Learning the Molecular Grammar of Protein Condensates from Sequence
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Uniprot at EMBL-EBI's Role in CTTV
Barbara P. Palka, Daniel Gonzalez, Edd Turner, Xavier Watkins, Maria J. Martin, Claire O’Donovan European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK UniProt at EMBL-EBI’s role in CTTV: contributing to improved disease knowledge Introduction The mission of UniProt is to provide the scientific community with a The Centre for Therapeutic Target Validation (CTTV) comprehensive, high quality and freely accessible resource of launched in Dec 2015 a new web platform for life- protein sequence and functional information. science researchers that helps them identify The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of therapeutic targets for new and repurposed medicines. functional information on proteins, with accurate, consistent and rich CTTV is a public-private initiative to generate evidence on the annotation. As much annotation information as possible is added to each validity of therapeutic targets based on genome-scale experiments UniProtKB record and this includes widely accepted biological ontologies, and analysis. CTTV is working to create an R&D framework that classifications and cross-references, and clear indications of the quality of applies to a wide range of human diseases, and is committed to annotation in the form of evidence attribution of experimental and sharing its data openly with the scientific community. CTTV brings computational data. together expertise from four complementary institutions: GSK, Biogen, EMBL-EBI and Wellcome Trust Sanger Institute. UniProt’s disease expert curation Q5VWK5 (IL23R_HUMAN) This section provides information on the disease(s) associated with genetic variations in a given protein. The information is extracted from the scientific literature and diseases that are also described in the OMIM database are represented with a controlled vocabulary. -
Webnetcoffee
Hu et al. BMC Bioinformatics (2018) 19:422 https://doi.org/10.1186/s12859-018-2443-4 SOFTWARE Open Access WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks Jialu Hu1,2, Yiqun Gao1, Junhao He1, Yan Zheng1 and Xuequn Shang1* Abstract Background: The discovery of functionally conserved proteins is a tough and important task in system biology. Global network alignment provides a systematic framework to search for these proteins from multiple protein-protein interaction (PPI) networks. Although there exist many web servers for network alignment, no one allows to perform global multiple network alignment tasks on users’ test datasets. Results: Here, we developed a web server WebNetcoffee based on the algorithm of NetCoffee to search for a global network alignment from multiple networks. To build a series of online test datasets, we manually collected 218,339 proteins, 4,009,541 interactions and many other associated protein annotations from several public databases. All these datasets and alignment results are available for download, which can support users to perform algorithm comparison and downstream analyses. Conclusion: WebNetCoffee provides a versatile, interactive and user-friendly interface for easily running alignment tasks on both online datasets and users’ test datasets, managing submitted jobs and visualizing the alignment results through a web browser. Additionally, our web server also facilitates graphical visualization of induced subnetworks for a given protein and its neighborhood. To the best of our knowledge, it is the first web server that facilitates the performing of global alignment for multiple PPI networks. Availability: http://www.nwpu-bioinformatics.com/WebNetCoffee Keywords: Multiple network alignment, Webserver, PPI networks, Protein databases, Gene ontology Background tools [7–10] have been developed to understand molec- Proteins are involved in almost all life processes. -
The Biogrid Interaction Database
D470–D478 Nucleic Acids Research, 2015, Vol. 43, Database issue Published online 26 November 2014 doi: 10.1093/nar/gku1204 The BioGRID interaction database: 2015 update Andrew Chatr-aryamontri1, Bobby-Joe Breitkreutz2, Rose Oughtred3, Lorrie Boucher2, Sven Heinicke3, Daici Chen1, Chris Stark2, Ashton Breitkreutz2, Nadine Kolas2, Lara O’Donnell2, Teresa Reguly2, Julie Nixon4, Lindsay Ramage4, Andrew Winter4, Adnane Sellam5, Christie Chang3, Jodi Hirschman3, Chandra Theesfeld3, Jennifer Rust3, Michael S. Livstone3, Kara Dolinski3 and Mike Tyers1,2,4,* 1Institute for Research in Immunology and Cancer, Universite´ de Montreal,´ Montreal,´ Quebec H3C 3J7, Canada, 2The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada, 3Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, 4School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK and 5Centre Hospitalier de l’UniversiteLaval´ (CHUL), Quebec,´ Quebec´ G1V 4G2, Canada Received September 26, 2014; Revised November 4, 2014; Accepted November 5, 2014 ABSTRACT semi-automated text-mining approaches, and to en- hance curation quality control. The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org) is an open access database that houses genetic and protein in- INTRODUCTION teractions curated from the primary biomedical lit- Massive increases in high-throughput DNA sequencing erature for all major model organism species and technologies (1) have enabled an unprecedented level of humans. As of September 2014, the BioGRID con- genome annotation for many hundreds of species (2–6), tains 749 912 interactions as drawn from 43 149 pub- which has led to tremendous progress in the understand- lications that represent 30 model organisms. -
Unpacking the Origins of In-Cell Crowding Kim A
COMMENTARY COMMENTARY Unpacking the origins of in-cell crowding Kim A. Sharpa,1 The living cell, the fundamental unit of biological meaning that a large excluded volume is a property of organization, was discovered in its apparent simplicity all macromolecules. An extensive review covers much by van Leeuwenhoek in the 17th century. Scientists of the subsequent literature (5). Of course, solutes can since then have continued to unpack nested levels cause nonideal behavior through a second mecha- of amazingly complex cellular structure and organiza- nism, strong intermolecular interactions such as elec- tion, right down to the atomic level. However, one of trostatic and hydrophobic effects. Although crowding the cell’s simplest properties is not yet understood, is now often used as a synonym for any effects of con- perhaps even misunderstood. The interior of the cell centrated solutes, for the purpose of this commentary I contains a high concentration of dissolved solutes, prin- will take crowding to refer to the excluded volume cipally ions, metabolites, proteins, and RNA. In a word, effects, as originally defined (3, 4), because disentan- it is crowded in there. Estimates range from 30% to 40% gling size effects and interaction effects is precisely by volume occupied by protein and RNA solutes, where the advances of Smith et al. (2) lie. I also discuss depending on the cell type and compartment (1). Bio- effects on equilibria only. Given our recently revised chemists and biophysicists have long been concerned understanding of equilibrium effects, it seems prema- that these high concentrations impart significantly non- ture to discuss the more complex effects of crowding ideal solution behavior. -
How Can Biochemical Reactions Within Cells Differ from Those in Test Tubes?
ß 2015. Published by The Company of Biologists Ltd | Journal of Cell Science (2015) 000, 000–000 doi:10.1242/jcs.170183 CORRECTION How can biochemical reactions within cells differ from those in test tubes? Allen P. Minton There was an error published in J. Cell Sci. 119, 2863-2869. There is a typographical error in equation (2). The right-hand side of this equation should read ‘DFI,AB 2 (DFI,A+D FI,B)’. JCS and the author apologise for any confusion that this error might have caused. 1 Journal of Cell Science JCS170183.3d 22/2/15 09:24:29 The Charlesworth Group, Wakefield +44(0)1924 369598 - Rev 9.0.225/W (Oct 13 2006) Commentary 2863 How can biochemical reactions within cells differ from those in test tubes? Allen P. Minton Section on Physical Biochemistry, Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA e-mail: [email protected] Accepted 23 May 2006 Journal of Cell Science 119, 2863-2869 Published by The Company of Biologists 2006 doi:10.1242/jcs.03063 Summary Nonspecific interactions between individual macro- interactions tend to enhance the rate and extent of molecules and their immediate surroundings (‘background macromolecular associations in solution, whereas interactions’) within a medium as heterogeneous and predominately attractive background interactions tend to highly volume occupied as the interior of a living cell can enhance the tendency of macromolecules to associate on greatly influence the equilibria and rates of reactions in adsorbing surfaces. -
Machine Learning Models for Predicting Protein Condensate Formation from Sequence Determinants and Embeddings
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.26.354753; this version posted October 26, 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-ND 4.0 International license. Machine learning models for predicting protein condensate formation from sequence determinants and embeddings Kadi L. Saar,1;2;† Alexey S. Morgunov,1;3;† Runzhang Qi,1 William E. Arter,1 Georg Krainer,1 Alpha A. Lee2 & Tuomas P. J. Knowles1;2;∗ 1 Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK 2 Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, UK 3 Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge CB1 8DH, UK † These authors contributed equally ∗ To whom correspondence should be addressed: [email protected] Abstract Intracellular phase separation of proteins into biomolecular condensates is increasingly recognised as an important phenomenon for cellular compartmentalisation and regulation of biological function. Different hypotheses about the parameters that determine the ten- dency of proteins to form condensates have been proposed with some of them probed ex- perimentally through the use of constructs generated by sequence alterations. To broaden the scope of these observations, here, we established an in silico strategy for understanding on a global level the associations between protein sequence and condensate formation, and used this information to construct machine learning classifiers for predicting liquid–liquid phase separation (LLPS) from protein sequence. -
Effects of Macromolecular Crowding on Gene Expression Studied In
Effects of macromolecular crowding on gene expression studied in protocell models The work described in this thesis was supported by a European Research Council (ERC), Advanced Grant (246812 Intercom) and a VICI grant from the Netherlands Organisation for Scientific Research (NWO) ISBN: 978-94-6295-151-8 Cover design: Denis Arslanov and Ekaterina Sokolova Printed & Lay Out by: Proefschriftmaken.nl || Uitgeverij BOXPress Published by: Uitgeverij BOXPress, ’s-Hertogenbosch Effects of macromolecular crowding on gene expression studied in protocell models Proefschrift ter verkrijging van de graad van doctor aan de Radboud Universiteit Nijmegen op gezag van de rector magnificus prof. dr. Th.L.M. Engelen, volgens besluit van het college van decanen in het openbaar te verdedigen op dinsdag 12 mei 2015 om 14.30 uur precies door Ekaterina Alexandrovna Sokolova geboren op 30 augustus 1987 te Angren (Uzbekistan) Promotor: Prof. dr. W. T. S. Huck Manuscriptcommissie: Prof. dr. ir. J. C. M. van Hest (voorzitter) Prof. dr. H. N. W. Lekkerkerker (Universiteit Utrecht) Dr. V. Noireaux (University of Minnesota, VS) Effects of macromolecular crowding on gene expression studied in protocell models Doctoral Thesis to obtain the degree of doctor from Radboud University Nijmegen on the authority of the Rector Magnificus prof. dr. Th.L.M. Engelen, according to the decision of the Council of Deans to be defended in public on Tuesday, May 12, 2015 at 14.30 hours by Ekaterina Alexandrovna Sokolova Born on August 30, 1987 in Angren (Uzbekistan) Supervisor: Prof. dr. W. T. S. Huck Doctoral Thesis Committee: Prof. dr. ir. J. C. M. van Hest (chairman) Prof. -
The Ubiquitin Proteasome System in Neuromuscular Disorders: Moving Beyond Movement
International Journal of Molecular Sciences Review The Ubiquitin Proteasome System in Neuromuscular Disorders: Moving Beyond Movement 1, , 2, 3,4 Sara Bachiller * y , Isabel M. Alonso-Bellido y , Luis Miguel Real , Eva María Pérez-Villegas 5 , José Luis Venero 2 , Tomas Deierborg 1 , José Ángel Armengol 5 and Rocío Ruiz 2 1 Experimental Neuroinflammation Laboratory, Department of Experimental Medical Science, Lund University, Sölvegatan 19, 221 84 Lund, Sweden; [email protected] 2 Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Sevilla/Instituto de Biomedicina de Sevilla-Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41012 Sevilla, Spain; [email protected] (I.M.A.-B.); [email protected] (J.L.V.); [email protected] (R.R.) 3 Unidad Clínica de Enfermedades Infecciosas, Hospital Universitario de Valme, 41014 Sevilla, Spain; [email protected] 4 Departamento de Especialidades Quirúrgicas, Bioquímica e Inmunología, Facultad de Medicina, 29071 Universidad de Málaga, Spain 5 Departamento de Fisiología, Anatomía y Biología Celular, Universidad Pablo de Olavide, 41013 Sevilla, Spain; [email protected] (E.M.P.-V.); [email protected] (J.Á.A.) * Correspondence: [email protected] These authors contributed equally to the work. y Received: 14 July 2020; Accepted: 31 August 2020; Published: 3 September 2020 Abstract: Neuromuscular disorders (NMDs) affect 1 in 3000 people worldwide. There are more than 150 different types of NMDs, where the common feature is the loss of muscle strength. These disorders are classified according to their neuroanatomical location, as motor neuron diseases, peripheral nerve diseases, neuromuscular junction diseases, and muscle diseases. Over the years, numerous studies have pointed to protein homeostasis as a crucial factor in the development of these fatal diseases. -
The Uniprot Knowledgebase BLAST
Introduction to bioinformatics The UniProt Knowledgebase BLAST UniProtKB Basic Local Alignment Search Tool A CRITICAL GUIDE 1 Version: 1 August 2018 A Critical Guide to BLAST BLAST Overview This Critical Guide provides an overview of the BLAST similarity search tool, Briefly examining the underlying algorithm and its rise to popularity. Several WeB-based and stand-alone implementations are reviewed, and key features of typical search results are discussed. Teaching Goals & Learning Outcomes This Guide introduces concepts and theories emBodied in the sequence database search tool, BLAST, and examines features of search outputs important for understanding and interpreting BLAST results. On reading this Guide, you will Be aBle to: • search a variety of Web-based sequence databases with different query sequences, and alter search parameters; • explain a range of typical search parameters, and the likely impacts on search outputs of changing them; • analyse the information conveyed in search outputs and infer the significance of reported matches; • examine and investigate the annotations of reported matches, and their provenance; and • compare the outputs of different BLAST implementations and evaluate the implications of any differences. finding short words – k-tuples – common to the sequences Being 1 Introduction compared, and using heuristics to join those closest to each other, including the short mis-matched regions Between them. BLAST4 was the second major example of this type of algorithm, From the advent of the first molecular sequence repositories in and rapidly exceeded the popularity of FastA, owing to its efficiency the 1980s, tools for searching dataBases Became essential. DataBase searching is essentially a ‘pairwise alignment’ proBlem, in which the and Built-in statistics. -
Aggresomal Sequestration and STUB1-Mediated Ubiquitylation During Mammalian Proteaphagy of Inhibited Proteasomes
Aggresomal sequestration and STUB1-mediated ubiquitylation during mammalian proteaphagy of inhibited proteasomes Won Hoon Choia,b, Yejin Yuna,b, Seoyoung Parka,c, Jun Hyoung Jeona,b, Jeeyoung Leea,b, Jung Hoon Leea,c, Su-A Yangd, Nak-Kyoon Kime, Chan Hoon Jungb, Yong Tae Kwonb, Dohyun Hanf, Sang Min Lime, and Min Jae Leea,b,c,1 aDepartment of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 03080 Seoul, Korea; bDepartment of Biomedical Sciences, Seoul National University Graduate School, 03080 Seoul, Korea; cNeuroscience Research Institute, Seoul National University College of Medicine, 03080 Seoul, Korea; dScience Division, Tomocube, 34109 Daejeon, Korea; eConvergence Research Center for Diagnosis, Korea Institute of Science and Technology, 02792 Seoul, Korea; and fProteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, 03080 Seoul, Korea Edited by Richard D. Vierstra, Washington University in St. Louis, St. Louis, MO, and approved July 1, 2020 (received for review November 18, 2019) The 26S proteasome, a self-compartmentalized protease complex, additional LC3-interacting region; the target cargoes can be plays a crucial role in protein quality control. Multiple levels of docked onto phosphatidylethanolamine-modified LC3 (LC3-II) regulatory systems modulate proteasomal activity for substrate on the expanding phagophore membrane, enveloped by an hydrolysis. However, the destruction mechanism of mammalian autophagosome, and eventually degraded in the autolysosomes. proteasomes is poorly understood. We found that inhibited pro- Notably, the enzymatic cascade attaching the lipid moiety at the teasomes are sequestered into the insoluble aggresome via C-terminal glycine of the cleaved LC3 protein in autophagy re- HDAC6- and dynein-mediated transport. -
RTL8 Promotes Nuclear Localization of UBQLN2 to Subnuclear Compartments Associated with Protein Quality Control
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.21.440788; this version posted April 22, 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. Title: RTL8 promotes nuclear localization of UBQLN2 to subnuclear compartments associated with protein quality control Harihar Milaganur Mohan1,2, Amit Pithadia1, Hanna Trzeciakiewicz1, Emily V. Crowley1, Regina Pacitto1 Nathaniel Safren1,3, Chengxin Zhang4, Xiaogen Zhou4, Yang Zhang4, Venkatesha Basrur5, Henry L. Paulson1,*, Lisa M. Sharkey1,* 1. Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200 2. Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109- 2200 3. Present address: Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 4. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2200 5. Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109. *Corresponding authors: Henry Paulson: Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200; [email protected]; Tel. (734) 615-5632; Fax. (734) 615-5655 Lisa M Sharkey: Department of Neurology, University of Michigan, Ann Arbor, MI 48109-2200; [email protected]; Tel. (734) 763-3496; Fax (734) 615-5655 Keywords: Ubiquilin, UBQLN2, RTL8, Nuclear Protein Quality Control, Ubiquitin Proteasome System Declarations Funding: This work was supported by NIH 9R01NS096785-06, 1P30AG053760-01, The Amyotrophic Lateral Sclerosis Foundation and the UM Protein Folding Disease Initiative. Conflicts of interest/Competing interests: None declared Availability of data and material: • The authors confirm that the data supporting the findings in this are available within the article, at repository links provided within the article, and within its supplementary files. -
Deciphering the Molecular Profile of Plaques, Memory Decline And
ORIGINAL RESEARCH ARTICLE published: 16 April 2014 AGING NEUROSCIENCE doi: 10.3389/fnagi.2014.00075 Deciphering the molecular profile of plaques, memory decline and neuron loss in two mouse models for Alzheimer’s disease by deep sequencing Yvonne Bouter 1†,Tim Kacprowski 2,3†, Robert Weissmann4, Katharina Dietrich1, Henning Borgers 1, Andreas Brauß1, Christian Sperling 4, Oliver Wirths 1, Mario Albrecht 2,5, Lars R. Jensen4, Andreas W. Kuss 4* andThomas A. Bayer 1* 1 Division of Molecular Psychiatry, Georg-August-University Goettingen, University Medicine Goettingen, Goettingen, Germany 2 Department of Bioinformatics, Institute of Biometrics and Medical Informatics, University Medicine Greifswald, Greifswald, Germany 3 Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany 4 Human Molecular Genetics, Department for Human Genetics of the Institute for Genetics and Functional Genomics, Institute for Human Genetics, University Medicine Greifswald, Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany 5 Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria Edited by: One of the central research questions on the etiology of Alzheimer’s disease (AD) is the Isidro Ferrer, University of Barcelona, elucidation of the molecular signatures triggered by the amyloid cascade of pathological Spain events. Next-generation sequencing allows the identification of genes involved in disease Reviewed by: Isidro Ferrer, University of Barcelona, processes in an unbiased manner. We have combined this technique with the analysis of Spain two AD mouse models: (1) The 5XFAD model develops early plaque formation, intraneu- Dietmar R. Thal, University of Ulm, ronal Ab aggregation, neuron loss, and behavioral deficits. (2)TheTg4–42 model expresses Germany N-truncated Ab4–42 and develops neuron loss and behavioral deficits albeit without plaque *Correspondence: formation.