australia 4 School of Molecular and Cellular Biology, University of Leeds, Leeds, U.K. # corresponding authors: [email protected]; [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.06.23.449515; this version posted June 24, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Abstract Insect-specific flaviviruses (ISFs) circulate in nature due to vertical transmission in mosquitoes and do not infect vertebrates. ISFs include two distinct lineages – classical ISFs (cISFs) that evolved independently and dual host associated ISFs (dISFs) that are proposed to diverge from mosquito-borne flaviviruses (MBFs). Compared to pathogenic flaviviruses, ISFs are relatively poorly studied, and their molecular biology remains largely unexplored. -
Giri Narasimhan ECS 254A; Phone: X3748 [email protected] July 2011
BSC 4934: QʼBIC Capstone Workshop" Giri Narasimhan ECS 254A; Phone: x3748 [email protected] http://www.cs.fiu.edu/~giri/teach/BSC4934_Su11.html July 2011 7/19/11 Q'BIC Bioinformatics 1 Modular Nature of Proteins" Proteins# are collections of “modular” domains. For example, Coagulation Factor XII F2 E F2 E K Catalytic Domain F2 E K K Catalytic Domain PLAT 7/21/10 Modular Nature of Protein Structures" Example: Diphtheria Toxin 7/21/10 Domain Architecture Tools" CDART# " #Protein AAH24495; Domain Architecture; " #It’s domain relatives; " #Multiple alignment for 2nd domain SMART# 7/21/10 Active Sites" Active sites in proteins are usually hydrophobic pockets/ crevices/troughs that involve sidechain atoms. 7/21/10 Active Sites" Left PDB 3RTD (streptavidin) and the first site located by the MOE Site Finder. Middle 3RTD with complexed ligand (biotin). Right Biotin ligand overlaid with calculated alpha spheres of the first site. 7/21/10 Secondary Structure Prediction Software" 7/21/10 PDB: Protein Data Bank" #Database of protein tertiary and quaternary structures and protein complexes. http:// www.rcsb.org/pdb/ #Over 29,000 structures as of Feb 1, 2005. #Structures determined by " # NMR Spectroscopy " # X-ray crystallography " # Computational prediction methods #Sample PDB file: Click here [▪] 7/21/10 Protein Folding" Unfolded Rapid (< 1s) Molten Globule State Slow (1 – 1000 s) Folded Native State #How to find minimum energy configuration? 7/21/10 Protein Structures" #Most proteins have a hydrophobic core. #Within the core, specific interactions take place between amino acid side chains. #Can an amino acid be replaced by some other amino acid? " # Limited by space and available contacts with nearby amino acids #Outside the core, proteins are composed of loops and structural elements in contact with water, solvent, other proteins and other structures. -
Nilsson C. L. (Ed.)
Else_AT-NILSSON_prelims.qxd 6/8/2007 06:29 PM Page i Lectins Analytical Technologies This page intentionally left blank Else_AT-NILSSON_prelims.qxd 6/8/2007 06:29 PM Page iii Lectins Analytical Technologies Edited by Carol L. Nilsson National High Magnetic Field Laboratory Florida State University Tallahassee, FL, USA Amsterdam – Boston – Heidelberg – London – New York – Oxford – Paris San Diego – San Francisco – Singapore – Sydney – Tokyo Else_AT-NILSSON_prelims.qxd 6/8/2007 06:29 PM Page iv Elsevier Radarweg 29, PO Box 211, 1000 AE Amsterdam, The Netherlands Linacre House, Jordan Hill, Oxford OX2 8DP, UK First edition 2007 Copyright © 2007 Elsevier B.V. All rights reserved No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone (+44) (0) 1865 843830; fax (+44) (0) 1865 853333; email: [email protected]. Alternatively you can submit your request online by visiting the Elsevier web site at http://www.elsevier.com/locate/permissions, and selecting Obtaining permission to use Elsevier material Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the -
Strategies and Challenges for the Next Generation of Therapeutic Antibodies
FOCUS ON THERAPEUTIC ANTIBODIES PERSPECTIVES ‘validated targets’, either because prior anti- TIMELINE bodies have clearly shown proof of activity in humans (first-generation approved anti- Strategies and challenges for the bodies on the market for clinically validated targets) or because a vast literature exists next generation of therapeutic on the importance of these targets for the disease mechanism in both in vitro and in vivo pharmacological models (experi- antibodies mental validation; although this does not necessarily equate to clinical validation). Alain Beck, Thierry Wurch, Christian Bailly and Nathalie Corvaia Basically, the strategy consists of develop- ing new generations of antibodies specific Abstract | Antibodies and related products are the fastest growing class of for the same antigens but targeting other therapeutic agents. By analysing the regulatory approvals of IgG-based epitopes and/or triggering different mecha- biotherapeutic agents in the past 10 years, we can gain insights into the successful nisms of action (second- or third-generation strategies used by pharmaceutical companies so far to bring innovative drugs to antibodies, as discussed below) or even the market. Many challenges will have to be faced in the next decade to bring specific for the same epitopes but with only one improved property (‘me better’ antibod- more efficient and affordable antibody-based drugs to the clinic. Here, we ies). This validated approach has a high discuss strategies to select the best therapeutic antigen targets, to optimize the probability of success, but there are many structure of IgG antibodies and to design related or new structures with groups working on this class of target pro- additional functions. -
M.Sc. [Botany] 346 13
cover page as mentioned below: below: mentioned Youas arepage instructedcover the to updateupdate to the coverinstructed pageare asYou mentioned below: Increase the font size of the Course Name. Name. 1. IncreaseCourse the theof fontsize sizefont ofthe the CourseIncrease 1. Name. use the following as a header in the Cover Page. Page. Cover 2. the usein the followingheader a as as a headerfollowing the inuse the 2. Cover Page. ALAGAPPAUNIVERSITY UNIVERSITYALAGAPPA [Accredited with ’A+’ Grade by NAAC (CGPA:3.64) in the Third Cycle Cycle Third the in (CGPA:3.64) [AccreditedNAAC by withGrade ’A+’’A+’ Gradewith by NAAC[Accredited (CGPA:3.64) in the Third Cycle and Graded as Category–I University by MHRD-UGC] MHRD-UGC] by University and Category–I Graded as as Graded Category–I and University by MHRD-UGC] M.Sc. [Botany] 003 630 – KARAIKUDIKARAIKUDI – 630 003 346 13 EDUCATION DIRECTORATEDISTANCE OF OF DISTANCEDIRECTORATE EDUCATION BIOLOGICAL TECHNIQUES IN BOTANY I - Semester BOTANY IN TECHNIQUES BIOLOGICAL M.Sc. [Botany] 346 13 cover page as mentioned below: below: mentioned Youas arepage instructedcover the to updateupdate to the coverinstructed pageare asYou mentioned below: Increase the font size of the Course Name. Name. 1. IncreaseCourse the theof fontsize sizefont ofthe the CourseIncrease 1. Name. use the following as a header in the Cover Page. Page. Cover 2. the usein the followingheader a as as a headerfollowing the inuse the 2. Cover Page. ALAGAPPAUNIVERSITY UNIVERSITYALAGAPPA [Accredited with ’A+’ Grade by NAAC (CGPA:3.64) in the Third Cycle Cycle Third the in (CGPA:3.64) [AccreditedNAAC by withGrade ’A+’’A+’ Gradewith by NAAC[Accredited (CGPA:3.64) in the Third Cycle and Graded as Category–I University by MHRD-UGC] MHRD-UGC] by University and Category–I Graded as as Graded Category–I and University by MHRD-UGC] M.Sc. -
In Vitro Selection for Catalytic Activity with Ribosome Display Patrick Amstutz,† Joelle N
Published on Web 07/17/2002 In Vitro Selection for Catalytic Activity with Ribosome Display Patrick Amstutz,† Joelle N. Pelletier,†,‡ Armin Guggisberg,§ Lutz Jermutus,†,⊥ Sandro Cesaro-Tadic,† Christian Zahnd,† and Andreas Plu¨ckthun*,† Biochemisches Institut, UniVersita¨tZu¨rich, Winterthurerstrasse 190, CH-8057 Zu¨rich, Switzerland, and Organisch-Chemisches Institut der UniVersita¨tZu¨rich, Winterthurerstrasse 190, CH-8057 Zu¨rich, Switzerland Received February 8, 2002 Abstract: We report what is, to our knowledge, the first in vitro selection for catalytic activity based on catalytic turnover by using ribosome display, a method which does not involve living cells at any step. RTEM-â-lactamase was functionally displayed on ribosomes as a complex with its encoding mRNA. We designed and synthesized a mechanism-based inhibitor of â-lactamase, biotinylated ampicillin sulfone, appropriate for selection of catalytic activity of the ribosome-displayed â-lactamase. This derivative of ampicillin inactivated â-lactamase in a specific and irreversible manner. Under appropriate selection conditions, active RTEM-â-lactamase was enriched relative to an inactive point mutant over 100-fold per ribosome display selection cycle. Selection for binding, carried out with â-lactamase inhibitory protein (BLIP), gave results similar to selection with the suicide inhibitor, indicating that ribosome display is similarly efficient in catalytic activity and affinity selections. In the future, the capacity to select directly for enzymatic activity using an entirely in vitro process may allow for a significant increase in the explorable sequence space relative to existing strategies. Naturally occurring enzymes catalyze a wide variety of selection methods sample the entire library in a single experi- chemical reactions and are increasingly used in pharmaceutical, mental step. -
In Vivo Mrna Display Enables Large-Scale Proteomics by Next Generation Sequencing
In vivo mRNA display enables large-scale proteomics by next generation sequencing Panos Oikonomoua,b,c,1, Roberto Salatinob, and Saeed Tavazoiea,b,c,1 aDepartment of Biological Sciences, Columbia University, New York, NY 10027; bDepartment of Systems Biology, Columbia University, New York, NY 10032; and cDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, NY10032 Edited by Jack W. Szostak, Massachusetts General Hospital, Boston, MA, and approved August 25, 2020 (received for review February 11, 2020) Large-scale proteomic methods are essential for the functional between genotype and phenotype, whereby a protein or peptide characterization of proteins in their native cellular context. How- is linked to its encoding nucleic acid. For example, in phage ever, proteomics has lagged far behind genomic approaches in display, the nucleic acid encoding the capsid displayed peptide is scalability, standardization, and cost. Here, we introduce in vivo contained within the phage (33). The resulting collection of mRNA display, a technology that converts a variety of proteomics displayed peptides can be used for the in vitro characterization of applications into a DNA sequencing problem. In vivo-expressed protein interactions, protein engineering, and selection of human proteins are coupled with their encoding messenger RNAs antibody fragment libraries (34–36). Alternative in vitro methods (mRNAs) via a high-affinity stem-loop RNA binding domain inter- linking nucleotide information to phenotype include mRNA action, enabling high-throughput identification of proteins with display (37, 38), ribosome display (39), and yeast display (40). In high sensitivity and specificity by next generation DNA sequenc- the past decade, many of these technologies have been coupled ing. -
WO 2014/152006 A2 25 September 2014 (25.09.2014) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2014/152006 A2 25 September 2014 (25.09.2014) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, A61K 39/395 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (21) International Application Number: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, PCT/US20 14/026804 KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, (22) International Filing Date: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 13 March 2014 (13.03.2014) OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, (25) Filing Language: English TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (26) Publication Language: English ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 61/791,953 15 March 2013 (15.03.2013) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, (71) Applicant: INTRINSIC LIFESCIENCES, LLC UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, [US/US]; 505 Coast Boulevard South, Suite 408, La Jolla, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, California 92037 (US). -
WO 2018/144999 Al 09 August 2018 (09.08.2018) W ! P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/144999 Al 09 August 2018 (09.08.2018) W ! P O PCT (51) International Patent Classification: Lennart; c/o Orionis Biosciences NV, Rijvisschestraat 120, A61K 38/00 (2006.01) C07K 14/555 (2006.01) Zwijnaarde, B-9052 (BE). TAVERNIER, Jan; c/o Orionis A61K 38/21 (2006.01) C12N 15/09 (2006.01) Biosciences NV, Rijvisschestraat 120, Zwijnaarde, B-9052 C07K 14/52 (2006.01) (BE). (21) International Application Number: (74) Agent: ALTIERI, Stephen, L. et al; Morgan, Lewis & PCT/US2018/016857 Bockius LLP, 1111 Pennsylvania Avenue, NW, Washing ton, D.C. 20004 (US). (22) International Filing Date: 05 February 2018 (05.02.2018) (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (25) Filing Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, (26) Publication Language: English CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (30) Priority Data: HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, 62/454,992 06 February 2017 (06.02.2017) US KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (71) Applicants: ORIONIS BIOSCIENCES, INC. [US/US]; MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 275 Grove Street, Newton, MA 02466 (US). -
Improving Protein Therapeutics Through Quantitative Molecular Engineering Approaches and a Cell-Based Oral Delivery Platform
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2013 Improving Protein Therapeutics Through Quantitative Molecular Engineering Approaches and A Cell-Based Oral Delivery Platform Ting Wun Ng University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biomedical Commons Recommended Citation Ng, Ting Wun, "Improving Protein Therapeutics Through Quantitative Molecular Engineering Approaches and A Cell-Based Oral Delivery Platform" (2013). Publicly Accessible Penn Dissertations. 784. https://repository.upenn.edu/edissertations/784 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/784 For more information, please contact [email protected]. Improving Protein Therapeutics Through Quantitative Molecular Engineering Approaches and A Cell-Based Oral Delivery Platform Abstract Proteins, with their ability to perform a variety of highly specific biological functions, have emerged as an important class of therapeutics. However, to fully harness their therapeutic potential, proteins often need to be optimized by molecular engineering; therapeutic efficacy can be improved by modulating protein properties such as binding affinity/specificity, half-life, bioavailability, and immunogenicity. In this work, we first present an introductory example in which a mechanistic mathematical model was used to improve target selection for directed evolution of an aglycosylated Fc domain of an antibody to enhance -
EURL ECVAM Recommendation on Non-Animal-Derived Antibodies
EURL ECVAM Recommendation on Non-Animal-Derived Antibodies EUR 30185 EN Joint Research Centre This publication is a Science for Policy report by the Joint Research Centre (JRC), the European Commission’s science and knowledge service. It aims to provide evidence-based scientific support to the European policymaking process. The scientific output expressed does not imply a policy position of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of this publication. For information on the methodology and quality underlying the data used in this publication for which the source is neither Eurostat nor other Commission services, users should contact the referenced source. EURL ECVAM Recommendations The aim of a EURL ECVAM Recommendation is to provide the views of the EU Reference Laboratory for alternatives to animal testing (EURL ECVAM) on the scientific validity of alternative test methods, to advise on possible applications and implications, and to suggest follow-up activities to promote alternative methods and address knowledge gaps. During the development of its Recommendation, EURL ECVAM typically mandates the EURL ECVAM Scientific Advisory Committee (ESAC) to carry out an independent scientific peer review which is communicated as an ESAC Opinion and Working Group report. In addition, EURL ECVAM consults with other Commission services, EURL ECVAM’s advisory body for Preliminary Assessment of Regulatory Relevance (PARERE), the EURL ECVAM Stakeholder Forum (ESTAF) and with partner organisations of the International Collaboration on Alternative Test Methods (ICATM). Contact information European Commission, Joint Research Centre (JRC), Chemical Safety and Alternative Methods Unit (F3) Address: via E. -
Generation of Novel Intracellular Binding Reagents Based on the Human Γb-Crystallin Scaffold
Generation of novel intracellular binding reagents based on the human γB-crystallin scaffold Dissertation zur Erlangung des akademischen Grades doctor rerum naturalium (Dr. rer. nat.) vorgelegt der Naturwissenschaftlichen Fakultät I-Biowissenschaften der Martin-Luther-Universität Halle-Wittenberg Institut für Biochemie und Biotechnologie von Ewa Mirecka geboren am 17. Dezember 1976 in Gdynia, Polen Table of contents Table of contents 1. INTRODUCTION.........................................................................................................1 1.1 Monoclonal antibodies as a biomolecular scaffold..........................................................1 1.2 Binding molecules derived from non-immunoglobulin scaffolds.....................................3 1.2.1 Alternative protein scaffolds – general considerations............................................................ 3 1.2.2 Application of alternative binding molecules ........................................................................... 6 1.3 Affilin – novel binding molecules based on the human γB-crystallin scaffold................... 6 1.3.1 Human γB-crystallin as a molecular scaffold........................................................................... 6 1.3.2 Generation of a human γB-crystallin library and selection of first-generation Affilin molecules ................................................................................................................................ 8 1.4 Selection of binding proteins by phage display ...................................................................