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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 (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Navarro Cantero, Susana (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Rodríguez Santiago, Luis (Universitat Autònoma de Barcelona. Departament de Química) ;
Ventura, Salvador (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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2.
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18 p, 1.7 MB |
MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments
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Martins, Pedro M. (Universidade do Porto. Instituto de Ciências Biomédicas Abel Salazar) ;
Navarro Cantero, Susana (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Silva, Alexandra (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Pinto, Maria F. (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Sárkány, Zsuzsa (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Figueiredo, Francisco (Universidade do Porto. Instituto de Ciências Biomédicas Abel Salazar) ;
Barbosa Pereira, Pedro José (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Pinheiro, Francisca (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bednarikova, Zuzana (Slovak Academy of Sciences. Department of Biophysics) ;
Burdukiewicz, Michal (Warsaw University of Technology. Faculty of Mathematics and Information Science) ;
Galzitskaya, Oxxana V. (Russian Academy of Sciences. Institute of Theoretical and Experimental Biophysics) ;
Gazova, Zuzana (Slovak Academy of Sciences. Department of Biophysics) ;
Gomes, Cláudio M. (Universidade de Lisboa. Departamento de Química e Bioquímica) ;
Pastore, Annalisa (Centre at King's College London. the Maurice Wohl Clinical Neuroscience Institute) ;
Serpell, Louise C. (University of Sussex. School of Life Sciences) ;
Skrabana, Rostislav (Slovak Academy of Sciences. Institute of Neuroimmunology) ;
Smirnovas, Vytautas (Vilnius University. Institute of Biotechnology) ;
Ziaunys, Mantas (Vilnius University. Institute of Biotechnology) ;
Otzen, Daniel E. (Aarhus University. Department of Molecular Biology and Genetics) ;
Ventura, Salvador (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Macedo-Ribeiro, Sandra (Universidade do Porto. Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde) ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. [...]
2020 - 10.3389/fnmol.2020.582488
Frontiers in molecular neuroscience, Vol. 13 (November 2020) , art. 582488
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3.
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12 p, 2.4 MB |
Inhibition of α-synuclein aggregation and mature fibril disassembling with a minimalistic compound, ZPDm
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Peña Díaz, Samuel (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pujols, Jordi (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pinheiro, Francisca (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Santos Suárez, Jaime (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pallarès i Goitiz, Irantzu (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Navarro Cantero, Susana (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Conde Gimenez, María (Universidad de Zaragoza. Instituto Aragonés de Investigaciones Sanitarias) ;
García, Jesús (Institut de Recerca Biomèdica) ;
Salvatella, Xavier (Institució Catalana de Recerca i Estudis Avançats) ;
Dalfo Capella, Esther (Universitat Autònoma de Barcelona. Facultat de Medicina) ;
Sancho, Javier (Universidad de Zaragoza. Instituto Aragonés de Investigaciones Sanitarias) ;
Ventura, Salvador (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular
Synucleinopathies are a group of disorders characterized by the accumulation of α-Synuclein amyloid inclusions in the brain. Preventing α-Synuclein aggregation is challenging because of the disordered nature of the protein and the stochastic nature of fibrillogenesis, but, at the same time, it is a promising approach for therapeutic intervention in these pathologies. [...]
2020 - 10.3389/fbioe.2020.588947
Frontiers in Bioengineering and Biotechnology, Vol. 8 (October 2020) , art. 588947
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4.
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10 p, 3.4 MB |
Rational design of small molecules able to inhibit α-synuclein amyloid aggregation for the treatment of Parkinson's disease
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Vittorio, Serena (Università degli Studi di Messina Viale Palatucci. Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali) ;
Adornato, Ilenia (Università degli Studi di Messina Viale Palatucci. Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali) ;
Gitto, Rosaria (Università degli Studi di Messina Viale Palatucci. Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali) ;
Peña Díaz, Samuel (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
De Luca, Laura (Università degli Studi di Messina Viale Palatucci. Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali) ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular
Parkinson's disease is one of the most common neurodegenerative disorders in elderly age. One of the mechanisms involved in the neurodegeneration appears related to the aggregation of the presynaptic protein alpha synuclein (α-syn) into toxic oligomers and fibrils. [...]
2020 - 10.1080/14756366.2020.1816999
Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 35, Issue 1 (September 2020) , p. 1727-1735
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5.
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12 p, 1.4 MB |
DispHred : a server to predict pH-dependent order-disorder transitions in intrinsically disordered proteins
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Santos Suárez, Jaime (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Iglesias, Valentin (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pintado Grima, Carlos (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Santos-Suárez, Juan (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Universitat Autònoma de Barcelona.
Departament de Bioquímica i de Biologia Molecular
The natively unfolded nature of intrinsically disordered proteins (IDPs) relies on several physicochemical principles, of which the balance between a low sequence hydrophobicity and a high net charge appears to be critical. [...]
2020 - 10.3390/ijms21165814
International journal of molecular sciences, Vol. 21, Issue 16 (August 2020) , art. 5814
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6.
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15 p, 4.1 MB |
Biasing the native α-synuclein conformational ensemble towards compact states abolishes aggregation and neurotoxicity
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Carija, Anita (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pinheiro, Francisca (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Pujols, Jordi (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Brás, Inês C. (University Medicine Göttingen) ;
Lázaro, Diana Fernandes (University Medicine Göttingen) ;
Santambrogio, Carlo (University of Milano-Bicocca. Dipartimento di Biotecnologie e Bioscienze) ;
Grandori, Rita (University of Milano-Bicocca. Dipartimento di Biotecnologie e Bioscienze) ;
Outeiro, Tiago F. (Max Planck Institute for Experimental Medicine) ;
Navarro Cantero, Susana (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
The aggregation of α-synuclein (α-syn) into amyloid fibrils is a major pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. The mechanisms underlying the structural transition of soluble and innocuous α-syn to aggregated neurotoxic forms remains largely unknown. [...]
2019 - 10.1016/j.redox.2019.101135
Redox biology, Vol. 22 (April 2019) , art. 101135
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8.
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18 p, 3.6 MB |
hnRNPDL phase separation is regulated by alternative splicing and disease-causing mutations accelerate its aggregation
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Batlle Carreras, Cristina (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Yang, Peiguo (St. Jude Children's Research Hospital. Department of Cell and Molecular Biology) ;
Coughlin, Maura (St. Jude Children's Research Hospital. Department of Cell and Molecular Biology) ;
Messing, James (Howard Hughes Medical Institute) ;
Pesarrodona Roches, Mireia (Institut de Recerca Biomèdica) ;
Szulc, Elzbieta (Institut de Recerca Biomèdica) ;
Salvatella, Xavier (Institut de Recerca Biomèdica) ;
Kim, Hong Joo (St. Jude Children's Research Hospital. Department of Cell and Molecular Biology) ;
Taylor, J. Paul (Howard Hughes Medical Institute) ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Prion-like proteins form multivalent assemblies and phase separate into membraneless organelles. Heterogeneous ribonucleoprotein D-like (hnRNPDL) is a RNA-processing prion-like protein with three alternative splicing (AS) isoforms, which lack none, one, or both of its two disordered domains. [...]
2020 - 10.1016/j.celrep.2019.12.080
Cell reports, Vol. 30, issue 4 (Jan. 2020) , p. 1117-1128
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9.
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12 p, 5.4 MB |
The biofilm-associated surface protein Esp of Enterococcus faecalis forms amyloid-like fibers
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Taglialegna, Agustina (Consejo Superior de Investigaciones Científicas (Espanya). Instituto de Agrobiotecnología) ;
Matilla-Cuenca, Leticia (Consejo Superior de Investigaciones Científicas (Espanya). Instituto de Agrobiotecnología) ;
Dorado-Morales, Pedro (Universidad Pública de Navarra. Departamento de Salud) ;
Navarro Cantero, Susana (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Garnett, James A. (Centre for Host Microbiome Interactions. Dental institute. King's College London) ;
Lasa, Iñigo (Universidad Pública de Navarra. Departamento de Salud) ;
Valle, Jaione (Consejo Superior de Investigaciones Científicas (Espanya). Instituto de Agrobiotecnología)
Functional amyloids are considered as common building block structures of the biofilm matrix in different bacteria. In previous work, we have shown that the staphylococcal surface protein Bap, a member of the Biofilm-Associated Proteins (BAP) family, is processed and the fragments containing the N-terminal region become aggregation-prone and self-assemble into amyloid-like structures. [...]
2020 - 10.1038/s41522-020-0125-2
npj biofilms and microbiomes, Vol. 6, issue 1 (2020) , art. 15
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8 p, 674.6 KB |
DisProt : intrinsic protein disorder annotation in 2020
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Hatos, Andras (University of Padova. Department of Biomedical Sciences) ;
Hajdu-Soltész, Borbála (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Monzon, Alexander M. (Department of Biomedical Sciences. University of Padova) ;
Palopoli, Nicolas (Departamento de Ciencia y Tecnología. Universidad Nacional de Quilmes-CONICET) ;
Álvarez, Lucía (Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO. Universidad Nacional de San Martín) ;
Aykac-Fas, Burcu (Computational Biology Laboratory. Danish Cancer Society Research Center) ;
Bassot, Claudio (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Benítez, Guillermo I. (Departamento de Ciencia y Tecnología. Universidad Nacional de Quilmes-CONICET) ;
Bevilacqua, Martina (Department of Biomedical Sciences. University of Padova) ;
Chasapi, Anastasia (Biological Computation and Process Laboratory. Chemical Process and Energy Resources Institute. Centre for Research and Technology Hellas) ;
Chemes, Lucía (Departamento de Fisiología y Biología Molecular y Celular (DFBMC). Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires) ;
Davey, NormanE. (Division of Cancer Biology. Institute of Cancer Research) ;
Davidović, Radoslav (Laboratory for Bioinformatics and Computational Chemistry. Institute of Nuclear Sciences Vinca. University of Belgrade) ;
Dunker, A. Keith (Center for Computational Biology and Bioinformatics. Indiana University School of Medicine) ;
Elofsson, Arne (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Gobeill, Julien (Swiss Institute of Bioinformatics and HES-SO\HEG) ;
Foutel, Nicolás S.G. (Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Biotecnológicas IIBIO. Universidad Nacional de San Martín) ;
Sudha, Govindarajan (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Guharoy, Mainak (VIB-VUB Center for Structural Biology. Flanders Institute for Biotechnology (VIB)) ;
Horvath, Tamas (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Iglesias, Valentin (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Kajava, Andrey V. (Institut de Biologie Computationnelle(IBC)) ;
Kovacs, Orsolya P. (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Lamb, John (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Lambrughi, Matteo (Computational Biology Laboratory. Danish Cancer Society Research Center) ;
Lazar, Tamas (VIB-VUB Center for Structural Biology. Flanders Institute for Biotechnology (VIB)) ;
Leclercq, Jeremy Y. (Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM). UMR 5237 CNRS. Université Montpellier) ;
Leonardi, Emanuela (Fondazione Istituto di Ricerca Pediatrica (IRP). Città della Speranza) ;
MacEdo-Ribeiro, Sandra (Instituto de Biologia Molecular e Celular (IBMC). Instituto de Investigação e Inovação em Saúde (i3S). Universidade Do Porto) ;
MacOssay-Castillo, Mauricio (VIB-VUB Center for Structural Biology. Flanders Institute for Biotechnology (VIB)) ;
Maiani, Emiliano (Computational Biology Laboratory. Danish Cancer Society Research Center) ;
Manso, José A. (Instituto de Biologia Molecular e Celular (IBMC). Instituto de Investigação e Inovação em Saúde (i3S). Universidade Do Porto) ;
Marino-Buslje, Cristina (Bioinformatics Unit. Fundación Instituto Leloir) ;
Martínez-Pérez, Elisabeth (Bioinformatics Unit. Fundación Instituto Leloir) ;
Mészáros, Bálint (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Mičetić, Ivan (Department of Biomedical Sciences. University of Padova) ;
Minervini, Giovanni (Department of Biomedical Sciences. University of Padova) ;
Murvai, Nikoletta (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Necci, Marco (Department of Biomedical Sciences. University of Padova) ;
Ouzounis, Christos A. (Biological Computation and Process Laboratory. Chemical Process and Energy Resources Institute. Centre for Research and Technology Hellas) ;
Pajkos, Mátyás (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Paladin, Lisanna (Department of Biomedical Sciences. University of Padova) ;
Pancsa, Rita (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Papaleo, Elena (Translational Disease Systems Biology. Faculty of Health and Medical Sciences. Novo Nordisk Foundation Center. Protein Research University of Copenhagen) ;
Parisi, Gustavo (Departamento de Ciencia y Tecnología. Universidad Nacional de Quilmes-CONICET) ;
Pasche, Emilie (Swiss Institute of Bioinformatics and HES-SO\HEG) ;
Barbosa Pereira, Pedro J. (Instituto de Biologia Molecular e Celular (IBMC). Instituto de Investigação e Inovação em Saúde (i3S). Universidade Do Porto) ;
Promponas, Vasilis J. (Bioinformatics Research Laboratory. Department of Biological Sciences. University of Cyprus) ;
Pujols, Jordi (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Quaglia, Federica (Department of Biomedical Sciences. University of Padova) ;
Ruch, Patrick (Swiss Institute of Bioinformatics and HES-SO\HEG) ;
Salvatore, Marco (Department of Biochemistry and Biophysics and Science for Life Laboratory. Stockholm University. Box 1031) ;
Schad, Eva (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Szabo, Beata (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Szaniszló, Tamás (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Tamana, Stella (Bioinformatics Research Laboratory. Department of Biological Sciences. University of Cyprus) ;
Tantos, Agnes (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Veljkovic, Nevena (Laboratory for Bioinformatics and Computational Chemistry. Institute of Nuclear Sciences Vinca. University of Belgrade) ;
Ventura, Salvador (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Vranken, Wim (Interuniversity Institute of Bioinformatics in Brussels (IB2). ULB-VUB) ;
Dosztányi, Zsuzsanna (MTA-ELTE Lendület Bioinformatics Research Group. Department of Biochemistry. Eötvös Loránd University) ;
Tompa, Peter (Institute of Enzymology. Research Centre for Natural Sciences. Hungarian Academy of Sciences) ;
Tosatto, Silvio C.E. (CNR Institute of Neurosceince) ;
Piovesan, Daminao (Department of Biomedical Sciences. University of Padova)
The Database of Protein Disorder (DisProt, URL: https://disprot. org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. [...]
2020 - 10.1093/nar/gkz975
Nucleic acids research, Vol. 48, issue D1 (Jan. 2020) , p. D269-D276
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