Bending-torsional elasticity and energetics of the plus-end microtubule tip

Microtubules (MTs), mesoscopic cellular filaments, grow primarily by the addition of GTP-bound tubulin dimers at their dynamic flaring plus-end tips. They operate as chemomechanical energy transducers with stochastic transitions to an astounding shortening motion upon hydrolyzing GTP to GDP. Time-resolved dynamics of the MT tip—a key determinant of this behavior—as a function of nucleotide state, internal lattice strain, and stabilizing lateral interactions have not been fully understood. Here we use atomistic simulations to study the spontaneous relaxation of complete GTP-MT and GDP-MT tip models from unfavorable straight to relaxed splayed conformations and to comprehensively characterize the elasticity of MT tips. Our simulations reveal the dominance of viscoelastic dynamics of MT protofilaments during the relaxation process, driven by the stored bending-torsional strain and counterbalanced by the interprotofilament interactions. We show that the posthydrolysis MT tip is exposed to higher activation energy barriers for straight lattice formation, which translates into its inability to elongate. Our study provides an information-driven Brownian ratchet mechanism for the elastic energy conversion and release by MT tips and offers insights into the mechanoenzymatics of MTs

Choice of fluorophore affects dynamic DNA nanostructures

The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modelling, we demonstrate for 12 different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation—without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices

Le Service Européen pour l’action Extérieure á l’heure de son épreuve : Une contribution tenforcée de l’UE au maintien de la paix ?

Cet article a pour objet de s’intéresser à l’impact que la mise en place d’un nouvel organe comme le Service Européen pour l’Action Extérieure, extrêmement original et innovateur du point de vue institutionnel, pourrait avoir à court et moyen terme sur la capacité de l’UE pour décoller défnitivement en tant qu’acteur majeur et partenaire vraiment crédible dans le domaine du maintien de la paix. Le moment semble opportun pour le faire dans la mesure où, après quelques quatre ans d’existence et une fois surmontés un certain nombre de teething problems, un processus de réflexion sur les faiblesses et potentialités du SEAE est en cours au sein du système institutionnel de l’UE en vue d’une éventuelle révision de sa Décision de base.En este trabajo se propone un análisis del impacto que la creación y puesta en funcionamiento de un nuevo órgano tan original e innovador desde el punto de vista institucional como el Servicio Europeo de Acción Exterior podría ejercer, a corto y medio plazo, sobre la capacidad de la UE para afanzarse como actor realmente signifcativo y socio internacional creíble en el campo del mantenimiento de la paz. El momento parece oportuno para ello en la medida en que, tras cuatro años de existencia y una vez superado un buen número de difcultades iniciales, se ha abierto un proceso de reflexión sobre las defciencias y potencialidades del SEAE que podría conducir a una revisión de su Decisión fundacional.This paper aims to analyse the impact that the setup and functioning of a new body, as original and innovative from an institutional point of view as the European External Action Service, could have in the consolidation of the EU’s position as a signifcant and reliable international partner in peacekeeping, both in the short and medium terms. This timing appears appropriate to do so insofar as, after four years of existence and having overcome a signifcant number of teething problems, a reflection process on the weaknesses and potentialities of the EEAS is currently in place and could eventually lead to a review of its founding Decision

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density

Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit.

Microtubules (MTs) are key components of the cytoskeleton and play a central role in cell division and development. MT assembly is known to be associated with a structural change in αβ-tubulin dimers from kinked to straight conformations. How GTP binding renders individual dimers polymerization-competent, however, is still unclear. Here, we have characterized the conformational dynamics and energetics of unassembled tubulin using atomistic molecular dynamics and free energy calculations. Contradictory to existing allosteric and lattice models, we find that GTP-tubulin favors a broad range of almost isoenergetic curvatures, whereas GDP-tubulin has a much lower bending flexibility. Moreover, irrespective of the bound nucleotide and curvature, two conformational states exist differing in location of the anchor point connecting the monomers that affects tubulin bending, with one state being strongly favored in solution. Our findings suggest a new combined model in which MTs incorporate and stabilize flexible GTP-dimers with a specific anchor point state