Article
Biochemistry & Molecular Biology
Mihaly Varadi, Stephen Anyango, David Armstrong, John Berrisford, Preeti Choudhary, Mandar Deshpande, Nurul Nadzirin, Sreenath S. Nair, Lukas Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom Blundell, Kelly P. Brock, Jose Maria Carazo, Jiri Damborsky, Alessia David, Sucharita Dey, Roland Dunbrack, Juan Fernandez Recio, Franca Fraternali, Toby Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivak, Manjeet Kumar, Emmanuel D. Levy, Nir London, Jose Ramon Macias, Madhusudhan M. Srivatsan, Debora S. Marks, Lennart Martens, Stuart A. McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar S. Sorzano, Jan Stourac, Joanna Sulkowska, Radka Svobodova, Natalia Tichshenko, Silvio C. E. Tosatto, Wim Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet Thornton, Michael Sternberg, Christine Orengo, Sameer Velankar
Summary: PDBe-KB is an open collaboration platform that aims to integrate functional and biophysical annotations from world-leading specialist data resources, serving the Protein Data Bank. By developing standardized data exchange formats and integrating functional annotations from partner resources, PDBe-KB aims to place macromolecular structure data in a biological context and provide valuable biological insights.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Virology
Pedro J. de Pablo, Carmen San Martin
Summary: Understanding the assembly and disassembly of adenoviruses is challenging due to their complexity. Cryoelectron microscopy and atomic force microscopy have provided insights into the structure and function of adenoviruses, particularly the roles of core proteins.
CURRENT OPINION IN VIROLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Maria Benko, Koki Aoki, Niklas Arnberg, Andrew J. Davison, Marcela Echavarria, Michael Hess, Morris S. Jones, Gyozo L. Kajan, Adriana E. Kajon, Suresh K. Mittal, Iva I. Podgorski, Carmen San Martin, Goran Wadell, Hidemi Watanabe, Balazs Harrach
Summary: The family Adenoviridae consists of non-enveloped viruses with linear dsDNA genomes and medium-sized icosahedral capsids. Adenoviruses have been found in vertebrates from fish to humans. The family is divided into six genera, each of which is more prevalent in certain animal groups. The outcome of infection can range from subclinical to lethal disease.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
R. Sanchez-Garcia, J. R. Macias, C. O. S. Sorzano, J. M. Carazo, J. Segura
Summary: Computational approaches for predicting protein-protein interfaces are important for understanding protein assemblies. The performance of these methods can be improved by selecting specific training datasets. BIPSPI+ is an upgraded version trained on carefully curated datasets, providing better predictions and new functionalities.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
J. Jimenez de la Morena, P. Conesa, Y. C. Fonseca, F. P. de Isidro-Gomez, D. Herreros, E. Fernandez-Gimenez, D. Strelak, E. Moebel, T. O. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J. J. Conesa, A. Cuervo, P. Losana, I. Sanchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Castano-Diez, A. Koster, J. G. Piccirillo, J. L. Vilas, J. Oton, R. Marabini, C. O. S. Sorzano, J. M. Carazo
Summary: This article introduces the extension of Scipion framework, called ScipionTomo, aiming to simplify image processing and analysis in cryogenic electron tomography. Developed by a collaborative multidisciplinary team, it combines the knowledge of Scipion developers with functionalities requested by beta testers and integrates third-party software packages.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Cristina Ramos, Rogelio Hernandez-Tamayo, Maria Lopez-Sanz, Begona Carrasco, Ester Serrano, Juan C. Alonso, Peter L. Graumann, Silvia Ayora
Summary: This study explores the role of RecD2 in DNA replication and its interaction with RecA. The results demonstrate that RecD2 counteracts the inhibition of leading and lagging strand synthesis by physically interacting with RecA. Additionally, RecD2 overcomes replicative stress by modulating RecA-mediated DNA strand exchange and branch migration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
C. O. S. Sorzano, A. Jimenez-Moreno, D. Maluenda, M. Martinez, E. Ramirez-Aportela, J. Krieger, R. Melero, A. Cuervo, J. Conesa, J. Filipovic, P. Conesa, L. del Cano, Y. C. Fonseca, J. Jimenez-de la Morena, P. Losana, R. Sanchez-Garcia, D. Strelak, E. Fernandez-Gimenez, F. P. de Isidro-Gomez, D. Herreros, J. L. Vilas, R. Marabini, J. M. Carazo
Summary: This article discusses potential problems in cryo-electron microscopy and provides solutions. These problems include sample-related issues and algorithm-related issues. Instabilities in estimating key parameters throughout the processing workflow can significantly affect the reliability of the entire process. The article also proposes a new method to detect parameter bias.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
James Michael Krieger, Carlos Oscar S Sorzano, Jose Maria Carazo, Ivet Bahar
Summary: Cryo-electron microscopy (cryoEM) is an important technique for studying the structure and dynamics of large and dynamic supramolecular complexes. Due to the unique characteristics of these molecular systems, traditional approaches are not suitable for structural modeling and molecular dynamics simulations, necessitating the development of new computational methods and models. Elastic network models, normal mode analysis, and ensemble analyses have played a significant role in this field.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Jose Luis Vilas, Jose Maria Carazo, Carlos Oscar S. Sorzano
Summary: This article reviews the main contributions of image processing to the current reconstruction workflow of single particle analysis (SPA) in cryo-electron microscopy (CryoEM), emphasizing the time evolution of algorithms across different steps.
Article
Microbiology
Ashrafali M. Ismail, Amrita Saha, Ji S. Lee, David F. Painter, Yinghua Chen, Gurdeep Singh, Gabriela N. Condezo, James Chodosh, Carmen San Martin, Jaya Rajaiya
Summary: In this study, the interaction between adenovirus protein pIIIa and host cellular proteins USP9x and RANBP2 was investigated. It was found that USP9x negatively regulates viral replication and protein expression, while RANBP2 is important for pIIIa transport and viral assembly. These findings have potential implications in the development of new antiviral therapeutics.
Article
Biophysics
Aida Sanz Calderon, Miguel Cantero, Uxia Perez, Paula Ortega-Gonzalez, Carmen San Martin, Pedro. J. de Pablo, Miguel Manso Silvan, Mercedes Hernando-Perez
Summary: Studies on the adsorption of viruses on surfaces with optimized properties have attracted attention due to their influence on the retention, orientation, and stability of viral capsids. Additionally, viruses can be used as cages or vectors in various fields. The physical properties of virus nanocages, such as their mechanical response and surface charge distribution, are crucial for their applications. This study demonstrates the strong surface interactions of two viruses on homogeneous hydrophobic surfaces and compares their mechanical properties with those on mica and graphite surfaces. The functionalized surfaces are validated as platforms for the characterization of virus particles, contributing to the understanding of their physical properties.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Multidisciplinary Sciences
Natalia Martin-Gonzalez, Alfonso Gomez-Gonzalez, Mercedes Hernando-Perez, Michael Bauer, Urs F. Greber, Carmen San Martin, Pedro J. de Pablo
Summary: Protein V in human adenovirus connects the inner capsid surface to the outer genome layer, providing mechanical reinforcement and facilitating genome release.
Article
Biochemistry & Molecular Biology
E. Fernandez-Gimenez, M. M. Martinez, R. Marabini, D. Strelak, R. Sanchez-Garcia, J. M. Carazo, C. O. S. Sorzano
Summary: Single particle analysis is widely used in cryo-electron microscopy to obtain the near-atomic structure of biological macromolecules. However, current projection subtraction methods have limitations in fully removing the signal of components that are not of interest. Therefore, we have developed a new and more precise projection subtraction method, which has shown improved performance compared to existing methods.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Physical
C. O. S. Sorzano, J. L. Vilas, E. Ramirez-Aportela, J. Krieger, D. del Hoyo, D. Herreros, E. Fernandez-Gimenez, D. Marchan, 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
Summary: This article proposes a new map validation scheme that takes into account not only the agreement between maps and models, but also factors such as 2D classes, particles, angles, coordinates, defoci, and micrographs. The scheme uses a progressive classification system to qualitatively evaluate the validation status of the results.
FARADAY DISCUSSIONS
(2022)