Infrastructure for transnational access and discovery in structural biology

Livrables

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

Publications

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

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

The CCP4 suite: integrative software for macromolecular crystallography

Auteurs: 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,
Publié dans: Acta Crystallogr D Struct Biol., 2023, ISSN 2059-7983
Éditeur: IUCr
DOI: 10.1107/s2059798323003595

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 12/1, 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-021-23327-1

Studies on the Interaction between Model Proteins and Fluorinated Ionic Liquids

Auteurs: Alves MMS, Melo MN, Mertens HDT, Pereiro AB, Archer M
Publié dans: Pharmaceutics, 2023, ISSN 1999-4923
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/pharmaceutics15010157

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

Auteurs: 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
Publié dans: ChemBioChem, Numéro 24, 2023, ISSN 1439-4227
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202200760

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

Auteurs: 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
Publié dans: Journal of Structural Biology, Numéro 213/1, 2021, Page(s) 107695, ISSN 1047-8477
Éditeur: 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

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

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

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

Whole-proteome structures shed new light on posttranslational modifications

Auteurs: Robbie P. Joosten, Jon Agirre
Publié dans: PLoS Biol, 2022, ISSN 1545-7885
Éditeur: Public Library of Science
DOI: 10.1371/journal.pbio.3001673

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

Auteurs: 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
Publié dans: Journal of Cell Biology, 2024, ISSN 1540-8140
Éditeur: 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

Auteurs: Letizia Barbieri, Enrico Luchinat
Publié dans: Journal of Visualized Experiments, Numéro 169, 2021, ISSN 1940-087X
Éditeur: 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

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

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 15, 2024, ISSN 2041-1723
Éditeur: 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

Auteurs: 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
Publié dans: Angew Chem Int Ed Engl., 2022, ISSN 1433-7851
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202205858

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

Auteurs: Beatrice Balboni, Roberto Marotta, Francesco Rinaldi, Giulia Milordini, Giulia Varignani, Stefania Girotto, Andrea Cavalli
Publié dans: Communications Biology, Numéro 7, 2024, ISSN 2399-3642
Éditeur: Nature Portfolio
DOI: 10.1038/s42003-024-06644-1

Structural conservation of antibiotic interaction with ribosomes

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

Protein delivery to living cells by thermal stimulation for biophysical investigation

Auteurs: Torricella F, Barbieri L, Bazzurro V, Diaspro A, Banci L.
Publié dans: Scientific Reports, Numéro 20452322, 2022, ISSN 2045-2322
Éditeur: 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

Auteurs: Andriianov A, Trigüis S, Drobiazko A, Sierro N, Ivanov NV, Selmer M, Severinov K, Isaev A.
Publié dans: Cell Reports, 2023, ISSN 2211-1247
Éditeur: Cell Press
DOI: 10.1016/j.celrep.2023.112972

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

Auteurs: Shu Zhou, Maosen Ruan, Yunyan Li, Jing Yang, Suwen Bai, Christian Richter, Harald Schwalbe, Can Xie, Bing Shen & Junfeng Wang
Publié dans: Cell Research, 2020, ISSN 1001-0602
Éditeur: 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

Auteurs: Premetis GE, Stathi A, Papageorgiou AC, Labrou NE.
Publié dans: FEBS Journal, 2022, ISSN 1742-464X
Éditeur: Blackwell Publishing Inc.
DOI: 10.1111/febs.16686

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

Auteurs: 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.
Publié dans: Acta Crystallogr D Struct Biol, 2022, ISSN 2059-7983
Éditeur: John Wiley and Sons Inc.
DOI: 10.1107/s2059798322001978

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

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

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

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

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

Auteurs: Marco Schiavina, Ruth Konrat, Irene Ceccolini, Borja Mateos, Robert Konrat, Isabella C. Felli, Roberta Pierattelli
Publié dans: Journal of Magnetic Resonance, Numéro 354, 2023, Page(s) 107539, ISSN 1090-7807
Éditeur: Academic Press
DOI: 10.1016/j.jmr.2023.107539

A Sample Preparation Pipeline for Microcrystals at the VMXm Beamline

Auteurs: Adam D. Crawshaw, Emma V. Beale, Anna J. Warren, Andrew Stallwood, Graham Duller, Jose Trincao, Gwyndaf Evans
Publié dans: Journal of Visualized Experiments, Numéro 172, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/62306

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

Auteurs: Camponeschi F, Piccioli M, Banci L.
Publié dans: Molecules, 2022, ISSN 1420-3049
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules27238218

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

Auteurs: Pierson E, De Pol F, Fillet M, Wouters J.
Publié dans: Commun Biol., 2023, ISSN 2399-3642
Éditeur: Springer Nature
DOI: 10.1038/s42003-023-05402-z

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

Auteurs: Hay IM, Shamin M, Caroe ER, Mohammed ASA, Svergun DI, Jeffries CM, Graham SC, Sharpe HJ, Deane JE.
Publié dans: Journal of Biological Chemistry, 2022, ISSN 0021-9258
Éditeur: 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

Auteurs: Epasto LM, Che K, Kozak F, Selimovic A, Kadeřávek P, Kurzbach D.
Publié dans: Science Advances, 2022, ISSN 2375-2548
Éditeur: 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

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

Fixed Target Serial Data Collection at Diamond Light Source

Auteurs: 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
Publié dans: Journal of Visualized Experiments, Numéro 168, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/62200

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

Auteurs: 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.
Publié dans: Nature Communications, 2024, ISSN 2041-1723
Éditeur: 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

Auteurs: Da Vela S, Saudino G, Lucarelli F, Banci L, Svergun DI, Ciofi-Baffoni S.
Publié dans: J Mol Biol, 2023, ISSN 0022-2836
Éditeur: 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

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

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

Auteurs: 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
Publié dans: Science Advances, 2022, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abo0517

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

Auteurs: David Beriashvili, Raymond D. Schellevis, Federico Napoli, Markus Weingarth, Marc Baldus
Publié dans: Journal of Visualized Experiments, Numéro 169, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/62197

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

Auteurs: Pearce NM, Skyner R, Krojer T.
Publié dans: Front. Mol. Biosci., Numéro Section Structural BIology, 2022, ISSN 2296-889X
Éditeur: Lausanne
DOI: 10.3389/fmolb.2022.861491

In-cell NMR: Why and how?

Auteurs: Theillet FX, Luchinat E.
Publié dans: Progress in Nuclear Magnetic Resonance Spectroscopy, 2022, ISSN 0079-6565
Éditeur: 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)

Auteurs: Ying Wang, John Kirkpatrick, Susanne zur Lage, Sophie M. Korn, Konstantin Neißner, Harald Schwalbe, Andreas Schlundt, Teresa Carlomagno
Publié dans: Biomolecular NMR Assignments, 2021, ISSN 1874-2718
Éditeur: 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

Auteurs: 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
Publié dans: Journal of Biological Chemistry, Numéro 00219258, 2022, ISSN 0021-9258
Éditeur: 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

Auteurs: 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
Publié dans: Journal of Cell Science, Numéro 135, 2023, ISSN 0021-9533
Éditeur: 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

Auteurs: 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.
Publié dans: ACS Chemical Biology, 2024, ISSN 1554-8929
Éditeur: American Chemical Society
DOI: 10.1021/acschembio.3c00720

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

Auteurs: 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
Publié dans: Journal of Molecular Biology, 2022, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2022.167720

Progression of herpesvirus infection remodels mitochondrial organization and metabolism

Auteurs: 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
Publié dans: PLoS Pathog, 2024, ISSN 1553-7374
Éditeur: Public Library of Science
DOI: 10.1371/journal.ppat.1011829

Phase distortion-free paramagnetic NMR spectra

Auteurs: Enrico Ravera
Publié dans: Journal of Magnetic Resonance Open, Numéro 8-9, 2021, Page(s) 100022, ISSN 2666-4410
Éditeur: Elsevier Inc
DOI: 10.1016/j.jmro.2021.100022

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

Auteurs: Nina Eleni Christou, Karine Giandoreggio-Barranco, Isabel Ayala, Oleksandr Glushonkov, Virgile Adam, Dominique Bourgeois, Bernhard Brutscher
Publié dans: Journal of the American Chemical Society, Numéro 143/19, 2021, Page(s) 7521-7530, ISSN 0002-7863
Éditeur: American Chemical Society
DOI: 10.1021/jacs.1c02442

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

Auteurs: Giovanni Saudino, Dafne Suraci, Veronica Nasta, Simone Ciofi-Baffoni, Lucia Banci
Publié dans: International Journal of Molecular Sciences, Numéro 22/9, 2021, Page(s) 4848, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22094848

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

Auteurs: Diana Müller, Irene Bessi, Christian Richter, and Harald Schwalbe
Publié dans: Angewandte Chemie (International Edition), 2021, ISSN 1433-7851
Éditeur: 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

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

OUP accepted manuscript

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

Auteurs: Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Alessio Nocentini, Claudiu T. Supuran, and Lucia Banci
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Structural studies of β-glucosidase from the thermophilic bacterium <i>Caldicellulosiruptor saccharolyticus</i>

Auteurs: Anastasia I. Sotiropoulou, Dimitris G. Hatzinikolaou, Evangelia D. Chrysina
Publié dans: Acta Crystallographica Section D Structural Biology, Numéro 80, 2024, Page(s) 733-743, ISSN 2059-7983
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Controlling the incorporation of fluorinated amino acids in human cells and its structural impact

Auteurs: Azzurra Costantino, Lan B. T. Pham, Letizia Barbieri, Vito Calderone, Gili Ben‐Nissan, Michal Sharon, Lucia Banci, Enrico Luchinat
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Exploring the druggability of conserved RNA regulatory elements in the SARS‐CoV‐2 genome

Auteurs: Sridhar Sreeramulu, Christian Richter, Hannes Berg, Maria A Wirtz Martin, Betül Ceylan, Tobias Matzel, Jennifer Adam, Nadide Altincekic, Kamal Azzaoui, Jasleen Kaur Bains, Marcel J.J. Blommers, Jan Ferner, Boris Fürtig, M. Göbel, J Tassilo Grün, Martin Hengesbach, Katharina F. Hohmann, Daniel Hymon, Bozana Knezic, Jason Martins, Klara R Mertinkus, Anna Niesteruk, Stephen A Peter, Dennis J Pype
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Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action

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

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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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The Extended Hadamard Transform: Sensitivity-Enhanced NMR Experiments Among Labile and Non-Labile 1Hs of SARS-CoV-2-derived RNAs

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Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

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A thermosensitive gel matrix for bioreactor-assisted in-cell NMR of nucleic acids and proteins

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Rapid protein delivery to living cells for biomolecular investigation

Auteurs: Francesco Torricella, Alessio Bonucci, Panagis Polykretis, Francesca Cencetti, Lucia Banci
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Biochemical and Structural Characterization of CRH-1, a Carbapenemase from Chromobacterium haemolyticum Related to KPC β-Lactamases

Auteurs: Brunetti F, Ghiglione B, Gudeta DD, Gutkind G, Guardabassi L, Klinke S, Power P.
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Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein

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Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography

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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

Auteurs: Siebert H-C, Eckert T, Bhunia A, Klatte N, Mohri M, Siebert S, Kozarova A, Hudson JW, Zhang R, Zhang N, Li L, Gousias K, Kanakis D, Yan M, Jiménez-Barbero J, Kožár T, Nifantiev NE, Vollmer C, Brandenburger T, Kindgen-Milles D, Haak T, Petridis AK.
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Structure-function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role

Auteurs: Kosinas C, Zerva A, Topakas E, Dimarogona M.
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A modular platform for automated cryo-FIB workflows

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Single Particle Cryo-Electron Microscopy: From Sample to Structure

Auteurs: Joshua B.R. White, Daniel P. Maskell, Andrew Howe, Martin Harrow, Daniel K. Clare, C. Alistair Siebert, Emma L. Hesketh, Rebecca F. Thompson
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Determination of intracellular protein–ligand binding affinity by competition binding in-cell NMR

Auteurs: Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Matteo Pennestri, Alessio Nocentini, Claudiu T. Supuran, Lucia Banci
Publié dans: Acta Crystallographica Section D Structural Biology, Numéro 77/10, 2021, Page(s) 1270-1281, ISSN 2059-7983
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Updated restraint dictionaries for carbohydrates in the pyranose form

Auteurs: Atanasova M, Nicholls RA, Joosten RP, Agirre J.
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Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium

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Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine

Auteurs: Hallier DC, Smales GJ, Seitz H, Hahn MB.
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Image processing tools for the validation of CryoEM maps

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Publié dans: Faraday Discussions, 2022, ISSN 1364-5498
Éditeur: Royal Society of Chemistry
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The Coming of Age of In-Cell Solution NMR

Auteurs: Luchinat E, Cremonini M, Banci L
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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

Auteurs: Steinebrei M, Baur J, Pradhan A, Kupfer N, Wiese S, Hegenbart U, Schönland SO, Schmidt M, Fändrich M.
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Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates

Auteurs: Tatjana Barthel, Franziska U. Huschmann, Dirk Wallacher, Christian G. Feiler, Gerhard Klebe, Manfred S. Weiss, Jan Wollenhaupt
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Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images

Auteurs: Nina Vyas, Stephan Kunne, Thomas M. Fish, Ian M. Dobbie, Maria Harkiolaki, Perrine Paul-Gilloteaux
Publié dans: STAR Protocols, Numéro 2/2, 2021, Page(s) 100529, ISSN 2666-1667
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Cryo-EM and Single-Particle Analysis with Scipion

Auteurs: A. Jiménez-Moreno, L. del Caño, M. Martínez, E. Ramírez-Aportela, A. Cuervo, R. Melero, R. Sánchez-García, D. Strelak, E. Fernández-Giménez, F.P. de Isidro-Gómez, D. Herreros, P. Conesa, Y. Fonseca, D. Maluenda, J. Jiménez de la Morena, J.R. Macías, P. Losana, R. Marabini, J.M. Carazo, C.O.S. Sorzano
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Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

Auteurs: Strelak D, Jiménez-Moreno A, Vilas JL, Ramírez-Aportela E, Sánchez-García R, Maluenda D, Vargas J, Herreros D, Fernández-Giménez E, de Isidro-Gómez FP, Horacek J, Myska D, Horacek M, Conesa P, Fonseca-Reyna YC, Jiménez J, Martínez M, Harastani M, Jonić S, Filipovic J, Marabini R, Carazo JM, Sorzano COS
Publié dans: Molecules, 2021, ISSN 1420-3049
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Oxidation of the Mycobacterium tuberculosis key virulence factor Protein Tyrosine Phosphatase A (MptpA) reduces its phosphatase activity

Auteurs: Niesteruk A,Sreeramulu S, Jonker HRA, Richter C, Schwalbe H.
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Real-time NMR spectroscopy in the study of biomolecular kineticsand dynamics

Auteurs: György Pintér, Katharina F. Hohmann, J. Tassilo Grün, Julia Wirmer-Bartoschek, Clemens Glaubitz, Boris Fürtig, Harald Schwalbe
Publié dans: Magnetic Resonance Discussions, 2021, ISSN 2699-0059
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Identification and Characterization of an RRM‐Containing, RNA Binding Protein in Acinetobacter baumannii

Auteurs: Ciani C, Pérez‐Ràfols A, Bonomo I, Micaelli M, Esposito A, Zucal C, Belli R, D’Agostino VG, Bianconi I, Calderone V, Cerofolini L, Massidda O, Whalen MB, Fragai M, Provenzani A.
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Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed

Auteurs: Joosten RP, Nicholls RA, Agirre J.
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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

Auteurs: Gustavo M. A. Lima, Elmir Jagudin, Vladimir O. Talibov, Laila S. Benz, Costantino Marullo, Tatjana Barthel, Jan Wollenhaupt, Manfred S. Weiss, Uwe Mueller
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Optimization of the Lead Compound NVP-BHG712 as Colorectal Cancer Inhibitor

Auteurs: Tröster A, DiPrima M, Jores N, Kudlinzki D, Sreeramulu S, Gande SL, Linhard V, Ludig D, Schug A, Saxena K, Reinecke M, Heinzlmeir S, Leisegang MS, Wollenhaupt J, Lennartz F, Weiss MS, Kuster B, Tosato G, Schwalbe H.
Publié dans: Chemistry, 2023, ISSN 0947-6539
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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

Auteurs: Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M
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Structural and molecular insights into a bifunctional glycoside hydrolase 30 xylanase specific to glucuronoxylan

Auteurs: Christina Pentari, Christos Kosinas, Efstratios Nikolaivits, Maria Dimarogona, Evangelos Topakas
Publié dans: Biotechnology and Bioengineering, Numéro 121, 2024, Page(s) 2067-2078, ISSN 0006-3592
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Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties

Auteurs: Maity A, Wulffelé J, Ayala I, Favier A, Adam V, Bourgeois D, Brutscher B
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Small molecule MMRi62 targets MDM4 for degradation and induces leukemic cell apoptosis regardless of p53 status

Auteurs: Lama R, Xu C, Galster SL, Querol-García J, Portwood S, Mavis CK, Ruiz FM, Martin D, Wu J, Giorgi MC, Bargonetti J, Wang ES, Hernandez-Ilizaliturri FJ, Koudelka GB, Chemler SR, Muñoz IG, Wang X
Publié dans: Frontiers in Oncology, 2022, ISSN 2234-943X
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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

Auteurs: Gelot C, Kovacs MT, Miron S, Mylne E, Haan A, Boeffard-Dosierre L, Ghouil R, Popova T, Dingli F, Loew D, Guirouilh-Barbat J, Del Nery E, Zinn-Justin S, Ceccaldi R.
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A Fijivirus Major Viroplasm Protein Shows RNA-Stimulated ATPase Activity by Adopting Pentameric and Hexameric Assemblies of Dimers

Auteurs: Gabriela Llauger, Roberto Melero, Demián Monti, Gabriela Sycz, Cristián Huck-Iriart, María L. Cerutti, Sebastián Klinke, Evelyn Mikkelsen, Ariel Tijman, Rocío Arranz, Victoria Alfonso, Sofía M. Arellano, Fernando A. Goldbaum, Yann G. J. Sterckx, José-María Carazo, Sergio B. Kaufman, Pablo D. Dans, Mariana del Vas, Lisandro H. Otero
Publié dans: mBio, Numéro 14, 2024, ISSN 2150-7511
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Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners

Auteurs: Agathe Marcelot, Ambre Petitalot, Virginie Ropars, Marie-Hélène Le Du, Camille Samson, Stevens Dubois, Guillaume Hoffmann, Simona Miron, Philippe Cuniasse, Jose Antonio Marquez, Robert Thai, François-Xavier Theillet, Sophie Zinn-Justin
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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

Auteurs: Deborah Grifagni, Vito Calderone, Stefano Giuntini, Francesca Cantini, Marco Fragai, Lucia Banci
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Dynamic interactions and Ca2+-binding modulate the holdase-type chaperone activity of S100B preventing tau aggregation and seeding

Auteurs: Guilherme G. Moreira, François-Xavier Cantrelle, Andrea Quezada, Filipa S. Carvalho, Joana S. Cristóvão, Urmi Sengupta, Nicha Puangmalai, Ana P. Carapeto, Mário S. Rodrigues, Isabel Cardoso, Güenter Fritz, Federico Herrera, Rakez Kayed, Isabelle Landrieu, Cláudio M. Gomes
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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

Auteurs: Giastas P, Papakyriakou A, Tsafaras G, Tzartos SJ, Zouridakis M.
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Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

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

Auteurs: Carlos Oscar S. Sorzano, Jose Maria Carazo
Publié dans: Acta Crystallographica Section D Structural Biology, Numéro 77/6, 2021, Page(s) 835-839, ISSN 2059-7983
Éditeur: IUCr
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Solid-state NMR - a complementary technique for protein framework characterization

Auteurs: Cerofolini L, Ramberg KO, Padilla LC, Antonik P, Ravera E, Luchinat C, Fragai M, Crowley PB.
Publié dans: Chemical Communications, 2023, ISSN 1364-548X
Éditeur: Royal Society of Chemistry
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Targeting EPHA2 with Kinase Inhibitors in Colorectal Cancer

Auteurs: Tröster A, Jores N, Mineev KS, Sreeramulu S, DiPrima M, Tosato G, Schwalbe H.
Publié dans: ChemMedChem, 2023, ISSN 1860-7179
Éditeur: Wiley - V C H Verlag GmbbH & Co.
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A 3D Cartographic Description of the Cell by Cryo Soft X-ray Tomography

Auteurs: Johannes Groen, Andrea Sorrentino, Lucía Aballe, Robert Oliete, Ricardo Valcárcel, Chidinma Okolo, Ilias Kounatidis, Maria Harkiolaki, Ana Joaquina Pérez-Berná, Eva Pereiro
Publié dans: Journal of Visualized Experiments, Numéro 169, 2021, ISSN 1940-087X
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Unraveling the mechanism of [4Fe‐4S] cluster assembly on the N‐terminal cluster binding site of NUBP1

Auteurs: Beatrice Bargagna, Sara Matteucci, Simone Ciofi‐Baffoni, Francesca Camponeschi, Lucia Banci
Publié dans: Protein Science, Numéro 32, 2023, ISSN 0961-8368
Éditeur: Cold Spring Harbor Laboratory Press
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Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Auteurs: Felix Weis, Wim J. H. Hagen, Martin Schorb, Simone Mattei
Publié dans: Journal of Visualized Experiments, Numéro 169, 2021, ISSN 1940-087X
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EFFECTS of BORON SUPPLEMENTATION on DAIRY CALVES’ HEALTH: A METABOLOMICS STUDY

Auteurs: Abdullah Basoglu, ADAM ABDEL-AZIZ ADAM, NURI BASPINAR, ALESSIA VIGNOLI, GAIAI MEONI, Leonardo Tenori, Erdem Gullersoy, Rumeyhisa Bicici
Publié dans: Assiut Veterinary Medical Journal, 2023, Page(s) 0-0, ISSN 2314-5226
Éditeur: The Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt
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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

Auteurs: Domenico Rizzo, Linda Cerofolini, Stefano Giuntini, Luisa Iozzino, Carlo Pergola, Francesca Sacco, Angelo Palmese, Enrico Ravera, Claudio Luchinat, Fabio Baroni, Marco Fragai
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Structure of the Borrelia bacteriophage φBB1 procapsid

Auteurs: Rūmnieks J, Füzik T, Tārs K.
Publié dans: Journal of Molecular Biology, 2023, ISSN 0022-2836
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Multitasking Pharmacophores Support Cabotegravir-Based Long-Acting HIV Pre-Exposure Prophylaxis (PrEP)

Auteurs: Wan Z, Shi M, Gong Y, Lucci M, Li J, Zhou J, Yang X-L, Lelli M, He X, Mao J.
Publié dans: Molecules, 2024, ISSN 1420-3049
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
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The COVID19-NMR Consortium: A Public Report on the Impact of this New Global Collaboration

Auteurs: Duchardt-Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Schwalbe H.
Publié dans: Angewandte Chemie, 2023, ISSN 1433-7851
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Structural and biochemical characterization of the C‐terminal region of the human <scp>RTEL</scp>1 helicase

Auteurs: Giuseppe Cortone, Melissa A. Graewert, Manil Kanade, Antonio Longo, Raghurama Hegde, Amaia González‐Magaña, Belén Chaves‐Arquero, Francisco J. Blanco, Luisa M. R. Napolitano, Silvia Onesti
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X-ray structure and enzymatic study of a bacterial NADPH oxidase highlight the activation mechanism of eukaryotic NOX

Auteurs: Isabelle Petit-Hartlein, Annelise Vermot, Michel Thepaut, Anne-Sophie Humm, Florine Dupeux, Jerome Dupuy, Vincent Chaptal, Jose Antonio Marquez, Susan ME Smith, Franck Fieschi
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Protein in-cell NMR spectroscopy at 1.2 GHz

Auteurs: Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Lucia Banci
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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

Auteurs: Riboni N, Bianchi F, Mattarozzi M, Caldara M, Gullì M, Graziano S, Maestri E, Marmiroli N, Careri M.
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Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein

Auteurs: Wiedemann C, Obika KB, Liebscher S, Jirschitzka J, Ohlenschläger O, Bordusa F.
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Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Auteurs: Nadide Altincekic, Sophie Marianne Korn, Nusrat Shahin Qureshi, Marie Dujardin, Martí Ninot-Pedrosa, Rupert Abele, Marie Jose Abi Saad, Caterina Alfano, Fabio C. L. Almeida, Islam Alshamleh, Gisele Cardoso de Amorim, Thomas K. Anderson, Cristiane D. Anobom, Chelsea Anorma, Jasleen Kaur Bains, Adriaan Bax, Martin Blackledge, Julius Blechar, Anja Böckmann, Louis Brigandat, Anna Bula, Matthias Büt
Publié dans: Frontiers in Molecular Biosciences, Numéro 8, 2021, ISSN 2296-889X
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Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

Auteurs: David Herreros, Roy R. Lederman, James Krieger, Amaya Jiménez-Moreno, Marta Martínez, David Myška, David Strelak, Jiri Filipovic, Ivet Bahar, Jose Maria Carazo, Carlos Oscar S. Sanchez
Publié dans: IUCrJ, Numéro 8/6, 2021, ISSN 2052-2525
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Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology

Auteurs: Conesa P, Fonseca YC, Jiménez de la Morena J, Sharov G, de la Rosa-Trevín JM, Cuervo A, García Mena A, Rodríguez de Francisco B, del Hoyo D, Herreros D, Marchan D, Strelak D, Fernández-Giménez E, Ramírez-Aportela E, de Isidro-Gómez FP, Sánchez I, Krieger J, Vilas JL, del Cano L, Gragera M, Iceta M, Martínez M, Losana P, Melero R, Marabini R, Carazo JM, Sorzano COS.
Publié dans: Biological Imaging, 2023, ISSN 2633-903X
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Structural deficits in key domains of Shank2 lead to alterations in postsynaptic nanoclusters and to a neurodevelopmental disorder in humans

Auteurs: Hassani Nia F, Woike D, Bento I, Niebling S, Tibbe D, Schulz K, Hirnet D, Skiba M, Hönck HH, Veith K, Günther C, Scholz T, Bierhals T, Driemeyer J, Bend R, Failla AV, Lohr C, Alai MG, Kreienkamp HJ
Publié dans: Molecular Psychiatry, 2022, ISSN 1359-4184
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Directed Evolution of Phi Class Glutathione Transferases Involved in Multiple-Herbicide Resistance of Grass Weeds and Crops

Auteurs: Ioannou E, Papageorgiou AC, Labrou NE.
Publié dans: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
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Analysis and validation of overall N-glycan conformation in Privateer

Auteurs: Dialpuri JS, Bagdonas H, Atanasova M, Schofield LC, Hekkelman ML, Joosten RP, Agirre J.
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Teixobactin kills bacteria by a two-pronged attack on the cell envelope

Auteurs: Shukla R, Lavore F, Maity S, Derks MGN, Jones CR, Vermeulen BJA, Melcrová A, Morris MA, Becker LM, Wang X, Kumar R, Medeiros-Silva J, van Beekveld RAM, Bonvin AMJJ, Lorent JH, Lelli M, Nowick JS, MacGillavry HD, Peoples AJ, Spoering AL, Ling LL, Hughes DE, Roos WH, Breukink E, Lewis K, Weingarth M.
Publié dans: Nature, 2022, ISSN 1476-4687
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Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism

Auteurs: Saridakis E, Vishwakarma R, Lai-Kee-Him J, Martin K, Simon I, Cohen-Gonsaud M, Coste F, Bron P, Margeat E, Boudvillain M
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Amyloid fibril structure from the vascular variant of systemic AA amyloidosis.

Auteurs: Banerjee S, Baur J, Daniel C, Pfeiffer PB, Hitzenberger M, Kuhn L, Wiese S, Bijzet J, Haupt C, Amann KU, Zacharias M, Hazenberg BPC, Westermark GT, Schmidt M, Fändrich M.
Publié dans: Nature Communications, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
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AlphaFill: enriching AlphaFold models with ligands and cofactors

Auteurs: Hekkelman ML, De Vries I, Joosten RP, Perrakis A
Publié dans: Nature Methods, Numéro 15487091, 2022, ISSN 1548-7091
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The structured organization of Deinococcus radiodurans' cell envelope

Auteurs: Farci D, Haniewicz P, Piano D.
Publié dans: Proc Natl Acad Sci U S A., 2022, ISSN 0027-8424
Éditeur: National Academy of Sciences
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splitSMLM, a spectral demixing method for high-precision multi-color localization microscopy applied to nuclear pore complexes

Auteurs: Andronov L, Genthial R, Hentsch D, Klaholz BP.
Publié dans: Communications Biology, Numéro 23993642, 2022, ISSN 2399-3642
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The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans

Auteurs: Farci D, Graça AT, Iesu L, de Sanctis D, Piano D.
Publié dans: Journal of Biological Chemistry, 2022, ISSN 0021-9258
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Improved detection of magnetic interactions in proteins based on long-lived coherences

Auteurs: Ianc O, Teleanu F, Ciumeică A, Lupulescu A, Sadet A, Vasos PR.
Publié dans: Communications Chemistry, 2024, ISSN 2399-3669
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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

Auteurs: Weishuai Yu, Imran Mohsin, Anastassios C. Papageorgiou and Duochuan Li
Publié dans: Catalysts, 2022, ISSN 2073-4344
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
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In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells

Auteurs: Víšková P, Ištvánková E, Ryneš J, Džatko Š, Loja T, Živković ML, Rigo R, El-Khoury R, Serrano-Chacón I, Damha MJ, González C, Mergny JL, Foldynová-Trantírková S, Trantírek L.
Publié dans: Nature Communications, 2024, ISSN 2041-1723
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PAXX binding to the NHEJ machinery explains functional redundancy with XLF

Auteurs: Seif-El-Dahan M, Kefala-Stavridi A, Frit P, Hardwick SW, Chirgadze DY, Maia De Oliviera T, Britton S, Barboule N, Bossaert M, Pandurangan AP, Meek K, Blundell TL, Ropars V, Calsou P, Charbonnier JB, Chaplin AK
Publié dans: Science Advances, 2023, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science
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Cryo-EM structure of a lysozyme-derived amyloid fibril from hereditary amyloidosis

Auteurs: Sara Karimi-Farsijani, Kartikay Sharma, Marijana Ugrina, Lukas Kuhn, Peter Benedikt Pfeiffer, Christian Haupt, Sebastian Wiese, Ute Hegenbart, Stefan O. Schönland, Nadine Schwierz, Matthias Schmidt, Marcus Fändrich
Publié dans: Nature Communications, Numéro 15, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
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Structural rearrangement of amyloid-β upon inhibitor binding suppresses formation of Alzheimer’s disease related oligomers

Auteurs: Tobias Lieblein, Rene Zangl, Janosch Martin, Jan Hoffmann, Marie J Hutchison, Tina Stark, Elke Stirnal, Thomas Schrader, Harald Schwalbe, Nina Morgner
Publié dans: eLife, Numéro 9, 2020, ISSN 2050-084X
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NMR quality control of fragment libraries for screening

Auteurs: Sridhar Sreeramulu, Christian Richter, Till Kuehn, Kamal Azzaoui, Marcel Jules José Blommers, Rebecca Del Conte, Marco Fragai, Nils Trieloff, Peter Schmieder, Marc Nazaré, Edgar Specker, Vladimir Ivanov, Hartmut Oschkinat, Lucia Banci, Harald Schwalbe
Publié dans: Journal of Biomolecular NMR, 2020, ISSN 0925-2738
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Development of in vitro-grown spheroids as a 3D tumor model system for solid-state NMR spectroscopy

Auteurs: Reinier Damman, Alessandra Lucini Paioni, Katerina T. Xenaki, Irati Beltrán Hernández, Paul M. P. van Bergen en Henegouwen, Marc Baldus
Publié dans: Journal of Biomolecular NMR, Numéro June 19 2020, 2020, ISSN 0925-2738
Éditeur: Kluwer Academic Publishers
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The basics of small-angle neutron scattering (SANS for new users of structural biology)

Auteurs: Cy M. Jeffries, Zuzanna Pietras, Dmitri I. Svergun
Publié dans: EPJ Web of Conferences, Numéro 236, 2020, Page(s) 03001, ISSN 2100-014X
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Structure-Based Identification and Functional Characterization of a Lipocalin in the Malaria Parasite Plasmodium falciparum

Auteurs: Paul-Christian Burda, Thomas Crosskey, Katharina Lauk, Aimo Zurborg, Christoph Söhnchen, Benjamin Liffner, Louisa Wilcke, Emma Pietsch, Jan Strauss, Cy M. Jeffries, Dmitri I. Svergun, Danny W. Wilson, Matthias Wilmanns, Tim-Wolf Gilberger
Publié dans: Cell Reports, Numéro 31/12, 2020, Page(s) 107817, ISSN 2211-1247
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Anomeric Selectivity of Trehalose Transferase with Rare l -Sugars

Auteurs: Luuk Mestrom, Stefan R. Marsden, Hessel van der Eijk, Jesper U. Laustsen, Cy M. Jeffries, Dmitri I. Svergun, Peter-Leon Hagedoorn, Isabel Bento, Ulf Hanefeld
Publié dans: ACS Catalysis, Numéro 10/15, 2020, Page(s) 8835-8839, ISSN 2155-5435
Éditeur: American Chemical Society
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19F‐NMR‐based fragment screening for 14 different biologically active RNAs and 10 DNA and protein counter‐screens

Auteurs: Oliver Binas, Vanessa de Jesus, Tom Landgraf, Albrecht Eduard Völklein, Jason Martins, Daniel Hymon, Hannes Berg, Jasleen Kaur Bains, Thomas Biedenbänder, Boris Fürtig, Santosh Lakshmi Gande, Anna Niesteruk, Andreas Oxenfarth, Nusrat Shahin Qureshi, Tatjana Schamber, Robbin Schnieders, Alix Tröster, Anna Wacker, Julia Wirmer-Bartoschek, Maria Alexandra Wirtz Martin, Elke Stirnal, Kamal Azzaoui
Publié dans: ChemBioChem, Numéro Aug 14 2020, 2020, ISSN 1439-4227
Éditeur: John Wiley & Sons Ltd.
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Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells

Auteurs: Nina Vyas, Nina Perry, Chidinma A. Okolo, Ilias Kounatidis, Thomas M. Fish, Kamal L. Nahas, Archana Jadhav, Mohamed A. Koronfel, Johannes Groen, Eva Pereiro, Ian M. Dobbie, Maria Harkiolaki
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Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM

Auteurs: Herreros D, Krieger JM, Fonseca Y, Conesa P, Harastani M, Vuillemot R, Hamitouche I, Serrano Gutiérrez R, Gragera M, Melero R, Jonic S, Carazo JM, Sorzano COS
Publié dans: Acta Crystallogr D Struct Biol, 2023, ISSN 2059-7983
Éditeur: IUCr
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3D Heteronuclear Magnetization Transfers for the Establishment of Secondary Structures in SARS-CoV-2-Derived RNAs

Auteurs: Jihyun Kim, Mihajlo Novakovic, Sundaresan Jayanthi, Adonis Lupulescu, Eriks Kupce, J. Tassilo Grün, Klara Mertinkus, Andreas Oxenfarth, Christian Richter, Robbin Schnieders, Julia Wirmer-Bartoschek, Harald Schwalbe, Lucio Frydman
Publié dans: Journal of the American Chemical Society, 2021, ISSN 0002-7863
Éditeur: American Chemical Society
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Heteronuclear decoupling with Rotor-Synchronized Phase-Alternated Cycles

Auteurs: Simion A, Schubeis T, Tanguy Le Marchand T, Vasilescu M, Pintacuda G, Lesage A, Filip C
Publié dans: The Journal of Chemical Physics, 2022, ISSN 0021-9606
Éditeur: American Institute of Physics
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Conservation and divergence of the G-interfaces of Drosophila melanogaster septins

Auteurs: de Freitas Fernandes A, Leonardo DA, Cavini IA, Rosa HVD, Vargas JA, D'Muniz Pereira H, Nascimento AS, Garratt RC
Publié dans: Cytoskeleton (Hoboken), 2022, ISSN 1949-3584
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The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble.

Auteurs: Irina Cornaciu, Raphael Bourgeas, Guillaume Hoffmann, Florine Dupeux, Anne-Sophie Humm, Vincent Mariaule, Andrea Pica, Damien Clavel, Gael Seroul, Peter Murphy, José Antonio Márquez
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An automated platform for structural analysis of membrane proteins through serial crystallography

Auteurs: Robert D. Healey, Shibom Basu, Anne-Sophie Humm, Cedric Leyrat, Xiaojing Cong, Jérome Golebiowski, Florine Dupeux, Andrea Pica, Sébastien Granier, José Antonio Márquez
Publié dans: bioRxiv, Numéro June 3, 2021, 2021, ISSN 0362-4331
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Direct Expression of Fluorinated Proteins in Human Cells for 19F In-Cell NMR Spectroscopy

Auteurs: Pham LBT, Costantino A, Barbieri L, Calderone V, Luchinat E, Banci L.
Publié dans: J Am Chem Soc, 2023, ISSN 0002-7863
Éditeur: American Chemical Society
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Shedding Light on Osteosarcoma Cell Differentiation: Impact on Biomineralization and Mitochondria Morphology

Auteurs: Rossi F, Picone G, Cappadone C, Sorrentino A, Columbaro M, Farruggia G, Catelli E, Sciutto G, Prati S, Oliete R, Pasini A, Pereiro E, Iotti S, Malucelli E
Publié dans: International Journal of Molecular Sciences, 2023, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin

Auteurs: Jan Wollenhaupt, Tatjana Barthel, Gustavo M. A. Lima, Alexander Metz, Dirk Wallacher, Elmir Jagudin, Franziska U. Huschmann, Thomas Hauß, Christian G. Feiler, Martin Gerlach, Michael Hellmig, Ronald Förster, Michael Steffien, Andreas Heine, Gerhard Klebe, Uwe Mueller, Manfred S. Weiss
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Éditeur: MYJoVE Corporation
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Unveiling the dimer/monomer propensities of Smad MH1-DNA complexes

Auteurs: Lidia Ruiz, Zuzanna Kaczmarska, Tiago Gomes, Eric Aragon, Carles Torner, Regina Freier, Blazej Baginski, Pau Martin-Malpartida, Natàlia de Martin Garrido, José. A. Marquez, Tiago N. Cordeiro, Radoslaw Pluta, Maria J. Macias
Publié dans: Computational and Structural Biotechnology Journal, Numéro 19, 2021, Page(s) 632-646, ISSN 2001-0370
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In‐cell NMR of functional riboswitch aptamers in eukaryotic cells

Auteurs: P. Broft, S. Dzatko, M. Krafcikova, Robert Hansel-Hertsch, A. Wacker, Volker Doetsch, L. Trantirek, Harald Schwalbe
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Éditeur: John Wiley & Sons Ltd.
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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

Auteurs: Melissa A. Graewert, Stefano Da Vela, Tobias W. Gräwert, Dmitry S. Molodenskiy, Clément E. Blanchet, Dmitri I. Svergun, Cy M. Jeffries
Publié dans: Crystals, Numéro 10/11, 2020, Page(s) 975, ISSN 2073-4352
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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

Auteurs: Mihajlo Novakovic, Eriks Kupce, Tali Scherf, Andreas Oxenfarth, Robbin Schnieders, Tassilo Grün, Julia Wirmer-Bartoschek, Christian Richter, Harald Schwalbe, Lucio Frydman
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Cryo-EM structure of the fully assembled Elongator complex.

Auteurs: Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NE, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S.
Publié dans: Nucleic Acid Research, 2023, ISSN 1362-4962
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The Molecular Chaperone CCT Sequesters Gelsolin and Protects it from Cleavage by Caspase-3

Auteurs: Cuéllar J, Vallin J, Svanström A, Maestro-López M, Bueno-Carrasco MT, Ludlam WG, Willardson BM, Valpuesta JM, Grantham J
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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Auteurs: Alice Douangamath, Ailsa Powell, Daren Fearon, Patrick M. Collins, Romain Talon, Tobias Krojer, Rachael Skyner, Jose Brandao-Neto, Louise Dunnett, Alexandre Dias, Anthony Aimon, Nicholas M. Pearce, Conor Wild, Tyler Gorrie-Stone, Frank von Delft
Publié dans: Journal of Visualized Experiments, Numéro 171, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
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Enlarging the scenario of site directed 19F labeling for NMR spectroscopy of biomolecules

Auteurs: Vitali V, Torricella F, Massai L, Messori L, Banci L.
Publié dans: Scientific reports, 2023, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-023-49247-2

Engineered Nonviral Protein Cages Modified for MR Imaging

Auteurs: Kaster MA, Levasseur MD, Edwardson TGW, Caldwell MA, Hofmann D, Licciardi G, Parigi G, Luchinat C, Hilvert D, Meade TJ
Publié dans: ACS Applied Bio Materials, 2023, ISSN 2576-6422
Éditeur: American Chemical Society
DOI: 10.1021/acsabm.2c00892

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

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

Auteurs: Vilas JL, Carazo JM, Sorzano COS
Publié dans: Chemical Reviews, 2022, ISSN 0009-2665
Éditeur: 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

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

Auteurs: 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.
Publié dans: Elife, 2022, ISSN 2050-084X
Éditeur: 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

Auteurs: Juliana Goncalves, A. Margarida Juliano, Nadia Charepe, Marta Alenquer, Diogo Athayde, Filipe Ferreira, Margarida Archer, Maria Joao Amorim, Fatima Serrano, Helena Soares
Publié dans: Cell Reports Medicine, 2021, ISSN 2666-3791
Éditeur: Cell Press
DOI: 10.1016/j.xcrm.2021.100468

The cryo-EM structure of the S-layer deinoxanthin-binding complex of Deinococcus radiodurans informs properties of its environmental interactions

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

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

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

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

Auteurs: Hans Wienk, Lucia Banci, Susan Daenke, Eva Pereiro, Harald Schwalbe, David Ian Stuart, Manfred S. Weiss, Anastassis Perrakis
Publié dans: Journal of Visualized Experiments, Numéro 177, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/63435

Molecular basis for transposase activation by a dedicated AAA+ ATPase

Auteurs: de la Gándara Á, Spínola-Amilibia M, Araújo-Bazán L, Núñez-Ramírez R, Berger JM, Arias-Palomo E.
Publié dans: Nature, 2024, ISSN 1476-4687
Éditeur: Springer Nature
DOI: 10.1038/s41586-024-07550-6

Modelling covalent linkages in CCP 4

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

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

Auteurs: 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
Publié dans: Angewandte Chemie International Edition, Numéro 62, 2023, ISSN 1433-7851
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202303202

Mixed‐Valence Compounds as Polarizing Agents for Overhauser Dynamic Nuclear Polarization in Solids**

Auteurs: Andrei Gurinov, Benedikt Sieland, Andrey Kuzhelev, Hossam Elgabarty, Thomas D. Kühne, Thomas Prisner, Jan Paradies, Marc Baldus, Konstantin L. Ivanov, Svetlana Pylaeva
Publié dans: Angewandte Chemie International Edition, Numéro 60/28, 2021, Page(s) 15371-15375, ISSN 1433-7851
Éditeur: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202103215

The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA

Auteurs: Holvec S, Barchet C, Lechner A, Fréchin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP
Publié dans: Nature Structural & Molecular Biology, 2024, ISSN 1545-9985
Éditeur: 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

Auteurs: 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.
Publié dans: RSC Medicinal Chemistry, 2024, ISSN 2632-8682
Éditeur: Royal Society of Chemistry
DOI: 10.1039/d3md00724c

AI revolutions in biology: The joys and perils of AlphaFold

Auteurs: Anastassis Perrakis, Titia K. Sixma
Publié dans: EMBO Reports, 2021, ISSN 1469-3178
Éditeur: EMBO Press
DOI: 10.15252/embr.202154046

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

Auteurs: Hyjek-Składanowska M, Anderson BA, Mykhaylyk V, Orr C, Wagner A, Poznański JT, Skowronek K, Seth P, Nowotny M
Publié dans: Nucleic Acid Research, 2022, ISSN 0305-1048
Éditeur: 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

Auteurs: 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
Publié dans: Nature Protocols, Numéro 16/6, 2021, Page(s) 2851-2885, ISSN 1754-2189
Éditeur: Nature Publishing Group
DOI: 10.1038/s41596-021-00522-4

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

Auteurs: Jana Moravcová, Matyáš Pinkas, Radka Holbová, Jiří Nováček
Publié dans: Journal of Visualized Experiments, Numéro 177, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/62351

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

Auteurs: Miglė Kišonaitė, Klemens Wild, Karine Lapouge, Thomas Ruppert, Irmgard Sinning
Publié dans: Nature Communications, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-27967-9

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

Auteurs: 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.
Publié dans: European Journal of Medicinal Chemistry, Numéro 02235234, 2022, ISSN 0223-5234
Éditeur: Elsevier BV
DOI: 10.1016/j.ejmech.2022.114857

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

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

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

Auteurs: Polimeni M, Zaccarelli E, Gulotta A, Lund M, Stradner A, Schurtenberger P
Publié dans: APL Bioengineering, 2024, ISSN 2473-2877
Éditeur: American Institute of Physics
DOI: 10.1063/5.0186642

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 14, 2023, ISSN 2041-1723
Éditeur: 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

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

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

Auteurs: Hannes Berg, M. A. Wirtz Martin, A. Niesteruk, C. Richter, S. Sreeramulu, H. Schwalbe
Publié dans: Journal of Visualized Experiments, Numéro 172, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/62262

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

Auteurs: Misbha Ud Din Ahmad, Alexander Fish, Jeroen Molenaar, Sridhar Sreeramulu, Christian Richter, Nadide Altincekic, Harald Schwalbe, Hans Wienk, Anastassis Perrakis
Publié dans: Journal of Visualized Experiments, Numéro 171, 2021, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/62469

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

Auteurs: Ramirez-Aportela E, Carazo JM, Sorzano COS
Publié dans: IUCrJ, 2022, ISSN 2052-2525
Éditeur: IUCr
DOI: 10.1107/s2052252522006959

Structural basis of CDNF interaction with the UPR regulator GRP78

Auteurs: 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
Publié dans: Nature Communications, Numéro 15, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-52478-0

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

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

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

Auteurs: 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
Publié dans: bioRxiv, 2022, ISSN 2692-8205
Éditeur: 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

Auteurs: 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.
Publié dans: bioRxiv, 2023, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.01.03.522595

Phase distortion-free pNMR spectra

Auteurs: Enrico Ravera
Publié dans: arXiv.org, 2021, ISSN 2331-8422
Éditeur: arXiv.org / Cornell University

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

Auteurs: Düring J, Wolter M, Toplak J, Torres C, Dybkov O, Fokkens TJ, Urlaub H, Steinchen W, Dienemann C, Lorenz S.
Publié dans: Research Square, 2023, ISSN 2693-5015
Éditeur: 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

Auteurs: Krieger JM, Sorzano COS, Carazo JM.
Publié dans: Preprints 2023, 2023080828, 2023, ISSN 2310-287X
Éditeur: Preprints
DOI: 10.20944/preprints202308.0828.v1

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

Auteurs: Sadet A, Ianc O, Teleanu F, Ciumeică A, Lupulescu A, Vasos P.
Publié dans: Research Square, 2024, ISSN 2693-5015
Éditeur: Springer Nature
DOI: 10.21203/rs.3.rs-3694602/v1

A Modular Platform for Streamlining Automated Cryo-FIB Workflows

Auteurs: Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoetz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J.
Publié dans: bioRxiv, 2021, ISSN 0362-4331
Éditeur: 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

Auteurs: Talachia Rosa L, Vernhes E, Soulet AL, Polard P, Fronzes R.
Publié dans: BioRxiv, 2024, ISSN 2692-8205
Éditeur: 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

Auteurs: Oberdick S, Jordanova K, Lundstrom J, Parigi G, Poorman M, Poorman G, Keenan K.
Publié dans: Research Square, 2023, ISSN 2693-5015
Éditeur: Research Square Company
DOI: 10.21203/rs.3.rs-2485292/v1

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

Auteurs: 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.
Publié dans: bioRxiv, 2024, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.01.18.576170

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

Auteurs: Arroyo-Urea S, Nazarova AL, Carrión-Antolí A, Bonifazi A, Battiti FO, Homing Lam J, Hauck Newman A, Katritch V, García-Nafría J.
Publié dans: Research Square, 2023, ISSN 2693-5015
Éditeur: 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

Auteurs: Kravikass M, Koren G, Saleh OA, Beck R.
Publié dans: arXiv, 2023, ISSN 2331-8422
Éditeur: Cornell University

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

Auteurs: 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.
Publié dans: Research Square, 2023, ISSN 2693-5015
Éditeur: Springer Nature
DOI: 10.21203/rs.3.rs-3734993/v1

Improvements on marker-free images alignment for electron tomography

Auteurs: Sorzano COS, De Isidro-Gomez F, Fernandez-Gimenez E, Herreros D, Marco S, Carazo JM, Messaoudi C.
Publié dans: BioRxiv, Numéro May 24 2020, 2020, ISSN 0362-4331
Éditeur: New York Times Company
DOI: 10.1101/2020.05.22.110445

Multitarget Virtual Screening for Drug Repurposing in COVID19

Auteurs: CO Sorzano, E Crisman, JM Carazo, R leon
Publié dans: ChemRxiv, Numéro July 17 2020, 2020, ISSN 2573-2293
Éditeur: 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.

Auteurs: Janssen AFJ, Marcelot A, Breusegem SY, Legrand P, Zinn-Justin S, Larrieu D
Publié dans: bioRxiv, 2022, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.02.25.481780

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

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

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

Auteurs: 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.
Publié dans: bioRxiv, 2023, ISSN 2692-8205
Éditeur: 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

Auteurs: Barret L, Schubeis T, Kugler V, Guyot L, Pintacuda G, Wagner R.
Publié dans: Methods Mol Biol. 2022, Numéro 2507, 2022, Page(s) 201-221, ISBN 978-1-0716-2367-1
Éditeur: Springer
DOI: 10.1007/978-1-0716-2368-8_11

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

Auteurs: Jana Moravcová, Radka Dopitová, Matyáš Pinkas, Jiří Nováček
Publié dans: Methods in Molecular Biology, Numéro Vol. 2305, Ch. 15, 2021
Éditeur: Springer
DOI: 10.1007/978-1-0716-1406-8

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

Auteurs: Moravcova J, Dopitova R, Pinkas M, Novacek J
Publié dans: Methods. Methods Mol Biol. 2021; 2305, 2021, Page(s) 301-322, ISBN 978-1-0716-1405-1
Éditeur: Springer
DOI: 10.1007/978-1-0716-1406-8_15

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

Auteurs: 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.
Publié dans: Methods. Methods Mol Biol. 2021; 2305, 2021, Page(s) 257-289, ISBN 978-1-0716-1405-1
Éditeur: Springer
DOI: 10.1007/978-1-0716-1406-8_13

Cryogenic Preparations of Biological Specimens for Cryo-Electron Tomography

Auteurs: D’Imprima E, Fung HKH, Zagoriy I, Mahamid J
Publié dans: Cryo-Electron Tomography - Structural Biology in situ, 2024, Page(s) 85-114, ISBN 978-3-031-51171-4
Éditeur: Springer Cham
DOI: 10.1007/978-3-031-51171-4_3

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

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

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

Auteurs: Gulotta A, Polimeni M, Lenton S, Starr CG, Kingsbury JS, Stradner A, Zaccarelli E, Schurtenberger P.
Publié dans: arXiv, 2023, ISSN 2331-8422
Éditeur: arXiv

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

Auteurs: Banerjee S
Publié dans: 2023
Éditeur: Banerjee S

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