keyword
MENU ▼
Read by QxMD icon Read
search

Sonia longhi

keyword
https://www.readbyqxmd.com/read/29286306/insidde-a-server-for-designing-artificial-disordered-proteins
#1
Antoine Schramm, Philippe Lieutaud, Stefano Gianni, Sonia Longhi, Christophe Bignon
InSiDDe (In Silico Disorder Design) is a program for the in silico design of intrinsically disordered proteins of desired length and disorder probability. The latter is assessed using IUPred and spans values ranging from 0.55 to 0.95 with 0.05 increments. One to ten artificial sequences per query, each made of 50 to 200 residues, can be generated by InSiDDe. We describe the rationale used to set up InSiDDe and show that an artificial sequence of 100 residues with an IUPred score of 0.6 designed by InSiDDe could be recombinantly expressed in E...
December 29, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29262365/interfacial-properties-of-ntail-an-intrinsically-disordered-protein
#2
Anaïs Bénarouche, Johnny Habchi, Alain Cagna, Ofelia Maniti, Agnès Girard-Egrot, Jean-François Cavalier, Sonia Longhi, Frédéric Carrière
Intrinsically disordered proteins (IDPs) lack stable secondary and tertiary structure under physiological conditions in the absence of their biological partners and thus exist as dynamic ensembles of interconverting conformers, often highly soluble in water. However, in some cases, IDPs such as the ones involved in neurodegenerative diseases can form protein aggregates and their aggregation process may be triggered by the interaction with membranes. Although the interfacial behavior of globular proteins has been extensively studied, experimental data on IDPs at the air/water (A/W) and water/lipid interfaces are scarce...
December 19, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29197511/partner-mediated-polymorphism-of-an-intrinsically-disordered-protein
#3
Christophe Bignon, Francesca Troilo, Stefano Gianni, Sonia Longhi
Intrinsically disordered proteins (IDPs) recognize their partners through molecular recognition elements (MoREs). The MoRE of the C-terminal intrinsically disordered domain of the measles virus nucleoprotein (NTAIL) is partly pre-configured as an α-helix in the free form and undergoes α-helical folding upon binding to the X domain (XD) of the viral phosphoprotein. Beyond XD, NTAIL also binds the major inducible heat shock protein 70 (hsp70). So far, no structural information is available for the NTAIL/hsp70 complex...
November 29, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29138428/structural-disorder-and-induced-folding-within-two-cereal-aba-stress-and-ripening-asr-proteins
#4
Karama Hamdi, Edoardo Salladini, Darragh P O'Brien, Sébastien Brier, Alexandre Chenal, Ines Yacoubi, Sonia Longhi
Abscisic acid (ABA), stress and ripening (ASR) proteins are plant-specific proteins involved in plant response to multiple abiotic stresses. We previously isolated the ASR genes and cDNAs from durum wheat (TtASR1) and barley (HvASR1). Here, we show that HvASR1 and TtASR1 are consistently predicted to be disordered and further confirm this experimentally. Addition of glycerol, which mimics dehydration, triggers a gain of structure in both proteins. Limited proteolysis showed that they are highly sensitive to protease degradation...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28994375/-how-is-transcription-reinitiation-governed-in-measles-virus
#5
Louis-Marie Bloyet, Philippe Roche, Denis Gerlier, Sonia Longhi
No abstract text is available yet for this article.
October 2017: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/28972216/the-henipavirus-v-protein-is-a-prevalently-unfolded-protein-with-a-zinc-finger-domain-involved-in-binding-to-ddb1
#6
Edoardo Salladini, Vincent Delauzun, Sonia Longhi
Henipaviruses are severe human pathogens within the Paramyxoviridae family. Beyond the P protein, the Henipavirus P gene also encodes the V protein which shares with P its N-terminal, intrinsically disordered region (PNT) and possesses a unique C-terminal domain predicted to be folded and to bind zinc (ZnFD). Henipavirus V proteins antagonize IFN signaling through PNT-mediated binding to STAT1, and several paramyxoviral V proteins promote STAT1 degradation through binding to DDB1. Structural and molecular information on Henipavirus V proteins is lacking, and their ability to interact with DDB1 has not been documented yet...
October 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28661120/analyzing-the-folding-and-binding-steps-of-an-intrinsically-disordered-protein-by-protein-engineering
#7
Daniela Bonetti, Francesca Troilo, Angelo Toto, Maurizio Brunori, Sonia Longhi, Stefano Gianni
Intrinsically disordered proteins (IDPs) are functionally active despite lacking a well-defined three-dimensional structure. Such proteins often undergo a disorder-to-order transition, or induced folding, when binding to their specific physiological partner. Because of cooperativity, the folding and binding steps typically appear as a single event, and therefore, induced folding is extremely difficult to characterize experimentally. In this perspective, the interaction between the disordered C-terminal domain of the measles virus nucleoprotein NTAIL and the folded X domain of the viral phosphoprotein (XD) is particularly interesting because the inherent complexity of the observed kinetics allows characterization of the binding and folding steps individually...
July 25, 2017: Biochemistry
https://www.readbyqxmd.com/read/28600653/how-order-and-disorder-within-paramyxoviral-nucleoproteins-and-phosphoproteins-orchestrate-the-molecular-interplay-of-transcription-and-replication
#8
REVIEW
Sonia Longhi, Louis-Marie Bloyet, Stefano Gianni, Denis Gerlier
In this review, we summarize computational and experimental data gathered so far showing that structural disorder is abundant within paramyxoviral nucleoproteins (N) and phosphoproteins (P). In particular, we focus on measles, Nipah, and Hendra viruses and highlight both commonalities and differences with respect to the closely related Sendai virus. The molecular mechanisms that control the disorder-to-order transition undergone by the intrinsically disordered C-terminal domain (NTAIL) of their N proteins upon binding to the C-terminal X domain (XD) of the homologous P proteins are described in detail...
September 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28459531/the-folding-pathway-of-the-kix-domain
#9
Francesca Troilo, Daniela Bonetti, Angelo Toto, Lorenzo Visconti, Maurizio Brunori, Sonia Longhi, Stefano Gianni
The KIX domain is an 89-residues globular domain with an important role in mediating protein-protein interactions. The presence of two distinct binding sites in such a small domain makes KIX a suitable candidate to investigate the effect of the potentially divergent demands between folding and function. Here, we report an extensive mutational analysis of the folding pathway of the KIX domain, based on 30 site-directed mutants, which allow us to assess the structures of both the transition and denatured states...
June 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28328918/simultaneous-quantification-of-protein-order-and-disorder
#10
Pietro Sormanni, Damiano Piovesan, Gabriella T Heller, Massimiliano Bonomi, Predrag Kukic, Carlo Camilloni, Monika Fuxreiter, Zsuzsanna Dosztanyi, Rohit V Pappu, M Madan Babu, Sonia Longhi, Peter Tompa, A Keith Dunker, Vladimir N Uversky, Silvio C E Tosatto, Michele Vendruscolo
No abstract text is available yet for this article.
March 22, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/27965415/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#11
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
No abstract text is available yet for this article.
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27936158/modulation-of-re-initiation-of-measles-virus-transcription-at-intergenic-regions-by-pxd-to-ntail-binding-strength
#12
Louis-Marie Bloyet, Joanna Brunel, Marion Dosnon, Véronique Hamon, Jenny Erales, Antoine Gruet, Carine Lazert, Christophe Bignon, Philippe Roche, Sonia Longhi, Denis Gerlier
Measles virus (MeV) and all Paramyxoviridae members rely on a complex polymerase machinery to ensure viral transcription and replication. Their polymerase associates the phosphoprotein (P) and the L protein that is endowed with all necessary enzymatic activities. To be processive, the polymerase uses as template a nucleocapsid made of genomic RNA entirely wrapped into a continuous oligomer of the nucleoprotein (N). The polymerase enters the nucleocapsid at the 3'end of the genome where are located the promoters for transcription and replication...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27899601/disprot-7-0-a-major-update-of-the-database-of-disordered-proteins
#13
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...
January 4, 2017: 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
76785
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"