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14 p, 2.8 MB |
Critical assessment of protein intrinsic disorder prediction
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Necci, Marco (University of Padua. Department of Biomedical Sciences) ;
Piovesan, Damiano (University of Padua. Department of Biomedical Sciences) ;
Hoque, M.T. (University of New Orleans. Computer Science) ;
Walsh, I. (Agency for Science, Technology and Research. Bioprocessing Technology Institute) ;
Iqbal, S. (Broad Institute of MIT and Harvard. Center for Psychiatric Research) ;
Vendruscolo, M. (University of Cambridge. Centre for Misfolding Diseases. Department of Chemistry) ;
Sormanni, P. (University of Cambridge. Centre for Misfolding Diseases. Department of Chemistry) ;
Wang, C. (Columbia University. Department of Medicine) ;
Raimondi, D. (ESAT-STADIUS. KU Leuven) ;
Sharma, R. (Fiji National University) ;
Zhou, Y. (Griffith University. Institute for Glycomics and School of Information and Communication Technology) ;
Litfin, T. (Griffith University. Institute for Glycomics and School of Information and Communication Technology) ;
Galzitskaya, Oxxana V (Russian Academy of Sciences. Institute of Theoretical and Experimental Biophysics) ;
Lobanov, M.Y. (Russian Academy of Sciences. Institute of Protein Research) ;
Vranken, W. (Vrije Universiteit Brussel. Interuniversity Institute of Bioinformatics in Brussels) ;
Wallner, B. (Linköping University. Department of Physics, Chemistry and Biology) ;
Mirabello, C. (Linköping University. Department of Physics, Chemistry and Biology) ;
Malhis, N. (University of British Columbia. Michael Smith Laboratories) ;
Dosztányi, Z. (Eötvös Loránd University. Department of Biochemistry) ;
Erdős, G. (Eötvös Loránd University. Department of Biochemistry) ;
Mészáros, B. (European Molecular Biology Laboratory. Structural and Computational Biology Unit) ;
Gao, J. (Nankai University. School of Mathematical Sciences and LPMC) ;
Wang, K. (Nankai University. School of Mathematical Sciences and LPMC) ;
Hu, G. (Nankai University. School of Statistics and Data Science) ;
Wu, Z. (Nankai University. School of Mathematical Sciences and LPMC) ;
Sharma, A. (University of the South Pacific. School of Engineering and Physics) ;
Hanson, J. (Griffith University. School of Engineering and Built Environment. Signal Processing Laboratory Griffith University. School of Engineering and Built Environment. Signal Processing Laboratory Signal Processing Laboratory. School of Engineering and Built Environment. Griffith University) ;
Callebaut, I. (Sorbonne Université. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie. Muséum National d'Histoire Naturelle) ;
Bitard-Feildel, T. (Sorbonne Université. Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie. Muséum National d'Histoire Naturelle) ;
Orlando, G. (VIB-KU Leuven. Switch Laboratorium.) ;
Peng, Z. (Tianjin University. Center for Applied Mathematics) ;
Xu, J. (Toyota Technological Institute at Chicago) ;
Wang, S. (Toyota Technological Institute at Chicago) ;
Jones, D.T. (University College London) ;
Cozzetto, D. (University College London) ;
Meng, F. (University of Alberta. Department of Electrical and Computer Engineering) ;
Yan, J. (University of Alberta. Department of Electrical and Computer Engineering) ;
Gsponer, J. (University of British Columbia. Michael Smith Laboratories) ;
Cheng, J. (University of Missouri. Department of Electrical Engineering and Computer Science) ;
Wu, T. (University of Missouri. Department of Electrical Engineering and Computer Science) ;
Kurgan, L. (Virginia Commonwealth University. Department of Computer Science) ;
Promponas, V.J. (University of Cyprus. Department of Biological Sciences. Bioinformatics Research Laboratory) ;
Tamana, S. (University of Cyprus. Department of Biological Sciences. Bioinformatics Research Laboratory) ;
Marino-Buslje, C. (Fundación Instituto Leloir (Buenos Aires, Argentina)) ;
Martínez-Pérez, E. (Fundación Instituto Leloir (Buenos Aires, Argentina)) ;
Chasapi, Anastasia (Centre for Research & Technology Hellas. Chemical Process & Energy Resources Institute) ;
Ouzounis, C. (Centre for Research & Technology Hellas. Chemical Process & Energy Resources Institute) ;
Dunker, A.K. (Indiana University School of Medicine. Center for Computational Biology and Bioinformatics) ;
Kajava, A.V. (University of Montpellier. Centre de Recherche en Biologie cellulaire de Montpellier) ;
Leclercq, J.Y. (University of Montpellier. Centre de Recherche en Biologie cellulaire de Montpellier) ;
Aykac-Fas, B. (Danish Cancer Society Research Center) ;
Lambrughi, M. (Danish Cancer Society Research Center) ;
Maiani, Emiliano (Danish Cancer Society Research Center) ;
Papaleo, E. (Danish Cancer Society Research Center) ;
Chemes, L.B. (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas) ;
Álvarez, L. (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas) ;
González-Foutel, N.S. (Universidad Nacional de San Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas) ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Pujols, Jordi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Palopoli, N. (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología) ;
Benítez, G.I. (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología) ;
Parisi, G. (Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología) ;
Bassot, Claudio (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Elofsson, A. (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Govindarajan, S. (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Lamb, J. (Stockholm University. Department of Biochemistry and Biophysics and Science for Life Laboratory) ;
Salvatore, M. (Copenhagen University. Department of Biology) ;
Hatos, A. (University of Padua. Department of Biomedical Sciences) ;
Monzon, A.M. (University of Padua. Department of Biomedical Sciences) ;
Bevilacqua, M. (University of Padua. Department of Biomedical Sciences) ;
Mičetić, I. (University of Padua. Department of Biomedical Sciences) ;
Minervini, G. (University of Padua. Department of Biomedical Sciences) ;
Paladin, L. (University of Padua. Department of Biomedical Sciences) ;
Quaglia, F. (University of Padua. Department of Biomedical Sciences) ;
Leonardi, E. (University of Padova - Pediatric Research Institute. Città della Speranza. Department of Woman and Child Health) ;
Davey, N. (The Institute of Cancer Research. Chelsea) ;
Horvath, T. (Research Centre for Natural Sciences. Institute of Enzymology) ;
Kovacs, O.P. (Research Centre for Natural Sciences. Institute of Enzymology) ;
Murvai, Nikoletta (Research Centre for Natural Sciences. Institute of Enzymology) ;
Pancsa, R. (Research Centre for Natural Sciences. Institute of Enzymology) ;
Schad, Eva (Research Centre for Natural Sciences. Institute of Enzymology) ;
Szabo, B. (Research Centre for Natural Sciences. Institute of Enzymology) ;
Tantos, A. (Research Centre for Natural Sciences. Institute of Enzymology) ;
Macedo-Ribeiro, S. (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Manso, J.A. (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Pereira, P.J.B. (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Davidović, R. (University of Belgrade. Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia.) ;
Veljkovic, N. (University of Belgrade. Vinča Institute of Nuclear Sciences - National Institute of thе Republic of Serbia.) ;
Hajdu-Soltész, B. (Eötvös Loránd University. Department of Biochemistry) ;
Pajkos, M. (Eötvös Loránd University. Department of Biochemistry) ;
Szaniszló, T. (Eötvös Loránd University. Department of Biochemistry) ;
Guharoy, M. (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Lazar, T. (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Macossay-Castillo, M. (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Tompa, P. (Vrije Universiteit Brussel. Structural Biology Brussels) ;
Tosatto, Silvio (University of Padua. Department of Biomedical Sciences)
Intrinsically disordered proteins, defying the traditional protein structure-function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. [...]
2021 - 10.1038/s41592-021-01117-3
Nature Methods, Vol. 18 (May 2021) , p. 472-481
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14 p, 2.5 MB |
Disease-associated mutations impacting BC-loop flexibility trigger long-range transthyretin tetramer destabilization and aggregation
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Esperante, Sebastián A. (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Varejāo, Nathalia (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Pinheiro, Francisca (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Sant'Anna, Ricardo (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Luque-Ortega, Juan Román (Centro de Investigaciones Biológicas Margarita Salas) ;
Alfonso, Carlos (Centro de Investigaciones Biológicas Margarita Salas) ;
Sora, Valentina (Technical University of Denmark. Cancer Systems Biology, Health and Technology Department) ;
Papaleo, Elena (Technical University of Denmark. Cancer Systems Biology, Health and Technology Department) ;
Rivas, Germán (Centro de Investigaciones Biológicas Margarita Salas) ;
Reverter i Cendrós, David (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Hereditary transthyretin amyloidosis (ATTR) is an autosomal dominant disease characterized by the extracellular deposition of the transport protein transthyretin (TTR) as amyloid fibrils. Despite the progress achieved in recent years, understanding why different TTR residue substitutions lead to different clinical manifestations remains elusive. [...]
2021 - 10.1016/j.jbc.2021.101039
Journal of biological chemistry, Vol. 297, Issue 3 (September 2021) , art. 101039
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15 p, 2.9 MB |
MED15 prion-like domain forms a coiled-coil responsible for its amyloid conversion and propagation
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Batlle Carreras, Cristina (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Calvo, Isabel (Institut de Ciència i Tecnologia de Barcelona. Institut de Recerca en Biomedicina) ;
Iglesias, Valentin (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
J. Lynch, Cian (Institut de Ciència i Tecnologia de Barcelona. Institut de Recerca en Biomedicina) ;
Gil-Garcia, Marcos (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Serrano, Manuel (Institut de Ciència i Tecnologia de Barcelona. Institut de Recerca en Biomedicina) ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular
A disordered to β-sheet transition was thought to drive the functional switch of Q/N-rich prions, similar to pathogenic amyloids. However, recent evidence indicates a critical role for coiled-coil (CC) regions within yeast prion domains in amyloid formation. [...]
2021 - 10.1038/s42003-021-01930-8
Communications Biology, Vol. 4 (March 2021) , art. 414
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9 p, 1.1 MB |
Atomistic fibrillar architectures of polar prion-inspired heptapeptides
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Peccati, Francesca (Centro de Investigación Cooperativa en Biociencias. Basque Research and Technology Alliance) ;
Díaz-Caballero, Marta (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Navarro, Susanna (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Rodríguez Santiago, Luis (Universitat Autònoma de Barcelona. Departament de Química) ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Sodupe Roure, Mariona (Universitat Autònoma de Barcelona. Departament de Química) ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular ;
Universitat Autònoma de Barcelona.
Departament de Química
This article provides the computational prediction of the atomistic architectures resulting from self-assembly of the polar heptapeptide sequences NYNYNYN, SYSYSYS and GYGYGYG. Using a combination of molecular dynamics and a newly developed tool for non-covalent interaction analysis, we uncover the properties of a new class of bionanomaterials, including hydrogen-bonded polar zippers, and the relationship between peptide composition, fibril geometry and weak interaction networks. [...]
2020 - 10.1039/d0sc05638c
Chemical science, Vol. 11, Issue 48 (December 2020) , p. 13143-13151
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