Publications

2020

  • publication

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

    Nikolaos Louros, Gabriele Orlando, Matthias De Vleeschouwer, Frederic Rousseau, Joost Schymkowitz
    Nat Commun
    PubMed
  • publication

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

    Margarita Monge-Morera, Marlies A Lambrecht, Lomme J Deleu, Rodrigo Gallardo, Nikolaos N Louros, Matthias De Vleeschouwer, Frederic Rousseau, Joost Schymkowitz, Jan A Delcour
    Biomacromolecules 2020 Mar 23
    PubMed
  • publication

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

    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
    Cell Rep . 2020 Apr 14;31(2):107512
    PubMed
  • publication

    Entropic Bristles Tune the Seeding Efficiency of Prion-Nucleating Fragments.

    Michiels E, Liu S, Gallardo R, Louros N, Mathelié-Guinlet M, Dufrêne Y, Schymkowitz J, Vorberg I, Rousseau F
    Cell Rep. 2020 Feb 25;30(8):2834-2845.e3
    PubMed
  • publication

    Defective SEC61α1 Underlies a Novel Cause of Autosomal Dominant Severe Congenital Neutropenia

    Erika Van Nieuwenhove, John S Barber, Julika Neumann, Elien Smeets 3, Mathijs Willemsen 2, Emanuela Pasciuto 2, Teresa Prezzemolo 2, Vasiliki Lagou 2, Laura Seldeslachts 4, Bert Malengier-Devlies 5, Mieke Metzemaekers 6, Sarah Haßdenteufel 7, Axelle Kerstens 8, Rob van der Kant 9, Frederic Rousseau 9, Joost Schymkowitz 9, Daniele Di Marino , Sven Lang, Richard Zimmermann, Susan Schlenner, Sebastian Munck, Paul Proost, Patrick Matthys, Christine Devalck, Nancy Boeckx, Frank Claessens, Carine Wouters, Stephanie Humblet-Baron, Isabelle Meyts, Adrian Liston
    J Allergy Clin Immunol . 2020 Apr 20;S0091-6749(20)30488-7
    PubMed
  • publication

    Preparation of Amorphous Solid Dispersions by Cryomilling: Chemical and Physical Concerns Related to Active Pharmaceutical Ingredients and Carriers

    Pas T, Bergonzi A, Michiels E, Rousseau F, Schymkowitz J, Koekoekx R, Clasen C, Vergauwen B, Van den Mooter G
    Mol Pharm. 2020 Feb 12. doi: 10.1021
    PubMed
  • publication

    Nanomaterials to avoid and destroy protein aggregates

    FélixSauvage, JoostSchymkowitz, FredericRousseau, Bela Z.Schmidt. KatrienRemaut, KevinBraeckmans, Stefaan C.De Smedt
    Nanotoday 11 January 2020, 100837
  • publication

    Reverse Engineering Synthetic Antiviral Amyloids

    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
    Nat Commun. 2020 Jun 5;11(1):2832.
    PubMed
  • publication

    Exposure of a Cryptic Hsp70 Binding Site Determines the Cytotoxicity of the ALS-associated SOD1-mutant A4V

    Filip Claes, Stanislav Rudyak, Angela S Laird, Nikolaos Louros, Jacinte Beerten, Maja Debulpaep, Emiel Michiels, Rob van der Kant, Joost Van Durme, Greet De Baets, Bert Houben, Meine Ramakers, Kristy Yuan, Serene S L Gwee, Sara Hernandez, Kerensa Broersen, Mikael Oliveberg, Barbara Moahamed, Janine Kirstein, Wim Robberecht, Frederic Rousseau , Joost Schymkowitz
    Protein Eng Des Sel . 2020 May 13;gzaa008. doi: 10.1093/protein/gzaa008
    PubMed
  • publication

    Autonomous Aggregation Suppression by Acidic Residues Explains Why Chaperones Favour Basic Residues

    Bert Houben, Emiel Michiels, Meine Ramakers, Katerina Konstantoulea, Nikolaos Louros, Joffré Verniers, Rob van der Kant, Matthias De Vleeschouwer, Nuno Chicória, Thomas Vanpoucke, Rodrigo Gallardo, Joost Schymkowitz, Frederic Rousseau
    EMBO J , e102864 2020 Apr 1
    PubMed

2019

  • publication

    SolubiS: Optimizing Protein Solubility by Minimal Point Mutations.

    van der Kant R, van Durme J, Rousseau F, Schymkowitz J
    Methods in Molecular Biology. 2019;1873:317-333.
    PubMed
  • publication

    Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability

    Cacace R, Heeman B, Van Mossevelde S, De Roeck A, Hoogmartens J, De Rijk P, Gossye H, De Vos K, De Coster W, Strazisar M, De Baets G, Schymkowitz J, Rousseau F, Geerts N, De Pooter T, Peeters K, Sieben A, Martin JJ, Engelborghs S, Salmon E, Santens P, Vandenberghe R, Cras P, P De Deyn P, C van Swieten J, M van Duijn C, van der Zee J, Sleegers K, Van Broeckhoven C; BELNEU Consortium
    Acta Neuropathol. 2019 Mar 14. doi: 10.1007/s00401-019-01976-3
    PubMed
  • publication

    Differential proteostatic regulation of insoluble and abundant proteins

    Ramakrishnan R, Houben B, Rousseau F, Schymkowitz J
    Bioinformatics. 2019 Mar 23. pii: btz214. doi: 10.1093/bioinformatics/btz214.
    PubMed
  • publication

    Conditions Governing Food Protein Amyloid Fibril Formation—Part I: Egg and Cereal Proteins

    Koen J.A. Jansens Marlies A. Lambrecht Ine Rombouts Margarita Monge Morera Kristof Brijs Frederic Rousseau Joost Schymkowitz Jan A. Delcour
    Comprehensive Reviews in Food Science and Food Safety
    https://onlinelibrary.wiley.com/doi/10.1111/1541-4337.12462
  • publication

    Protein Homeostasis Database: protein quality control in E. coli.

    Ramakrishnan R, Houben B, Kreft Ł, Botzki A, Schymkowitz J, Rousseau F1
    Bioinformatics. 2019 Aug 8. pii: btz628
    PubMed
  • publication

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

    Louros N, Konstantoulea K, De Vleeschouwer M, Ramakers M, Schymkowitz J, Rousseau F1
    Nucleic Acids Res. 2019 Sep 2. pii: gkz758.
    PubMed
  • publication

    Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants

    Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Pal LR, Radivojac P, Rousseau F, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Väliaho J, Repo S, Moult J, Brenner SE, Friedberg I
    Hum Mutat. 2019 Jul 13. doi: 10.1002/humu.23868.
    PubMed
  • publication

    Structural Basis of the Subcellular Topology Landscape of Escherichia coli.

    Loos MS, Ramakrishnan R, Vranken W, Tsirigotaki A, Tsare EP, Zorzini V, Geyter J, Yuan B, Tsamardinos I, Klappa M, Schymkowitz J, Rousseau F, Karamanou S, Economou A
    Front Microbiol. 2019 Jul 24;10:1670.
    PubMed
  • publication

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

    van der Kant R, Bauer J, Karow-Zwick AR, Kube S, Garidel P, Blech M, Rousseau F, Schymkowitz J
    Protein Eng Des Sel. 2019 Sep 19.
    PubMed
  • publication

    Evaluation of [11C]NMS-E973 as a PET tracer for in vivo visualisation of HSP90.

    Vermeulen K, Naus E, Ahamed M, Attili B, Siemons M, Luyten K, Celen S, Schymkowitz J, Rousseau F,, Bormans G
    Theranostics. 2019 Jan 1;9(2):554-572
    PubMed

2018

  • publication

    TRANSCELLULAR SPREADING OF TAU IN TAUOPATHIES

    Demaegd K, Schymkowitz J, Rousseau F
    Chembiochem. 2018 Aug 22. doi: 10.1002/cbic.201800288
    PubMed
  • publication

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

    Bogaert E, Boeynaems S, Kato M, Guo L, Caulfield TR, Steyaert J, Scheveneels W, Wilmans N, Haeck W, Hersmus N, Schymkowitz J, Rousseau F, Shorter J, Callaerts P, Robberecht W, Van Damme P, Van Den Bosch L
    Cell Rep. 2018 Jul 17;24(3):529-537.e4.
    PubMed
  • publication

    Rational Design of Amyloid-Like Fibrillary Structures for Tailoring Food Protein Techno-Functionality and Their Potential Health Implications

    K. J. A. Jansens, I. Rombouts, C. Grootaert, K. Brijs, J. Van Camp, P. Van der Meeren, F. Rousseau, J. Schymkowitz, and J. A. Delcour
    Comprehensive Reviews in Food Science and Food Safety, vol. 18, no. 1, pp. 84–105, Nov. 2018.
  • publication

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

    Khodaparast L, Khodaparast L, Gallardo R, Louros NN, Michiels E, Ramakrishnan R, Ramakers M, Claes F, Young L, Shahrooei M, Wilkinson H, Desager M, Mengistu Tadesse W, Nilsson KPR, Hammarström P, Aertsen A, Carpentier S, Van Eldere J, Rousseau F, Schymkowitz J
    Nat Commun. 2018 Feb 28;9(1):866. doi: 10.1038/s41467-018-03131-0.
    PubMedhttps://www.ncbi.nlm.nih.gov/pubmed/29491361
  • publication

    Comprehensive subcellular topologies of polypeptides in Streptomyces

    Tsolis KC, Tsare EP, Orfanoudaki G, Busche T, Kanaki K, Ramakrishnan R, Rousseau F, Schymkowitz J, Rückert C, Kalinowski J, Anné J, Karamanou S, Klapa M, Economou A
    Microb Cell Fact. 2018 Mar 15;17(1):43. doi: 10.1186/s12934-018-0892-0.
    PubMed
  • publication

    Protein Phase Separation: A New Phase in Cell Biology

    Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, Van Den Bosch L, Tompa P, Fuxreiter M
    Trends Cell Biol. 2018 Mar 27. pii: S0962-8924(18)30028-X
    PubMedhttps://www.ncbi.nlm.nih.gov/pubmed/29602697
  • publication

    Hsp90 Mediates Membrane Deformation and Exosome Release

    Lauwers E, Wang YC, Gallardo R, Van der Kant R, Michiels E, Swerts J, Baatsen P, Zaiter SS, McAlpine SR, Gounko NV, Rousseau F, Schymkowitz J, Verstreken P
    Mol Cell. 2018 Sep 6;71(5):689-702.e9.
    PubMed

2017

  • publication

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

    Szaruga M, Munteanu B, Lismont S, Veugelen S, Horré K, Mercken M, Saido TC, Ryan NS, De Vos T, Savvides SN, Gallardo R, Schymkowitz J, Rousseau F, Fox NC, Hopf C, De Strooper B, Chávez-Gutiérrez L
    Cell. 2017 Jul 27;170(3):443-456.e14
    PubMed
  • publication

    Prediction and reduction of the aggregation of monoclonal antibodies

    van der Kant R, Karow-Zwick AR, Van Durme J, Blech M, Gallardo R, Seeliger D, Aßfalg K, Baatsen P, Compernolle G, Gils A, Studts JM, Schulz P, Garidel P, Schymkowitz J, Rousseau F
    J Mol Biol. 2017 Mar 17. pii: S0022-2836(17)30118-3.
    PubMed
  • publication

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

    De Smet F, Saiz Rubio M, Hompes D, Naus E, De Baets G, Langenberg T, Hipp M, Houben B, Claes F, Charbonneau S, Blanco JD, Plaisance S, Ramkissoon S, Ramkissoon L, Simons C, van den Brandt P, Weijenberg M, Van England M, Lambrechts S, Amant F, D'Hoore A, Ligon KL, Sagaert X, Schymkowitz J, Rousseau F
    J Pathol. 2016 Dec 30. doi: 10.1002/path.4872.
    PubMed
  • publication

    Selective Knockdowns in Maize by Sequence-Specific Protein Aggregation.

    Camilla Betti, Joost Schymkowitz, Frederic Rousseau, and Eugenia Russinova
    Methods Mol Biol. 2018;1676:109-127
    PubMed
  • publication

    Phase Separation of C9orf72 Dipeptide Repeats Perturbs Stress Granule Dynamics

    Boeynaems S, Bogaert E, Kovacs D, Konijnenberg A, Timmerman E, Volkov A, Guharoy M, De Decker M, Jaspers T, Ryan VH, Janke AM, Baatsen P, Vercruysse T, Kolaitis RM, Daelemans D, Taylor JP, Kedersha N, Anderson P, Impens F, Sobott F, Schymkowitz J, Rousseau F, Fawzi NL, Robberecht W, Van Damme P, Tompa P, Van Den Bosch L
    Mol Cell. 2017 Mar 16;65(6):1044-1055.e5.
    PubMed
  • publication

    Identifying rescuers of misfolding

    Langenberg, T., Schymkowitz, J. and F. Rousseau
    Nat Biomed Eng, 2017;1:782-783

2016

  • publication

    Protein aggregation: A rescue by chaperones.

    Schymkowitz J, Rousseau F
    Nat Chem Biol. 2016 Jan 19;12(2):58-9
    PubMed
  • publication

    Restricted Location of PSEN2/γ-Secretase Determines Substrate Specificity and Generates an Intracellular Aβ Pool.

    Sannerud R, Esselens C, Ejsmont P, Mattera R, Rochin L, Tharkeshwar AK, De Baets G, De Wever V, Habets R, Baert V, Vermeire W, Michiels C, Groot AJ, Wouters R, Dillen K, Vints K, Baatsen P, Munck S, Derua R, Waelkens E, Basi GS, Mercken M, Vooijs M, Bollen M, Schymkowitz J, Rousseau F, Bonifacino JS, Van Niel G, De Strooper B, Annaert W
    Cell. 2016 Jun 9. pii: S0092-8674(16)30568-2. doi: 10.1016
    PubMed
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    Post-translational Control of the Temporal Dynamics of Transcription Factor Activity Regulates Neurogenesis.

    Quan XJ, Yuan L, Tiberi L, Claeys A, De Geest N, Yan J, van der Kant R, Xie WR, Klisch TJ, Shymkowitz J, Rousseau F, Bollen M, Beullens M, Zoghbi HY, Vanderhaeghen P, Hassan BA.
    Cell. 2016 Jan 28;164(3):460-75. doi: 10.1016
    PubMed
  • publication

    Structural hot spots for the solubility of globular proteins

    Ganesan A, Siekierska A, Beerten J, Brams M, Van Durme J, De Baets G, Van der Kant R, Gallardo R, Ramakers M, Langenberg T, Wilkinson H, De Smet F, Ulens C, Rousseau F, Schymkowitz J
    Nat Commun. 2016 Feb 24;7:10816. doi: 10.1038/ncomms10816.
    PubMedpdf
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    Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling.

    Egea-Jimenez AL, Gallardo R, Garcia-Pino A, Ivarsson Y, Wawrzyniak AM, Kashyap R, Loris R, Schymkowitz J, Rousseau F, Zimmermann P
    Nat Commun. 2016 Jul 8;7:12101.
    PubMed
  • publication

    Sequence-specific protein aggregation generates defined protein knockdowns in plants.

    Betti C, Vanhoutte I, Coutuer S, De Rycke RM, Mishev K, Vuylsteke M, Aesaert S, Rombaut D, Gallardo R, De Smet F, Xu J, Van Lijsebettens M, Van Breusegem F, Inzé D, Rousseau F, Schymkowitz J, Russinova E
    Plant Physiol. 2016 May 4. pii: pp.00335.2016.
    PubMed
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    From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

    Zafra Ruano A, Cilia E, Couceiro JR, Ruiz Sanz J, Schymkowitz J, Rousseau F, Luque I, Lenaerts T
    PLoS Comput Biol. 2016 May 23;12(5):e1004938. doi: 10.1371
    PubMed
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    Solubis: a webserver to reduce protein aggregation through mutation.

    Van Durme J, De Baets G, Van Der Kant R, Ramakers M, Ganesan A, Wilkinson H, Gallardo R, Rousseau F, Schymkowitz J
    Protein Eng Des Sel. 2016 Aug;29(8):285-9.
  • publication

    Drosophila screen connects nuclear transport genes to DPR pathology in c9ALS/FTD

    Boeynaems S, Bogaert E,, Michiels E,, Gijselinck I,, Sieben A, Jovičić A, De Baets G, Scheveneels W, Steyaert J, Cuijt I, Verstrepen KJ, Callaerts P, Rousseau F, Schymkowitz J, Cruts M, Van Broeckhoven C, Van Damme P, Gitler AD, Robberecht W, Van Den Bosch L
    Sci Rep. 2016 Feb 12;6:20877. doi: 10.1038/srep20877.
    PubMed
  • publication

    De novo design of a biologically active amyloid

    Gallardo R, Ramakers M, De Smet F, Claes F, Khodaparast L1, Khodaparast L, Couceiro JR, Langenberg T, Siemons M, Nyström S, Young LJ, Laine RF, Young L, Radaelli E, Benilova I, Kumar M, Staes , Desager M, Beerens M, Vandervoort P, Luttun A, Gevaert K, Bormans G, Dewerchin M, Van Eldere J, Carmeliet P, Vande Velde G, Verfaillie C, Kaminski CF, De Strooper B, Hammarström P, Nilsson KP, Serpell L, Schymkowitz J, Rousseau F
    Science. 2016 Nov 11;354(6313). pii: aah4949.
    PubMedfull pdf

2015

  • publication

    WALTZ-DB: a benchmark database of amyloidogenic hexapeptides.

    Beerten J, Van Durme J, Gallardo R, Capriotti E, Serpell L, Rousseau F, Schymkowitz J4
    Bioinformatics 2015 Jan 18. pii: btv027
    PubMed
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    Solubis: optimize your protein

    De Baets G, Van Durme J, van der Kant R, Schymkowitz J, Rousseau F2
    Bioinformatics. 2015 Mar 19. pii: btv162. [Epub ahead of print]
    PubMed
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    Structure of the Extracellular Domain of Matrix Protein 2 of Influenza A Virus in Complex with a Protective Monoclonal Antibody

    Cho KJ, Schepens B, Seok JH, Kim S, Roose K, Lee JH, Gallardo R, Hamme EV, Schymkowitz J, Rousseau F, Fiers W, Saelens X, Kim KH
    J Virol. 2015 Jan 21. pii: JVI.02576-14.
    PubMed
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    Variable Glutamine-Rich Repeats Modulate Transcription Factor Activity

    Gemayel R, Chavali S, Pougach K, Legendre M, Zhu B, Boeynaems S, van der Zande E, Gevaert K, Rousseau F, Schymkowitz J, Babu MM, Verstrepen KJ
    Mol Cell. 2015 Aug 5. pii: S1097-2765(15)00534-1
    PubMed
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    Protein aggregation as an antibiotic design strategy

    Bednarska NG,, Van Eldere J, Gallardo R, Ganesan A, Ramakers M, Vogel I, Baatsen P, Staes A, Goethals M, Hammarström P, Nilsson KP, Gevaert K, Schymkowitz J, Rousseau F
    Mol Microbiol. 2015 Nov 12. doi: 10.1111/mmi.13269
    PubMed
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    Amyloids or Prions? That is the Question.

    Sabate R, Rousseau F, Schymkowitz J, Batlle C, Ventura S.
    Prion 2015 Jun 3:0
    PubMed
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    PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores

    Zambrano R, Conchillo-Sole O, Iglesias V, Illa R, Rousseau F, Schymkowitz J, Sabate R, Daura X, Ventura S.
    Nucleic Acids Res. 2015 May 14. pii: gkv490.
    PubMed
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    What Makes a Protein Sequence a Prion?

    Raimon Sabate, Frederic Rousseau, Joost Schymkowitz, Salvador Ventura
    PLoS Comput Biol. 2015 Jan 8;11(1):e1004013.
    PubMed
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    Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms

    Greet De Baets, Loic Van Doorn, Frederic Rousseau, Joost Schymkowitz
    PLoS Comput Biol. 2015 Sep 4;11(9):e1004374.
    PubMed

2014

  • publication

    Predicting aggregation-prone sequences in proteins.

    De Baets G, Schymkowitz J, Rousseau F.
    Essays Biochem. 2014 Aug 18;56(1):41-52
    PubMed
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    Sequence-dependent internalisation of aggregating peptides.

    Couceiro JR, Gallardo R, De Smet F, De Baets G, Baatsen P, Annaert W, Roose K, Saelens X, Schymkowitz J, Rousseau F.
    J Biol Chem. 2014 Nov 12. pii: jbc.M114.586636.
    PubMed
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    The Alzheimer Disease Protective Mutation A2T Modulates Kinetic and Thermodynamic Properties of Amyloid-β (Aβ) Aggregation.

    Benilova I, Gallardo R, Ungureanu AA, Castillo Cano V, Snellinx A, Ramakers M, Bartic C, Rousseau F, Schymkowitz J, De Strooper B.
    J Biol Chem. 2014 Nov 7;289(45):30977-89
    PubMed
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    A genome-wide sequence-structure analysis suggests aggregation gatekeepers constitute an evolutionary constrained functional class

    De Baets G, Van Durme J, Rousseau F, Schymkowitz J
    J Mol Biol. 2014 Jun 12;426(12):2405-12.
    PubMed
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    Selectivity of Aggregation-Determining Interactions.

    Ganesan A, Debulpaep M, Wilkinson H, Van Durme J, De Baets G, Jonckheere W, Ramakers M, Ivarsson Y, Zimmermann P, Van Eldere J, Schymkowitz J, Rousseau F.
    J Mol Biol. 2014.09.027
    PubMed
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    Horizontal gene transfer from human host to HIV-1 reverse transcriptase confers drug resistance and partly compensates for replication deficits.

    Megens S, Vaira D, De Baets G, Dekeersmaeker N, Schrooten Y, Li G, Schymkowitz J, Rousseau F, Vandamme AM, Moutschen M, Van Laethem K
    Virology. 2014 May;456-457:310-8.
    PubMed

2013

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    Exploring the sequence-structure relationship for amyloid peptides.

    Morris KL, Rodger A, Hicks MR, Debulpaep M, Schymkowitz J, Rousseau F, Serpell LC.
    Biochem J. 2013 Mar 1;450(2):275-83.
    PubMed
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    Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling

    Herbert C, Schieborr U, Saxena K, Juraszek J, De Smet F, Alcouffe C, Bianciotto M, Saladino G, Sibrac D, Kudlinzki D, Sreeramulu S, Brown A, Rigon P, Herault JP, Lassalle G, Blundell TL, Rousseau F, Gils A, Schymkowitz J, Tompa P, Herbert JM, Carmeliet P, Gervasio FL, Schwalbe H, Bono F.
    Cancer Cell. 2013 Apr 15;23(4):489-501.
    PubMed
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    Aggregation prone regions and gatekeeping residues in protein sequences.

    Beerten J, Schymkowitz J, Rousseau F.
    Curr Top Med Chem. 2013 Jan 4.
    PubMed
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    Motif discovery with data mining in 3d protein structure databases: discovery, validation and prediction of the u-shape zinc binding ("huf-zinc") motif.

    Maurer-Stroh S, Gao H, Han H, Baeten L, Schymkowitz J, Rousseau F, Zhang L, Eisenhaber F.
    J Bioinform Comput Biol. 2013 Feb;11(1):1340008
    PubMed
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    Protein aggregation in bacteria: the thin boundary between functionality and toxicity

    Bednarska NG, Schymkowitz J, Rousseau F, Van Eldere J.
    Microbiology. 2013 Sep:1795-806.
    PubMed
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    Protein-Peptide Complex Prediction through Fragment Interaction Patterns.

    Verschueren E, Vanhee P, Rousseau F, Schymkowitz J, Serrano L.
    Structure. 2013 Apr 9. pii: S0969-2126(13)00081-6.
    PubMed

2012

  • publication

    Implications of 3D domain swapping for protein folding, misfolding and function

    Rousseau F, Schymkowitz J, Itzhaki LS.
    Adv Exp Med Biol. 2012;747:137-52.
    PubMed
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    Peptides based on the presenilin-APP binding domain inhibit APP processing and Aβ production through interfering with the APP transmembrane domain.

    Esselens C, Sannerud R, Gallardo R, Baert V, Kaden D, Serneels L, De Strooper B, Rousseau F, Multhaup G, Schymkowitz J, Langedijk JP, Annaert W.
    FASEB J. 2012 Sep;26(9):3765-78.
    PubMed
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    A comparative analysis of the aggregation behavior of amyloid-β peptide variants

    Vandersteen A, Hubin E, Sarroukh R, Baets GD, Schymkowitz J, Rousseau F, Subramaniam V, Raussens V, Wenschuh H, Wildemann D, Broersen K.
    FEBS Lett. 2012 Oct 24.
    PubMed
  • publication

    The mechanism of γ-Secretase dysfunction in familial Alzheimer disease

    Chávez-Gutiérrez L, Bammens L, Benilova I, Vandersteen A, Benurwar M, Borgers M, Lismont S, Zhou L, Van Cleynenbreugel S, Esselmann H, Wiltfang J, Serneels L, Karran E, Gijsen H, Schymkowitz J, Rousseau F, Broersen K, De Strooper B
    EMBO J. 2012 Apr 13;31(10):2261-74.
    PubMed
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    Structural basis for increased toxicity of pathological Aβ42:Aβ40 ratios in Alzheimer's disease

    Pauwels K, Williams TL, Morris KL, Jonckheere W, Vandersteen A, Kelly G, Schymkowitz J, Rousseau F, Pastore A, Serpell LC, Broersen K.
    J Biol Chem. 2012 Feb 17;287(8):5650-60
    PubMed
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    α-Galactosidase Aggregation Is a Determinant of Pharmacological Chaperone Efficacy on Fabry Disease Mutants.

    Siekierska A, De Baets G, Reumers J, Gallardo R, Rudyak S, Broersen K, Couceiro J, Van Durme J, Schymkowitz J, Rousseau F.
    J Biol Chem. 2012 Aug 17;287(34):28386-97.
    PubMed
  • publication

    Molecular plasticity regulates oligomerization and cytotoxicity of the multi-peptide length Aβ pool

    Vandersteen A, Masman MF, De Baets G, Jonckheere W, Van der Werf K, Marrink SJ, Rozenski J, Benilova I, De Strooper B, Subramaniam V, Schymkowitz J, Rousseau F, Broersen K.
    J Biol Chem. 2012 Sep 19
    PubMed
  • publication

    Aggregation gatekeepers modulate protein homeostasis of aggregating sequences and affect bacterial fitness

    Beerten J, Jonckheere W, Rudyak S, Xu J, Wilkinson H, De Smet F, Schymkowitz J, Rousseau F.
    Protein Eng Des Sel. 2012 Jul;25(7):357-66.
    PubMed
  • publication

    SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

    De Baets G, Van Durme J, Reumers J, Maurer-Stroh S, Vanhee P, Dopazo J, Schymkowitz J, Rousseau F
    Nucleic Acids Res. 2012 Jan;40(1):D935-9.
    PubMed

2011

  • publication

    Protein design with fragment databases

    Verschueren E, Vanhee P, van der Sloot AM, Serrano L, Rousseau F, Schymkowitz J
    Curr Opin Struct Biol. 2011 21:1-8
    PubMed
  • publication

    Redox proteomics of protein-bound methionine oxidation.

    Ghesquiere B, Jonckheere V, Colaert N, Van Durme J, Timmerman E, Goethals M, Schymkowitz J, Rousseau F, Vandekerckhove J, Gevaert K.
    Mol Cell Proteomics. 2011 May;10(5):M110.006866
    PubMed
  • publication

    BriX: a database of protein building blocks for structural analysis, modeling and design.

    Vanhee P, Verschueren E, Baeten L, Stricher F, Serrano L, Rousseau F, Schymkowitz J.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D435-42.
    PubMed
  • publication

    Gain of function of mutant p53 by coaggregation with multiple tumor suppressors.

    Xu J, Reumers J, Couceiro JR, De Smet F, Gallardo R, Rudyak S, Cornelis A, Rozenski J, Zwolinska A, Marine JC, Lambrechts D, Suh YA, Rousseau F, Schymkowitz J.
    Nat Chem Biol. 2011 May;7(5):285-95.
    PubMed
  • publication

    An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins

    De Baets G, Reumers J, Delgado Blanco J, Dopazo J, Schymkowitz J, Rousseau F.
    PLoS Comput Biol. 2011 Jun;7(6):e1002090.
    PubMed
  • publication

    Computational design of peptide ligands.

    Vanhee P, van der Sloot AM, Verschueren E, Serrano L, Rousseau F, Schymkowitz J.
    Trends Biotechnol. 2011 May;29(5):231-9.
    PubMed
  • publication

    A standardized and biocompatible preparation of aggregate-free amyloid beta peptide for biophysical and biological studies of Alzheimer's disease

    Broersen K, Jonckheere W, Rozenski J, Vandersteen A, Pauwels K, Pastore A, Rousseau F, Schymkowitz J
    Protein Eng Des Sel. 2011 Sep;24(9):743-50.
    PubMed
  • publication

    A graphical interface for the FoldX forcefield.

    Van Durme J, Delgado J, Stricher F, Serrano L, Schymkowitz J, Rousseau F.
    Bioinformatics 2011;27(12): 1711-1712
    PubMed

2010

  • publication

    The culprit behind amyloid beta peptide related neurotoxicity in Alzheimer's disease: oligomer size or conformation?

    Broersen K, Rousseau F, Schymkowitz J.
    Alzheimers Res Ther. 2010 Jul 14;2(4):12.
    PubMed
  • publication

    Structural diversity of PDZ-lipid interactions.

    Gallardo R, Ivarsson Y, Schymkowitz J, Rousseau F, Zimmermann P.
    Chembiochem. 2010 Mar 1;11(4):456-67. Review.
    PubMed
  • publication

    Neurotoxicity of Alzheimer's disease Aβ peptides is induced by small changes in the Aβ42 to Aβ40 ratio.

    Kuperstein I, Broersen K, Benilova I, Rozenski J, Jonckheere W, Debulpaep M, Vandersteen A, Segers-Nolten I, Van Der Werf K, Subramaniam V, Braeken D, Callewaert G, Bartic C, D'Hooge R, Martins IC, Rousseau F, Schymkowitz J, De Strooper B.
    EMBO J. 2010 Oct 6;29(19):3408-20.
    PubMed
  • publication

    Increased monomerization of mutant HSPB1 leads to protein hyperactivity in Charcot-Marie-Tooth neuropathy.

    Almeida-Souza L, Goethals S, de Winter V, Dierick I, Gallardo R, Van Durme J, Irobi J, Gettemans J, Rousseau F, Schymkowitz J, Timmerman V, Janssens S.
    J Biol Chem. 2010 Apr 23;285(17):12778-86.
    PubMed
  • publication

    Exploring the sequence determinants of amyloid structure using position-specific scoring matrices.

    Maurer-Stroh S, Debulpaep M, Kuemmerer N, Lopez de la Paz M, Martins IC, Reumers J, Morris KL, Copland A, Serpell L, Serrano L, Schymkowitz JW, Rousseau F.
    Nat Methods. 2010 Mar;7(3):237-42.
    PubMed
  • publication

    PepX: a structural database of non-redundant protein-peptide complexes.

    Vanhee P, Reumers J, Stricher F, Baeten L, Serrano L, Schymkowitz J, Rousseau F.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D545-51.
    PubMed

2009

  • publication

    Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations.

    Reumers J, Schymkowitz J, Rousseau F.
    BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S9.
    PubMed
  • publication

    Information theoretical quantification of cooperativity in signalling complexes.

    Lenaerts T, Ferkinghoff-Borg J, Schymkowitz J, Rousseau F.
    BMC Syst Biol. 2009 Jan 16;3:9.
    PubMed
  • publication

    Protein domains as information processing units.

    Lenaerts T, Schymkowitz J, Rousseau F.
    Curr Protein Pept Sci. 2009 Apr;10(2):133-45.
    PubMed
  • publication

    Protein sequences encode safeguards against aggregation.

    Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F.
    Hum Mutat. 2009 Mar;30(3):431-7.
    PubMed
  • publication

    Proteome-wide substrate analysis indicates substrate exclusion as a mechanism to generate caspase-7 versus caspase-3 specificity.

    Demon D, Van Damme P, Vanden Berghe T, Deceuninck A, Van Durme J, Verspurten J, Helsens K, Impens F, Wejda M, Schymkowitz J, Rousseau F, Madder A, Vandekerckhove J, Declercq W, Gevaert K, Vandenabeele P.
    Mol Cell Proteomics. 2009 Dec;8(12):2700-14.
    PubMed
  • publication

    Analysis of protein processing by N-terminal proteomics reveals novel species-specific substrate determinants of granzyme B orthologs.

    Van Damme P, Maurer-Stroh S, Plasman K, Van Durme J, Colaert N, Timmerman E, De Bock PJ, Goethals M, Rousseau F, Schymkowitz J, Vandekerckhove J, Gevaert K.
    Mol Cell Proteomics. 2009 Feb;8(2):258-72.
    PubMed
  • publication

    Accurate prediction of DnaK-peptide binding via homology modelling and experimental data.

    Van Durme J, Maurer-Stroh S, Gallardo R, Wilkinson H, Rousseau F, Schymkowitz J.
    PLoS Comput Biol. 2009 Aug;5(8):e1000475.
    PubMed
  • publication

    Protein-peptide interactions adopt the same structural motifs as monomeric protein folds.

    Vanhee P, Stricher F, Baeten L, Verschueren E, Lenaerts T, Serrano L, Rousseau F, Schymkowitz J.
    Structure. 2009 Aug 12;17(8):1128-36.
    PubMed

2008

  • publication

    Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure.

    Lenaerts T, Ferkinghoff-Borg J, Stricher F, Serrano L, Schymkowitz JW, Rousseau F.
    BMC Struct Biol. 2008 Oct 8;8:43.
    PubMed
  • publication

    Lipids revert inert Abeta amyloid fibrils to neurotoxic protofibrils that affect learning in mice.

    Martins IC, Kuperstein I, Wilkinson H, Maes E, Vanbrabant M, Jonckheere W, Van Gelder P, Hartmann D, D'Hooge R, De Strooper B, Schymkowitz J, Rousseau F.
    EMBO J. 2008 Jan 9;27(1):224-33.
    PubMed
  • publication

    Genetic variability in the mitochondrial serine protease HTRA2 contributes to risk for Parkinson disease.

    Bogaerts V, Nuytemans K, Reumers J, Pals P, Engelborghs S, Pickut B, Corsmit E, Peeters K, Schymkowitz J, De Deyn PP, Cras P, Rousseau F, Theuns J, Van Broeckhoven C.
    Hum Mutat. 2008 Jun;29(6):832-40.
    PubMed
  • publication

    Analysis of the transthyretin-like (TTL) gene family in Ostertagia ostertagi - Comparison with other strongylid nematodes and Caenorhabditis elegans.

    Saverwyns H, Visser A, Van Durme J, Power D, Morgado I, Kennedy MW, Knox DP, Schymkowitz J, Rousseau F, Gevaert K, Vercruysse J, Claerebout E, Geldhof P.
    Int J Parasitol. 2008 May 10.
    PubMed
  • publication

    Hybrid N-glycans on the host protective activation-associated secreted proteins of Ostertagia ostertagi and their importance in immunogenicity.

    Meyvis Y, Callewaert N, Gevaert K, Timmerman E, Van Durme J, Schymkowitz J, Rousseau F, Vercruysse J, Claerebout E, Geldhof P.
    Mol Biochem Parasitol. 2008 Sep;161(1):67-71.
    PubMed
  • publication

    Genetic variability in progranulin contributes to risk for clinically diagnosed Alzheimer disease.

    Brouwers N, Sleegers K, Engelborghs S, Maurer-Stroh S, Gijselinck I, van der Zee J, Pickut BA, Van den Broeck M, Mattheijssens M, Peeters K, Schymkowitz J, Rousseau F, Martin JJ, Cruts M, De Deyn PP, Van Broeckhoven C.
    Neurology. 2008 Aug 26;71(9):656-64.
    PubMed
  • publication

    Progranulin genetic variability contributes to amyotrophic lateral sclerosis.

    Sleegers K, Brouwers N, Maurer-Stroh S, van Es MA, Van Damme P, van Vught PW, van der Zee J, Serneels S, De Pooter T, Van den Broeck M, Cruts M, Schymkowitz J, De Jonghe P, Rousseau F, van den Berg LH, Robberecht W, Van Broeckhoven C.
    Neurology. 2008 Jul 22;71(4):253-9.
    PubMed
  • publication

    Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm.

    Sánchez IE, Beltrao P, Stricher F, Schymkowitz J, Ferkinghoff-Borg J, Rousseau F, Serrano L.
    PLoS Comput Biol. 2008 Apr 4;4(4):e1000052.
    PubMed
  • publication

    Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.

    Reumers J, Conde L, Medina I, Maurer-Stroh S, Van Durme J, Dopazo J, Rousseau F, Schymkowitz J.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D825-9.
    PubMed
  • publication

    Reconstruction of protein backbones from the BriX collection of canonical protein fragments.

    Baeten L, Reumers J, Tur V, Stricher F, Lenaerts T, Serrano L, Rousseau F, Schymkowitz J.
    PLoS Comput Biol. 2008 May 23;4(5):e1000083.
    PubMed
  • publication

    ALS precursor finally shaken into fibrils.

    Rousseau F, Schymkowitz J, Oliveberg M.
    Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18649-50.
    PubMed

2007

  • publication

    Mutations other than null mutations producing a pathogenic loss of progranulin in frontotemporal dementia.

    van der Zee J, Le Ber I, Maurer-Stroh S, Engelborghs S, Gijselinck I, Camuzat A, Brouwers N, Vandenberghe R, Sleegers K, Hannequin D, Dermaut B, Schymkowitz J, Campion D, Santens P, Martin JJ, Lacomblez L, De Pooter T, Peeters K, Mattheijssens M, Vercelletto M, Van den Broeck M, Cruts M, et al.
    Hum Mutat. 2007 Apr;28(4):416.
    PubMed

2006

  • publication

    SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs.

    Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F.
    Bioinformatics. 2006 Sep 1;22(17):2183-5.
    PubMed
  • publication

    Protein aggregation and amyloidosis: confusion of the kinds?

    Rousseau F, Schymkowitz J, Serrano L.
    Curr Opin Struct Biol. 2006 Feb;16(1):118-26. Review.
    PubMed
  • publication

    Domain swapping in p13suc1 results in formation of native-like, cytotoxic aggregates.

    Rousseau F, Wilkinson H, Villanueva J, Serrano L, Schymkowitz JW, Itzhaki LS.
    J Mol Biol. 2006 Oct 20;363(2):496-505.
    PubMed
  • publication

    PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes.

    Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, Rousseau F, Schymkowitz J, Dopazo J.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W621-5.
    PubMed
  • publication

    How evolutionary pressure against protein aggregation shaped chaperone specificity.

    Rousseau F, Serrano L, Schymkowitz JW.
    J Mol Biol. 2006 Feb 3;355(5):1037-47. Epub 2005 Nov 28.
    PubMed

2005

  • publication

    A systems biology perspective on protein structural dynamics and signal transduction.

    Rousseau F, Schymkowitz J.
    Curr Opin Struct Biol. 2005 Feb;15(1):23-30. Review.
    PubMed
  • publication

    SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs.

    Reumers J, Schymkowitz J, Ferkinghoff-Borg J, Stricher F, Serrano L, Rousseau F.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D527-32.
    PubMed
  • publication

    Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations.

    Kiel C, Wohlgemuth S, Rousseau F, Schymkowitz J, Ferkinghoff-Borg J, Wittinghofer F, Serrano L.
    J Mol Biol. 2005 May 6;348(3):759-75.
    PubMed
  • publication

    The FoldX web server: an online force field.

    Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W382-8.
    PubMed
  • publication

    Prediction of water and metal binding sites and their affinities by using the Fold-X force field.

    Schymkowitz JW, Rousseau F, Martins IC, Ferkinghoff-Borg J, Stricher F, Serrano L.
    Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10147-52.
    PubMed

2004

  • publication

    Intermediates control domain swapping during folding of p13suc1.

    Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS.
    J Biol Chem. 2004 Feb 27;279(9):8368-77.
    PubMed
  • publication

    A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins.

    Linding R, Schymkowitz J, Rousseau F, Diella F, Serrano L.
    J Mol Biol. 2004 Sep 3;342(1):345-53.
    PubMed
  • publication

    Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins.

    Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L.
    Nat Biotechnol. 2004 Oct;22(10):1302-6.
    PubMed

2003

  • publication

    The unfolding story of three-dimensional domain swapping.

    Rousseau F, Schymkowitz JW, Itzhaki LS.
    Structure. 2003 Mar;11(3):243-51. Review.
    PubMed

2002

  • publication

    Folding and association of the human cell cycle regulatory proteins ckshs1 and ckshs2.

    Seeliger MA, Schymkowitz JW, Rousseau F, Wilkinson HR, Itzhaki LS.
    Biochemistry. 2002 Jan 29;41(4):1202-10.
    PubMed
  • publication

    Characterisation of the BRCT domains of the breast cancer susceptibility gene product BRCA1.

    Ekblad CM, Wilkinson HR, Schymkowitz JW, Rousseau F, Freund SM, Itzhaki LS.
    J Mol Biol. 2002 Jul 12;320(3):431-42.
    PubMed
  • publication

    Surfing on protein folding energy landscapes.

    Schymkowitz JW, Rousseau F, Serrano L.
    Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):15846-8.
    PubMed
  • publication

    The structure of the transition state for folding of domain-swapped dimeric p13suc1.

    Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS.
    Structure. 2002 May;10(5):649-57.
    PubMed

2001

  • publication

    Observation of signal transduction in three-dimensional domain swapping.

    Schymkowitz JW, Rousseau F, Wilkinson HR, Friedler A, Itzhaki LS.
    Nat Struct Biol. 2001 Oct;8(10):888-92.
    PubMed
  • publication

    Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues.

    Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS.
    Proc Natl Acad Sci U S A. 2001 May 8;98(10):5596-601.
    PubMed

2000

  • publication

    Sequence conservation provides the best prediction of the role of proline residues in p13suc1.

    Schymkowitz JW, Rousseau F, Itzhaki LS.
    J Mol Biol. 2000 Aug 4;301(1):199-204.
    PubMed
  • publication

    The folding pathway of the cell-cycle regulatory protein p13suc1: clues for the mechanism of domain swapping.

    Schymkowitz JW, Rousseau F, Irvine LR, Itzhaki LS.
    Structure. 2000 Jan 15;8(1):89-100.
    PubMed

1998

  • publication

    Stability and folding of the cell cycle regulatory protein, p13(suc1).

    Rousseau F, Schymkowitz JW, Sánchez del Pino M, Itzhaki LS.
    J Mol Biol. 1998 Nov 27;284(2):503-19.
    PubMed