The determinants of cross-seeding of protein aggregation: a Multiple TANGO

Intrinsic and extrinsic determinants of protein folding, aggregation and abundance

Author(s): Reshmi Ramakrishnan
Published in: 2020
Publisher: KU Leuven

PROTEIN AGGREGATION AS A NEW STRATEGY TO COMBAT GRAM NEGATIVE BACTERIA : PROTEÏNEAGGREGATIE ALS EEN NIEUWE STRATEGIE OM BACTERIËN TE BESTRIJDEN

Author(s): Khodaparast, Ladan
Published in: Issue 2, 2017
Publisher: KU Leuven

Aggregation as a mechanism for p53 oncogenic transformation: clinical relevance and new tools for its study : Aggregatie als een mechanisme voor p53-gemedieerde oncogene transformatie: klinische relevantie en nieuwe manieren om dit te bestuderen.

Author(s): Saiz Rubio, Mirian
Published in: Issue 1, 2017
Publisher: KU Leuven

Targeting protein aggregation during cancer development

Author(s): Evelyne Naus
Published in: 2019
Publisher: KU Leuven

Processing Induced Changes in Food Proteins: Amyloid Formation during Boiling of Hen Egg White

Author(s): Margarita Monge-Morera, Marlies A. Lambrecht, Lomme J. Deleu, Rodrigo Gallardo, Nikolaos N. Louros, Matthias De Vleeschouwer, Frederic Rousseau, Joost Schymkowitz, Jan A. Delcour
Published in: Biomacromolecules, Issue 21/6, 2020, Page(s) 2218-2228, ISSN 1525-7797
Publisher: American Chemical Society
DOI: 10.1021/acs.biomac.0c00186

Nuclear inclusion bodies of mutant and wild-type p53 in cancer: a hallmark of p53 inactivation and proteostasis remodelling by p53 aggregation

Author(s): Frederik De Smet, Mirian Saiz Rubio, Daphne Hompes, Evelyne Naus, Greet De Baets, Tobias Langenberg, Mark S Hipp, Bert Houben, Filip Claes, Sarah Charbonneau, Javier Delgado Blanco, Stephane Plaisance, Shakti Ramkissoon, Lori Ramkissoon, Colinda Simons, Piet van den Brandt, Matty Weijenberg, Manon Van England, Sandrina Lambrechts, Frederic Amant, André D'Hoore, Keith L Ligon, Xavier Sagaert, Joos
Published in: The Journal of Pathology, Issue 242/1, 2017, Page(s) 24-38, ISSN 0022-3417
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/path.4872

Prediction and Reduction of the Aggregation of Monoclonal Antibodies

Author(s): Rob van der Kant, Anne R. Karow-Zwick, Joost Van Durme, Michaela Blech, Rodrigo Gallardo, Daniel Seeliger, Kerstin Aßfalg, Pieter Baatsen, Griet Compernolle, Ann Gils, Joey M. Studts, Patrick Schulz, Patrick Garidel, Joost Schymkowitz, Frederic Rousseau
Published in: Journal of Molecular Biology, Issue 429/8, 2017, Page(s) 1244-1261, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2017.03.014

Sequence-specific protein aggregation generates defined protein knockdowns in plants

Author(s): Camilla Betti, Isabelle Vanhoutte, Silvie Coutuer, Riet Maria De Rycke, Kiril Mishev, Marnik Vuylsteke, Stijn Aesaert, Debbie Rombaut, Rodrigo Gallardo, Frederik De Smet, Jie Xu, Mieke Van Lijsebettens, Frank Van Breusegem, Dirk Inzé, Frederic Rousseau, Joost Schymkowitz, Eugenia Russinova
Published in: Plant Physiology, 2016, Page(s) pp.00335.2016, ISSN 0032-0889
Publisher: American Society of Plant Biologists
DOI: 10.1104/pp.16.00335

Alzheimer’s-Causing Mutations Shift Aβ Length by Destabilizing γ-Secretase-Aβn Interactions

Author(s): Maria Szaruga, Bogdan Munteanu, Sam Lismont, Sarah Veugelen, Katrien Horré, Marc Mercken, Takaomi C. Saido, Natalie S. Ryan, Tatjana De Vos, Savvas N. Savvides, Rodrigo Gallardo, Joost Schymkowitz, Frederic Rousseau, Nick C. Fox, Carsten Hopf, Bart De Strooper, Lucía Chávez-Gutiérrez
Published in: Cell, Issue 170/3, 2017, Page(s) 443-456.e14, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2017.07.004

Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics

Author(s): Steven Boeynaems, Elke Bogaert, Denes Kovacs, Albert Konijnenberg, Evy Timmerman, Alex Volkov, Mainak Guharoy, Mathias De Decker, Tom Jaspers, Veronica H. Ryan, Abigail M. Janke, Pieter Baatsen, Thomas Vercruysse, Regina-Maria Kolaitis, Dirk Daelemans, J. Paul Taylor, Nancy Kedersha, Paul Anderson, Francis Impens, Frank Sobott, Joost Schymkowitz, Frederic Rousseau, Nicolas L. Fawzi, Wim Robberecht
Published in: Molecular Cell, Issue 65/6, 2017, Page(s) 1044-1055.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/J.MOLCEL.2017.02.013

Structural hot spots for the solubility of globular proteins

Author(s): Ashok Ganesan, Aleksandra Siekierska, Jacinte Beerten, Marijke Brams, Joost Van Durme, Greet De Baets, Rob Van der Kant, Rodrigo Gallardo, Meine Ramakers, Tobias Langenberg, Hannah Wilkinson, Frederik De Smet, Chris Ulens, Frederic Rousseau, Joost Schymkowitz
Published in: Nature Communications, Issue 7, 2016, Page(s) 10816, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms10816

Solubis: a webserver to reduce protein aggregation through mutation

Author(s): Joost Van Durme, Greet De Baets, Rob Van Der Kant, Meine Ramakers, Ashok Ganesan, Hannah Wilkinson, Rodrigo Gallardo, Frederic Rousseau, Joost Schymkowitz
Published in: Protein Engineering Design and Selection, Issue 29/8, 2016, Page(s) 285-289, ISSN 1741-0126
Publisher: Oxford University Press
DOI: 10.1093/protein/gzw019

De novo design of a biologically active amyloid

Author(s): Rodrigo Gallardo, Meine Ramakers, Frederik De Smet, Filip Claes, Ladan Khodaparast, Laleh Khodaparast, José R. Couceiro, Tobias Langenberg, Maxime Siemons, Sofie Nyström, Laurence J. Young, Romain F. Laine, Lydia Young, Enrico Radaelli, Iryna Benilova, Manoj Kumar, An Staes, Matyas Desager, Manu Beerens, Petra Vandervoort, Aernout Luttun, Kris Gevaert, Guy Bormans, Mieke Dewerchin, Johan Van Eld
Published in: Science, Issue 354/6313, 2016, Page(s) aah4949, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aah4949

WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides

Author(s): Nikolaos Louros, Katerina Konstantoulea, Matthias De Vleeschouwer, Meine Ramakers, Joost Schymkowitz, Frederic Rousseau
Published in: Nucleic Acids Research, Issue 48/D1, 2019, Page(s) D389-D393, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz758

Adaption of human antibody λ and κ light chain architectures to CDR repertoires

Author(s): Rob van der Kant, Joschka Bauer, Anne R Karow-Zwick, Sebastian Kube, Patrick Garidel, Michaela Blech, Frederic Rousseau, Joost Schymkowitz
Published in: Protein Engineering, Design and Selection, Issue 32/3, 2019, Page(s) 109-127, ISSN 1741-0126
Publisher: Oxford University Press
DOI: 10.1093/protein/gzz012

Protein Homeostasis Database: protein quality control in E.coli

Author(s): Reshmi Ramakrishnan, Bert Houben, Łukasz Kreft, Alexander Botzki, Joost Schymkowitz, Frederic Rousseau
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz628

Differential proteostatic regulation of insoluble and abundant proteins

Author(s): Reshmi Ramakrishnan, Bert Houben, Frederic Rousseau, Joost Schymkowitz
Published in: Bioinformatics, Issue 35/20, 2019, Page(s) 4098-4107, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz214

Molecular Dissection of FUS Points at Synergistic Effect of Low-Complexity Domains in Toxicity

Author(s): Elke Bogaert, Steven Boeynaems, Masato Kato, Lin Guo, Thomas R. Caulfield, Jolien Steyaert, Wendy Scheveneels, Nathalie Wilmans, Wanda Haeck, Nicole Hersmus, Joost Schymkowitz, Frederic Rousseau, James Shorter, Patrick Callaerts, Wim Robberecht, Philip Van Damme, Ludo Van Den Bosch
Published in: Cell Reports, Issue 24/3, 2018, Page(s) 529-537.e4, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2018.06.070

Protein Phase Separation: A New Phase in Cell Biology

Author(s): Steven Boeynaems, Simon Alberti, Nicolas L. Fawzi, Tanja Mittag, Magdalini Polymenidou, Frederic Rousseau, Joost Schymkowitz, James Shorter, Benjamin Wolozin, Ludo Van Den Bosch, Peter Tompa, Monika Fuxreiter
Published in: Trends in Cell Biology, Issue 28/6, 2018, Page(s) 420-435, ISSN 0962-8924
Publisher: Elsevier BV
DOI: 10.1016/j.tcb.2018.02.004

Comprehensive subcellular topologies of polypeptides in Streptomyces

Author(s): Konstantinos C. Tsolis, Evridiki-Pandora Tsare, Georgia Orfanoudaki, Tobias Busche, Katerina Kanaki, Reshmi Ramakrishnan, Frederic Rousseau, Joost Schymkowitz, Christian Rückert, Jörn Kalinowski, Jozef Anné, Spyridoula Karamanou, Maria I. Klapa, Anastassios Economou
Published in: Microbial Cell Factories, Issue 17/1, 2018, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-018-0892-0

Aggregating sequences that occur in many proteins constitute weak spots of bacterial proteostasis

Author(s): Ladan Khodaparast, Laleh Khodaparast, Rodrigo Gallardo, Nikolaos N. Louros, Emiel Michiels, Reshmi Ramakrishnan, Meine Ramakers, Filip Claes, Lydia Young, Mohammad Shahrooei, Hannah Wilkinson, Matyas Desager, Wubishet Mengistu Tadesse, K. Peter R. Nilsson, Per Hammarström, Abram Aertsen, Sebastien Carpentier, Johan Van Eldere, Frederic Rousseau, Joost Schymkowitz
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-03131-0

Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms

Author(s): Greet De Baets, Loic Van Doorn, Frederic Rousseau, Joost Schymkowitz
Published in: PLOS Computational Biology, Issue 11/9, 2015, Page(s) e1004374, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1004374

Transcellular Spreading of Tau in Tauopathies

Author(s): Koen Demaegd, Joost Schymkowitz, Frederic Rousseau
Published in: ChemBioChem, Issue 19/23, 2018, Page(s) 2424-2432, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.201800288

Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins

Author(s): Tobias Langenberg, Rodrigo Gallardo, Rob van der Kant, Nikolaos Louros, Emiel Michiels, Ramon Duran-Romaña, Bert Houben, Rafaela Cassio, Hannah Wilkinson, Teresa Garcia, Chris Ulens, Joost Van Durme, Frederic Rousseau, Joost Schymkowitz
Published in: Cell Reports, Issue 31/2, 2020, Page(s) 107512, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.03.076

Reverse engineering synthetic antiviral amyloids

Author(s): Emiel Michiels, Kenny Roose, Rodrigo Gallardo, Ladan Khodaparast, Laleh Khodaparast, Rob van der Kant, Maxime Siemons, Bert Houben, Meine Ramakers, Hannah Wilkinson, Patricia Guerreiro, Nikolaos Louros, Suzanne J. F. Kaptein, Lorena Itatí Ibañez, Anouk Smet, Pieter Baatsen, Shu Liu, Ina Vorberg, Guy Bormans, Johan Neyts, Xavier Saelens, Frederic Rousseau, Joost Schymkowitz
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16721-8

Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues

Author(s): Bert Houben, Emiel Michiels, Meine Ramakers, Katerina Konstantoulea, Nikolaos Louros, Joffré Verniers, Rob der Kant, Matthias De Vleeschouwer, Nuno Chicória, Thomas Vanpoucke, Rodrigo Gallardo, Joost Schymkowitz, Frederic Rousseau
Published in: The EMBO Journal, Issue 39/11, 2020, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2019102864

Entropic Bristles Tune the Seeding Efficiency of Prion-Nucleating Fragments

Author(s): Emiel Michiels, Shu Liu, Rodrigo Gallardo, Nikolaos Louros, Marion Mathelié-Guinlet, Yves Dufrêne, Joost Schymkowitz, Ina Vorberg, Frederic Rousseau
Published in: Cell Reports, Issue 30/8, 2020, Page(s) 2834-2845.e3, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.01.098

Structure-based machine-guided mapping of amyloid sequence space reveals uncharted sequence clusters with higher solubilities

Author(s): Nikolaos Louros, Gabriele Orlando, Matthias De Vleeschouwer, Frederic Rousseau, Joost Schymkowitz
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-17207-3

Selective Knockdowns in Maize by Sequence-Specific Protein Aggregation

Author(s): Camilla Betti, Joost Schymkowitz, Frederic Rousseau, Eugenia Russinova
Published in: Methods in Molecular Biology, 2017, Page(s) 109-127
Publisher: Springer New York
DOI: 10.1007/978-1-4939-7315-6_6

SolubiS: Optimizing Protein Solubility by Minimal Point Mutations

Author(s): Rob van der Kant, Joost van Durme, Frederic Rousseau, Joost Schymkowitz
Published in: Protein Misfolding Diseases - Methods and Protocols, Issue 1873, 2019, Page(s) 317-333, ISBN 978-1-4939-8819-8
Publisher: Springer New York
DOI: 10.1007/978-1-4939-8820-4_21

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