Article
Multidisciplinary Sciences
Maria Teresa Bueno-Carrasco, Jorge Cuellar, Marte I. Flydal, Cesar Santiago, Trond-Andre Krakenes, Rune Kleppe, Jose R. Lopez-Blanco, Miguel Marcilla, Knut Teigen, Sara Alvira, Pablo Chacon, Aurora Martinez, Jose M. Valpuesta
Summary: Tyrosine hydroxylase (TH) is a key enzyme in the synthesis of dopamine (DA) and other catecholamines. This study used Cryo-EM to determine the structures of human TH with and without DA, as well as S40 phosphorylated TH. The study revealed the inhibitory and stabilizing effects of DA, as well as the counteraction by S40 phosphorylation, providing insights into the regulatory mechanisms of TH and dopamine homeostasis.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Arkadiusz W. Kulczyk, Carlos Oscar S. Sorzano, Przemyslaw Grela, Marek Tchorzewski, Nilgun E. Tumer, Xiao-Ping Li
Summary: This study uses cryo-EM to determine the structure of Shiga toxin 2a (Stx2a) complexed with the ribosomal P-stalk. The findings reveal the dynamics of the Stx2a-P-stalk interaction and suggest that the binding interface between Stx2a and the P-stalk could be a potential target for drug discovery.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Editorial Material
Physics, Multidisciplinary
Carlo Manzo, Gorka Munoz-Gil, Giovanni Volpe, Miguel Angel Garcia-March, Maciej Lewenstein, Ralf Metzler
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2023)
Article
Biochemistry & Molecular Biology
Tristan Bepler, Andrew J. Borst, Jonathan Bouvette, Giuseppe Cannone, Songye Chen, Anchi Cheng, Ao Cheng, Quanfu Fan, Fanis Grollios, Harshit Gupt, Meghna Gupta, Theo Humphreys, Paul T. Kim, Huihui Kuang, Yilai Li, Alex J. Noble, Ali Punjani, William J. Rice, Carlos Oscar S. Sorzano, Scott M. Stagg, Joshua Strauss, Lingbo Yu, Bridget Carragher, Clinton S. Potter
Summary: This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM. The workshop aimed to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
J. Garcia Condado, A. Munoz-Barrutia, C. O. S. Sorzano
Summary: Single-Particle Analysis by Cryo-Electron Microscopy is a technique used to determine the 3D structure of biological macromolecules. This article introduces HaPi, a method that automatically determines the handedness of macromolecule electron density maps solved by CryoEM. HaPi utilizes convolutional neural networks and a consensus strategy to determine the hand of the maps.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
C. O. S. Sorzano, M. A. Perez-de-la-Cruz Moreno, J. L. Vilas
Summary: This article investigates the absorption models of drugs in the body, including carrier mediated transport and saturable absorption. By studying the exact solutions of different absorption models, the differences between these models can be illustrated.
PHARMACEUTICAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
D. Herreros, R. R. Lederman, J. M. Krieger, A. Jimenez-Moreno, M. Martinez, D. Myska, D. Strelak, J. Filipovic, C. O. S. Sorzano, J. M. Carazo
Summary: The advancements in Cryo-EM Single Particle Analysis play a vital role in understanding the relationship between macromolecular structure and function in biological processes. Traditional approaches have limitations in fully characterizing the conformational landscape due to the small number of accurately reconstructed states. To overcome this, we propose an extension of the Zernike3D method that can extract continuous flexibility information directly from particle datasets. Additionally, the introduced ZART reconstruction algorithm minimizes blurring induced by molecular motions.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Nitzan Gonen, Caroline Eozenou, Richard Mitter, Maeva Elzaiat, Isabelle Stevant, Rona Aviram, Andreia Sofia Bernardo, Almira Chervova, Somboon Wankanit, Emmanuel Frachon, Pierre-Henri Commere, Sylvie Brailly-Tabard, Leo Valon, Laura Barrio Cano, Romain Levayer, Inas Mazen, Samy Gobaa, James C. Smith, Kenneth McElreavey, Robin Lovell-Badge, Anu Bashamboo
Summary: During embryonic development, signaling cascades determine the fate of gonads. Errors in this process result in disorders of sex development. This study provides a protocol for differentiating pluripotent cells into gonadal progenitors and demonstrates their equivalence to embryonic progenitors. The study also shows the potential of using induced pluripotent stem cells to model DSDs and investigate sex determination mechanisms.
Article
Biochemistry & Molecular Biology
D. Herreros, J. Kiska, E. Ramirez-Aportela, J. Filipovic, J. M. Carazo, C. O. S. Sorzano
Summary: The main purpose of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule. ZART is a new Algebraic Reconstruction Technique that can include continuous flexibility information to improve resolution and reduce motion blurring.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Maria Sanz-Paz, Thomas S. van Zanten, Carlo Manzo, Mathieu Mivelle, Maria F. Garcia-Parajo
Summary: Recently, the implementation of plasmonic nanoantennas has allowed for the investigation of nanoscale dynamics of biomolecules in living cells. However, previous studies were limited to single molecular species due to the narrow wavelength resonance of gold-based nanostructures. In this study, researchers used broadband aluminum-based nanoantennas to study molecular interactions on living cell membranes with higher resolution. They were able to detect transient interactions and distinguish molecular diffusion within nanoclusters. This work demonstrates the potential of broadband photonic antennas to study multiple molecular events and interactions in living cells with unprecedented spatiotemporal resolution.
Article
Biology
Enric Gutierrez-Martinez, Susana Benet Garrabe, Nicolas Mateos, Itziar Erkizia, Jon Ander Nieto-Garai, Maier Lorizate, Kyra J. E. Borgman, Carlo Manzo, Felix Campelo, Nuria Izquierdo-Useros, Javier Martinez-Picado, Maria F. Garcia-Parajo
Summary: The immunoglobulin-like lectin receptor CD169 (Siglec-1) on activated dendritic cells (DCs) mediates the capture of HIV-1 through binding to sialylated ligands. Activation of DCs leads to basal nanoclustering of Siglec-1, which enhances the receptor's avidity to gangliosides carrying sialic ligands. This facilitates the accumulation of viral particles in a single compartment.
Article
Chemistry, Analytical
David Strelak, Daniel Marchan, Jose Maria Carazo, Carlos O. S. Sorzano
Summary: This article conducts a comparative analysis of the quality and performance of commonly used software for movie alignment in Cryo-EM. The tested software includes FlexAlign, MotionCor2, Relion MotionCor, Warp, and CryoSPARC. The alignment precision, power spectra density, and performance scaling were compared using generated phantom data and real datasets.
Article
Immunology
Blanca Soler Palacios, Ricardo Villares, Pilar Lucas, Jose Miguel Rodriguez-Frade, Ana Cayuela, Jonathan G. Piccirillo, Manuel Lombardia, David Delgado Gestoso, Miguel Fernandez-Garcia, Cristina Risco, Coral Barbas, Fernando Corrales, Carlos Oscar S. Sorzano, Nuria Martinez-Martin, Jose Javier Conesa, Francisco J. Iborra, Mario Mellado
Summary: This study found that growth hormone can alter the metabolism of inflammatory macrophages, increase mitochondrial volume and alter mitochondrial dynamics. It reduces glycolysis and lactate production, and increases the density of the inner mitochondrial membrane. The results suggest that targeting macrophage metabolism could be a new approach for intervening in inflammatory diseases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Jesus Pineda, Benjamin Midtvedt, Harshith Bachimanchi, Sergio Noe, Daniel Midtvedt, Giovanni Volpe, Carlo Manzo
Summary: Despite recent improvements in microscopy acquisition methods, extracting quantitative information from biological experiments in crowded conditions is a challenging task. Pineda and colleagues propose a geometric deep-learning-based framework for automated trajectory linking and dynamical property estimation that is able to effectively deal with complex biological scenarios.
NATURE MACHINE INTELLIGENCE
(2023)
Correction
Chemistry, Physical
C. O. S. Sorzano, J. L. Vilas, E. Ramirez-Aportela, J. Krieger, D. del Hoyo, D. Herreros, E. Fernandez-Gimenez, D. Marchan, F. de Isidro Gomez, J. R. Macias, I Sanchez, L. del Cano, Y. Fonseca-Reyna, P. Conesa, A. Garcia-Mena, J. Burguet, J. Garcia Condado, J. Mendez Garcia, M. Martinez, A. Munoz-Barrutia, R. Marabini, J. Vargas, J. M. Carazo
FARADAY DISCUSSIONS
(2022)
