Infrastructure for transnational access and discovery in structural biology

Risultati finali

Initial Data Management plan
Second update of the iNEXT-Discovery Data Management plan

Second update of the iNEXTDiscovery Data Management plan

API for structure refinement and model building pipeline for fragment screening
Generation of PDB-Dev-compatible mmCIF files from models / restraints

Generation of PDBDevcompatible mmCIF files from models restraints

Report on standardized data model for fragment screening data

Report on standardized data model for fragment screening data EMBLEBI

Protocol and standards for NMR fragment screening experiments
API enabling communication between crystallization facilities and synchrotrons

API enabling communication between crystallization facilities and synchrotrons (EMBL-GR)

First update of the iNEXT-Discovery Data Management plan
Tools and protocols for BMRB deposition of protein interaction data
Database blueprint for NMR (meta)data for fragment screening

Database blueprint for NMR metadata for fragment screening

Protocols for joint NMR/cryo-EM structural refinement of membrane proteins and viral capsids

Protocols for joint NMRcryoEM structural refinement of membrane proteins and viral capsids

Instrument for automated measurement of ice thickness in cryo-EM

Instrument for automated measurement of ice thickness in cryoEM EMBLHD

Characterization of RNA refolding by in-cell NMR

Characterization of RNA refolding by incell NMR

Protocol isotope labelled photochemically locked RNAs in prokaryotes
New statistical model implemented in PanDDA software
NMR for kinetics and thermodynamics of protein-ligand interaction

NMR for kinetics and thermodynamics of proteinligand interaction

Approved schematic plan for iNEXT-Discovery ARIA
Scripts for automatization of 3D fiducialisation in SRCLXM
Report on Thematic Calls
Protocols for lamella production with cryo-FIB

Protocols for lamella production with cryoFIB

Provide grid maps scored based on ice thickness to microscope

Provide grid maps scored based on ice thickness to microscope EMBLHD

Workflow for real-time in-cell NMR measurements in the bioreactor

Workflow for realtime incell NMR measurements in the bioreactor

Data exchange standards for dataset exchange and analysis
First report on training activities
Data collection protocols optimized for ligand detection

Data collection protocols optimized for ligand detection (EMBL-GR)

Dissemination plan
First report on outreach and dissemination
Review of implementation quality and improved usage
Report on networking within the consortium and with (potential) users
Robust, automated sample evaluation workflow for single-particle cryo-EM

Robust automated sample evaluation workflow for singleparticle cryoEM

Optimised NMR experiments for light-induced kinetics and transitions

Optimised NMR experiments for lightinduced kinetics and transitions

In situ NMR laser illumination device combing at least 3 wavelengths
NMR methods for site-specific measurement of dynamical parameters

NMR methods for sitespecific measurement of dynamical parameters

Protocols for 3D fiducialisation for SRCLXM and SRCLEM
Scripts for cryo-FIB automatization

Scripts for cryoFIB automatization EMBLHD

Robust, automated implementation of sample evaluation workflow for cryo-ET

Robust automated implementation of sample evaluation workflow for cryoET

List of ARIA captured data for proposal and user experience evaluation approved
Web report of capabilities to conduct time-resolved NMR experiments
Report on outreach activities to attract industry users

Report on outreach activities to attract industry users EMBLGR

Proof of concept for advance data analysis pipelines at EMBL-GR
Protocol isotope labelled photochemically locked RNAs in eukaryotes
Sustainability Working Group meeting report
Analysis of binding location and affinity increase of ligated fragments
Second progress report
Software framework for custom-built data analysis pipelines

Software framework for custombuilt data analysis pipelines

Protocols to correlate cellular ssNMR with cryo-EM and microscopy readouts

Protocols to correlate cellular ssNMR with cryoEM and microscopy readouts

Report on expanding interaction possibilities with industry

Report on expanding interaction possibilities with industry (EMBL-GR)

Report on measures to compensate for the absence of hands-on on-site training

Report on measures to compensate for the absence of handson onsite training M24 NKI

ssNMR methods for kinetics of drug-receptor interaction in cell surfaces

ssNMR methods for kinetics of drugreceptor interaction in cell surfaces

First progress report
Investigation of RNA refolding from user application
Tool for identification of follow-up compounds from fragment hits

Tool for identification of followup compounds from fragment hits

Combining solution NMR and SAXS/SANS data for IDPs

Combining solution NMR and SAXSSANS data for IDPs

Light-induced transition in a photo-switchable fluorescent protein

Lightinduced transition in a photoswitchable fluorescent protein

Software tool for automated analysis of spectra
Management Guidelines in place
Cryo-EM image-based quality scores by on-the-fly image processing

CryoEM imagebased quality scores by onthefly image processing

Pubblicazioni

Ligand-Based Competition Binding by Real-Time 19F NMR in Human Cells

Autori: Luchinat E, Barbieri L, Davis B, Brough PA, Pennestri M, Banci L.
Pubblicato in: Journal of Medicinal Chemistry, 2024, ISSN 1520-4804
Editore: American Chemical Society
DOI: 10.1021/acs.jmedchem.3c01600

The CCP4 suite: integrative software for macromolecular crystallography

Autori: Agirre J, Atanasova M, Bagdonas H, Ballard CB, Baslé A, Beilsten-Edmands J, Borges RJ, Brown DG, Burgos-Mármol JJ, Berrisford JM, Bond PS, Caballero I, Catapano L, Chojnowski G, Cook AG, Cowtan KD, Croll TI, Debreczeni JÉ, Devenish NE, Dodson EJ, Drevon TR, Emsley P, Evans G, Evans PR, Fando M, Foadi J, Fuentes-Montero L, Garman EF, Gerstel M, Gildea RJ, Hatti K, Hekkelman ML, Heuser P, Hoh SW,
Pubblicato in: Acta Crystallogr D Struct Biol., 2023, ISSN 2059-7983
Editore: IUCr
DOI: 10.1107/s2059798323003595

Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology

Autori: Yulia Kargapolova, Rizwan Rehimi, Hülya Kayserili, Joanna Brühl, Konstantinos Sofiadis, Anne Zirkel, Spiros Palikyras, Athanasia Mizi, Yun Li, Gökhan Yigit, Alexander Hoischen, Stefan Frank, Nicole Russ, Jonathan Trautwein, Bregje van Bon, Christian Gilissen, Magdalena Laugsch, Eduardo Gade Gusmao, Natasa Josipovic, Janine Altmüller, Peter Nürnberg, Gernot Längst, Frank J. Kaiser, Erwan Watr
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-23327-1

Studies on the Interaction between Model Proteins and Fluorinated Ionic Liquids

Autori: Alves MMS, Melo MN, Mertens HDT, Pereiro AB, Archer M
Pubblicato in: Pharmaceutics, 2023, ISSN 1999-4923
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics15010157

Modulation of Aβ42 Aggregation Kinetics and Pathway by Low‐Molecular‐Weight Inhibitors

Autori: Marie‐Theres Hutchison, Giovanni Bellomo, Alexey Cherepanov, Elke Stirnal, Boris Fürtig, Christian Richter, Verena Linhard, Elina Gurewitsch, Moreno Lelli, Nina Morgner, Thomas Schrader, Harald Schwalbe
Pubblicato in: ChemBioChem, Numero 24, 2023, ISSN 1439-4227
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202200760

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

Autori: C.O.S. Sorzano, D. Semchonok, S.-C. Lin, Y.-C. Lo, J.L. Vilas, A. Jiménez-Moreno, M. Gragera, S. Vacca, D. Maluenda, M. Martínez, E. Ramírez-Aportela, R. Melero, A. Cuervo, J.J. Conesa, P. Conesa, P. Losana, L. del Caño, J. Jiménez de la Morena, Y.C. Fonseca, R. Sánchez-García, D. Strelak, E. Fernández-Giménez, F. de Isidro, D. Herreros, P.L. Kastritis, R. Marabini, B.D. Bruce, J.M. Caraz
Pubblicato in: Journal of Structural Biology, Numero 213/1, 2021, Pagina/e 107695, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2020.107695

Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors

Autori: Osipov EM, Munawar AH, Beelen S, Fearon D, Douangamath A, Wild C, Weeks SD, Van Aerschot A, Von Delft F, Strelkov SV.
Pubblicato in: RSC Chemical Biology, 2022, ISSN 2633-0679
Editore: Royal Society of Chemistry
DOI: 10.1039/d2cb00052k

Site-Selective Functionalized PD-1 Mutant for a Modular Immunological Activity against Cancer Cells

Autori: Fallarini S, Cerofolini L, Salobehaj M, Rizzo D, Gheorghita GR, Licciardi G, Capialbi DE, Zullo V, Sodini A, Nativi C, Fragai M.
Pubblicato in: Biomacromolecules, 2023, ISSN 1526-4602
Editore: American Chemical Society
DOI: 10.1021/acs.biomac.3c00893

Whole-proteome structures shed new light on posttranslational modifications

Autori: Robbie P. Joosten, Jon Agirre
Pubblicato in: PLoS Biol, 2022, ISSN 1545-7885
Editore: Public Library of Science
DOI: 10.1371/journal.pbio.3001673

UBAP2L ensures homeostasis of nuclear pore complexes at the intact nuclear envelope

Autori: Liao Y, Andronov L, Liu X, Lin J, Guerber L, Lu L, Agote-Arán A, Pangou E, Ran L, Kleiss C, Qu M, Schmucker S, Cirillo L, Zhang Z, Riveline D, Gotta M, Klaholz BP, Sumara I
Pubblicato in: Journal of Cell Biology, 2024, ISSN 1540-8140
Editore: Rockefeller University Press
DOI: 10.1083/jcb.202310006

Monitoring Protein-Ligand Interactions in Human Cells by Real-Time Quantitative In-Cell NMR using a High Cell Density Bioreactor

Autori: Letizia Barbieri, Enrico Luchinat
Pubblicato in: Journal of Visualized Experiments, Numero 169, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/62323

High-resolution structure of stem-loop 4 from the 5'-UTR of SARS-CoV-2 solved by solution state NMR

Autori: Vögele J, Hymon D, Martins J, Ferner J, Jonker HRA, Hargrove AE, Weigand JE, Wacker A, Schwalbe H, Wöhnert J, Duchardt-Ferner E.
Pubblicato in: Nucleic Acid Research, 2023, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad762

A bitopic agonist bound to the dopamine 3 receptor reveals a selectivity site

Autori: Sandra Arroyo-Urea, Antonina L. Nazarova, Ángela Carrión-Antolí, Alessandro Bonifazi, Francisco O. Battiti, Jordy Homing Lam, Amy Hauck Newman, Vsevolod Katritch, Javier García-Nafría
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-51993-4

Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development

Autori: Berg H, Wirtz Martin MA, Altincekic N, Alshamleh I, Kaur Bains J, Blechar J, Ceylan B, de Jesus V, Dhamotharan K, Fuks C, Gande SL, Hargittay B, Hohmann KF, Hutchinson MT, Korn SM, Krishnathas R, Kutz F, Linhard V, Matzel T, Meiser N, Niesteruk A, Pyper DJ, Schulte L, Trucks S, Azzaoui K, Blommers MJJ, Gadiya Y, Karki R, Zaliani A, Gribbon P, Almeida MDS, Anobom CD, Bula AL, Buetikofer M, Caruso
Pubblicato in: Angew Chem Int Ed Engl., 2022, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202205858

An integrative structural study of the human full-length RAD52 at 2.2 Å resolution

Autori: Beatrice Balboni, Roberto Marotta, Francesco Rinaldi, Giulia Milordini, Giulia Varignani, Stefania Girotto, Andrea Cavalli
Pubblicato in: Communications Biology, Numero 7, 2024, ISSN 2399-3642
Editore: Nature Portfolio
DOI: 10.1038/s42003-024-06644-1

Structural conservation of antibiotic interaction with ribosomes

Autori: Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmüller H, Nováček J, Wilson DN.
Pubblicato in: Nature Structural and Molecular Biology, 2023, ISSN 1545-9993
Editore: Nature Publishing Group
DOI: 10.1038/s41594-023-01047-y

Protein delivery to living cells by thermal stimulation for biophysical investigation

Autori: Torricella F, Barbieri L, Bazzurro V, Diaspro A, Banci L.
Pubblicato in: Scientific Reports, Numero 20452322, 2022, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-022-21103-9

Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase

Autori: Andriianov A, Trigüis S, Drobiazko A, Sierro N, Ivanov NV, Selmer M, Severinov K, Isaev A.
Pubblicato in: Cell Reports, 2023, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2023.112972

Solution structure of the voltage-gated Tim23 channel in complex with a mitochondrial presequence peptide

Autori: Shu Zhou, Maosen Ruan, Yunyan Li, Jing Yang, Suwen Bai, Christian Richter, Harald Schwalbe, Can Xie, Bing Shen & Junfeng Wang
Pubblicato in: Cell Research, 2020, ISSN 1001-0602
Editore: Kexue Chubaneshe/Science Press
DOI: 10.1038/s41422-020-00452-y

Characterization of a glycoside hydrolase endolysin from Acinetobacter baumannii phage AbTZA1 with high antibacterial potency and novel structural features

Autori: Premetis GE, Stathi A, Papageorgiou AC, Labrou NE.
Pubblicato in: FEBS Journal, 2022, ISSN 1742-464X
Editore: Blackwell Publishing Inc.
DOI: 10.1111/febs.16686

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

Autori: Sorzano COS, Jiménez-Moreno A, Maluenda D, Martínez M, Ramírez-Aportela E, Krieger J, Melero R, Cuervo A, Conesa J, Filipovic J, Conesa P, Del Caño L, Fonseca YC, Jiménez-de la Morena J, Losana P, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro-Gómez FP, Herreros D, Vilas JL, Marabini R, Carazo JM.
Pubblicato in: Acta Crystallogr D Struct Biol, 2022, ISSN 2059-7983
Editore: John Wiley and Sons Inc.
DOI: 10.1107/s2059798322001978

New restraints and validation approaches for nucleic acid structures in PDB-REDO

Autori: Ida de Vries, Tim Kwakman, Xiang-Jun Lu, Maarten L. Hekkelman, Mandar Deshpande, Sameer Velankar, Anastassis Perrakis, Robbie P. Joosten
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 77/9, 2021, ISSN 2059-7983
Editore: IUCr
DOI: 10.1107/s2059798321007610

Integrated NMR/Molecular Dynamics Determination of the Ensemble Conformation of a Thermodynamically Stable CUUG RNA Tetraloop

Autori: Oxenfarth A, Kümmerer F, Bottaro S, Schnieders R, Pinter G, Jonker HRA, Fürtig B, Richter C, Blackledge M, Lindorff-Larsen K, Schwalbe H
Pubblicato in: Journal of the American Chemical Society, 2023, ISSN 0002-7863
Editore: American Chemical Society
DOI: 10.1021/jacs.3c03578

Studies of proline conformational dynamics in IDPs by 13C-detected cross-correlated NMR relaxation

Autori: Marco Schiavina, Ruth Konrat, Irene Ceccolini, Borja Mateos, Robert Konrat, Isabella C. Felli, Roberta Pierattelli
Pubblicato in: Journal of Magnetic Resonance, Numero 354, 2023, Pagina/e 107539, ISSN 1090-7807
Editore: Academic Press
DOI: 10.1016/j.jmr.2023.107539

A Sample Preparation Pipeline for Microcrystals at the VMXm Beamline

Autori: Adam D. Crawshaw, Emma V. Beale, Anna J. Warren, Andrew Stallwood, Graham Duller, Jose Trincao, Gwyndaf Evans
Pubblicato in: Journal of Visualized Experiments, Numero 172, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/62306

The Intriguing mitoNEET: Functional and Spectroscopic Properties of a Unique [2Fe-2S] Cluster Coordination Geometry

Autori: Camponeschi F, Piccioli M, Banci L.
Pubblicato in: Molecules, 2022, ISSN 1420-3049
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules27238218

A morpheein equilibrium regulates catalysis in phosphoserine phosphatase SerB2 from Mycobacterium tuberculosis

Autori: Pierson E, De Pol F, Fillet M, Wouters J.
Pubblicato in: Commun Biol., 2023, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.1038/s42003-023-05402-z

Determinants of receptor tyrosine phosphatase homophilic adhesion: structural comparison of PTPRK and PTPRM extracellular domains

Autori: Hay IM, Shamin M, Caroe ER, Mohammed ASA, Svergun DI, Jeffries CM, Graham SC, Sharpe HJ, Deane JE.
Pubblicato in: Journal of Biological Chemistry, 2022, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2022.102750

Toward protein NMR at physiological concentrations by hyperpolarized water — Finding and mapping uncharted conformational spaces

Autori: Epasto LM, Che K, Kozak F, Selimovic A, Kadeřávek P, Kurzbach D.
Pubblicato in: Science Advances, 2022, ISSN 2375-2548
Editore: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abq5179

Structural basis for different membrane-binding properties of E. coli anaerobic and human mitochondrial β-oxidation trifunctional enzymes

Autori: Sah-Teli SK, Pinkas M, Hynönen MJ, Butcher SJ, Wierenga RK, Novacek J, Venkatesan R.
Pubblicato in: Structure, 2023, ISSN 0969-2126
Editore: Cell Press
DOI: 10.1016/j.str.2023.04.011

Fixed Target Serial Data Collection at Diamond Light Source

Autori: Sam Horrell, Danny Axford, Nicholas E. Devenish, Ali Ebrahim, Michael A. Hough, Darren A. Sherrell, Selina L. S. Storm, Ivo Tews, Jonathan A. R. Worrall, Robin L. Owen
Pubblicato in: Journal of Visualized Experiments, Numero 168, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/62200

Identification of potential aggregation hotspots on Aβ42 fibrils blocked by the anti-amyloid chaperone-like BRICHOS domain

Autori: Kumar R, Le Marchand T, Adam L, Bobrovs R, Chen G, Fridmanis J, Kronqvist N, Biverstål H, Jaudzems K, Johansson J, Pintacuda G, Abelein A.
Pubblicato in: Nature Communications, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-45192-4

Structural plasticity of NFU1 upon interaction with binding partners: insights into the mitochondrial [4Fe-4S] cluster pathway

Autori: Da Vela S, Saudino G, Lucarelli F, Banci L, Svergun DI, Ciofi-Baffoni S.
Pubblicato in: J Mol Biol, 2023, ISSN 0022-2836
Editore: Academic Press
DOI: 10.1016/j.jmb.2023.168154

Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release

Autori: Domenico Rizzo, Linda Cerofolini, Anna Pérez-Ràfols, Stefano Giuntini, Fabio Baroni, Enrico Ravera, Claudio Luchinat, Marco Fragai
Pubblicato in: Analytical Chemistry, 2021, ISSN 0003-2700
Editore: American Chemical Society
DOI: 10.1021/acs.analchem.1c01850

Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Autori: Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H
Pubblicato in: Science Advances, 2022, ISSN 2375-2548
Editore: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abo0517

High-Resolution Studies of Proteins in Natural Membranes by Solid-State NMR

Autori: David Beriashvili, Raymond D. Schellevis, Federico Napoli, Markus Weingarth, Marc Baldus
Pubblicato in: Journal of Visualized Experiments, Numero 169, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/62197

Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies.

Autori: Pearce NM, Skyner R, Krojer T.
Pubblicato in: Front. Mol. Biosci., Numero Section Structural BIology, 2022, ISSN 2296-889X
Editore: Lausanne
DOI: 10.3389/fmolb.2022.861491

In-cell NMR: Why and how?

Autori: Theillet FX, Luchinat E.
Pubblicato in: Progress in Nuclear Magnetic Resonance Spectroscopy, 2022, ISSN 0079-6565
Editore: Elsevier BV
DOI: 10.1016/j.pnmrs.2022.04.002

1H, 13C, and 15N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein)

Autori: Ying Wang, John Kirkpatrick, Susanne zur Lage, Sophie M. Korn, Konstantin Neißner, Harald Schwalbe, Andreas Schlundt, Teresa Carlomagno
Pubblicato in: Biomolecular NMR Assignments, 2021, ISSN 1874-2718
Editore: Springer Verlag
DOI: 10.1007/s12104-021-10019-6

Intrinsically disordered plant protein PARCL co-localizes with RNA in phase-separated condensates whose formation can be regulated by mutating the PLD

Autori: Ostendorp A, Ostendorp S, Zhou Y, Chaudron Z, Wolffram L, Rombi K, von Pein L, Falke S, Jeffries CM, Svergun DI, Betzel C, Morris RJ, Kragler F, Kehr J
Pubblicato in: Journal of Biological Chemistry, Numero 00219258, 2022, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2022.102631

Dissociation of β2m from MHC class I triggers formation of noncovalent transient heavy chain dimers

Autori: Cindy Dirscherl, Sara Löchte, Zeynep Hein, Janine-Denise Kopicki, Antonia Regina Harders, Noemi Linden, Andreas Karner, Johannes Preiner, Julian Weghuber, Maria Garcia-Alai, Charlotte Uetrecht, Martin Zacharias, Jacob Piehler, Peter Lanzerstorfer, Sebastian Springer
Pubblicato in: Journal of Cell Science, Numero 135, 2023, ISSN 0021-9533
Editore: The Company of Biologists Ltd.
DOI: 10.1242/jcs.259498

Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies

Autori: Altincekic N, Jores N, Löhr F, Richter C, Ehrhardt C, Blommers MJJ, Berg H, Öztürk S, Gande SL, Linhard V, Orts J, Abi Saad MJ, Bütikofer M, Kaderli J, Karlsson BG, Brath U, Hedenström M, Gröbner G, Sauer UH, Perrakis A, Langer J, Banci L, Cantini F, Fragai M, Grifagni D, Barthel T, Wollenhaupt J, Weiss MS, Robertson A, Bax A, Sreeramulu S, Schwalbe H.
Pubblicato in: ACS Chemical Biology, 2024, ISSN 1554-8929
Editore: American Chemical Society
DOI: 10.1021/acschembio.3c00720

Binding adaptation of GS-441524 diversifies macro domains and downregulate SARS-CoV-2 de-MARylation capacity

Autori: A.C. Tsika, A. Gallo, N.K. Fourkiotis, A.I. Argyriou, S. Sreeramulu, F. Löhr, V.V. Rogov, C. Richter, V. Linhard, S.L. Gande, N. Altincekic, R. Krishnathas, I. Elamri, H. Schwalbe, J. Wollenhaupt, M.S. Weiss, G.A. Spyroulias
Pubblicato in: Journal of Molecular Biology, 2022, ISSN 0022-2836
Editore: Academic Press
DOI: 10.1016/j.jmb.2022.167720

Progression of herpesvirus infection remodels mitochondrial organization and metabolism

Autori: Leclerc S, Gupta A, Ruokolainen V, Chen JH, Kunnas K, Ekman AA, Niskanen H, Belevich I, Vihinen H, Turkki P, Perez-Berna AJ, Kapishnikov S, Mäntylä E, Harkiolaki M, Dufour E, Hytönen V, Pereiro E, McEnroe T, Fahy K, Kaikkonen MU, Jokitalo E, Larabell CA, Weinhardt V, Mattola S, Aho V, Vihinen-Ranta M
Pubblicato in: PLoS Pathog, 2024, ISSN 1553-7374
Editore: Public Library of Science
DOI: 10.1371/journal.ppat.1011829

Phase distortion-free paramagnetic NMR spectra

Autori: Enrico Ravera
Pubblicato in: Journal of Magnetic Resonance Open, Numero 8-9, 2021, Pagina/e 100022, ISSN 2666-4410
Editore: Elsevier Inc
DOI: 10.1016/j.jmro.2021.100022

Disentangling Chromophore States in a Reversibly Switchable Green Fluorescent Protein: Mechanistic Insights from NMR Spectroscopy

Autori: Nina Eleni Christou, Karine Giandoreggio-Barranco, Isabel Ayala, Oleksandr Glushonkov, Virgile Adam, Dominique Bourgeois, Bernhard Brutscher
Pubblicato in: Journal of the American Chemical Society, Numero 143/19, 2021, Pagina/e 7521-7530, ISSN 0002-7863
Editore: American Chemical Society
DOI: 10.1021/jacs.1c02442

Molecular Basis of Multiple Mitochondrial Dysfunctions Syndrome 2 Caused by CYS59TYR BOLA3 Mutation

Autori: Giovanni Saudino, Dafne Suraci, Veronica Nasta, Simone Ciofi-Baffoni, Lucia Banci
Pubblicato in: International Journal of Molecular Sciences, Numero 22/9, 2021, Pagina/e 4848, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22094848

The folding landscapes of human telomeric RNA and DNA Gquadruplexesare markedly different

Autori: Diana Müller, Irene Bessi, Christian Richter, and Harald Schwalbe
Pubblicato in: Angewandte Chemie (International Edition), 2021, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202100280

Cost-Effective Protein Production in CHO Cells Following Polyethylenimine-Mediated Gene Delivery Showcased by the Production and Crystallization of Antibody Fabs

Autori: Meskova K, Martonova K, Hrasnova P, Sinska K, Skrabanova M, Fialova L, Njemoga S, Cehlar O, Parmar O, Kolenko P, Pevala V, Skrabana R.
Pubblicato in: Antibodies, 2023, ISSN 2073-4468
Editore: MDPI
DOI: 10.3390/antib12030051

OUP accepted manuscript

Autori: Tamas Lazar, Elizabeth Martínez-Pérez, Federica Quaglia, András Hatos, Lucía B Chemes, Javier A Iserte, Nicolás A Méndez, Nicolás A Garrone, Tadeo E Saldaño, Julia Marchetti, Ana Julia Velez Rueda, Pau Bernadó, Martin Blackledge, Tiago N Cordeiro, Eric Fagerberg, Julie D Forman-Kay, Maria S Fornasari, Toby J Gibson, Gregory-Neal W Gomes, Claudiu C Gradinaru, Teresa Head-Gordon, Malene Rin
Pubblicato in: Nucleic Acids Research, 2020, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa1021

Intracellular Binding/Unbinding Kinetics of Approved Drugs toCarbonic Anhydrase II Observed by in-Cell NMR

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Controlling the incorporation of fluorinated amino acids in human cells and its structural impact

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Exploring the druggability of conserved RNA regulatory elements in the SARS‐CoV‐2 genome

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Real-Time Quantitative In-Cell NMR: Ligand Binding and Protein Oxidation Monitored in Human Cells Using Multivariate Curve Resolution

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Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

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Biochemical and Structural Characterization of CRH-1, a Carbapenemase from Chromobacterium haemolyticum Related to KPC β-Lactamases

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Crystal structure of the Phospholipase A and acyltransferase 4 (PLAAT4) catalytic domain

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Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking

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Blood pH Analysis in Combination with Molecular Medical Tools in Relation to COVID-19 Symptoms

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Structure-function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role

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Single Particle Cryo-Electron Microscopy: From Sample to Structure

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Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR

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Updated restraint dictionaries for carbohydrates in the pyranose form

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Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium

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The Coming of Age of In-Cell Solution NMR

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Staphylococcus aureus sacculus mediates activities of M23 hydrolases

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Common transthyretin-derived amyloid fibril structures in patients with hereditary ATTR amyloidosis

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Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates

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Cryo-EM and Single-Particle Analysis with Scipion

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

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Oxidation of the Mycobacterium tuberculosis key virulence factor Protein Tyrosine Phosphatase A (MptpA) reduces its phosphatase activity

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Real-time NMR spectroscopy in the study of biomolecular kineticsand dynamics

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Identification and Characterization of an RRM‐Containing, RNA Binding Protein in Acinetobacter baumannii

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Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed

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Beta and Gamma Amino Acid-Substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases

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FragMAXapp : crystallographic fragment-screening data-analysis and project-management system

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Optimization of the Lead Compound NVP-BHG712 as Colorectal Cancer Inhibitor

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The missing link: covalent linkages in structural models

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A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity

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Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan

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Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties

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Small molecule MMRi62 targets MDM4 for degradation and induces leukemic cell apoptosis regardless of p53 status

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Program VUE: analysing distributions of cryo-EM projections using uniform spherical grids

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High-resolution cryo-EM performance comparison of two latest-generation cryo electron microscopes on the human ribosome

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Polθ is phosphorylated by PLK1 to repair double-strand breaks in mitosis

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A Fijivirus Major Viroplasm Protein Shows RNA-Stimulated ATPase Activity by Adopting Pentameric and Hexameric Assemblies of Dimers

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Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners

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The complex structure of Fomes fomentarius represents an architectural design for high-performance ultralightweight materials

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Evasion of cGAS and TRIM5 defines pandemic HIV

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SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design

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Dynamic interactions and Ca2+-binding modulate the holdase-type chaperone activity of S100B preventing tau aggregation and seeding

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Innovative Approach for a Classic Target: Fragment Screening on Trypanothione Reductase Reveals New Opportunities for Drug Design

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Structural Insights into the Role of β3 nAChR Subunit in the Activation of Nicotinic Receptors

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

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Solid-state NMR - a complementary technique for protein framework characterization

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Targeting EPHA2 with Kinase Inhibitors in Colorectal Cancer

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A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography

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EFFECTS of BORON SUPPLEMENTATION on DAIRY CALVES’ HEALTH: A METABOLOMICS STUDY

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Epitope Mapping and Binding Assessment by Solid-State NMR Provide a Way for the Development of Biologics under the Quality by Design Paradigm

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Multitasking Pharmacophores Support Cabotegravir-Based Long-Acting HIV Pre-Exposure Prophylaxis (PrEP)

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Structural and biochemical characterization of the C‐terminal region of the human <scp>RTEL</scp>1 helicase

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X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX

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NMR characterization and ligand binding site of the stem loop 2 motif (s2m) from the Delta variant of SARS-CoV-2

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Protein in-cell NMR spectroscopy at 1.2 GHz

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Ultra-high Performance Liquid Chromatography−Ion Mobility−High-Resolution Mass Spectrometry to Evaluate the Metabolomic Response of Durum Wheat to Sustainable Treatments

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Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein

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Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

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

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Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology

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Structural deficits in key domains of Shank2 lead to alterations in postsynaptic nanoclusters and to a neurodevelopmental disorder in humans

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Directed Evolution of Phi Class Glutathione Transferases Involved in Multiple-Herbicide Resistance of Grass Weeds and Crops

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Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism

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Amyloid fibril structure from the vascular variant of systemic AA amyloidosis.

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AlphaFill: enriching AlphaFold models with ligands and cofactors

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The structured organization of Deinococcus radiodurans' cell envelope

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splitSMLM, a spectral demixing method for high-precision multi-color localization microscopy applied to nuclear pore complexes

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The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans

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Improved detection of magnetic interactions in proteins based on long-lived coherences

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Purification and Structural Characterization of the Auxiliary Activity 9 Native Lytic Polysaccharide Monooxygenase from Thermoascus aurantiacus and Identification of Its C1- and C4-Oxidized Reaction Products

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In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells

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PAXX binding to the NHEJ machinery explains functional redundancy with XLF

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Cryo-EM structure of a lysozyme-derived amyloid fibril from hereditary amyloidosis

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Structural rearrangement of amyloid-β upon inhibitor binding suppresses formation of Alzheimer’s disease related oligomers

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NMR quality control of fragment libraries for screening

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Development of in vitro-grown spheroids as a 3D tumor model system for solid-state NMR spectroscopy

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The basics of small-angle neutron scattering (SANS for new users of structural biology)

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Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum

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Anomeric Selectivity of Trehalose Transferase with Rare l -Sugars

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19F‐NMR‐based fragment screening for 14 different biologically active RNAs and 10 DNA and protein counter‐screens

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Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells

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

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3D Heteronuclear Magnetization Transfers for the Establishment of Secondary Structures in SARS-CoV-2-Derived RNAs

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Heteronuclear decoupling with Rotor-Synchronized Phase-Alternated Cycles

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Conservation and divergence of the G-interfaces of Drosophila melanogaster septins

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The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble.

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An automated platform for structural analysis of membrane proteins through serial crystallography

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Direct Expression of Fluorinated Proteins in Human Cells for 19F In-Cell NMR Spectroscopy

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Shedding Light on Osteosarcoma Cell Differentiation: Impact on Biomineralization and Mitochondria Morphology

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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

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Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes

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In‐cell NMR of functional riboswitch aptamers in eukaryotic cells

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Adding Size Exclusion Chromatography (SEC) and Light Scattering (LS) Devices to Obtain High-Quality Small Angle X-Ray Scattering (SAXS) Data

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Magnetization transfer to enhance NOE cross‐peaks among labile protons: Applications to imino‐imino sequential walks in SARS‐CoV‐2‐derived RNAs

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Cryo-EM structure of the fully assembled Elongator complex.

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The Molecular Chaperone CCT Sequesters Gelsolin and Protects it from Cleavage by Caspase-3

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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

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Enlarging the scenario of site directed 19F labeling for NMR spectroscopy of biomolecules

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Engineered Nonviral Protein Cages Modified for MR Imaging

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Crystallographic Fragment Screening on the Shigella Type III Secretion System Chaperone IpgC

Autori: Gárdonyi M, Hasewinkel C, Wallbaum J, Wollenhaupt J, Weiss MS, Klebe G, Reuter K, Heine A
Pubblicato in: ACS Omega, 2023, ISSN 2470-1343
Editore: American Chemical Society
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Emerging Themes in CryoEM─Single Particle Analysis Image Processing

Autori: Vilas JL, Carazo JM, Sorzano COS
Pubblicato in: Chemical Reviews, 2022, ISSN 0009-2665
Editore: American Chemical Society
DOI: 10.1021/acs.chemrev.1c00850

X-ray structure of the metastable SEPT14-SEPT7 coiled coil reveals a hendecad region crucial for heterodimerization

Autori: Cavini IA, Winter AJ, D'Muniz Pereira H, Woolfson DN, Crump MP, Garratt RC
Pubblicato in: Acta Crystallogr D Struct Biol, 2023, ISSN 2059-7983
Editore: IUCr
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Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

Autori: Johansen NT, Bonaccorsi M, Bengtsen T, Larsen AH, Tidemand FG, Pedersen MC, Huda P, Berndtsson J, Darwish T, Yepuri NR, Martel A, Pomorski TG, Bertarello A, Sansom M, Rapp M, Crehuet R, Schubeis T, Lindorff-Larsen K, Pintacuda G, Arleth L.
Pubblicato in: Elife, 2022, ISSN 2050-084X
Editore: eLife Sciences Publications
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Secretory IgA and T cells targeting SARS-CoV-2 spike protein are transferred to the breastmilk upon mRNA vaccination

Autori: Juliana Goncalves, A. Margarida Juliano, Nadia Charepe, Marta Alenquer, Diogo Athayde, Filipe Ferreira, Margarida Archer, Maria Joao Amorim, Fatima Serrano, Helena Soares
Pubblicato in: Cell Reports Medicine, 2021, ISSN 2666-3791
Editore: Cell Press
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The cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions

Autori: Farci D, Haniewicz P, de Sanctis D, Iesu L, Kereïche S, Winterhalter M, Piano D.
Pubblicato in: J Biol Chem., 2022, ISSN 0021-9258
Editore: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2022.102031

1H‑Detected Biomolecular NMR under Fast Magic-Angle Spinning

Autori: Le Marchand T, Schubeis T, Bonaccorsi M, Paluch P, Lalli D, Pell AJ, Andreas LB, Jaudzems K, Stanek J, Pintacuda G.
Pubblicato in: Chemical Reviews, 2022, ISSN 1520-6890
Editore: ACS
DOI: 10.1021/acs.chemrev.1c00918

iNEXT-Discovery and Instruct-ERIC: Integrating High-End Services for Translational Research in Structural Biology

Autori: Hans Wienk, Lucia Banci, Susan Daenke, Eva Pereiro, Harald Schwalbe, David Ian Stuart, Manfred S. Weiss, Anastassis Perrakis
Pubblicato in: Journal of Visualized Experiments, Numero 177, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/63435

Molecular basis for transposase activation by a dedicated AAA+ ATPase

Autori: de la Gándara Á, Spínola-Amilibia M, Araújo-Bazán L, Núñez-Ramírez R, Berger JM, Arias-Palomo E.
Pubblicato in: Nature, 2024, ISSN 1476-4687
Editore: Springer Nature
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RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity

Autori: Morici M, Gabrielli S, Fujiwara K, Paternoga H, Beckert B, Bock LV, Chiba S, Wilson DN
Pubblicato in: Nature Communications, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-46761-3

Modelling covalent linkages in CCP 4

Autori: Robert A. Nicholls, Robbie P. Joosten, Fei Long, Marcin Wojdyr, Andrey Lebedev, Eugene Krissinel, Lucrezia Catapano, Marcus Fischer, Paul Emsley, Garib N. Murshudov
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 77/6, 2021, ISSN 2059-7983
Editore: IUCr
DOI: 10.1107/s2059798321001753

Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates

Autori: Linda Cerofolini, Kristian Vasa, Elisa Bianconi, Maria Salobehaj, Giulia Cappelli, Alice Bonciani, Giulia Licciardi, Anna Pérez‐Ràfols, Luis Padilla‐Cortés, Sabrina Antonacci, Domenico Rizzo, Enrico Ravera, Caterina Viglianisi, Vito Calderone, Giacomo Parigi, Claudio Luchinat, Antonio Macchiarulo, Stefano Menichetti, Marco Fragai
Pubblicato in: Angewandte Chemie International Edition, Numero 62, 2023, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
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Mixed‐Valence Compounds as Polarizing Agents for Overhauser Dynamic Nuclear Polarization in Solids**

Autori: Andrei Gurinov, Benedikt Sieland, Andrey Kuzhelev, Hossam Elgabarty, Thomas D. Kühne, Thomas Prisner, Jan Paradies, Marc Baldus, Konstantin L. Ivanov, Svetlana Pylaeva
Pubblicato in: Angewandte Chemie International Edition, Numero 60/28, 2021, Pagina/e 15371-15375, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
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The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA

Autori: Holvec S, Barchet C, Lechner A, Fréchin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP
Pubblicato in: Nature Structural & Molecular Biology, 2024, ISSN 1545-9985
Editore: Nature Portfolio
DOI: 10.1038/s41594-024-01274-x

Design, Quality and Validation of the EU-OPENSCREEN Fragment Library Poised to a High-Throughput Screening Collection

Autori: Jalencas X, Berg H, Espeland LO, Sreeramulu S, Kinnen F, Richter C, Georgiou C, Yadrykhinsky V, Specker E, Jaudzems K, Mileti T, Harmel R, Gribbon P, Schwalbe H, Brenk R, Jirgensons A, Zaliani A, Mestres J.
Pubblicato in: RSC Medicinal Chemistry, 2024, ISSN 2632-8682
Editore: Royal Society of Chemistry
DOI: 10.1039/d3md00724c

AI revolutions in biology: The joys and perils of AlphaFold

Autori: Anastassis Perrakis, Titia K. Sixma
Pubblicato in: EMBO Reports, 2021, ISSN 1469-3178
Editore: EMBO Press
DOI: 10.15252/embr.202154046

Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding

Autori: Hyjek-Składanowska M, Anderson BA, Mykhaylyk V, Orr C, Wagner A, Poznański JT, Skowronek K, Seth P, Nowotny M
Pubblicato in: Nucleic Acid Research, 2022, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkac774

Sample preparation strategies for efficient correlation of 3D SIM and soft X-ray tomography data at cryogenic temperatures

Autori: Chidinma A. Okolo, Ilias Kounatidis, Johannes Groen, Kamal L. Nahas, Stefan Balint, Thomas M. Fish, Mohamed A. Koronfel, Aitziber L. Cortajarena, Ian M. Dobbie, Eva Pereiro, Maria Harkiolaki
Pubblicato in: Nature Protocols, Numero 16/6, 2021, Pagina/e 2851-2885, ISSN 1754-2189
Editore: Nature Publishing Group
DOI: 10.1038/s41596-021-00522-4

Preparation and Cryo-FIB micromachining of <em>Saccharomyces cerevisiae</em> for Cryo-Electron Tomography

Autori: Jana Moravcová, Matyáš Pinkas, Radka Holbová, Jiří Nováček
Pubblicato in: Journal of Visualized Experiments, Numero 177, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/62351

High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation

Autori: Miglė Kišonaitė, Klemens Wild, Karine Lapouge, Thomas Ruppert, Irmgard Sinning
Pubblicato in: Nature Communications, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-27967-9

Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARSCoV-2

Autori: Di Micco S, Rahimova R, Sala M,Scala MC, Vivenzio G, Musella S, Andrei G, Remans K, Mammri L, Snoeck R, Bifulco G, Di Matteo F, Vestuto V, Campiglia P, Márquez JA, Fasano A.
Pubblicato in: European Journal of Medicinal Chemistry, Numero 02235234, 2022, ISSN 0223-5234
Editore: Elsevier BV
DOI: 10.1016/j.ejmech.2022.114857

The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services

Autori: Fromm SA, O'Connor KM, Purdy M, Bhatt PR, Loughran G, Atkins JF, Jomaa A, Mattei S.
Pubblicato in: Nature communications, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-36742-3

A multi-scale numerical approach to study monoclonal antibodies in solution

Autori: Polimeni M, Zaccarelli E, Gulotta A, Lund M, Stradner A, Schurtenberger P
Pubblicato in: APL Bioengineering, 2024, ISSN 2473-2877
Editore: American Institute of Physics
DOI: 10.1063/5.0186642

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

Autori: 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
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-35791-y

Integration of NMR Spectroscopy in an Analytical Workflow to Evaluate the Effects of Oxidative Stress on Abituzumab: Beyond the Fingerprint of mAbs

Autori: Cerofolini L, Ravera E, Fischer C, Trovato A, Sacco F, Palinsky W, Angiuoni G, Fragai M, Baroni F.
Pubblicato in: Analytical Chemistry, 2023, ISSN 1520-6882
Editore: ACS Publications
DOI: 10.1021/acs.analchem.3c00317

NMR-based Fragment Screening in a Minimum Sample but Maximum Automation Mode

Autori: Hannes Berg, M. A. Wirtz Martin, A. Niesteruk, C. Richter, S. Sreeramulu, H. Schwalbe
Pubblicato in: Journal of Visualized Experiments, Numero 172, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/62262

Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery

Autori: Misbha Ud Din Ahmad, Alexander Fish, Jeroen Molenaar, Sridhar Sreeramulu, Christian Richter, Nadide Altincekic, Harald Schwalbe, Hans Wienk, Anastassis Perrakis
Pubblicato in: Journal of Visualized Experiments, Numero 171, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
DOI: 10.3791/62469

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

Autori: Ramirez-Aportela E, Carazo JM, Sorzano COS
Pubblicato in: IUCrJ, 2022, ISSN 2052-2525
Editore: IUCr
DOI: 10.1107/s2052252522006959

Structural basis of CDNF interaction with the UPR regulator GRP78

Autori: Melissa A. Graewert, Maria Volkova, Klara Jonasson, Juha A. E. Määttä, Tobias Gräwert, Samara Mamidi, Natalia Kulesskaya, Johan Evenäs, Richard E. Johnsson, Dmitri Svergun, Arnab Bhattacharjee, Henri J. Huttunen
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-52478-0

TIR domains produce histidine-ADPR conjugates as immune signaling molecules in bacteria

Autori: Sabonis D, Avraham C, Lu A, Herbst E, Silanskas A, Leavitt A, Yirmiya E, Zaremba M, Amitai G, Kranzusch PJ, Sorek R, Tamulaitiene G.
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.01.03.573942

Macrophage activation of cGAS and TRIM5 distinguish pandemic and non-pandemic HIV

Autori: Lorena Zuliani Alvarez, Morten L. Govasli, Jane Rasaiyaah, Chris Monit, Stephen O. Perry, Rebecca P. Sumner, Simon McAlpine-Scott, Claire Dickson, K. M. Rifat Faysal, Laura Hilditch, Richard J. Miles, Frederic Bibollet-Ruche, Beatrice H. Hahn, Till Boecking, Nikos Pinotsis, Leo C. James, David A. Jacques, Greg J. Towers
Pubblicato in: bioRxiv, 2022, ISSN 2692-8205
Editore: bioRxiv
DOI: 10.1101/2022.01.21.477263

An original potentiating mechanism revealed by the cryoEM structures of the human α7 nicotinic receptor in complex with nanobodies

Autori: Prevost MS, Barilone N, Dejean De La Batie G, Pons S, Ayme G, England P, Gielen M, Bontems F, Pehau-Arnaudet G, Maskos U, Lafaye P, Corringer P-J.
Pubblicato in: bioRxiv, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.01.03.522595

Phase distortion-free pNMR spectra

Autori: Enrico Ravera
Pubblicato in: arXiv.org, 2021, ISSN 2331-8422
Editore: arXiv.org / Cornell University

Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1

Autori: Düring J, Wolter M, Toplak J, Torres C, Dybkov O, Fokkens TJ, Urlaub H, Steinchen W, Dienemann C, Lorenz S.
Pubblicato in: Research Square, 2023, ISSN 2693-5015
Editore: Springer Nature
DOI: 10.21203/rs.3.rs-3220888/v1

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

Autori: Krieger JM, Sorzano COS, Carazo JM.
Pubblicato in: Preprints 2023, 2023080828, 2023, ISSN 2310-287X
Editore: Preprints
DOI: 10.20944/preprints202308.0828.v1

Improved detection of magnetic interactions in proteins based on long-lived coherences

Autori: Sadet A, Ianc O, Teleanu F, Ciumeică A, Lupulescu A, Vasos P.
Pubblicato in: Research Square, 2024, ISSN 2693-5015
Editore: Springer Nature
DOI: 10.21203/rs.3.rs-3694602/v1

A Modular Platform for Streamlining Automated Cryo-FIB Workflows

Autori: Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoetz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J.
Pubblicato in: bioRxiv, 2021, ISSN 0362-4331
Editore: New York Times Company
DOI: 10.1101/2021.05.19.444745

Structural basis for activation and mechanism of the bacterial hexameric motors RadA and ComM in DNA branch migration during homologous recombination

Autori: Talachia Rosa L, Vernhes E, Soulet AL, Polard P, Fronzes R.
Pubblicato in: BioRxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.02.15.580443

Iron Oxide Nanoparticles as Positive T1 Contrast Agents for Low-Field Magnetic Resonance Imaging at 64 mT

Autori: Oberdick S, Jordanova K, Lundstrom J, Parigi G, Poorman M, Poorman G, Keenan K.
Pubblicato in: Research Square, 2023, ISSN 2693-5015
Editore: Research Square Company
DOI: 10.21203/rs.3.rs-2485292/v1

EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control

Autori: Gemin O, Armijo V, Hons M, Bissardon C, Linares R, Bowler MW, Wolff G, Kovalev K, Babenko A, Salo VT, Schneider S, Rossi C, Lecomte L, Deckers T, Lauzier K, Janocha R, Felisaz F, Sinoir J, Galej WP, Mahamid J, Muller CW, Eustermann S, Mattei S, Cipriani F, Papp G.
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.01.18.576170

Inducible protein expression in stably transfected cells paves the way toward in-cell NMR studies in defined physiological states and 3D tissue cultures

Autori: Rynes J, Istvankova E, Krafcikova M, Luchinat E, Barbieri L, Banci L, Kamarytova K, Loja T, Fafilek B, Rico-Llanos G, Krejci P, Macurek L, Foldynova-Trantirkova S, Trantirek L.
Pubblicato in: ChemRxiv, 2024, ISSN 2573-2293
Editore: Cambridge Unversity Press
DOI: 10.26434/chemrxiv-2024-jqd66-v2

Structure of the dopamine D3 receptor bound to a bitopic agonist reveals a new specificity site in an expanded allosteric pocket

Autori: Arroyo-Urea S, Nazarova AL, Carrión-Antolí A, Bonifazi A, Battiti FO, Homing Lam J, Hauck Newman A, Katritch V, García-Nafría J.
Pubblicato in: Research Square, 2023, ISSN 2693-5015
Editore: Springer Nature
DOI: 10.21203/rs.3.rs-3433207/v1

From isolated polyelectrolytes to star-like assemblies: The role of sequence heterogeneity on the statistical structure of the intrinsically disordered Neurofilament-low tail domain

Autori: Kravikass M, Koren G, Saleh OA, Beck R.
Pubblicato in: arXiv, 2023, ISSN 2331-8422
Editore: Cornell University

DNA i-motif levels are overwhelmingly depleted in living human cells: insights from in-cell NMR.

Autori: Trantirek L, Viskova P, Istvankova E, Rynes J, Dzatko S, Loja T, Lenarcic Zivkovic M, Rigo R, El-Khoury R, Serano I, Damha M, Gonzalez C, Mergny JL, Foldynova-Trantirkova S.
Pubblicato in: Research Square, 2023, ISSN 2693-5015
Editore: Springer Nature
DOI: 10.21203/rs.3.rs-3734993/v1

Improvements on marker-free images alignment for electron tomography

Autori: Sorzano COS, De Isidro-Gomez F, Fernandez-Gimenez E, Herreros D, Marco S, Carazo JM, Messaoudi C.
Pubblicato in: BioRxiv, Numero May 24 2020, 2020, ISSN 0362-4331
Editore: New York Times Company
DOI: 10.1101/2020.05.22.110445

Multitarget Virtual Screening for Drug Repurposing in COVID19

Autori: CO Sorzano, E Crisman, JM Carazo, R leon
Pubblicato in: ChemRxiv, Numero July 17 2020, 2020, ISSN 2573-2293
Editore: American Chemical Society (ACS), Chinese Chemical Society, Chemical Society of Japan, German Chemical Society (GDCh) and the Royal Society of Chemistry

The BAF A12T mutation reduces BAF affinity to lamin A/C, preventing its recruitment to nuclear ruptures in Nestor Guillermo Progeria Syndrome cells.

Autori: Janssen AFJ, Marcelot A, Breusegem SY, Legrand P, Zinn-Justin S, Larrieu D
Pubblicato in: bioRxiv, 2022, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.02.25.481780

Intramolecular Structural Heterogeneity altered by Long-range Contacts in an Intrinsically Disordered Protein

Autori: Koren G, Meir S, Holschuh L, Mertens HDT, Ehm T, Yahalom N, Golombek A, Schwartz T, Svergun DI, Saleh OA, Dzubiella J, Beck R.
Pubblicato in: arXiv e-prints, 2022, ISSN 2331-8422
Editore: Cornell University
DOI: 10.48550/arxiv.2212.01894

Plasticity of the binding pocket in peptide transporters underpins 2 promiscuous substrate recognition

Autori: Kotov V, Killer M, Jungnickel KEJ, Lei J, Finocchio G, Steinke J, Bartels K, Strauss J, Dupeux F, Humm A-S, Cornaciu I, Márquez JA, Pardon E, Steyaert J, Löw C.
Pubblicato in: bioRxiv, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.02.14.528348

Production and Preparation of Isotopically Labeled Human Membrane Proteins in Pichia pastoris for Fast-MAS-NMR Analyses

Autori: Barret L, Schubeis T, Kugler V, Guyot L, Pintacuda G, Wagner R.
Pubblicato in: Methods Mol Biol. 2022, Numero 2507, 2022, Pagina/e 201-221, ISBN 978-1-0716-2367-1
Editore: Springer
DOI: 10.1007/978-1-0716-2368-8_11

Cryo-focused ion beam lamella preparation protocol for in situ Structural Biology

Autori: Jana Moravcová, Radka Dopitová, Matyáš Pinkas, Jiří Nováček
Pubblicato in: Methods in Molecular Biology, Numero Vol. 2305, Ch. 15, 2021
Editore: Springer
DOI: 10.1007/978-1-0716-1406-8

Cryo-Focused Ion Beam Lamella Preparation Protocol for in Situ Structural Biology

Autori: Moravcova J, Dopitova R, Pinkas M, Novacek J
Pubblicato in: Methods. Methods Mol Biol. 2021; 2305, 2021, Pagina/e 301-322, ISBN 978-1-0716-1405-1
Editore: Springer
DOI: 10.1007/978-1-0716-1406-8_15

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

Autori: Sorzano COS, Jiménez-Moreno A, Maluenda D, Ramírez-Aportela E, Martínez M, Cuervo A, Melero R, Conesa JJ, Sánchez-García R, Strelak D, Filipovic J, Fernández-Giménez E, de Isidro-Gómez F, Herreros D, Conesa P, Del Caño L, Fonseca Y, de la Morena JJ, Macías JR, Losana P, Marabini R, Carazo JM.
Pubblicato in: Methods. Methods Mol Biol. 2021; 2305, 2021, Pagina/e 257-289, ISBN 978-1-0716-1405-1
Editore: Springer
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Cryogenic Preparations of Biological Specimens for Cryo-Electron Tomography

Autori: D’Imprima E, Fung HKH, Zagoriy I, Mahamid J
Pubblicato in: Cryo-Electron Tomography - Structural Biology in situ, 2024, Pagina/e 85-114, ISBN 978-3-031-51171-4
Editore: Springer Cham
DOI: 10.1007/978-3-031-51171-4_3

Mixed-valence compounds as polarizing agents for Overhauser dynamic nuclear polarization in solids

Autori: Andrei Gurinov, Benedikt Sieland, Andrei Kuzhelev, Hossam Elgabarty, Thomas D. Kuhne, Thomas Prisner, Jan Paradies, Marc Baldus, Konstantin L. Ivanov, and Svetlana Pylaeva
Pubblicato in: Condensed Matter - arXiv.org, 2021
Editore: Cornell University

Combining scattering experiments and colloid theory to characterize charge effects in concentrated antibody solutions

Autori: Gulotta A, Polimeni M, Lenton S, Starr CG, Kingsbury JS, Stradner A, Zaccarelli E, Schurtenberger P.
Pubblicato in: arXiv, 2023, ISSN 2331-8422
Editore: arXiv

Structural analysis of human ex vivo amyloid fibrils from systemic AA amyloidosis

Autori: Banerjee S
Pubblicato in: 2023
Editore: Banerjee S

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