A synergistic approach toward understanding receptor signaling in the cell at very high resolution

Información del proyecto

HighResCells

Identificador del acuerdo de subvención: 810057

DOI

10.3030/810057

Proyecto cerrado

Fecha de la firma de la CE 24 Enero 2019

Fecha de inicio 1 Marzo 2019

Fecha de finalización 30 Noviembre 2024

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 8 273 457,00

Aportación de la UE

€ 8 273 457,00

Coordinado por

UNIVERSITAT ZURICH
Switzerland

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (46)

Gold nanomaterials and their potential use as cryo-electron tomography labels

Autores: Charlie Beales; Ohad Medalia
Publicado en: Crossref, Edición 8, 2022, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2022.107880

Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

Autores: Herreros, D; Lederman, RR; Krieger, J; Jimenez-Moreno, A; Martinez, M; Myska, D; Strelak, D; Filipovic, J; Bahar, I; Carazo, JM; Sanchez, COS
Publicado en: IUCrJ, Edición Volume 8| Part 6| November 2021| Pages 992-1005, 2021, ISSN 2052-2525
Editor: IUCRJ
DOI: 10.1107/s2052252521008903

A network of mixed actin polarity in the leading edge of spreading cells.

Autores: Wen-Lu Chung, Matthias Eibauer, Wenhong Li, Rajaa Boujemaa-Paterski, Benjamin Geiger , Ohad Medalia
Publicado en: Communications Biology, 2022, ISSN 2399-3642
Editor: Springer Nature
DOI: 10.1038/s42003-022-04288-7

Structural analysis of receptors and actin polarity in platelet protrusions

Autores: Sorrentino S, Conesa JJ, Cuervo A, Melero R, Martins B, Fernandez-Gimenez E, de Isidro-Gomez FP, de la Morena J, Studt JD, Sorzano COS, Eibauer M, Carazo JM, Medalia O.
Publicado en: PNAS Vol. 118 | No. 37, 2021, ISSN 1091-6490
Editor: PNAS
DOI: 10.1073/pnas.2105004118

Differential cellular responses to adhesive interactions with galectin-8- and fibronectin-coated substrates

Autores: Li W, Sancho A, Chung WL, Vinik Y, Groll J, Zick Y, Medalia O, Bershadsky AD, Geiger B.
Publicado en: Journal of Cell Science, 2021, ISSN 0021-9533
Editor: The Company of Biologists Ltd.
DOI: 10.1242/jcs.252221

One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes

Autores: Zilu Ye, Pierre Sabatier, Javier Martin-Gonzalez, Akihiro Eguchi, Maico Lechner, Ole Østergaard, Jingsheng Xie, Yuan Guo, Lesley Schultz, Rafaela Truffer, Dorte B. Bekker-Jensen, Nicolai Bache, Jesper V. Olsen
Publicado en: Nature Communications, Edición 15, 2024, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-024-46777-9

A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions

Autores: F.P. de Isidro-Gómez, J.L. Vilas, P. Losana, J.M. Carazo, C.O.S. Sorzano
Publicado en: Journal of Structural Biology, Edición 216, 2024, Página(s) 108056, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2023.108056

Differential ultracentrifugation enables deep plasma proteomics through enrichment of extracellular vesicles

Autores: Kverneland, AH, Østergaard O, Emdal KB, Svane IM, Olsen JV
Publicado en: Proteomics, 2022, ISSN 1615-9853
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/pmic.202200039

ScipionTomo: Towards Cryo-Electron Tomography Software Integration, Reproducibility, and Validation

Autores: J. Jiménez de la Morena, P. Conesa, Y.C. Fonseca, F.P. de Isidro-Gómez, D. Herreros, E. Fernández-Giménez, D. Strelak, E. Moebel, T.O. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J.J. Conesa, A. Cuervo, P. Losana, I. Sánchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Castaño-Díez, A. Koster, J.G. Piccirillo, J.L. Vilas, J. Otón, R. Marabini, C.O.S. Sorz
Publicado en: Journal of Structural Biology, 2022, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2022.107872

BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction

Autores: R. Sanchez-Garcia, J.R. Macias, C.O.S. Sorzano, J.M. Carazo, J. Segura
Publicado en: Journal of Molecular Biology, 2022, ISSN 0022-2836
Editor: Academic Press
DOI: 10.1016/j.jmb.2022.167556

Local defocus estimation in single particle analysis in cryo-electron microscopy.

Autores: Fernandez-Gimenez, E; Carazo, J M; Sorzano, C O S
Publicado en: Journal of Structural Biology, 2023, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2023.108030

Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN

Autores: D. Herreros, C.P. Mata, C. Noddings, D. Irene, J. Krieger, D.A. Agard, M.-D. Tsai, C.O.S. Sorzano, J.M. Carazo
Publicado en: bioRxiv, 2024, ISSN 2692-8205
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.09.16.613176

FSC-Q: a CryoEM map-to-atomic model quality validation based on the local Fourier shell correlation.

Autores: Erney Ramírez-Aportela; David Maluenda; Yunior C. Fonseca; Pablo Conesa; Roberto Marabini; J. Bernard Heymann; José María Carazo; C.O.S. Sorzano
Publicado en: Nature Communications, Edición 4, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-20295-w

Proteomic investigation of Cbl and Cbl-b in neuroblastoma cell differentiation highlights roles for SHP-2 and CDK16

Autores: Pedersen, A.K., Pfeiffer, A., Karemore, G., Akimov, V., Bekker-Jensen, D.B., Blagoev, B., Francavilla, C., and Olsen, J.V.
Publicado en: iScience, Volume 24, Edición 4,, 2021, ISSN 0092-8674
Editor: Cell Press
DOI: 10.1016/j.isci.2021.102321

Phosphoproteomic investigation of targets of protein phosphatases in EGFR signaling

Autores: Akihiro Eguchi, Jesper V. Olsen
Publicado en: Scientific Reports, Edición 14, 2024, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-024-58619-1

Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition

Autores: Ulises H. Guzman, Ana Martinez-Val, Zilu Ye, Eugen Damoc, Tabiwang N. Arrey, Anna Pashkova, Santosh Renuse, Eduard Denisov, Johannes Petzoldt, Amelia C. Peterson, Florian Harking, Ole Østergaard, Rasmus Rydbirk, Susana Aznar, Hamish Stewart, Yue Xuan, Daniel Hermanson, Stevan Horning, Christian Hock, Alexander Makarov, Vlad Zabrouskov, Jesper V. Olsen
Publicado en: Nature Biotechnology, Edición 42, 2024, Página(s) 1855-1866, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.1038/s41587-023-02099-7

Protein dynamics developments for the large scale and cryoEM: case study of <i>ProDy</i> 2.0

Autores: Ivet Bahar; James Krieger; Carlos Oscar S. Sorzano; Jose Maria Carazo Garcia
Publicado en: Crossref, Edición 8, 2022, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1107/s2059798322001966

Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids

Autores: Ana Martínez-Val, Kyle Fort, Claire Koenig, Leander Van der Hoeven, Giulia Franciosa, Thomas Moehring, Yasushi Ishihama, Yu-Ju Chen, Alexander Makarov, Yue Xuan, Jesper V Olsen
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-39347-y

Proteomics of resistance to Notch1 inhibition in acute lymphoblastic leukemia reveals targetable kinase signatures

Autores: Franciosa, G., Smits, J.G.A., Minuzzo, S., Martinez-Val, A., Indraccolo, S., and Olsen, J.V.
Publicado en: Nature communications, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-22787-9

Real-time correction of chromatic aberration in optical fluorescence microscopy

Autores: Ana Cayuela López, Pablo Conesa, Ana María Oña Blanco, José Antonio Gómez-Pedrero, Carlos Oscar S Sorzano
Publicado en: Methods and Applications in Fluorescence, Edición 11, 2023, Página(s) 045001, ISSN 2050-6120
Editor: bioRxiv
DOI: 10.1088/2050-6120/ace153

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

Autores: C. O. S. Sorzano, A. Jiménez-Moreno, D. Maluenda, M. Martínez, E. Ramírez-Aportela, J. Krieger, R. Melero, A. Cuervo, J. Conesa, J. Filipovic, P. Conesa, L. del Caño, Y. C. Fonseca, J. Jiménez-de la Morena, P. Losana, R. Sánchez-García, D. Strelak,E. Fernández-Giménez, F. P. de Isidro-Gómez, D. Herreros, J. L. Vilas, R. Marabinid and J. M. Carazo
Publicado en: Acta Crystallographica Section D: Structural Biology, 2022, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1107/s2059798322001978

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

Autores: David Střelák, Jiří Filipovič, Amaya Jiménez-Moreno, Jose Carazo, Carlos Sánchez Sorzano
Publicado en: Electronics, Edición 9/6, 2020, Página(s) 1040, ISSN 2079-9292
Editor: Electronics (MDPI)
DOI: 10.3390/electronics9061040

Emerging Themes in CryoEM─Single Particle Analysis Image Processing

Autores: Jose Luis Vilas; Jose Maria Carazo; Carlos Oscar S. Sorzano
Publicado en: Crossref, Edición 12, 2023, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1021/acs.chemrev.1c00850

Principal component analysis is limited to low-resolution analysis in cryoEM

Autores: Sorzano, COS; Carazo, JM
Publicado en: INT UNION CRYSTALLOGRAPHY - ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2021, ISSN 2059-7983
Editor: INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/s2059798321002291

Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography

Autores: Chunyang Wang; Matthias Wojtynek; Ohad Medalia
Publicado en: Crossref, Edición 10, 2023, ISSN 0346-251X
Editor: Pergamon Press Ltd.
DOI: 10.1016/j.jbior.2022.100923

Unveiling the polarity of actin filaments by cryo-electron tomography

Autores: Bruno Martins, Simona Sorrentino, Wen-Lu Chung, Meltem Tatli, Ohad Medalia, Matthias Eibauer
Publicado en: Structure, Volume 29, Edición 5, 6 May 2021, Pages 488-498.e4, 2021, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1016/j.str.2020.12.014

Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM

Autores: D. Herreros, J. M. Krieger, Y. Fonseca, P. Conesa, M. Harastani, R. Vuillemot, I. Hamitouche, R. Serrano Gutiérrez, M. Gragera, R. Melero, S. Jonic, J. M. Carazo and C. O. Sorzano
Publicado en: Acta Crystallographica Section D: Structural Biology, 2023, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1107/s2059798323004497

The Actin Network Interfacing Diverse Integrin-Mediated Adhesions

Autores: Geiger B, Boujemaa-Paterski R, Winograd-Katz SE, Balan Venghateri J, Chung WL, Medalia O.
Publicado en: Biomolecules, 2023, ISSN 2218-273X
Editor: MDPI
DOI: 10.3390/biom13020294

ZART: a novel multiresolution reconstruction algorithm with motion-blur correction for single particle analysis

Autores: D. Herreros, J. Kiska, E. Ramírez-Aportela, J. Filipovic, J.M. Carazo, C.O.S. Sorzano
Publicado en: Journal of Molecular Biology, 2023, ISSN 0022-2836
Editor: Academic Press
DOI: 10.1016/j.jmb.2023.168088

Measurement of local resolution in electron tomography

Autores: J.L. Vilas, J. Oton, C. Messaoudi, R. Melero, P. Conesa, E. Ramirez-Aportela, J. Mota, M. Martinez, A. Jimenez, R. Marabini, J.M. Carazo, J. Vargas, C.O.S. Sorzano
Publicado en: Journal of Structural Biology: X, Edición 4, 2020, Página(s) 100016, ISSN 2590-1524
Editor: Journal of Structural Biology: X (Elsevier Inc)
DOI: 10.1016/j.yjsbx.2019.100016

Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools

Autores: Erney Ramírez-Aportela; Jose M. Carazo; Carlos Oscar S. Sorzano
Publicado en: Crossref, Edición 11, 2022, ISSN 2052-2525
Editor: IUCrJ
DOI: 10.1107/s2052252522006959

Structures of neurokinin 1 receptor in complex with Gq and Gs proteins reveal substance P binding mode and unique activation features

Autores: Christian Thom, Janosch Ehrenmann, Santiago Vacca, Yann Waltenspühl, Jendrik Schöppe, Ohad Medalia, Andreas Plückthun
Publicado en: S C I E N C E A D V A N C E S, 2021, ISSN 2375-2548
Editor: American Association for the Advancement of Science’s
DOI: 10.1126/sciadv.abk2872

Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Autores: Martinez-Val, A., Bekker-Jensen, D.B., Steigerwald, S., Koenig, C., Ostergaard, O., Mehta, A., Tran, T., Sikorski, K., Torres-Vega, E., Kwasniewicz, E., et al.
Publicado en: Nature Communications, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-27398-y

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.

Autores: Krieger, JM; Sorzano, COS; Carazo, JM
Publicado en: International Journal of molecular Science, 2023, ISSN 1422-0067
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms241814245

Measuring local-directional resolution and local anisotropy in cryo-EM maps

Autores: Jose Luis Vilas, Hemant D. Tagare, Javier Vargas, Jose Maria Carazo, Carlos Oscar S. Sorzano
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-13742-w

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion

Autores: Strelak, D; Jimenez-Moreno, A; Vilas, JL; Ramirez-Aportela, E; Sanchez-Garcia, R; Maluenda, D; Vargas, J; Herreros, D; Fernandez-Gimenez, E; de Isidro-Gomez, FP; Horacek, J; Myska, D; Horacek, M; Conesa, P; Fonseca-Reyna, YC; Jimenez, J; Martinez, M; Harastani, M; Jonic, S; Filipovic, J; Marabini, R; Carazo, JM; Sorzano, COS.
Publicado en: MOLECULES Special Edición Cryo-EM and Hybrid Methods Development: Current Progress and Future Perspectives), Edición Volume 26 Edición 20, 2021, ISSN 1420-3049
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26206224

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

Autores: E. Fernández-Giménez, M.M. Martínez, R. Marabini, D. Strelak, R. Sánchez-García, J.M. Carazo, C.O.S. Sorzano
Publicado en: Journal of Structural Biology, 2023, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2023.108024

Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods

Autores: Sorzano, COS; Jimenez-Moreno, A; Maluenda, D; Ramirez-Aportela, E; Martinez, M; Cuervo, A; Melero, R; Conesa, JJ; Sanchez-Garcia, R; Strelak, D; Filipovic, J; Fernandez-Gimenez, E; de Isidro-Gomez, F; Herreros, D; Conesa, P; del Cano, L; Fonseca, Y; de la Morena, JJ; Macias, JR; Losana, P; Marabini, R; Carazo, JM
Publicado en: Structural Proteomics pp 257-289, 2021, ISSN 1064-3745
Editor: Humana Press, Inc.
DOI: 10.1007/978-1-0716-1406-8_13

Multi-layered proteomics identifies insulin-induced upregulation of the EphA2 receptor via the ERK pathway which is dependent on low IGF1R level

Autores: Sarah Hyllekvist Jørgensen, Kristina Bennet Emdal, Anna-Kathrine Pedersen, Lene Nygaard Axelsen, Helene Faustrup Kildegaard, Damien Demozay, Thomas Åskov Pedersen, Mads Grønborg, Rita Slaaby, Peter Kresten Nielsen, Jesper Velgaard Olsen
Publicado en: Scientific Reports, Edición 14, 2024, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-024-77817-5

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

Autores: Ruben Sanchez Garcia; Josué Gómez-Blanco; Ana Maria Cuervo; José María Carazo; Carlos Oscar S. Sorzano; Javier Vargas
Publicado en: Communications Biology, Edición 2, 2021, ISSN 2399-3642
Editor: SpringerNature
DOI: 10.1101/2020.06.12.148296

Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

Autores: Dorte B. Bekker-Jensen, Oliver M. Bernhardt, Alexander Hogrebe, Ana Martinez-Val, Lynn Verbeke, Tejas Gandhi, Christian D. Kelstrup, Lukas Reiter, Jesper V. Olsen
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-14609-1

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

Autores: Roberto Melero, Carlos Oscar S. Sorzano, Brent Foster, José-Luis Vilas, Marta Martínez, Roberto Marabini, Erney Ramírez-Aportela, Ruben Sanchez-Garcia, David Herreros, Laura del Caño, Patricia Losana, Yunior C. Fonseca-Reyna, Pablo Conesa, Daniel Wrapp, Pablo Chacon, Jason S. McLellan, Hemant D. Tagare, Jose-Maria Carazo
Publicado en: IUCrJ, Edición 7/6, 2020, ISSN 2052-2525
Editor: International Union of Crystallography
DOI: 10.1107/s2052252520012725

Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials

Autores: D. Herreros, R. R. Lederman, J. M. Krieger, A. Jiménez-Moreno, M. Martínez, D. Myška, D. Strelak, J. Filipovic, C. O. S. Sorzano & J. M. Carazo
Publicado en: Nature Communications, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-35791-y

Deep Proteome Analysis of Cerebrospinal Fluid from Pediatric Patients with Central Nervous System Cancer

Autores: Christian Mirian, Ole Østergaard, Maria Thastrup, Signe Modvig, Jon Foss-Skiftesvik, Jane Skjøth-Rasmussen, Marianne Berntsen, Josefine Britze, Alex Christian Yde Nielsen, René Mathiasen, Kjeld Schmiegelow, Jesper Velgaard Olsen
Publicado en: Journal of Proteome Research, Edición 23, 2024, Página(s) 5048-5063, ISSN 1535-3893
Editor: American Chemical Society
DOI: 10.1021/acs.jproteome.4c00471

Cryo-EM density maps adjustment for subtraction, consensus and sharpening.

Autores: E. Fernández-Giménez; María Jesús Martínez; Rubén J. Sánchez-García; Roberto Marabini; Erney Ramírez-Aportela; Pablo Conesa; José María Carazo; Carlos Oscar S. Sorzano
Publicado en: Journal of Structural Biology, Edición 5, 2021, ISSN 1047-8477
Editor: Academic Press
DOI: 10.1016/j.jsb.2021.107780

Cryo-EM and Single-Particle Analysis with Scipion

Autores: Jimenez-Moreno, A; del Cano, L; Martinez, M; Ramirez-Aportela, E; Cuervo, A; Melero, R ; Sanchez-Garcia, R; Strelak, D; Fernandez-Gimenez, E; de Isidro-Gomez, FP; Herreros, D; Conesa, P; Fonseca, Y; Maluenda, D; de la Morena, JJ ; Macias, JR; Losana, P; Marabini, R; Carazo, JM; Sorzano, COS
Publicado en: Biochemistry, 2021, ISSN 1940-087X
Editor: MYJoVE Corporation
DOI: 10.3791/62261

Non-peer reviewed articles (3)

Spatiotemporal Proteomics Deciphers Functional Selectivity of EGFR ligands

Autores: Akihiro Eguchi,  Kristina B. Emdal, Zilu Ye,  Ulises H. Guzmán,  Jesper V. Olsen
Publicado en: Biorxiv.org, 2023, ISSN 2692-8205
Editor: BioRxiv
DOI: 10.1101/2023.09.13.557663

Structural basis for the activation and ligand recognition of the human oxytocin receptor

Autores: Yann Waltenspühl, Janosch Ehrenmann, Santiago Vacca, Christian Thom, Ohad Medalia, Andreas Plückthun
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-31325-0

A Vaccinia-based system for directed evolution of GPCRs in mammalian cells

Autores: Christoph Klenk, Maria Scrivens, Anina Niederer, Shuying Shi, Loretta Mueller, Elaine Gersz, Maurice Zauderer, Ernest S. Smith, Ralf Strohner & Andreas Plückthun
Publicado en: Nature Communications, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-37191-8