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Your search keyword '"Melero, Roberto [0000-0001-9467-9381]"' showing total 2 results
Start Over Author "Melero, Roberto [0000-0001-9467-9381]" Topic cryo-electron microscopy
2 results on '"Melero, Roberto [0000-0001-9467-9381]"'

1. Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

Author

Pablo Chacón, Laura del Cano, José María Carazo, Pablo Conesa, Roberto Marabini, Erney Ramírez-Aportela, C.O.S. Sorzano, Hemant D. Tagare, Jason S. McLellan, Daniel Wrapp, Patricia Losana, Rubén J. Sánchez-García, Brent Foster, José Luis Vilas, David Herreros, Roberto Melero, Yunior C. Fonseca-Reyna, Marta Martínez, Consejo Superior de Investigaciones Científicas (España), Comunidad de Madrid, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Ministerio de Educación, Cultura y Deporte (España), Instituto de Salud Carlos III, European Commission, National Institutes of Health (US), Melero, Roberto [0000-0001-9467-9381], Martínez, Marta [0000-0002-8435-5540], Marabini, Roberto [0000-0001-7876-1684], Sánchez-García, Ruben [0000-0001-6156-3542], Melero, Roberto, Martínez, Marta, Marabini, Roberto, Sánchez-García, Ruben, and UAM. Departamento de Ingeniería Informática

Subjects
conformational flexibility, Computer science, Image processing, Spike, cryo-electron microscopy, Instability, Biochemistry, Conformational flexibility, Domain (mathematical analysis), Article, Domain (software engineering), 03 medical and health sciences, 0302 clinical medicine, General Materials Science, Statistical physics, Cluster analysis, 030304 developmental biology, Interpretability, Informática, Physics, Flexibility (engineering), 0303 health sciences, Crystallography, SARS-CoV-2, State (functional analysis), General Chemistry, spike, Condensed Matter Physics, Research Papers, Cryo-electron microscopy (cryo-EM), image processing, Data set, sars-cov-2, QD901-999, Principal component analysis, Spike (software development), Algorithm, 030217 neurology & neurosurgery
Abstract

Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results., The authors would like to acknowledge financial support from CSIC (PIE/COVID-19 No. 202020E079), the Comunidad de Madrid through grant CAM (S2017/BMD-3817), the Spanish Ministry of Science and Innovation through projects SEV 2017-0712, FPU-2015/264 and PID2019-104757RB-I00/AEI/FEDER, the Instituto de Salud Carlos III [PT17/0009/0010 (ISCIII-SGEFI/ERDF)], and the European Union and Horizon 2020 through grants INSTRUCT–ULTRA (INFRADEV-03-2016-2017, Proposal 731005), EOSC Life (INFRAEOSC-04-2018, Proposal 824087), HighResCells (ERC-2018-SyG, Proposal 810057), IMpaCT (WIDESPREAD-03-2018, Proposal 857203), CORBEL (INFRADEV-1-2014-1, Proposal 654248) and EOSC–Synergy (EINFRA-EOSC-5, Proposal 857647). HDT and BF were supported by NIH grant GM125769 and JSM was supported by NIH grant R01-AI127521.

Published
2020
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2. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Author

Zachary Freyberg, Roberto Marabini, Carlos Oscar S. Sorzano, F Cazals, A. Jimenez, David Maluenda, Y. Rancel, Rubén J. Sánchez-García, María Jesús Martínez, L. del Cano, Javier Mota, Roberto Melero, José María Carazo, José Luis Vilas, Pablo Conesa, Joan Segura, Slavica Jonic, Javier Vargas, Ivet Bahar, James Krieger, Tomáš Majtner, Erney Ramírez-Aportela, Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Biocomputing Unit [Madrid], Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), McGill University = Université McGill [Montréal, Canada], Algorithms, Biology, Structure (ABS), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Universidad Autonoma de Madrid (UAM), ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), UAM. Departamento de Ingeniería Informática, Tratamiento de Señales Biomédicas (ING EPS-011), Ministerio de Economía y Competitividad (España), Comunidad de Madrid, Instituto de Salud Carlos III, National Institutes of Health (US), European Commission, Carazo, J. M, Sorzano, Carlos Óscar S., Marabini, Roberto, Melero, Roberto, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Universidad Autónoma de Madrid (UAM), Carazo, J. M [0000-0003-0788-8447], Sorzano, Carlos Óscar S. [0000-0002-9473-283X], Marabini, Roberto [0000-0001-7876-1684], and Melero, Roberto [0000-0001-9467-9381]

Subjects
Materials science, Macromolecular Substances, Molecular Conformation, Biophysics, Single particle analysis, Electrons, Molecular Dynamics Simulation, [INFO.INFO-CG]Computer Science [cs]/Computational Geometry [cs.CG], Biochemistry, law.invention, 03 medical and health sciences, Imaging, Three-Dimensional, Image processing, Structural Biology, Normal mode, law, Continuous heterogeneity, Image Processing, Computer-Assisted, Genetics, Electron microscopy, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Informática, Principal Component Analysis, 0303 health sciences, 030302 biochemistry & molecular biology, Proteins, Single-particle analysis, Condensed Matter Physics, 3. Good health, Microscopy, Electron, Thermodynamics, Normal-mode analysis, Electron microscope, Cryo-Electron Microscopy, Algorithms, Macromolecule
Abstract

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed., Spanish Ministry of Economy and Competitiveness through grants BIO2013-44647-R and BIO2016-76400-R (AEI/FEDER, UE), Comunidad Autonoma de Madrid through grant S2017/BMD-3817, Instituto de Salud Carlos III through grants PT13/0001/0009 and PT17/0009/0010, the European Union (EU) and Horizon 2020 through West-Life (EINFRA-2015-1, Proposal 675858), CORBEL (INFRADEV-1-2014-1, Proposal 654248), ELIXIR–EXCELERATE (INFRADEV-3-2015, Proposal 676559), iNEXT (INFRAIA-1-2014-2015, Proposal 653706), EOSCpilot (INFRADEV-04-2016, Proposal 739563) and the National Institutes of Health (P41GM 103712) (IB).

Published
2019

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