Membrane models for molecular simulations of peripheral membrane proteins

Peripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their interfacial-binding site with membrane lipids remain difficult to observe directly. Their binding and unbinding mechanism, the conformational changes of the PMPs and their influence on the membrane structure are notoriously challenging to study experimentally. Molecular dynamics simulations are particularly useful to fill some knowledge-gaps and provide hypothesis that can be experimentally challenged to further our understanding of PMP-membrane recognition. Because of the time-scales of PMP-membrane binding events and the computational costs associated with molecular dynamics simulations, membrane models at different levels of resolution are used and often combined in multiscale simulation strategies. We here review membrane models belonging to three classes: atomistic, coarse-grained and implicit. Differences between models are rooted in the underlying theories and the reference data they are parameterized against. The choice of membrane model should therefore not only be guided by its computational efficiency. The range of applications of each model is discussed and illustrated using examples from the literature.publishedVersio

Hepatitis E virus RNA replication polyprotein: taking structural biology seriously

International audienceHepatitis E virus (HEV) infects approximately 20 million individuals each year allaround the world, both in developing and industrialized countries. It leads to 40,000–70,000 deaths annually, especially in immunocompromised patients and pregnant women.Despite its recognized major public health issue status and zoonotic potential, no specifictreatment is available. Indeed, HEV life cycle characterization is hampered by the lackof efficient infectious cell culture systems or in vivo models. A better knowledge of HEVvirology is therefore needed. By providing descriptions of the three-dimensional structuresof viral proteins at atomic level, structural biology can be a powerful tool to understandviral replication and help develop specific antivirals. In this comment, we describe how bothexperimental and advanced computational structural biology help to decipher HEV virologyand make a case for heeding its lessons

High rates of breast conservation for large ductal and lobular invasive carcinomas combining multimodality strategies

The literature reports low rates of breast conservation after neoadjuvant chemotherapy for operable breast cancers not amenable to initial breast-conserving surgery. This study aims to compare the outcome of lobular vs ductal carcinomas after neoadjuvant chemotherapy. Between 1989 and 1999, 750 patients with clinical stage II/IIIA ductal (672) or lobular (78) invasive breast carcinomas were treated at the Institut Curie with primary anthracycline-based polychemotherapy followed by either breast conservation (surgery and/or radiotherapy) or mastectomy. Median follow-up was 10 years. Clinical response to primary chemotherapy was significantly worse for lobular than for ductal carcinomas (47 vs 60%; P=0.04), but only histological grade remained predictive in multivariate analysis. Breast conservation was high for both ductal and lobular carcinomas (65 and 54%; P=0.07), due, in part, to the use of radiotherapy, either exclusive or preoperative, for respectively 26 and 40% of patients. The lobular type had no adverse effect, neither on locoregional control nor on overall survival, even in the group of patients treated with breast conservation

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Dynamique d'assemblage de la capside des norovirus

Noroviruses are the leading cause of acute viral gastroenteritis in humans and animas. Each year, they are responsible for 220 000 deaths and cost close to 65 billion euros.It’s a small single-stranded positive sense RNA virus. The capsid is composed of 90 dimers of a single structural protein (VP1) which consists of two main domains: the protruding domain (P) exposed to the biological environment, and the shell domain (S) which is the assembly module of the capsid .Using computational approaches such as homology modelling, simulated annealing, molecular dynamic simulations in all atoms and coarse grains systems, we are looking to determine the molecular basis of norovirus capsid assembly.Our results on the capsid assembly brick (dimer of VP1) indicate the presence of an asymmetry that can have a role in the first stages of self-assembly, which we confirm experimentally by SAXS.Our results on larger VP1 assemblages (pentamer and hexamer of dimers) also reveal a disruption of symmetry in the pentamer of dimer, leaving a preferred position for the insertion of an additional dimer and promoting anisotropic growth.We complete and specify the assembly model originally published by our team in 2013.Le norovirus est le virus de la gastroentérite virale aiguë chez les humains et les animaux. Chaque année, il est responsable de la mort de près de 220 000 personnes et un coût de près de 65 milliards d’euros.C’est un petit virus à ARN simple brin de polarité positive. Sa capside icosaédrique est composée de 90 dimères d’une seule protéine structurale (VP1) à deux domaines : le domaine de spicule (P) exposé à l’environnement biologique, et le domaine shell (S) qui est le module d’assemblage de la capside. Un intermédiaire d'assemblage serait le pentamère de dimères, mais expérimentalement c'est un intermédiaire de 10-11 dimères qui a été rapporté.En utilisant des approches computationnelles (modélisation par homologie, recuit simulé, simulation de dynamique moléculaire avec des systèmes tout atomes ou en gros grains) nous cherchons à déterminer les bases moléculaires de l’assemblage de la capside des norovirus.Nos résultats sur la brique d’assemblage de la capside (dimère de VP1) indiquent la présence d’une asymétrie pouvant avoir un rôle dans les premières étapes d’autoassemblage, que nous confirmons expérimentalement par SAXS.Nos résultats sur de plus gros assemblages (pentamère et hexamère de dimère) révèlent également une rupture de symétrie dans le pentamère de dimère, laissant une position privilégiée pour l’insertion d’un dimère supplémentaire et favorisant une croissance anisotropique.Nous complétons et précisons ainsi le modèle d’assemblage initialement publié par notre équipe en 2013

Norovirus Capsid Assembly

Le norovirus est le virus de la gastroentérite virale aiguë chez les humains et les animaux. Chaque année, il est responsable de la mort de près de 220 000 personnes et un coût de près de 65 milliards d’euros.C’est un petit virus à ARN simple brin de polarité positive. Sa capside icosaédrique est composée de 90 dimères d’une seule protéine structurale (VP1) à deux domaines : le domaine de spicule (P) exposé à l’environnement biologique, et le domaine shell (S) qui est le module d’assemblage de la capside. Un intermédiaire d'assemblage serait le pentamère de dimères, mais expérimentalement c'est un intermédiaire de 10-11 dimères qui a été rapporté.En utilisant des approches computationnelles (modélisation par homologie, recuit simulé, simulation de dynamique moléculaire avec des systèmes tout atomes ou en gros grains) nous cherchons à déterminer les bases moléculaires de l’assemblage de la capside des norovirus.Nos résultats sur la brique d’assemblage de la capside (dimère de VP1) indiquent la présence d’une asymétrie pouvant avoir un rôle dans les premières étapes d’autoassemblage, que nous confirmons expérimentalement par SAXS.Nos résultats sur de plus gros assemblages (pentamère et hexamère de dimère) révèlent également une rupture de symétrie dans le pentamère de dimère, laissant une position privilégiée pour l’insertion d’un dimère supplémentaire et favorisant une croissance anisotropique.Nous complétons et précisons ainsi le modèle d’assemblage initialement publié par notre équipe en 2013.Noroviruses are the leading cause of acute viral gastroenteritis in humans and animas. Each year, they are responsible for 220 000 deaths and cost close to 65 billion euros.It’s a small single-stranded positive sense RNA virus. The capsid is composed of 90 dimers of a single structural protein (VP1) which consists of two main domains: the protruding domain (P) exposed to the biological environment, and the shell domain (S) which is the assembly module of the capsid .Using computational approaches such as homology modelling, simulated annealing, molecular dynamic simulations in all atoms and coarse grains systems, we are looking to determine the molecular basis of norovirus capsid assembly.Our results on the capsid assembly brick (dimer of VP1) indicate the presence of an asymmetry that can have a role in the first stages of self-assembly, which we confirm experimentally by SAXS.Our results on larger VP1 assemblages (pentamer and hexamer of dimers) also reveal a disruption of symmetry in the pentamer of dimer, leaving a preferred position for the insertion of an additional dimer and promoting anisotropic growth.We complete and specify the assembly model originally published by our team in 2013

Effets de l activité physique adaptée sur la fonction aérobie et la fatigue chez des patientes atteintes d un cancer du sein en situation adjuvante et néo-adjuvante

Objectifs. Le but de cette étude est d'évaluer la fonction cardio-pulmonaire mesurée par la VO2pic dans le cancer du sein avant un traitement (CT-RT) et après la réalisation d'un programme d'activité physique adaptée (APA). Méthodes. Le bras A (entraînement en endurance et résistance) et le bras B (groupe contrôle). Cette étude inclus 3 temps d'évaluation. (T0 : avant CT-RT) ; T1 (semaine 27) and T2 : évaluation finale à 54 semaines). Les examens réalisés sont une épreuve d'effort cardio-pulmonaire évaluant la VO2pic, un test de marche de 6 min 5TM6), des tests de la force musculaire, des explorations fonctionnelles respiratoires, l'évaluation de l'activité physique à l'aide du questionnaire IPAQ, de la fatigue (MFI 20), qualité de vie (EORTC QLQ-C30), de l'anxiété et de la dépression (HADS) et pour finir une évaluation de la composition corporelle. Résultats. Entre juin 2012 et juin 2013 44 patientes ont été incluses dans l'étude. A T0, la moyenne d'âge était de 52,3 +- 11,7 ans pour le bras A et de 48,8 +-8 pour le bras B. Avant traitement la VO2pic était de 22,5 +- 4,4 ml.kg-1.min-1pour le bras A et de 23,4 +- 5,1 ml.min-1kg-1 pour le bras B. Après traitement, en analyse par intention de traiter, la différence entre nos 2 groupes était de 2,3 ml.min-1kg-1, alors qu'en analyse per-protocole cette différence est de 3,49 ml.min-1kg-1 et est significative. La distance de marche s'améliore de 21,75 +- 7,15 m pour le bras A (P=.016) et diminue de 9,54 +- 6,82 m pour le bras B (P=.0,43). Conclusions. Notre étude a réussi à prouver qu'un entraînement individualisé et à domicile est faisable et sûr pour des patientes atteintes d'un cancer du sein en situation adjuvante ou néoadjuvante.LIMOGES-BU Médecine pharmacie (870852108) / SudocSudocFranceF

De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation

International audienceHepatitis E virus (HEV), a major cause of acute viral hepatitis, is a single-stranded, positive-sense RNA virus. As such, it encodes a 1700-residue replication polyprotein pORF1 that directs synthesis of new viral RNA in infected cells. Here we report extensive modeling with AlphaFold2 of the full-length pORF1, and its production by in vitro translation. From this, we give a detailed update on the breakdown into domains of HEV pORF1. We also provide evidence that pORF1’s N-terminal domain is likely to oligomerize to form a dodecameric pore, homologously to what has been described for Chikungunya virus. Beyond providing accurate folds for its five domains, our work highlights that there is no canonical protease encoded in pORF1 and that flexibility in several functionally important regions rather than proteolytic processing may serve to regulate HEV RNA synthesis

Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.

International audienceA molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to the most complex carbohydrate molecules have been considered and can be depicted. This concerns the monosaccharide identification and classification, conformations, location in single or multiple branched chains, depiction of secondary structural elements and the essential constituting elements in very complex structures. Particular attention was given to cope with the accepted nomenclature and pictorial representation used in glycoscience. This achievement provides a continuum between the most popular ways to depict the primary structures of complex carbohydrates to visualizing their 3D structures while giving the users many options to select the most appropriate modes of representations including new features such as those provided by the use of textures to depict some molecular properties. These developments are incorporated in a stand-alone viewer capable of displaying molecular structures, biomacromolecule surfaces and complex interactions of biomacromolecules, with powerful, artistic and illustrative rendering methods. They result in an open source software compatible with multiple platforms, i.e., Windows, MacOS and Linux operating systems, web pages, and producing publication-quality figures. The algorithms and visualization enhancements are demonstrated using a variety of carbohydrate molecules, from glycan determinants to glycoproteins and complex protein-carbohydrate interactions, as well as very complex mega-oligosaccharides and bacterial polysaccharides and multi-stranded polysaccharide architectures

Dissecting peripheral protein-membrane interfaces.

Peripheral membrane proteins (PMPs) include a wide variety of proteins that have in common to bind transiently to the chemically complex interfacial region of membranes through their interfacial binding site (IBS). In contrast to protein-protein or protein-DNA/RNA interfaces, peripheral protein-membrane interfaces are poorly characterized. We collected a dataset of PMP domains representative of the variety of PMP functions: membrane-targeting domains (Annexin, C1, C2, discoidin C2, PH, PX), enzymes (PLA, PLC/D) and lipid-transfer proteins (START). The dataset contains 1328 experimental structures and 1194 AphaFold models. We mapped the amino acid composition and structural patterns of the IBS of each protein in this dataset, and evaluated which were more likely to be found at the IBS compared to the rest of the domains' accessible surface. In agreement with earlier work we find that about two thirds of the PMPs in the dataset have protruding hydrophobes (Leu, Ile, Phe, Tyr, Trp and Met) at their IBS. The three aromatic amino acids Trp, Tyr and Phe are a hallmark of PMPs IBS regardless of whether they protrude on loops or not. This is also the case for lysines but not arginines suggesting that, unlike for Arg-rich membrane-active peptides, the less membrane-disruptive lysine is preferred in PMPs. Another striking observation was the over-representation of glycines at the IBS of PMPs compared to the rest of their surface, possibly procuring IBS loops a much-needed flexibility to insert in-between membrane lipids. The analysis of the 9 superfamilies revealed amino acid distribution patterns in agreement with their known functions and membrane-binding mechanisms. Besides revealing novel amino acids patterns at protein-membrane interfaces, our work contributes a new PMP dataset and an analysis pipeline that can be further built upon for future studies of PMPs properties, or for developing PMPs prediction tools using for example, machine learning approaches