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

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

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

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

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

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

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

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

Autori: Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Alessio Nocentini, Claudiu T. Supuran, and Lucia Banci
Pubblicato in: ACS Chemical Biology, 2020, ISSN 1554-8929
Editore: American Chemical Society
DOI: 10.1021/acschembio.0c00590

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

Autori: 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
Pubblicato in: Angewandte Chemie International Edition, 2021, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202103693

Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action

Autori: Weinhäupl K, Gragera M, Bueno-Carrasco MT, Arranz R, Krandor O, Akopian T, Soares R, Rubin E, Felix J, Fraga H
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.2022.102553

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

Autori: E. Fernández-Giménez, M. Martínez, R. Sánchez-García, R. Marabini, E. Ramírez-Aportela, P. Conesa, J.M. Carazo, C.O.S. Sorzano
Pubblicato in: Journal of Structural Biology, Numero 213/4, 2021, Pagina/e 107780, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2021.107780

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

Autori: Enrico Luchinat, Letizia Barbieri, Timothy F. Campbell, Lucia Banci
Pubblicato in: Analytical Chemistry, Numero 92/14, 2020, Pagina/e 9997-10006, ISSN 0003-2700
Editore: American Chemical Society
DOI: 10.1021/acs.analchem.0c01677

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

Autori: Kim J, Novakovic M, Jayanthi S, Lupulescu A, Kupče Ē, Grün JT, Mertinkus K, Oxenfarth A, Schwalbe H, Frydman L.
Pubblicato in: ChemPhysChem, 2022, ISSN 1439-4235
Editore: John Wiley & Sons Ltd.
DOI: 10.1002/cphc.202100704

Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

Autori: Mao J, Jin X, Shi M, Heidenreich D, Brown LJ, Brown RCD, Lelli M, He X, Glaubitz C.
Pubblicato in: Science Advances, 2024, ISSN 2375-2548
Editore: AAAS
DOI: 10.1126/sciadv.adj0384

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

Autori: Dzurov M, Pospíšilová Š, Krafčíková M, Trantírek L, Vojtová L, Ryneš J
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Rapid protein delivery to living cells for biomolecular investigation

Autori: 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

Autori: 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

Autori: Sacerdoti M, Gross LZF, Riley AM, Zehnder K, Ghode A, Klinke S, Anand GS, Paris K, Winkel A, Herbrand AK, Godage HY, Cozier GE, Süß E, Schulze JO, Pastor-Flores D, Bollini M, Cappellari MV, Svergun D, Gräwert MA, Aramendia PF, Leroux AE, Potter BVL, Camacho CJ, Biondi RM.
Pubblicato in: Science Signaling, 2023, ISSN 1937-9145
Editore: American Association for the Advancement of Science
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Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography

Autori: Bauda E, Gallet B, Moravcova J, Effantin G, Chan H, Novacek J, Jouneau PH, Rodrigues CDA, Schoehn G, Moriscot C, Morlot C
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Crystal structure of the Phospholipase A and acyltransferase 4 (PLAAT4) catalytic domain

Autori: Wehlin A, Cornaciu I, Marquez JM, Perrakis A, von Castelmur E.
Pubblicato in: Journal of Structural Biology, Numero 10478477, 2022, ISSN 1047-8477
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Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking

Autori: A. Metz, J. Wollenhaupt, S. Glöckner, N. Messini, S. Huber, T. Barthel, A. Mehrabed, H.-D. Gerber, A. Heine, G. Klebe and M. S. Weiss
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 77/8, 2021, ISSN 2059-7983
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Blood pH Analysis in Combination with Molecular Medical Tools in Relation to COVID-19 Symptoms

Autori: 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.
Pubblicato in: Biomedicines, 2023, ISSN 2227-9059
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Structure-function studies of a novel laccase-like multicopper oxidase from Thermothelomyces thermophila provide insights into its biological role

Autori: Kosinas C, Zerva A, Topakas E, Dimarogona M.
Pubblicato in: Acta Crystallogr D Struct Biol, 2023, ISSN 2059-7983
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A modular platform for automated cryo-FIB workflows

Autori: Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoelz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J
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Single Particle Cryo-Electron Microscopy: From Sample to Structure

Autori: 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

Autori: Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Matteo Pennestri, Alessio Nocentini, Claudiu T. Supuran, Lucia Banci
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Updated restraint dictionaries for carbohydrates in the pyranose form

Autori: Atanasova M, Nicholls RA, Joosten RP, Agirre J.
Pubblicato in: Acta Crystallogr D Struct Biol, 2022, ISSN 2059-7983
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Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium

Autori: Premetis GE, Stathi A, Papageorgiou AC, Labrou NE.
Pubblicato in: Scientific Reports, 2023, ISSN 2045-2322
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Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine

Autori: Hallier DC, Smales GJ, Seitz H, Hahn MB.
Pubblicato in: Phys Chem Chem Phys, 2023, ISSN 1463-9076
Editore: Royal Society of Chemistry
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Image processing tools for the validation of CryoEM maps

Autori: C.O.S. Sorzano, J.L. Vilas, E. Ramírez-Aportela, J. Krieger, D. del Hoyo, D. Herreros, E. Fernandez-Giménez, D. Marchán, J.R. Macías, I. Sánchez, L. del Caño, Y. Fonseca- Reyna, P. Conesa, A. García-Mena, J. Burguet, J. García Condado, J. Méndez García, M. Martínez, A. Muñoz-Barrutia, R. Marabini, J. Vargas, J.M. Carazo
Pubblicato in: Faraday Discussions, 2022, ISSN 1364-5498
Editore: Royal Society of Chemistry
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The Coming of Age of In-Cell Solution NMR

Autori: Luchinat E, Cremonini M, Banci L
Pubblicato in: Chemical Reviews, 2022, ISSN 0009-2665
Editore: American Chemical Society
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Staphylococcus aureus sacculus mediates activities of M23 hydrolases

Autori: Razew A, Laguri C, Vallet A, Bougault C, Kaus-Drobek M, Sabala I, Simorre JP.
Pubblicato in: Nature Communications, 2023, ISSN 2041-1723
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Common transthyretin-derived amyloid fibril structures in patients with hereditary ATTR amyloidosis

Autori: Steinebrei M, Baur J, Pradhan A, Kupfer N, Wiese S, Hegenbart U, Schönland SO, Schmidt M, Fändrich M.
Pubblicato in: Nature Communications, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
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Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates

Autori: Tatjana Barthel, Franziska U. Huschmann, Dirk Wallacher, Christian G. Feiler, Gerhard Klebe, Manfred S. Weiss, Jan Wollenhaupt
Pubblicato in: Journal of Applied Crystallography, Numero 54/1, 2021, Pagina/e 376-382, ISSN 1600-5767
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Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images

Autori: Nina Vyas, Stephan Kunne, Thomas M. Fish, Ian M. Dobbie, Maria Harkiolaki, Perrine Paul-Gilloteaux
Pubblicato in: STAR Protocols, Numero 2/2, 2021, Pagina/e 100529, ISSN 2666-1667
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Cryo-EM and Single-Particle Analysis with Scipion

Autori: 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

Autori: 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
Pubblicato in: Molecules, 2021, ISSN 1420-3049
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
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Oxidation of the Mycobacterium tuberculosis key virulence factor Protein Tyrosine Phosphatase A (MptpA) reduces its phosphatase activity

Autori: Niesteruk A,Sreeramulu S, Jonker HRA, Richter C, Schwalbe H.
Pubblicato in: FEBS letters, 2022, ISSN 1873-3468
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Real-time NMR spectroscopy in the study of biomolecular kineticsand dynamics

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

Autori: 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.
Pubblicato in: Biomolecules, 2022, ISSN 2218-273X
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Towards Consistency in Geometry Restraints for Carbohydrates in the Pyranose form: Modern Dictionary Generators Reviewed

Autori: Joosten RP, Nicholls RA, Agirre J.
Pubblicato in: Curr Med Chem., 2022, ISSN 1875-533X
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Beta and Gamma Amino Acid-Substituted Benzenesulfonamides as Inhibitors of Human Carbonic Anhydrases

Autori: Balandis B, Šimkūnas T, Paketurytė-Latvė V, Michailovienė V, Mickevičiūtė A, Manakova E, Gražuli S, Belyakov S, Kairys V, Mickevičius V, Zubrienė A, Matulis D.
Pubblicato in: Pharmaceuticals, 2022, ISSN 1424-8247
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
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FragMAXapp : crystallographic fragment-screening data-analysis and project-management system

Autori: Gustavo M. A. Lima, Elmir Jagudin, Vladimir O. Talibov, Laila S. Benz, Costantino Marullo, Tatjana Barthel, Jan Wollenhaupt, Manfred S. Weiss, Uwe Mueller
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 77/6, 2021, ISSN 2059-7983
Editore: IUCr
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Optimization of the Lead Compound NVP-BHG712 as Colorectal Cancer Inhibitor

Autori: 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.
Pubblicato in: Chemistry, 2023, ISSN 0947-6539
Editore: John Wiley & Sons Ltd.
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The missing link: covalent linkages in structural models

Autori: Robert A. Nicholls, Marcin Wojdyr, Robbie P. Joosten, Lucrezia Catapano, Fei Long, Marcus Fischer, Paul Emsley, Garib N. Murshudov
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 77/6, 2021, ISSN 2059-7983
Editore: IUCr
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A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity

Autori: Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M
Pubblicato in: Chemical Science, 2023, ISSN 2041-6520
Editore: Royal Society of Chemistry
DOI: 10.1039/d3sc02117c

Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties

Autori: Maity A, Wulffelé J, Ayala I, Favier A, Adam V, Bourgeois D, Brutscher B
Pubblicato in: Advanced Science, 2023, ISSN 2198-3844
Editore: WIley
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Small molecule MMRi62 targets MDM4 for degradation and induces leukemic cell apoptosis regardless of p53 status

Autori: 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
Pubblicato in: Frontiers in Oncology, 2022, ISSN 2234-943X
Editore: Frontiers Media S. A.
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High-resolution cryo-EM performance comparison of two latest-generation cryo electron microscopes on the human ribosome

Autori: Fréchin L, Holvec S, von Loeffelholz O, Hazemann I, Klaholz BP
Pubblicato in: Journal of Structural BIology, 2022, ISSN 1047-8477
Editore: Academic Press
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Polθ is phosphorylated by PLK1 to repair double-strand breaks in mitosis

Autori: 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.
Pubblicato in: Nature, 2023, ISSN 0028-0836
Editore: Nature Publishing Group
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Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners

Autori: 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
Pubblicato in: Nucleic Acids Research, 2021, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkab184

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

Autori: Pylkkänen R, Werner D, Bishoyi A, Weil D, Scoppola E, Wagermaier W, Safeer A, Bahri S, Baldus M, Paananen A, Penttilä M, Szilvay GR, Mohammadi P.
Pubblicato in: Science Advances, 2023, ISSN 2375-2548
Editore: American Association for the Advancement of Science
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Evasion of cGAS and TRIM5 defines pandemic HIV

Autori: Zuliani-Alvarez L, Govasli ML, Rasaiyaah J, Monit C, Perry SO, Sumner RP, McAlpine-Scott S, Dickson C, Rifat Faysal KM, Hilditch L, Miles RJ, Bibollet-Ruche F, Hahn BH, Boecking T, Pinotsis N, James LC, Jacques DA, Towers GJ.
Pubblicato in: nature microbiology, Numero 20585276, 2022, ISSN 2058-5276
Editore: Nature Portfolio
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SARS-CoV-2 M pro inhibition by a zinc ion: structural features and hints for drug design

Autori: Deborah Grifagni, Vito Calderone, Stefano Giuntini, Francesca Cantini, Marco Fragai, Lucia Banci
Pubblicato in: Chemical Communications, Numero 57/64, 2021, Pagina/e 7910-7913, ISSN 1359-7345
Editore: Royal Society of Chemistry
DOI: 10.1039/d1cc02956h

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

Autori: 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
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
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Innovative Approach for a Classic Target: Fragment Screening on Trypanothione Reductase Reveals New Opportunities for Drug Design

Autori: Fiorillo A, Colotti G, Exertier C, Liuzzi A, Seghetti F, Salerno A, Caciolla J, Ilari A.
Pubblicato in: Frontiers in molecular biosciences, 2022, ISSN 2296-889X
Editore: Frontiers Media S.A.
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Structural Insights into the Role of β3 nAChR Subunit in the Activation of Nicotinic Receptors

Autori: Giastas P, Papakyriakou A, Tsafaras G, Tzartos SJ, Zouridakis M.
Pubblicato in: Molecules, 2022, ISSN 1420-3049
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
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Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

Autori: Anna Wacker, Julia E Weigand, Sabine R Akabayov, Nadide Altincekic, Jasleen Kaur Bains, Elnaz Banijamali, Oliver Binas, Jesus Castillo-Martinez, Erhan Cetiner, Betül Ceylan, Liang-Yuan Chiu, Jesse Davila-Calderon, Karthikeyan Dhamotharan, Elke Duchardt-Ferner, Jan Ferner, Lucio Frydman, Boris Fürtig, José Gallego, J Tassilo Grün, Carolin Hacker, Christina Haddad, Martin Hähnke, Martin Hengesb
Pubblicato in: Nucleic Acids Research, Numero 48/22, 2020, Pagina/e 12415-12435, ISSN 0305-1048
Editore: Oxford University Press
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Principal component analysis is limited to low-resolution analysis in cryoEM

Autori: Carlos Oscar S. Sorzano, Jose Maria Carazo
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 77/6, 2021, Pagina/e 835-839, ISSN 2059-7983
Editore: IUCr
DOI: 10.1107/s2059798321002291

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

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

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

Autori: Johannes Groen, Andrea Sorrentino, Lucía Aballe, Robert Oliete, Ricardo Valcárcel, Chidinma Okolo, Ilias Kounatidis, Maria Harkiolaki, Ana Joaquina Pérez-Berná, Eva Pereiro
Pubblicato in: Journal of Visualized Experiments, Numero 169, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
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Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Autori: Felix Weis, Wim J. H. Hagen, Martin Schorb, Simone Mattei
Pubblicato in: Journal of Visualized Experiments, Numero 169, 2021, ISSN 1940-087X
Editore: MYJoVE Corporation
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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

Autori: Domenico Rizzo, Linda Cerofolini, Stefano Giuntini, Luisa Iozzino, Carlo Pergola, Francesca Sacco, Angelo Palmese, Enrico Ravera, Claudio Luchinat, Fabio Baroni, Marco Fragai
Pubblicato in: Journal of the American Chemical Society, 2022, ISSN 0002-7863
Editore: American Chemical Society
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Structure of the Borrelia bacteriophage φBB1 procapsid

Autori: Rūmnieks J, Füzik T, Tārs K.
Pubblicato in: Journal of Molecular Biology, 2023, ISSN 0022-2836
Editore: Academic Press
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Multitasking Pharmacophores Support Cabotegravir-Based Long-Acting HIV Pre-Exposure Prophylaxis (PrEP)

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

Autori: Duchardt-Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Schwalbe H.
Pubblicato in: Angewandte Chemie, 2023, ISSN 1433-7851
Editore: John Wiley & Sons Ltd.
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Protein in-cell NMR spectroscopy at 1.2 GHz

Autori: Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Lucia Banci
Pubblicato in: Journal of Biomolecular NMR, 2021, ISSN 0925-2738
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10858-021-00358-w

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

Autori: Riboni N, Bianchi F, Mattarozzi M, Caldara M, Gullì M, Graziano S, Maestri E, Marmiroli N, Careri M.
Pubblicato in: J Agric Food Chem, 2023, ISSN 0021-8561
Editore: American Chemical Society
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Backbone and side chain resonance assignment of the intrinsically disordered human DBNDD1 protein

Autori: Wiedemann C, Obika KB, Liebscher S, Jirschitzka J, Ohlenschläger O, Bordusa F.
Pubblicato in: Biomol NMR Assign., 2022, ISSN 1874-2718
Editore: Springer Verlag
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Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

Autori: 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
Pubblicato in: Frontiers in Molecular Biosciences, Numero 8, 2021, ISSN 2296-889X
Editore: Frontiers Media SA
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Approximating deformation fields for the analysis of continuous heterogeneity of biological macromolecules by 3D Zernike polynomials

Autori: 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
Pubblicato in: IUCrJ, Numero 8/6, 2021, ISSN 2052-2525
Editore: IUCrJ
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Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology

Autori: 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.
Pubblicato in: Biological Imaging, 2023, ISSN 2633-903X
Editore: Cambridge University Press
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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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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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PAXX binding to the NHEJ machinery explains functional redundancy with XLF

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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

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Emerging Themes in CryoEM─Single Particle Analysis Image Processing

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

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Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

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Secretory IgA and T cells targeting SARS-CoV-2 spike protein are transferred to the breastmilk upon mRNA vaccination

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

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

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

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AI revolutions in biology: The joys and perils of AlphaFold

Autori: Anastassis Perrakis, Titia K. Sixma
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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
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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
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Preparation and Cryo-FIB micromachining of <em>Saccharomyces cerevisiae</em> for Cryo-Electron Tomography

Autori: Jana Moravcová, Matyáš Pinkas, Radka Holbová, Jiří Nováček
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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
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Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARSCoV-2

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

Autori: Polimeni M, Zaccarelli E, Gulotta A, Lund M, Stradner A, Schurtenberger P
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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.
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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
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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
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Higher resolution in cryo-EM by the combination of macromolecular prior knowledge and image-processing tools

Autori: Ramirez-Aportela E, Carazo JM, Sorzano COS
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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

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
DOI: 10.1007/978-1-0716-1406-8_13

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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