Academic literature on the topic 'Cryo EM 2'

Structural biology continues to benefit from an expanding toolkit, which is helping to gain unprecedented insight into the assembly and organization of multi-protein machineries, enzyme mechanisms and ligand/inhibitor binding. During the last ten years, cryoEM has become widely available and has provided a major boost to structure determination of membrane proteins and large multi-protein complexes. Many of the structures have now been made available at resolutions around 2 Å, where fundamental questions regarding enzyme mechanisms can be addressed. Over the years, the abbreviation cryoEM has been understood to stand for different things. We wish the wider community to engage and clarify the definition of cryoEM so that the expanding literature involving cryoEM is unified.

Background: The effect of Dps-DNA co-crystals formation, which occurs in stressed Escherichia coli cells exposed to extreme conditions, is well described in the literature. However, the exact mechanisms of co-crystals formation are yet to be postulated remaining largely unknown. Here we summarize the results obtained by our group over the last few years using cryo-Electron Microscopy (cryo-EM) and Small Angle X-ray Scattering (SAXS). Methods: Samples for cryo-EM were plunge frozen in liquid ethane with Vitrobot Mark IV and studied with Titan Krios (ThermoFisher Scientific, US) cryo-EM, equipped with Falcon 2 direct electron detector, Image corrector (CEOS, Germany), and Volta phase plate. Single Particle Analysis (SPA) and cryo-Electron Tomography (cryo-ET) studies were conducted with 300 kV accelerating voltage in low dose mode using EPU and Tomography software (ThermoFisher Scientific, US). Cryo-EM data processing was conducted using Warp, CryoSPARC, IMOD, EMAN, and Relion software packages. SAXS measurements were performed at the EMBL on the P12 BioSAXS beam line at the PETRAIII storage ring (DESY, Hamburg). Results: In this work, Dps-DNA complex formation is thoroughly studied using complementary cryo-EM (including SPA, cryo-ET, and subtomogram averaging) and SAXS methods. The formation of individual complexes of Dps with small linear DNA fragments and the Dps-Dps interaction was visualized using cryo-EM. It was found that Dps-DNA complex remains stable under various conditions and while the addition of different ions leads to the disruption of co-crystals, the process is completely or partially reversible. Conclusion: Recent studies conducted by our group showed that Dps-DNA co-crystals adopt triclinic or cubic crystal lattice (FEBS Lett., 2019; Biomolecules, 2020). Here we present the results on the studies of Dps interaction with small linear DNA fragments, demonstrate the effects of MgCl2, FeSO4, and EDTA on the Dps-DNA complex and individual Dps protein structure, discuss the influence of the temperature and time on the co-crystals.

The recently reported “UK variant” (B.1.1.7) of SARS-CoV-2 is thought to be more infectious than previously circulating strains as a result of several changes, including the N501Y mutation. We present a 2.9-Å resolution cryo-electron microscopy (cryo-EM) structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. This additional interaction provides a structural explanation for the increased ACE2 affinity of the N501Y mutant, and likely contributes to its increased infectivity. However, this mutation does not result in large structural changes, enabling important neutralization epitopes to be retained in the spike receptor binding domain. We confirmed this through biophysical assays and by determining cryo-EM structures of spike protein ectodomains bound to 2 representative potent neutralizing antibody fragments.

X-ray crystallography and cryo-electron microscopy (cryo-EM) are complementary techniques for structure determination. Crystallography usually reveals more detailed information, while cryo-EM is an extremely useful technique for studying large-sized macromolecules. As the gap between the resolution of crystallography and cryo-EM data narrows, the cryo-EM map of a macromolecule could serve as an initial model to solve the phase problem of crystal diffraction for high-resolution structure determination. FSEARCH is a procedure to utilize the low-resolution molecular shape for crystallographic phasing. The IPCAS (Iterative Protein Crystal structure Automatic Solution) pipeline is an automatic direct-methods-aided dual-space iterative phasing and model-building procedure. When only an electron-density map is available as the starting point, IPCAS is capable of generating a completed model from the phases of the input map automatically, without the requirement of an initial model. In this study, a hybrid method integrating X-ray crystallography with cryo-EM to help with structure determination is presented. With a cryo-EM map as the starting point, the workflow of the method involves three steps. (1) Cryo-EM map replacement: FSEARCH is utilized to find the correct translation and orientation of the cryo-EM map in the crystallographic unit cell and generates the initial low-resolution map. (2) Phase extension: the phases calculated from the correctly placed cryo-EM map are extended to high-resolution X-ray data by non-crystallographic symmetry averaging with phenix.resolve. (3) Model building: IPCAS is used to generate an initial model using the phase-extended map and perform model completion by iteration. Four cases (the lowest cryo-EM map resolution being 6.9 Å) have been tested for the general applicability of the hybrid method, and almost complete models have been generated for all test cases with reasonable R work/R free. The hybrid method therefore provides an automated tool for X-ray structure determination using a cryo-EM map as the starting point.

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Althoughα-helices can be detected from density maps at 5–8 Å resolutions,β-strands are challenging to detect at such density maps due to close-spacing ofβ-strands. The variety of shapes ofβ-sheets adds the complexity ofβ-strands detection from density maps. We propose a new approach to model traces ofβ-strands forβ-barrel density regions that are extracted from cryo-EM density maps. In the test containing eightβ-barrels extracted from experimental cryo-EM density maps at 5.5 Å–8.25 Å resolution,StrandRollerdetected about 74.26% of the amino acids in theβ-strands with an overall 2.05 Å 2-way distance between the detectedβ-traces and the observed ones, if the best of the fifteen detection cases is considered.

La capacité d'une cellule à faciliter le mouvement sélectif et rapide des ions et des petites molécules à travers la membrane plasmique est un processus biologique indispensable. Les canaux potassiques à rectification entrante (Kir) sont des protéines membranaires intégrales qui fournissent des voies sélectives aux ions K+ à travers la membrane cellulaire autrement imperméable, le long des gradients électrochimiques. Les canaux Kir permettent le passage des ions K+ dans les deux sens et régulent diverses fonctions chez les humains, notamment la fréquence cardiaque, le tonus vasculaire, la sécrétion d'insuline et l'équilibre salin et hydrique. L'importance physiologique des canaux Kir est mise en évidence par le fait que des défauts génétiquement héréditaires de ces gènes entraînent des maladies humaines (canalopathies). Nous nous intéressons particulièrement au syndrome d'Andersen, où des mutations du gène KCNJ2 codant pour la protéine Kir2.1 sont directement impliquées. Le syndrome d'Andersen (AS) est une maladie rare caractérisée par des arythmies cardiaques, des dysmorphies multiples et des paralysies périodiques. Le traitement disponible pour les patients atteints d’AS est empirique plutôt que rationnel en raison de la manque de connaissance de ce canal Kir2.1. Cette thèse visait à identifier les différences entre le canal Kir2.1 de type sauvage et deux canaux mutants causant l’AS afin de trouver des liens entre la structure et la fonction du Kir2.1 humain en utilisant une combinaison d'approches biochimiques, structurelles et fonctionnelles. Dans cette étude, nous avons exprimé le canal Kir2.1 humain dans la levure et l'avons purifié dans un détergent. Nous avons caractérisé l'interaction entre Kir2.1 et l'activateur essentiel PIP2, résolu par cryo-EM la première structure d'un canal Kir humain et exploré la reconstitution dans des systèmes modèles sans détergent comme les amphipols et les nanodisques. Les résultats de cette étude fourniront une base structurale et fonctionnelle pour mieux comprendre les mécanismes impliqués dans les canaux Kir et les effets de leurs mutations. Ce manuscrit est divisé en trois parties. La première partie présente les canaux Kir et l'état de l'art. La deuxième partie porte sur la caractérisation du canal potassique humain Kir2.1, la détermination de sa structure par cryo-EM et l'impact des mutations sur sa structure et sa fonction. La troisième partie présente deux mutations dans l'homologue bactérien KirBac3.1, qui partage des caractéristiques structurelles avec Kir2.1, pour donner un aperçu du mécanisme d’ouverture et fermeture des canaux Kir
The ability of a cell to facilitate the selective and rapid movement of ions and small molecules across the plasma membrane is one of the most fundamental biological processes. Inward rectifier potassium (Kir) channels are integral membrane proteins that provide K+-selective pathways across the otherwise impermeable cell membrane along the electrochemical gradients. Kir channels support the flow of K+ ions into and out of the cell and regulate various functions in the human body, including heart rate, vascular tone, insulin secretion, and salt and fluid balance. The physiological significance of Kir channels is highlighted by the fact that genetically-inherited defects in these genes result in human diseases (channelopathies). We are particularly interested in Andersen’s syndrome, where mutations in the KCNJ2 gene coding for Kir2.1 protein are directly involved. Andersen’s syndrome (AS) is a rare disease characterized by cardiac arrhythmias, dysmorphic features, and periodic paralysis. The available treatment for AS patients is empirical rather than rational due to the lack of knowledge of this Kir2.1 channel. This thesis aimed to identify the differences between the wild-type Kir2.1 channel and two mutant AS-causing channels to find links between the structure and the function of human Kir2.1 using a combination of biochemical, structural, and functional approaches. In this study, we recombinantly expressed the human Kir2.1 channel in yeast and purified it in detergent. We characterized the interaction between Kir2.1 and the essential activator PIP2, solved the first human Kir channel structure by cryo-EM, and explored reconstitution in detergent-free systems like amphipols and nanodiscs. The findings of this study will provide a structural and functional base to understand better the mechanisms involved in Kir channels and the effects of their mutations. This manuscript is divided into three parts. The first part introduces Kir channels and state-of-the-art. The second part focuses on the characterization of the human potassium channel Kir2.1, the determination of its structure by cryo-EM, and the impact of mutations on its structure and function. The third part presents two mutations in the bacterial homolog KirBac3.1, which shares structural features with Kir2.1, to provide insight into the gating mechanism of Kir channels

La régulation de la transcription est un processus dynamique faisant intervenir le recrutement de complexes protéiques impliqués dans le remodelage de la chromatine. Parmi eux, mon travail s’est focalisé sur le complexe NuRD (Nucleosome Remodeling and histone Deacetylation) et sa sous-unité de liaison à l’ADN CpG MBD3. Pour cela une approche de biologie structurale intégrative combinant la préparation biochimique, la caractérisation biophysique et l’étude structurale par cryo-EM et cristallographie aux rayons-X a été mise en place. Les caractérisations biophysiques de MBD3 ont permis de mettre en évidence son interaction avec un ADN non-modifié CpG et des cristaux diffractant jusqu’à 3.9 Å ont été obtenu. De plus la région désordonnée en aval du domaine de liaison a été identifiée et son impact dans la formation de complexe caractérisé. Des cristaux pour les différentes constructions en complexe avec l’ADN ont été obtenus et sont actuellement optimisés. Enfin l’optimisation de la purification et la préparation du complexe, ont permis la visualisation du complexe NuRD et mettent en avant pour la première fois une organisation en domaines du complexe
Transcription regulation of chromatin is a very dynamic process regulated through the recruitment of chromatin-remodeling complexes. My work focuses on NuRD for Nucleosome remodeling and histones deacetylation complex a 1 MDa multi-subunit protein complex and its subunit MBD3 a CpG-binding protein and more precisely on an integrated biology approach of this molecular assembly and its interaction with DNA. It combines biochemical preparation, biophysical characterization, single particle cryo-eletron microscopy and x-ray crystallography. Biophysical analysis show that MBD domain of MBD3 interacts with unmodified CpG DNA, a crystal diffracting up to 3.9 Å were obtained. Moreover a C-terminal intrinsically disordered region of MBD3 were identified and despite is inherent disorder seems to increase the binding affinity of MBD3 for DNA. Crystals were obtained for both constructs in complex with DNA and are currently optimized.Cryo-EM study of NuRD complex allows us to develop and optimized purification and grids preparation for the visualization of the complex. The present results reveal a domain organization of the complex never identify before

Une approche de biologie structurale intégrative a été mise à profit pour l'étude de l’organisation structurale du complexe NuRD. Mon travail s'est focalisé essentiellement sur trois sous-unités du complexe: MBD3, RbAp46 et RbAp48. J'ai mis en place les protocoles de production et de purification de ces différentes sous-unités, et les ai caractérisé biophysiquement par diverses méthodes. Nous avons ensuite entrepris des études de liaisons sur des nucléosomes reconstitués au laboratoire. Pour MBD3, l'optimisation du complexe nous a permis d'obtenir des cristaux diffractant jusqu'à 7 A de résolution. Parallèlement, une reconstruction 3D préliminaire à partir de données de cryo-microscopie électronique a pu être obtenue à 25A de résolution. Pour RbAp46/48, nous avons pu montrer que ces protéines formaient un complexe stable avec le nucléosome, pavant la voie pour leur future étude structurale par cryo-microscopie électronique ou cristallographie aux rayons-X
An integrative structural biology approach has been used to study the structural organization of the NuRD complex.My work focused especially on three subunits of this complex: MBD3, RbAp46 and RbAp48. I set up the preparation of the individual subunits and characterized them by various biophysical methods. We next carried out binding assays with homemade human nucleosomes. For MBD3, optimization of the complex led to crystals diffracting up to 7 Å. In parallel, a preliminary 3-D reconstruction at 25 Å resolution has been solved in cryo-EM. For RbAp46/48, crystal we were able to show that these proteins form stable complexes with the nucleosome, paving the way for future structural analysis by cryo-EM or X-ray crystallography

Today, we make many choices with an eye to how those choices influence how others see us. For example, we try to give others a favorable impression of our general capacities, such as wealth, health, vigor, intelligence, knowledge, skills, conscientiousness, and artistic sense. With this in mind, we try to appear impressive in our arts, sports, schooling, hobbies, vocabularies, and other markers. For example, we plausibly pay extra for visibly nice clothes, cars, houses, etc., in part to show that we can afford such things. We use big words and witty banter in part to show our intelligence and schooling. We go to school in part to show our intelligence, conscientiousness, and conformity. We play sports in part to show our intelligence, health, strength, self-control, toughness, and cooperativeness. We play music in part to show our intelligence, self-control, passion, and creativity. We also try to give others a favorable impression of our loyalties and connections. That is, we try to credibly show that we feel strong positive ties toward certain individuals and groups, who feel similarly toward us. We can also try to show negative feelings toward rivals and outsiders. With this in mind, we choose with whom we spend our time, who we praise or criticize, and our styles of clothing, music, movies, etc. We follow gossip, news, and fashion in part to help show that we are well connected to respected sources of information. We enjoy stories and participate in politics in part to convince associates of our moral sympathies. We sometimes even cry for help, to show who will come running. Today, we spend a large fraction of our energy and wealth on such “signaling,” both because humans naturally care greatly about gaining status and respect in the eyes of others, and because being rich allows us to attend more to such concerns. As mentioned in Chapter 2, Era Values section, in terms of simple functionality, we seem today to spend excessive amounts on schools, medicine, financial intermediation, and huge projects. In contrast, while ems share most of our desires for respect, they live in a more competitive world, where they can less afford to indulge such desires.

Introdução: A Classificação de risco em Obstetrícia faz parte da Política Nacional de Humanização, tendo como base o Manual de Acolhimento e Classificação de Risco em Obstetrícia (A&CRO). Inclui protocolo de Classificação de Risco, uma ferramenta de apoio à decisão clínica que pretende viabilizar o acesso qualificado e o atendimento com resolutividade, em tempo adequado para cada caso. O Acolhimento e Classificação em Obstetrícia tem sido realizado no Hospital das Clínicas de Botucatu pelas residentes do Programa de Enfermagem Obstétrica, através de sistema eletrônico. Objetivo: Descrever o treinamento de Classificação de Risco em obstetrícia para residentes de enfermagem de um hospital escola. Método: Trata-se de um relato de experiência vivenciado no Programa de Residência de Enfermagem Obstétrica da FMB – UNESP – Botucatu. O treinamento é realizado com os residentes, no início do programa e as estratégias pedagógicas são a exposição teórica e simulações gravadas, seguidas de exercícios de classificação. Resultados: O treinamento é realizado em cinco etapas: 1. Estudo do Manual de A&CRO e suas contribuições para a segurança das pacientes; 2. Apresentação de cinco casos fictícios de classificação, gravados e tendo como atores os residentes e uma tutora do programa como paciente; 3. Classificação dos casos; 4. Discussão dos casos entre pares de residentes; 5. Discussão em grupo sobre a classificação dos casos. Os casos enfocam diferentes queixas mais comuns de gestantes e puérperas. O treinamento tem sido considerado como um facilitador para a inserção do enfermeiro residente no campo de atuação, sendo que eles expressam que os exercícios de simulação facilitam a coleta dos dados e a tomada de decisão no momento de classificar. Conclusão: A estratégia pedagógica atingiu os objetivos de treinamento, sendo apropriada a utilização da simulação gravada, que permitiu uma leitura particular para enfermeiros residentes que estão em fase de treinamento.