62 research outputs found
Dataset: Polystyrene and SARS-CoV-2 S protein MD simulations
No full textCoordinates (input files and equilibrated structures) corresponding to the MD simulations reported in Sahihi and Faraudo, J. Chem. Inf. Model. 2022, 62, 16, 3814–3824 https://doi.org/10.1021/acs.jcim.2c00562 . Please cite this publication and the dataset in any use of the data.
The coordinate files in pdb format include fully glycosylated structures of the S1 subunit of SARS-CoV-2 spike protein (up and down confirmations) and a polystyrene slab
Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface
No full text[Image: see text] A prominent feature of coronaviruses is the presence of a large glycoprotein spike (S) protruding from the viral particle. The specific interactions of a material with S determine key aspects such as its possible role for indirect transmission or its suitability as a virucidal material. Here, we consider all-atom molecular dynamics simulations of the interaction between a polymer surface (polystyrene) and S in its up and down conformations. Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects. Also, previous atomic force microscopy (AFM) experiments showed substantial adhesion of S over polystyrene, stronger than in other common materials. Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π–π interactions with S amino acids and glycans. The interaction was stronger for the case of S in the up conformation, which exposes one highly flexible receptor binding domain (RBD) that adjusts its conformation to interact with the polymer surface. In this case, the interaction has similar contributions from the RBD and glycans. In the case of S in the down conformation, the interaction with the polystyrene surface was weaker and it was dominated by glycans located near the RBD. We do not find significant structural changes in the conformation of S, a result which is in deep contrast to our previous results with another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2 virions may adsorb strongly over plastic surfaces without significantly affecting their infectivity
Comment on “Nanoscale Wetting of Crystalline Cellulose”
No full textThis work was supported by the Spanish Ministry of Science and Innovation through Grant No. RTI2018-096273-B-I00, and the “Severo Ochoa” Grant No. CEX2019-000917-S for Centres of Excellence in R&D awarded to ICMABPeer reviewe
Interaction between SARS-CoV-2 spike glycoprotein and human skin models: a molecular dynamics study
No full textThe possibility of contamination of human skin by infectious virions plays an important role in indirect transmission of respiratory viruses but little is known about the fundamental physico-chemical aspects of the virus-skin interactions. In the case of coronaviruses, the interaction with surfaces (including the skin surface) is mediated by their large glycoprotein spikes that protrude from (and cover) the viral envelope. Here, we perform all atomic simulations between the SARS-CoV-2 spike glycoprotein and human skin models. We consider an "oily" skin covered by sebum and a "clean" skin exposing the stratum corneum. The simulations show that the spike tries to maximize the contacts with stratum corneum lipids, particularly ceramides, with substantial hydrogen bonding. In the case of "oily" skin, the spike is able to retain its structure, orientation and hydration over sebum with little interaction with sebum components. Comparison of these results with our previous simulations of the interaction of SARS-CoV-2 spike with hydrophilic and hydrophobic solid surfaces, suggests that the"soft" or "hard" nature of the surface plays an essential role in the interaction of the spike protein with materials.This work was supported by the Spanish Ministry of Science
and Innovation through Grant No. RTI2018-096273-B-I00, the
“Severo Ochoa” Grant No.CEX2019-000917-S for Centres of Excellence in R&D awarded to ICMAB and the FPI grant PRE2020-
093689 awarded to M.D. We thank the CESGA supercomputing
center for computer time and technical support at the Finisterrae supercomputer. M.D. is enrolled in the Material Sciences PhD
program of the Universitat Autonoma de Barcelona.Peer reviewe
L'Anatomia artística a l"Escola de Belles Arts de Barcelona. Els casos de Jeroni Faraudo (1823-1886) i de Tiberio Ávila (1843-1932)
No full text[cat] Aquest article se centra en la significació i transcendència de l"assignatura d"Anatomia artística a l"Escola de Belles Arts de Barcelona durant la segona meitat del segle XIX i principis de segle XX. S"empren, com a fil conductor, les figures de Jeroni Faraudo i Condeminas (1823-1886) i de Tiberio Ávila Rodríguez (1843-1932), els dos primers professors que impartiren la matèria i que romanen, en l"actualitat, pràcticament inèdits. El coneixement de l"ideari de Faraudo i d"Ávila permet completar el panorama de l"evolució de les idees estètiques a la Catalunya del moment i, alhora, contribueix a la comprensió de l"erosió de la primacia de l"antic en l"aprenentatge oficial de les arts a Catalunya. [spa] Este artículo se centra en la significación y transcendencia de la asignatura de Anatomía artística en la Escuela de Bellas Artes de Barcelona durante la segunda mitad del siglo XIX y principios de siglo XX. Se emplean, como hilo conductor, las figuras de Gerónimo Faraudo Condeminas (1823-1886) y de Tiberio Ávila Rodríguez (1843-1932), los dos primeros profesores que impartieron la materia y que permanecen, en la actualidad, prácticamente inéditos. El conocimiento del ideario de Faraudo y de Ávila permite completar el panorama de la evolución de las ideas estéticas en la Cataluña del momento y, al mismo tiempo, contribuye a la comprensión de la erosión de la primacía del antiguo en el aprendizaje oficial de las artes en Cataluña. [eng]This article focuses on the subject of Artistic Anatomy at the Barcelona School of Fine Arts during the second half of the 19th and early 20th centuries, discussing its signification. The connecting thread of this article are Jeroni Faraudo i Condeminas (1823-1886) and Tiberio Ávila Rodríguez (1843-1932), its first two teachers, who remain nowadays practically unknown. The knowledge of their ideas completes the history of contemporary Catalan aesthetics and also contributes to the comprehension of the erosion in the primacy of the use of ancient models in the official artistic teaching in Catalonia
A comparative evaluation of a new fully automated assay for von Willebrand factor collagen binding activity to an established method
No full textIntroduction: Laboratory diagnosis of von Willebrand disease (VWD) is made by the measurement of von Willebrand factor (VWF) protein level and its activities. Current VWF activity tests include ristocetin cofactor and collagen binding (VWF:CB) assays. Aim: We have undertaken an evaluation of a new fully automated VWF:CB assay relative to an established enzyme-linked immunosorbent assay (ELISA) method. Methods: The two analytical systems operate with different detection principles: a chemiluminescent method performed on ACL AcuStar Analyzer (the former) and a colorimetric ELISA by Asserachrom Stago (the latter) (type III collagen from human placenta). The HemosIL AcuStar VWF:CB assay is a chemiluminescent 2-step immunoassay that uses magnetic particles coated with a type III collagen triple-helical peptide. VWF:CB levels were determined in 50 healthy subjects and 100 VWD patients (22 type 1, 73 type 2 and 5 type 3). Results: Eleven VWD samples reported VWF:CB values below the lower detection limit of one or both methods. The new method showed a good correlation with the ELISA method (r >.9, mean bias 3.85 IU/dL) in both healthy and VWD samples. One of 150 samples gave inconsistent results using the two assays, leading to an uncertain diagnosis of VWD type 1 (ELISA method) or type 2 MCB (fully automated method). Conclusion: The new assay is rapid and simple to use, with its ready-to-use reagent cartridges. This VWF:CB assay, in addition to the measurement of VWF:Ag and VWF:RCo made on the same platform, gives additional information for the diagnosis of VWD in both nonspecialized and reference laboratories
L'Anatomia artística a l"Escola de Belles Arts de Barcelona. Els casos de Jeroni Faraudo (1823-1886) i de Tiberio Ávila (1843-1932)
No full text[cat] Aquest article se centra en la significació i transcendència de l"assignatura d"Anatomia artística a l"Escola de Belles Arts de Barcelona durant la segona meitat del segle XIX i principis de segle XX. S"empren, com a fil conductor, les figures de Jeroni Faraudo i Condeminas (1823-1886) i de Tiberio Ávila Rodríguez (1843-1932), els dos primers professors que impartiren la matèria i que romanen, en l"actualitat, pràcticament inèdits. El coneixement de l"ideari de Faraudo i d"Ávila permet completar el panorama de l"evolució de les idees estètiques a la Catalunya del moment i, alhora, contribueix a la comprensió de l"erosió de la primacia de l"antic en l"aprenentatge oficial de les arts a Catalunya. [spa] Este artículo se centra en la significación y transcendencia de la asignatura de Anatomía artística en la Escuela de Bellas Artes de Barcelona durante la segunda mitad del siglo XIX y principios de siglo XX. Se emplean, como hilo conductor, las figuras de Gerónimo Faraudo Condeminas (1823-1886) y de Tiberio Ávila Rodríguez (1843-1932), los dos primeros profesores que impartieron la materia y que permanecen, en la actualidad, prácticamente inéditos. El conocimiento del ideario de Faraudo y de Ávila permite completar el panorama de la evolución de las ideas estéticas en la Cataluña del momento y, al mismo tiempo, contribuye a la comprensión de la erosión de la primacía del antiguo en el aprendizaje oficial de las artes en Cataluña. [eng]This article focuses on the subject of Artistic Anatomy at the Barcelona School of Fine Arts during the second half of the 19th and early 20th centuries, discussing its signification. The connecting thread of this article are Jeroni Faraudo i Condeminas (1823-1886) and Tiberio Ávila Rodríguez (1843-1932), its first two teachers, who remain nowadays practically unknown. The knowledge of their ideas completes the history of contemporary Catalan aesthetics and also contributes to the comprehension of the erosion in the primacy of the use of ancient models in the official artistic teaching in Catalonia
Effect of surfactants on SARS-CoV-2: Molecular Dynamics Simulations
No full textSurfactants are commonly used as disinfection agents in personal care products against bacteria and viruses, including SARS-CoV-2. However, there is a lack of understanding of the molecular mechanisms of the inactivation of viruses by surfactants. Here, we employ coarse grain (CG) and all-atom (AA) molecular dynamics simulations to investigate the interaction between general families of surfactants and the SARS-CoV-2 virus. To this end, we considered a CG model of a full virion. Overall, we found that surfactants have only a small impact over the virus envelope, being inserted into the envelope without dissolving it or generating pores, at the conditions considered here. However, we found that surfactants may induce a deep impact on the spike protein of the virus (responsible for its infectivity), easily covering it and inducing its collapse over the envelope surface of the virus. AA simulations confirmed that both negatively and positively charged surfactants are able to extensively adsorb over the spike protein and get inserted into the virus envelope. Our results suggest that the best strategy for the design of surfactants as virucidal agents will be to focus on those strongly interacting with the spike protein.This work was supported by the Spanish Ministry of Science and Innovation through Grant No. PID2021-124297NBC33, the “Severo Ochoa” Grant No. CEX2019-000917-S for
Centres of Excellence in R&D awarded to ICMAB and the
FPI grant PRE2020-093689 awarded to M. D. We thank the
CESGA supercomputing center for computer time and technical support at the Finisterrae supercomputer.
We thank Dr. Alvin Yu and Prof. G.A.Voth (University
of Chicago) for their help on the implementation of the virus
model and for providing us the code for the "Two Gaussian"
potential.
M. D. is enrolled in the Material Sciences PhD program of
the Universitat Autonoma de BarcelonaN
Computer Simulation of the interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals
No full textCoinage metals like silver, gold and copper are historically known as materials with anti-infective properties; but the mechanism behind these properties is not yet clear, and several features seem to be effective in this regard. Here, we used an all-atom molecular dynamics simulation method to investigate the interaction of up and down conformations of the S1 subunit of the SARS-CoV-2 spike protein with the (100) surface of Au, Ag and Cu. Our results revealed that spike protein is adsorbed onto the surface of these metals, being the Cu-metal with the highest interaction with the spike and Au, the metal which induces bigger structural changes in the spike. In our simulations, we considered the spike protein in both its up and down conformations. We found that the affinity of the metals for the up-conformation was higher than their affinity for the down conformation of the spike protein due to the interactions with the receptor binding domain that is exposed in the up conformation but hidden in the down conformation.
Comparing the present results for metals with those obtained in our previous MD simulations with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in the spike, larger than those obtained in our previous studies.This work was supported by Grant PID2021-124297NB-C33 funded by MCIN/AEI/
10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the
“European Union” or by the “European Union NextGenerationEU/PRTR” and by the “Severo
Ochoa” Program for Centers of Excellence in R&D (CEX2019-000917-S) awarded to ICMAB.
We thank the Spanish national supercomputing network (BSC-RES) for the award of computer
time at the Minotauro supercomputer. M Sahihi is supported by the European Union Horizon
2020 research and innovation programme under Marie Sklodowska-Curie Action Individual
Fellowship Grant Agreement No. 101026158.N
Licence with proverbs and other features in three Catalan translators of Franklin, Rojas and Rabelais: Gateà Vidal 1868, Antoni Bulbuena 1914, Lluís Faraudo 1929
No full textSón nombrosos els autors del darrer terç del segle XIX i principis del XX que dediquen part de la seva obra a traslladar clàssics i autors contemporanis al català. La traducció juga durant la Renaixença i el Noucentisme un paper destacat en el procés de consolidació i recuperació del català com a llengua literària. En aquest context, ens proposem fer una pinzellada il lustrada dels criteris paremiològics de tres traductors catalans d’obres clàssiques de tres llengües majoritàries: anglès, castellà i francès. Els torsimanys mostren a bastament la seva competència paremiològica, tot i que es permeten algunes llicències, sovint enginyoses i amenes, que la professionalització de l’ofici de la traducció actual no admetria. Gaietà Vidal, el 1868, fa de Lo camí de la fortuna de Benjamin Franklin, obra estructurada al voltant de cent aforismes, un anostrament més semblant a una recreació que a una traducció; Antoni Bulbena, traductor “vitalici” del Quixot al català, trasllada 383 parèmies de La Celestina el 1914; i finalment, Lluís Faraudo, que gira a la nostra llengua obres de François Rabelais des de 1909, farcides de jocs lingüístics i manipulacions fraseològiques, publica Gargantua l’any 1929.A number of authors of the late nineteenth and early twentieth centuries translated classic and contemporary works into Catalan. Translation plays an important role during the Renaixença and Noucentisme periods in consolidating the r ecovery of Catalan as a literary language. In this context, our aim is to give some illustrative examples of criteria for proverb translation in three Catalan translators of three classic works written in three worldwide languages: English, Spanish and Fre nch. The three translators exhibit their skill in translating proverbs while indulging at times in poetic license which, though often ingenious and entertaining, would fly in the face of professional translation practice today. Gaietà Vidal, in 1868, transforms Benjamin Franklin ́s Lo camí de la fortuna and its more than 100 aphorisms into a work that seems more are -‐‑ creation than a translation; Antoni Bulbena, “ lifelong ” translator of Don Quixote into Catalan, translates 383 proverbs from Celestina in 1914; finally, Lluís Faraudo, whose translations of works by François Rabelais from 1909 onward are rich in wordplay and idiomatic legerdemain, published Gargantua in 1929
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