Protein Binder (Probi) As a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution
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The Wnt Pathway Scaffold Protein Axin Promotes Signaling Specificity by Suppressing Competing Kinase Reactions
bioRxiv preprint doi: https://doi.org/10.1101/768242; this version posted September 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. The Wnt pathway scaffold protein Axin promotes signaling specificity by suppressing competing kinase reactions Maire Gavagan1,2, Erin Fagnan1,2, Elizabeth B. Speltz1, and Jesse G. Zalatan1,* 1Department of Chemistry, University of Washington, Seattle, WA 98195, USA 2These authors contributed equally to this work *Correspondence: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/768242; this version posted September 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 GSK3β is a multifunctional kinase that phosphorylates β-catenin in the Wnt signaling network and also acts on other protein targets in response to distinct cellular signals. To test the long-standing hypothesis that the scaffold protein Axin specifically accelerates β-catenin phosphorylation, we measured GSK3β reaction rates with multiple substrates in a minimal, biochemically-reconstituted system. We observed an unexpectedly small, ~2-fold Axin-mediated rate increase for the β-catenin reaction. The much larger effects reported previously may have arisen because Axin can rescue GSK3β from an inactive state that occurs only under highly specific conditions. -
CK1 Is Required for a Mitotic Checkpoint That Delays Cytokinesis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Current Biology 23, 1920–1926, October 7, 2013 ª2013 Elsevier Ltd All rights reserved http://dx.doi.org/10.1016/j.cub.2013.07.077 Report CK1 Is Required for a Mitotic Checkpoint that Delays Cytokinesis Alyssa E. Johnson,1 Jun-Song Chen,1 isoforms were detected, which collapsed into a discrete ladder and Kathleen L. Gould1,* upon phosphatase treatment (Figure 1A, lanes 1 and 2). These 1Department of Cell and Developmental Biology, Vanderbilt bands are ubiquitinated isoforms because they collapse into a University School of Medicine, Nashville, TN 37232, USA single band in the absence of dma1+ (Figure 1A, lane 4) and Dma1 is required for Sid4 ubiquitination [6]. In dma1D cells, a single slower-migrating form of Sid4 was detected, which Summary was collapsed by phosphatase treatment, indicating that Sid4 is phosphorylated in vivo (Figure 1A, lanes 3 and 4). In vivo Failure to accurately partition genetic material during cell radiolabeling experiments validated Sid4 as a phosphoprotein division causes aneuploidy and drives tumorigenesis [1]. and revealed that Sid4 is phosphorylated on serines and thre- Cell-cycle checkpoints safeguard cells from such catastro- onines (see Figures S1A–S1C available online). The constitu- phes by impeding cell-cycle progression when mistakes tive presence of an unmodified Sid4 isoform indicates that arise. FHA-RING E3 ligases, including human RNF8 [2] and only a subpopulation of Sid4 is modified (Figure 1A). Collec- CHFR [3] and fission yeast Dma1 [4], relay checkpoint signals tively, these data indicate that Sid4 is ubiquitinated and phos- by binding phosphorylated proteins via their FHA domains phorylated in vivo. -
Impact of Digestive Inflammatory Environment and Genipin
International Journal of Molecular Sciences Article Impact of Digestive Inflammatory Environment and Genipin Crosslinking on Immunomodulatory Capacity of Injectable Musculoskeletal Tissue Scaffold Colin Shortridge 1, Ehsan Akbari Fakhrabadi 2 , Leah M. Wuescher 3 , Randall G. Worth 3, Matthew W. Liberatore 2 and Eda Yildirim-Ayan 1,4,* 1 Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH 43606, USA; [email protected] 2 Department of Chemical Engineering, College of Engineering, University of Toledo, Toledo, OH 43606, USA; [email protected] (E.A.F.); [email protected] (M.W.L.) 3 Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH 43614, USA; [email protected] (L.M.W.); [email protected] (R.G.W.) 4 Department of Orthopaedic Surgery, University of Toledo Medical Center, Toledo, OH 43614, USA * Correspondence: [email protected]; Tel.: +1-419-530-8257; Fax: +1-419-530-8030 Abstract: The paracrine and autocrine processes of the host response play an integral role in the success of scaffold-based tissue regeneration. Recently, the immunomodulatory scaffolds have received huge attention for modulating inflammation around the host tissue through releasing anti- inflammatory cytokine. However, controlling the inflammation and providing a sustained release of anti-inflammatory cytokine from the scaffold in the digestive inflammatory environment are predicated upon a comprehensive understanding of three fundamental questions. (1) How does the Citation: Shortridge, C.; Akbari release rate of cytokine from the scaffold change in the digestive inflammatory environment? (2) Fakhrabadi, E.; Wuescher, L.M.; Can we prevent the premature scaffold degradation and burst release of the loaded cytokine in the Worth, R.G.; Liberatore, M.W.; digestive inflammatory environment? (3) How does the scaffold degradation prevention technique Yildirim-Ayan, E. -
A Deeply Glimpse Into Protein Fold Recognition
International Journal of Sciences Research Article (ISSN 2305-3925) Volume 2, Issue June 2013 http://www.ijSciences.com A Deep Glimpse into Protein Fold Recognition Ahmed Sharaf Eldin1, Taysir Hassan A. Soliman2, Mohammed Ebrahim Marie3, Marwa Mohamed M. Ghareeb4 1Information Systems Department, Faculty of Computers and Information, Helwan University, Cairo, Egypt 2Supervisor of Information Systems Department, Faculty of Computers and Information, Assiut University, Assiut, Egypt 3Information Systems Department, Faculty of Computers and Information, Helwan University, Cairo, Egypt 4Assistant Lecturer, Information Systems Department, Modern Academy, Cairo, Egypt Abstract: The rapid growth in genomic and proteomic data causes a lot of challenges that are raised up and need powerful solutions. It is worth noting that UniProtKB/TrEMBL database Release 28-Nov-2012 contains 28,395,832 protein sequence entries, while the number of stored protein structures in Protein Data Bank (PDB, 4- 12-2012) is 65,643. Thus, the need of extracting structural information through computational analysis of protein sequences has become very important, especially, the prediction of the fold of a query protein from its primary sequence has become very challenging. The traditional computational methods are not powerful enough to address theses challenges. Researchers have examined the use of a lot of techniques such as neural networks, Monte Carlo, support vector machine and data mining techniques. This paper puts a spot on this growing field and covers the main approaches and perspectives to handle this problem. Keywords: Protein fold recognition, Neural network, Evolutionary algorithms, Meta Servers. research has been conducted towards this goal in the I. INTRODUCTION late years. Especially, the prediction of the fold of a Proteins transport oxygen to cells, prevent harmful query protein from its primary sequence has become infections, convert chemical energy into mechanical very challenging. -
Crosstalk Between Casein Kinase II and Ste20-Related Kinase Nak1
University of Massachusetts Medical School eScholarship@UMMS GSBS Student Publications Graduate School of Biomedical Sciences 2013-03-05 Crosstalk between casein kinase II and Ste20-related kinase Nak1 Lubos Cipak University of Vienna Et al. Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_sp Part of the Biochemistry Commons, Cell Biology Commons, Cellular and Molecular Physiology Commons, and the Molecular Biology Commons Repository Citation Cipak L, Gupta S, Rajovic I, Jin Q, Anrather D, Ammerer G, McCollum D, Gregan J. (2013). Crosstalk between casein kinase II and Ste20-related kinase Nak1. GSBS Student Publications. https://doi.org/ 10.4161/cc.24095. Retrieved from https://escholarship.umassmed.edu/gsbs_sp/1850 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Student Publications by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. EXTRA VIEW Cell Cycle 12:6, 884–888; March 15, 2013; © 2013 Landes Bioscience Crosstalk between casein kinase II and Ste20-related kinase Nak1 Lubos Cipak,1,2,† Sneha Gupta,3,† Iva Rajovic,1 Quan-Wen Jin,3,4 Dorothea Anrather,1 Gustav Ammerer,1 Dannel McCollum3,* and Juraj Gregan1,5,* 1Max F. Perutz Laboratories; Department of Chromosome Biology; University of Vienna; Vienna, Austria; 2Cancer Research Institute; Slovak Academy of Sciences; Bratislava, Slovak Republic; 3Department of Microbiology and Physiological Systems and Program in Cell Dynamics; University of Massachusetts Medical School; Worcester, MA USA; 4Department of Biological Medicine; School of Life Sciences; Xiamen University; Xiamen, China; 5Department of Genetics; Comenius University; Bratislava, Slovak Republic †These authors contributed equally to this work. -
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. -
Electrical Synaptic Transmission Requires a Postsynaptic Scaffolding Protein
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.03.410696; this version posted December 4, 2020. 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 4.0 International license. TITLE: Electrical synaptic transmission requires a postsynaptic scaffolding protein Abagael M. Lasseigne1*, Fabio A. Echeverry2*, Sundas Ijaz2*, Jennifer Carlisle Michel1*, E. Anne Martin1, Audrey J. Marsh1, Elisa Trujillo1, Kurt C. Marsden3, Alberto E. Pereda2#, Adam C. Miller1#@ * denotes co-first author # denotes co-corresponding author @ denotes lead contact Affiliations: 1 Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA 2 Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA 3 Department of Biological Sciences, NC State University, Raleigh, NC 27695, USA Correspondence: [email protected] [email protected] Keywords: gap junction; connexin; ZO1 ZO-1; synaptic development; electrical coupling 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.03.410696; this version posted December 4, 2020. 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 4.0 International license. SUMMARY Electrical synaptic transmission relies on neuronal gap junctions containing channels constructed by Connexins. While at chemical synapses neurotransmitter-gated ion channels are critically supported by scaffolding proteins, it is unknown if channels at electrical synapses require similar scaffold support. -
Modeling and Predicting Super-Secondary Structures of Transmembrane Beta-Barrel Proteins Thuong Van Du Tran
Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins Thuong van Du Tran To cite this version: Thuong van Du Tran. Modeling and predicting super-secondary structures of transmembrane beta-barrel proteins. Bioinformatics [q-bio.QM]. Ecole Polytechnique X, 2011. English. NNT : 2011EPXX0104. pastel-00711285 HAL Id: pastel-00711285 https://pastel.archives-ouvertes.fr/pastel-00711285 Submitted on 23 Jun 2012 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. THESE` pr´esent´ee pour obtenir le grade de DOCTEUR DE L’ECOLE´ POLYTECHNIQUE Sp´ecialit´e: INFORMATIQUE par Thuong Van Du TRAN Titre de la th`ese: Modeling and Predicting Super-secondary Structures of Transmembrane β-barrel Proteins Soutenue le 7 d´ecembre 2011 devant le jury compos´ede: MM. Laurent MOUCHARD Rapporteurs Mikhail A. ROYTBERG MM. Gregory KUCHEROV Examinateurs Mireille REGNIER M. Jean-Marc STEYAERT Directeur Laboratoire d’Informatique UMR X-CNRS 7161 Ecole´ Polytechnique, 91128 Plaiseau CEDEX, FRANCE Composed with LATEX !c Thuong Van Du Tran. All rights reserved. Contents Introduction 1 1Fundamentalreviewofproteins 5 1.1 Introduction................................... 5 1.2 Proteins..................................... 5 1.2.1 Aminoacids............................... 5 1.2.2 Properties of amino acids . -
Final List of NGF Publications (2001-2007)
Final List of NGF Publications (2001-2007) (1) Abahuni N, Gispert S, Bauer P, Riess O, Krüger R, Becker T, Auburger G. Mitochondrial translation initiation factor 3 gene polymorphism associated with Parkinson's disease. Neurosci Lett. 2007 Mar 6;414(2):126-9. (2) Abarca C, Albrecht U, Spanagel R. Cocaine sensitization and reward are influenced by circadian genes and rhythm. Proc. Natl. Acad. Sci. USA 2002; 99, 9026-9030 (3) Abdelaziz AI, Segaric J, Bartsch H, Petzhold D, Schlegel WP, Kott M, Seefeldt I, Klose J, Bader M, Haase H, Morano I. Functional characterization of the human atrial essential myosin light chain (hALC-1) in a transgenic rat model. J Mol Med. 2004 Apr;82(4):265-74. (4) Abdollahi A, Hahnfeldt P, Maercker C, Grone HJ, Debus J, Ansorge W, Folkman J, Hlatky L, Huber PE. Endostatin's antiangiogenic signaling network. Mol Cell. 2004 Mar 12;13(5):649-63. (5) Abe K, Fuchs H, Lisse T, Hans W, de Angelis MH. New ENU-induced semidominant mutation, Ali18, causes inflammatory arthritis, dermatitis, and osteoporosis in the mouse. Mamm Genome. 2006 Sep 8; [Epub ahead of print] (6) Abe M, Westermann F, Nakagawara A, Takato T, Schwab M, Ushijima T. Marked and independent prognostic significance of the CpG island methylator phenotype in neuroblastomas. Cancer Lett. 2007 Mar 18;247(2):253- 258. (7) Abeysinghe SS, Chuzhanova N, Krawczak M, Ball EV, Cooper DN. Translocation and gross deletion breakpoints in human inherited disease and cancer I. Nucleotide composition and recombination-associated motifs. Hum Mutat. 2003; 22:229-244 (8) Abeysinghe SS, Stenson PD, Krawczak M, Cooper DN. -
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 ................................................................... -
A Tri-Gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition
A Tri-Gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition Author Paliwal, Kuldip K, Sharma, Alok, Lyons, James, Dehzangi, Abdollah Published 2014 Journal Title IEEE Transactions on NanoBioscience DOI https://doi.org/10.1109/TNB.2013.2296050 Copyright Statement © 2014 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. Downloaded from http://hdl.handle.net/10072/67288 Griffith Research Online https://research-repository.griffith.edu.au A Tri-gram Based Feature Extraction Technique Using Linear Probabilities of Position Specific Scoring Matrix for Protein Fold Recognition Kuldip K. Paliwal, Member, IEEE, Alok Sharma, Member, IEEE, James Lyons, Abdollah Dhezangi, Member, IEEE protein structure in a reasonable amount of time. Abstract— In biological sciences, the deciphering of a three The prime objective of protein fold recognition is to find the dimensional structure of a protein sequence is considered to be an fold of a protein sequence. Assigning of protein fold to a important and challenging task. The identification of protein folds protein sequence is a transitional stage in the recognition of from primary protein sequences is an intermediate step in three dimensional structure of a protein. The protein fold discovering the three dimensional structure of a protein. This can be done by utilizing feature extraction technique to accurately recognition broadly covers feature extraction task and extract all the relevant information followed by employing a classification task.