A5078992474- Advanced Electron Microscopy Techniques and Applications
- Electron and X-Ray Spectroscopy Techniques
- Enzyme Structure and Function
- Machine Learning in Materials Science
- Protein Structure and Dynamics
- Advanced X-ray Imaging Techniques
- Bacterial Genetics and Biotechnology
- Force Microscopy Techniques and Applications
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Photosynthetic Processes and Mechanisms
- Bacteriophages and microbial interactions
- SARS-CoV-2 and COVID-19 Research
- Hormonal Regulation and Hypertension
- ATP Synthase and ATPases Research
- Lipid Membrane Structure and Behavior
- Glycosylation and Glycoproteins Research
- Microtubule and mitosis dynamics
- Cellular transport and secretion
- Plant Diversity and Evolution
- Microbial Community Ecology and Physiology
- Adrenal Hormones and Disorders
- Monoclonal and Polyclonal Antibodies Research
- Hydrogen embrittlement and corrosion behaviors in metals
- Cancer Research and Treatments
Centro Nacional de Biotecnología
2018-2023
Universidad Autónoma de Madrid
2019-2022
Consejo Superior de Investigaciones Científicas
2014-2021
Biocom
2020-2021
Instituto de Química Física Blas Cabrera
2013-2017
Centro de Investigaciones Biológicas Margarita Salas
2013-2016
Hospital General Universitario Gregorio Marañón
2013
The prediction of protein-protein complexes from the structures unbound components is a challenging and powerful strategy to decipher mechanism many essential biological processes. We present user-friendly docking server based on an improved version FRODOCK that includes complementary knowledge-based potential. web interface provides very effective tool explore select models interactively screen them against experimental distance constraints. competitive success rates efficiency achieved...
Recent technological advances and computational developments have allowed the reconstruction of Cryo-Electron Microscopy (cryo-EM) maps at near-atomic resolution. On a typical workflow once cryo-EM map has been calculated, sharpening process is usually performed to enhance visualization, step that proven very important in key task structural modeling. However, approaches, general, neglects local quality map, which clearly suboptimal.Here, new method for density proposed. The algorithm, named...
Significance PRC1 (protein regulator of cytokinesis 1) is critical to cellular architecture through its interaction with microtubules form antiparallel microtubule arrays, like those in the spindle midzone. Here, cryo-EM studies describe, close atomic detail, surface. Together previous studies, our structure leads a model how promotes establishment stable, higher-order arrays.
In this article, a method is presented to estimate new local quality measure for 3D cryoEM maps that adopts the form of 'local resolution' type information. The algorithm (
Cell division protein FtsZ is the organizer of cytokinetic Z-ring in most bacteria and a target for new antibiotics. assembles with GTP into filaments that hydrolyze nucleotide at association interface between monomers then disassemble. We have replaced FtsZ's non-nucleotide synthetic inhibitors bacterial division. searched these small molecules among compounds from literature, virtual screening (VS), our in-house library (UCM), employing fluorescence anisotropy primary assay. From screens...
Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of SARS-CoV-2 spike in prefusion state have been analysed. These studies revealed concerted motions involving receptor-binding domain (RBD), N-terminal domain, subdomains 1 2 around previously characterized 1-RBD-up state, which modeled as elastic deformations. It is shown that this data set there are not well defined, stable conformations, but...
Abstract In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, number solved atomic models. It is widely accepted that quality maps varies locally; therefore, evaluation maps-derived structural models must be done locally as well. this article, a method for local analysis map-to-model fit presented. The algorithm uses comparison two maps. first FSC (Fourier shell correlation) between full map and model, while second calculated half...
Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands macromolecules that are assumed be structurally identical combined into single map representing Coulomb potential macromolecule under study. This article discusses possible caveats along image-processing path and how avoid them obtain reliable structure. Some these problems very known in community. These may referred as...
The assembly switch of cell division protein FtsZ monitored with a fluorescent probe targeting the cleft between domains.
The calcitonin receptor (CTR) is a class B G protein-coupled (GPCR) that responds to the peptide hormone (CT). CTs are clinically approved for treatment of bone diseases. We previously reported 4.1 Å structure activated CTR bound salmon CT (sCT) and heterotrimeric Gs protein by cryo-electron microscopy (Liang, Y.-L., et al. Phase-plate cryo- EM GPCR-G complex. Nature 2017, 546, 118–123). In current study, we have reprocessed electron micrographs yield 3.3 map This has allowed us model...
The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one the hurdles preventing many structural analyses from yielding high-resolution structures. Although existence mostly related to grid preparation, this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others these detrimental conditions. We exemplify argument with...
Essential cell division protein FtsZ is considered an attractive target in the search for antibacterials with novel mechanisms of action to overcome resistance problem. undergoes GTP-dependent assembly at midcell form Z-ring, a dynamic structure that evolves until final constriction cell. Therefore, molecules able inhibit its activity will eventually disrupt bacterial viability. In this work, we report new series small replace GTP and specifically FtsZ, blocking process. These synthesized...
Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here major extension that allows processing EM while the data being acquired. This approach helps to detect problems early stages, saves computing time and provides users with detailed evaluation...
Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and tomography, designed managed by the Biocomputing Unit Spanish National Center Biotechnology, although with contributions many other developers over world. During its 25 years existence, underwent changes updates. While there were publications related to new functionality added Xmipp, no single publication on as a since 2013. In this article, we give overview...
Advances in cryo-electron microscopy (cryo-EM) have made it possible to obtain structures of large biological macromolecules at near-atomic resolution. This "resolution revolution" has encouraged the use and development modeling tools able produce high-quality atomic models from cryo-EM density maps. Unfortunately, many practical problems appear when combining different packages same processing workflow, which make difficult these by non-experts and, therefore, reduce their utility. We...
Photosystem I (PSI) is one of two photosystems involved in oxygenic photosynthesis. PSI cyanobacteria exists monomeric, trimeric, and tetrameric forms, contrast to the strictly monomeric form plants algae. The organization raises questions about its structural, physiological, evolutionary significance. Here we report ∼3.72 Å resolution cryo-electron microscopy structure from thermophilic, unicellular cyanobacterium Chroococcidiopsis sp. TS-821. resolves 44 subunits 448 cofactor molecules. We...
Abstract Image-processing pipelines require the design of complex workflows combining many different steps that bring raw acquired data to a final result with biological meaning. In image-processing domain cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds must be performed obtain three-dimensional structure macromolecule by integrating spread over thousands micrographs containing millions copies allegedly same macromolecule. The execution such complicated demands...
One of the main purposes CryoEM Single Particle Analysis is to reconstruct three-dimensional structure a macromolecule thanks acquisition many particle images representing different poses sample. By estimating orientation each projected particle, it possible recover underlying 3D volume by multiple reconstruction methods, usually working either in Fourier or real space. However, from works under assumption that all particles dataset correspond same conformation macromolecule. Although this...
Electron microscopy of macromolecular structures is an approach that in increasing demand the field structural biology. The automation image acquisition has greatly increased potential throughput electron microscopy. Here, focus on possibilities Scipion to implement flexible and robust image-processing workflows allow electron-microscope operator user monitor quality acquisition, assessing very simple measures or obtaining a first estimate initial volume, data resolution heterogeneity,...