Correction
Biochemical Research Methods
Emmanuel Moebel, Antonio Martinez-Sanchez, Lorenz Lamm, Ricardo D. Righetto, Wojciech Wietrzynski, Sahradha Albert, Damien Lariviere, Eric Fourmentin, Stefan Pfeffer, Julio Ortiz, Wolfgang Baumeister, Tingying Peng, Benjamin D. Engel, Charles Kervrann
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)
Editorial Material
Microbiology
Ricardo D. Righetto, Benjamin D. Engel
NATURE MICROBIOLOGY
(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)
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
Biochemistry & Molecular Biology
Leonardo Cassari, Angela Pavan, Giulia Zoia, Monica Chinellato, Elena Zeni, Alessandro Grinzato, Sylvia Rothenberger, Laura Cendron, Monica Dettin, Antonella Pasquato
Summary: The SARS-CoV-2 virus displays unique characteristics and has a high ability to spread among humans. The virus relies on Furin for its invasion and replication, and though there are mutations in the amino acid sequence, the dependence on Furin remains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Microbiology
Gabriela Llauger, Roberto Melero, Demian Monti, Gabriela Sycz, Cristian Huck-Iriart, Maria L. Cerutti, Sebastian Klinke, Evelyn Mikkelsen, Ariel Tijman, Rocio Arranz, Victoria Alfonso, Sofia M. Arellano, Fernando A. Goldbaum, Yann G. J. Sterckx, Jose-Maria Carazo, Sergio B. Kaufman, Pablo D. Dans, Mariana del Vas, Lisandro H. Otero
Summary: The mal de Rio Cuarto virus (MRCV) is a major cause of maize disease in Argentina, replicating in various plants and insects. The C-arm region of the major viroplasm protein P9-1 is essential for the formation of viroplasm-like structures and RNA binding. The study uncovers the structural versatility of a fijivirus major viroplasm protein and provides insights into its mechanism of action.
Article
Biochemistry & Molecular Biology
Johannes F. Hevler, Pascal Albanese, Alfredo Cabrera-Orefice, Alisa Potter, Andris Jankevics, Jelena Misic, Richard A. Scheltema, Ulrich Brandt, Susanne Arnold, Albert J. R. Heck
Summary: The tricarboxylic acid cycle is a central pathway for energy production in eukaryotic cells and plays a key role in aerobic respiration across all life kingdoms. The 2-oxoglutarate dehydrogenase complex (OGDHC) is a crucial enzyme in this cycle, generating NADH by oxidatively decarboxylating 2-oxoglutarate to succinyl-CoA. We provide evidence that MRPS36 is an important component of eukaryotic OGDHC, supported by cross-linking mass spectrometry data and phylogenetic analyses. We propose that MRPS36 evolved as an E3 adaptor protein, functionally replacing the peripheral subunit-binding domain (PSBD) in eukaryotic E2o.
Article
Biochemical Research Methods
D. Herreros, J. M. Krieger, Y. Fonseca, P. Conesa, M. Harastani, R. Vuillemot, I. Hamitouche, R. Serrano Gutierrez, M. Gragera, R. Melero, S. Jonic, J. M. Carazo, C. O. S. Sorzano
Summary: In this work, a new framework called the Flexibility Hub is proposed, which automatically handles intercommunication between different heterogeneity software, simplifying the task of combining the software into workflows and maximizing the quality and quantity of information extracted from flexibility analysis.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Federica Tonolo, Alessandro Grinzato, Alberto Bindoli, Maria Pia Rigobello
Summary: The increasing need for redox imbalance in chronic diseases has led to a focus on compounds with antioxidant activity. Bioactive peptides, as natural molecules with health-promoting effects, have gained interest. Recent studies have explored the effects of bioactive peptides in the cellular environment and found that they can modulate specific pathways. This review focuses on the structure-function correlation of antioxidant bioactive peptides, considering their molecular mechanism and the activation of specific signaling pathways. The correlation between molecular docking analysis and cellular effects is highlighted. This knowledge is important for proposing the use of bioactive peptides in functional foods or nutraceuticals.
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
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
Biochemistry & Molecular Biology
Dmitry A. Semchonok, Jyotirmoy Mondal, Connor J. Cooper, Katrina Schlum, Meng Li, Muhamed Amin, Carlos O. S. Sorzano, Erney Ramirez-Aportela, Panagiotis L. Kastritis, Egbert J. Boekema, Albert Guskov, Barry D. Bruce
Summary: The tetrameric structure of photosystem I in cyanobacteria has been studied, showing that the tetramer is arranged through two different interfaces. The localization of chlorophyll molecules allows for excitation energy transfer within and between monomers. Tetrameric PSI may play a significant role in the evolution of photosynthetic organisms.
PLANT COMMUNICATIONS
(2022)