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https://www.readbyqxmd.com/read/27899601/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#1
Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J Oldfield, Maria Cristina Aspromonte, Norman E Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N Uversky, A Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C E Tosatto
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. The current release holds information on more than 800 entries of IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist and function without a well-defined three-dimensional structure. We have re-curated previous entries to purge DisProt from conflicting cases, and also upgraded the functional classification scheme to reflect continuous advance in the field in the past 10 years or so...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27223650/serological-based-monitoring-of-a-cohort-of-patients-with-chronic-chagas-disease-treated-with-benznidazole-in-a-highly-endemic-area-of-northern-argentina
#2
Leticia L Niborski, Vanina Grippo, Sonia O Lafón, Gabriela Levitus, Facundo García-Bournissen, Juan C Ramirez, Juan M Burgos, Margarita Bisio, Natalia A Juiz, Vilma Ayala, María Coppede, Verónica Herrera, Crescencia López, Ana Contreras, Karina A Gómez, Juan C Elean, Hugo D Mujica, Alejandro G Schijman, Mariano J Levin, Silvia A Longhi
This study aimed to evaluate well-documented diagnostic antigens, named B13, 1F8 and JL7 recombinant proteins, as potential markers of seroconversion in treated chagasic patients. Prospective study, involving 203 patients treated with benznidazole, was conducted from endemic areas of northern Argentina. Follow-up was possible in 107 out of them and blood samples were taken for serology and PCR assays before and 2, 3, 6, 12, 24 and 36 months after treatment initiation. Reactivity against Trypanosoma cruzi lysate and recombinant antigens was measured by ELISA...
May 24, 2016: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/27115638/predicting-conformational-disorder
#3
Philippe Lieutaud, François Ferron, Sonia Longhi
In the last two decades, it has become increasingly evident that a large number of proteins are either fully or partially disordered. Intrinsically disordered proteins are ubiquitous proteins that fulfill essential biological functions while lacking a stable 3D structure. Their conformational heterogeneity is encoded at the amino acid sequence level, thereby allowing intrinsically disordered proteins or regions to be recognized based on their sequence properties. The identification of disordered regions facilitates the functional annotation of proteins and is instrumental for delineating boundaries of protein domains amenable to crystallization...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27002146/identification-and-structural-characterization-of-an-intermediate-in-the-folding-of-the-measles-virus-x-domain
#4
Daniela Bonetti, Carlo Camilloni, Lorenzo Visconti, Sonia Longhi, Maurizio Brunori, Michele Vendruscolo, Stefano Gianni
Although most proteins fold by populating intermediates, the transient nature of such states makes it difficult to characterize their structures. In this work we identified and characterized the structure of an intermediate of the X domain of phosphoprotein (P) of measles virus. We obtained this result by a combination of equilibrium and kinetic measurements and NMR chemical shifts used as structural restraints in replica-averaged metadynamics simulations. The structure of the intermediate was then validated by rationally designing four mutational variants predicted to affect the stability of this state...
May 13, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/26684000/fuzzy-regions-in-an-intrinsically-disordered-protein-impair-protein-protein-interactions
#5
EDITORIAL
Antoine Gruet, Marion Dosnon, David Blocquel, Joanna Brunel, Denis Gerlier, Rahul K Das, Daniela Bonetti, Stefano Gianni, Monika Fuxreiter, Sonia Longhi, Christophe Bignon
Despite the partial disorder-to-order transition that intrinsically disordered proteins often undergo upon binding to their partners, a considerable amount of residual disorder may be retained in the bound form, resulting in a fuzzy complex. Fuzzy regions flanking molecular recognition elements may enable partner fishing through non-specific, transient contacts, thereby facilitating binding, but may also disfavor binding through various mechanisms. So far, few computational or experimental studies have addressed the effect of fuzzy appendages on partner recognition by intrinsically disordered proteins...
February 2016: FEBS Journal
https://www.readbyqxmd.com/read/26387109/order-and-disorder-in-the-replicative-complex-of-paramyxoviruses
#6
REVIEW
Jenny Erales, David Blocquel, Johnny Habchi, Matilde Beltrandi, Antoine Gruet, Marion Dosnon, Christophe Bignon, Sonia Longhi
In this review we summarize available data showing the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed description of the molecular mechanisms that govern the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (XD) of the homologous P proteins. We also show that a significant flexibility persists within NTAIL-XD complexes, which therefore provide illustrative examples of "fuzziness"...
2015: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/26184170/structural-disorder-within-paramyxoviral-nucleoproteins-and-phosphoproteins-in-their-free-and-bound-forms-from-predictions-to-experimental-assessment
#7
Johnny Habchi, Sonia Longhi
We herein review available computational and experimental data pointing to the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed molecular description of the mechanisms governing the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (PXD) of the homologous P proteins...
July 10, 2015: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/26071376/structural-disorder-within-paramyxoviral-nucleoproteins
#8
REVIEW
Sonia Longhi
In this review I summarize available data pointing to the abundance of structural disorder within the nucleoprotein (N) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. I provide a detailed description of the molecular mechanisms that govern the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (XD) of the homologous phosphoproteins. I also show that a significant flexibility persists within NTAIL-XD complexes, which makes them illustrative examples of "fuzziness"...
September 14, 2015: FEBS Letters
https://www.readbyqxmd.com/read/25960280/insights-into-the-hendra-virus-ntail-xd-complex-evidence-for-a-parallel-organization-of-the-helical-more-at-the-xd-surface-stabilized-by-a-combination-of-hydrophobic-and-polar-interactions
#9
Jenny Erales, Matilde Beltrandi, Jennifer Roche, Maria Maté, Sonia Longhi
The Hendra virus is a member of the Henipavirus genus within the Paramyxoviridae family. The nucleoprotein, which consists of a structured core and of a C-terminal intrinsically disordered domain (N(TAIL)), encapsidates the viral genome within a helical nucleocapsid. N(TAIL) partly protrudes from the surface of the nucleocapsid being thus capable of interacting with the C-terminal X domain (XD) of the viral phosphoprotein. Interaction with XD implies a molecular recognition element (MoRE) that is located within N(TAIL) residues 470-490, and that undergoes α-helical folding...
August 2015: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/25637789/insights-into-the-coiled-coil-organization-of-the-hendra-virus-phosphoprotein-from-combined-biochemical-and-saxs-studies
#10
Matilde Beltrandi, David Blocquel, Jenny Erales, Pascale Barbier, Andrea Cavalli, Sonia Longhi
Nipah and Hendra viruses are recently emerged paramyxoviruses belonging to the Henipavirus genus. The Henipavirus phosphoprotein (P) consists of a large intrinsically disordered domain and a C-terminal domain (PCT) containing alternating disordered and ordered regions. Among these latter is the P multimerization domain (PMD). Using biochemical, analytical ultracentrifugation and small-angle X-ray scattering (SAXS) studies, we show that Hendra virus (HeV) PMD forms an elongated coiled-coil homotrimer in solution, in agreement with our previous findings on Nipah virus (NiV) PMD...
March 2015: Virology
https://www.readbyqxmd.com/read/25511246/demonstration-of-a-folding-after-binding-mechanism-in-the-recognition-between-the-measles-virus-ntail-and-x-domains
#11
Marion Dosnon, Daniela Bonetti, Angela Morrone, Jenny Erales, Eva di Silvio, Sonia Longhi, Stefano Gianni
In the past decade, a wealth of experimental data has demonstrated that a large fraction of proteins, while functional, are intrinsically disordered at physiological conditions. Many intrinsically disordered proteins (IDPs) undergo a disorder-to-order transition upon binding to their biological targets, a phenomenon known as induced folding. Induced folding may occur through two extreme mechanisms, namely conformational selection and folding after binding. Although the pre-existence of ordered structures in IDPs is a prerequisite for conformational selection, it does not necessarily commit to this latter mechanism, and kinetic studies are needed to discriminate between the two possible scenarios...
March 20, 2015: ACS Chemical Biology
https://www.readbyqxmd.com/read/25510932/molecular-basis-for-structural-heterogeneity-of-an-intrinsically-disordered-protein-bound-to-a-partner-by-combined-esi-im-ms-and-modeling
#12
Annalisa D'Urzo, Albert Konijnenberg, Giulia Rossetti, Johnny Habchi, Jinyu Li, Paolo Carloni, Frank Sobott, Sonia Longhi, Rita Grandori
Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered N(TAIL) domain and the phosphoprotein X domain (P(XD)) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase...
March 2015: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/25492314/dynamics-of-the-intrinsically-disordered-c-terminal-domain-of-the-nipah-virus-nucleoprotein-and-interaction-with-the-x-domain-of-the-phosphoprotein-as-unveiled-by-nmr-spectroscopy
#13
Lorenzo Baronti, Jenny Erales, Johnny Habchi, Isabella C Felli, Roberta Pierattelli, Sonia Longhi
We provide an atomic-resolution description based on NMR spectroscopy, of the intrinsically disordered C-terminal domain of the Nipah virus nucleoprotein (NTAIL ), both in its isolated state and within the nucleocapsid (NC). Within the NC the second half of NTAIL retains conformational behavior similar to that of isolated NTAIL , whereas the first half of NTAIL becomes much more rigid. In spite of the mostly disordered nature of NTAIL , chemical shifts and relaxation measurements show a significant degree of α-helical sampling in the molecular recognition element (MoRE) involved in binding to the X domain (XD) of the phosphoprotein, with this preconfiguration being more pronounced than in the NTAIL domain from the cognate Hendra virus...
January 19, 2015: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/25022622/elevated-antibody-reactivity-to-measles-virus-ncore-protein-among-patients-with-multiple-sclerosis-and-their-healthy-siblings-with-intrathecal-oligoclonal-immunoglobulin-g-production
#14
Linn Persson, Sonia Longhi, Johanna Enarsson, Oluf Andersen, Sara Haghigi, Staffan Nilsson, Martin Lagging, Maria Johansson, Tomas Bergström
BACKGROUND: Patients with multiple sclerosis (MS) and their healthy siblings with the MS oligoclonal bands (OCB) trait, (a hyperimmune condition in form of two or more CSF enriched OCBs) harbor in cerebrospinal fluid (CSF) and serum elevated immunoglobulin G (IgG) titers against measles crude whole-cell antigen. The underlying mechanism resulting in the increased IgG antibody reactivity to measles remains unclear. The response may represent specific IgG reactivity to measles antigens or unspecific auto-antibodies targeting cellular components in the crude whole virus antigens commonly used in detection assays...
September 2014: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/25008930/sequence-of-events-in-measles-virus-replication-role-of-phosphoprotein-nucleocapsid-interactions
#15
Joanna Brunel, Damien Chopy, Marion Dosnon, Louis-Marie Bloyet, Patricia Devaux, Erica Urzua, Roberto Cattaneo, Sonia Longhi, Denis Gerlier
UNLABELLED: The genome of nonsegmented negative-strand RNA viruses is tightly embedded within a nucleocapsid made of a nucleoprotein (N) homopolymer. To ensure processive RNA synthesis, the viral polymerase L in complex with its cofactor phosphoprotein (P) binds the nucleocapsid that constitutes the functional template. Measles virus P and N interact through two binding sites. While binding of the P amino terminus with the core of N (NCORE) prevents illegitimate encapsidation of cellular RNA, the interaction between their C-terminal domains, P(XD) and N(TAIL) is required for viral RNA synthesis...
September 2014: Journal of Virology
https://www.readbyqxmd.com/read/24914970/coiled-coil-deformations-in-crystal-structures-the-measles-virus-phosphoprotein-multimerization-domain-as-an-illustrative-example
#16
David Blocquel, Johnny Habchi, Eric Durand, Marion Sevajol, François Ferron, Jenny Erales, Nicolas Papageorgiou, Sonia Longhi
The structures of two constructs of the measles virus (MeV) phosphoprotein (P) multimerization domain (PMD) are reported and are compared with a third structure published recently by another group [Communie et al. (2013), J. Virol. 87, 7166-7169]. Although the three structures all have a tetrameric and parallel coiled-coil arrangement, structural comparison unveiled considerable differences in the quaternary structure and unveiled that the three structures suffer from significant structural deformation induced by intermolecular interactions within the crystal...
June 2014: Acta Crystallographica. Section D, Biological Crystallography
https://www.readbyqxmd.com/read/24823319/structural-disorder-in-viral-proteins
#17
REVIEW
Bin Xue, David Blocquel, Johnny Habchi, Alexey V Uversky, Lukasz Kurgan, Vladimir N Uversky, Sonia Longhi
No abstract text is available yet for this article.
July 9, 2014: Chemical Reviews
https://www.readbyqxmd.com/read/24739139/introducing-protein-intrinsic-disorder
#18
REVIEW
Johnny Habchi, Peter Tompa, Sonia Longhi, Vladimir N Uversky
No abstract text is available yet for this article.
July 9, 2014: Chemical Reviews
https://www.readbyqxmd.com/read/24452480/diversification-of-epr-signatures-in-site-directed-spin-labeling-using-a-%C3%AE-phosphorylated-nitroxide
#19
Nolwenn Le Breton, Marlène Martinho, Kuanysh Kabytaev, Jérémie Topin, Elisabetta Mileo, David Blocquel, Johnny Habchi, Sonia Longhi, Antal Rockenbauer, Jérôme Golebiowski, Bruno Guigliarelli, Sylvain R A Marque, Valérie Belle
Site Directed Spin Labeling (SDSL) combined with EPR spectroscopy is a very powerful approach to investigate structural transitions in proteins in particular flexible or even disordered ones. Conventional spin labels are based on nitroxide derivatives leading to classical 3-line spectra whose spectral shapes are indicative of the environment of the labels and thus constitute good reporters of structural modifications. However, the similarity of these spectral shapes precludes probing two regions of a protein or two partner proteins simultaneously...
March 7, 2014: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/24086133/atomic-resolution-description-of-the-interaction-between-the-nucleoprotein-and-phosphoprotein-of-hendra-virus
#20
Guillaume Communie, Johnny Habchi, Filip Yabukarski, David Blocquel, Robert Schneider, Nicolas Tarbouriech, Nicolas Papageorgiou, Rob W H Ruigrok, Marc Jamin, Malene Ringkjøbing Jensen, Sonia Longhi, Martin Blackledge
Hendra virus (HeV) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family. The HeV genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid. Recruitment of the viral polymerase onto the nucleocapsid template relies on the interaction between the C-terminal domain, N(TAIL), of N and the C-terminal X domain, XD, of the polymerase co-factor phosphoprotein (P). Here, we provide an atomic resolution description of the intrinsically disordered N(TAIL) domain in its isolated state and in intact nucleocapsids using nuclear magnetic resonance (NMR) spectroscopy...
2013: PLoS Pathogens
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