Infrastructure for transnational access and discovery in structural biology

Deliverables

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

Author(s): Luchinat E, Barbieri L, Davis B, Brough PA, Pennestri M, Banci L.
Published in: Journal of Medicinal Chemistry, 2024, ISSN 1520-4804
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.3c01600

The CCP4 suite: integrative software for macromolecular crystallography

Author(s): 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,
Published in: Acta Crystallogr D Struct Biol., 2023, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798323003595

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

Author(s): 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
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23327-1

Studies on the Interaction between Model Proteins and Fluorinated Ionic Liquids

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

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

Author(s): 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
Published in: Journal of Structural Biology, Issue 213/1, 2021, Page(s) 107695, ISSN 1047-8477
Publisher: 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

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

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

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

Whole-proteome structures shed new light on posttranslational modifications

Author(s): Robbie P. Joosten, Jon Agirre
Published in: PLoS Biol, 2022, ISSN 1545-7885
Publisher: 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

Author(s): Letizia Barbieri, Enrico Luchinat
Published in: Journal of Visualized Experiments, Issue 169, 2021, ISSN 1940-087X
Publisher: 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

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

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

Author(s): 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
Published in: Angew Chem Int Ed Engl., 2022, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202205858

Structural conservation of antibiotic interaction with ribosomes

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

Protein delivery to living cells by thermal stimulation for biophysical investigation

Author(s): Torricella F, Barbieri L, Bazzurro V, Diaspro A, Banci L.
Published in: Scientific Reports, Issue 20452322, 2022, ISSN 2045-2322
Publisher: 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

Author(s): Andriianov A, Trigüis S, Drobiazko A, Sierro N, Ivanov NV, Selmer M, Severinov K, Isaev A.
Published in: Cell Reports, 2023, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.112972

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

Author(s): Shu Zhou, Maosen Ruan, Yunyan Li, Jing Yang, Suwen Bai, Christian Richter, Harald Schwalbe, Can Xie, Bing Shen & Junfeng Wang
Published in: Cell Research, 2020, ISSN 1001-0602
Publisher: 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

Author(s): Premetis GE, Stathi A, Papageorgiou AC, Labrou NE.
Published in: FEBS Journal, 2022, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.16686

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

Author(s): 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.
Published in: Acta Crystallogr D Struct Biol, 2022, ISSN 2059-7983
Publisher: John Wiley and Sons Inc.
DOI: 10.1107/s2059798322001978

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

Author(s): Ida de Vries, Tim Kwakman, Xiang-Jun Lu, Maarten L. Hekkelman, Mandar Deshpande, Sameer Velankar, Anastassis Perrakis, Robbie P. Joosten
Published in: Acta Crystallographica Section D Structural Biology, Issue 77/9, 2021, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798321007610

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

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

A Sample Preparation Pipeline for Microcrystals at the VMXm Beamline

Author(s): Adam D. Crawshaw, Emma V. Beale, Anna J. Warren, Andrew Stallwood, Graham Duller, Jose Trincao, Gwyndaf Evans
Published in: Journal of Visualized Experiments, Issue 172, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62306

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

Author(s): Camponeschi F, Piccioli M, Banci L.
Published in: Molecules, 2022, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules27238218

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

Author(s): Pierson E, De Pol F, Fillet M, Wouters J.
Published in: Commun Biol., 2023, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-023-05402-z

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

Author(s): Hay IM, Shamin M, Caroe ER, Mohammed ASA, Svergun DI, Jeffries CM, Graham SC, Sharpe HJ, Deane JE.
Published in: Journal of Biological Chemistry, 2022, ISSN 0021-9258
Publisher: 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

Author(s): Epasto LM, Che K, Kozak F, Selimovic A, Kadeřávek P, Kurzbach D.
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: 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

Author(s): Sah-Teli SK, Pinkas M, Hynönen MJ, Butcher SJ, Wierenga RK, Novacek J, Venkatesan R.
Published in: Structure, 2023, ISSN 0969-2126
Publisher: Cell Press
DOI: 10.1016/j.str.2023.04.011

Fixed Target Serial Data Collection at Diamond Light Source

Author(s): 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
Published in: Journal of Visualized Experiments, Issue 168, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62200

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

Author(s): 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.
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: 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

Author(s): Da Vela S, Saudino G, Lucarelli F, Banci L, Svergun DI, Ciofi-Baffoni S.
Published in: J Mol Biol, 2023, ISSN 0022-2836
Publisher: 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

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

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

Author(s): 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
Published in: Science Advances, 2022, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abo0517

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

Author(s): David Beriashvili, Raymond D. Schellevis, Federico Napoli, Markus Weingarth, Marc Baldus
Published in: Journal of Visualized Experiments, Issue 169, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62197

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

Author(s): Pearce NM, Skyner R, Krojer T.
Published in: Front. Mol. Biosci., Issue Section Structural BIology, 2022, ISSN 2296-889X
Publisher: Lausanne
DOI: 10.3389/fmolb.2022.861491

In-cell NMR: Why and how?

Author(s): Theillet FX, Luchinat E.
Published in: Progress in Nuclear Magnetic Resonance Spectroscopy, 2022, ISSN 0079-6565
Publisher: 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)

Author(s): Ying Wang, John Kirkpatrick, Susanne zur Lage, Sophie M. Korn, Konstantin Neißner, Harald Schwalbe, Andreas Schlundt, Teresa Carlomagno
Published in: Biomolecular NMR Assignments, 2021, ISSN 1874-2718
Publisher: 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

Author(s): 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
Published in: Journal of Biological Chemistry, Issue 00219258, 2022, ISSN 0021-9258
Publisher: 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

Author(s): 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.
Published in: ACS Chemical Biology, 2024, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/acschembio.3c00720

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

Author(s): 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
Published in: Journal of Molecular Biology, 2022, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2022.167720

Phase distortion-free paramagnetic NMR spectra

Author(s): Enrico Ravera
Published in: Journal of Magnetic Resonance Open, Issue 8-9, 2021, Page(s) 100022, ISSN 2666-4410
Publisher: Elsevier Inc
DOI: 10.1016/j.jmro.2021.100022

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

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

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

Author(s): Giovanni Saudino, Dafne Suraci, Veronica Nasta, Simone Ciofi-Baffoni, Lucia Banci
Published in: International Journal of Molecular Sciences, Issue 22/9, 2021, Page(s) 4848, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22094848

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

Author(s): Diana Müller, Irene Bessi, Christian Richter, and Harald Schwalbe
Published in: Angewandte Chemie (International Edition), 2021, ISSN 1433-7851
Publisher: 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

Author(s): Meskova K, Martonova K, Hrasnova P, Sinska K, Skrabanova M, Fialova L, Njemoga S, Cehlar O, Parmar O, Kolenko P, Pevala V, Skrabana R.
Published in: Antibodies, 2023, ISSN 2073-4468
Publisher: MDPI
DOI: 10.3390/antib12030051

OUP accepted manuscript

Author(s): 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
Published in: Nucleic Acids Research, 2020, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1021

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

Author(s): Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Alessio Nocentini, Claudiu T. Supuran, and Lucia Banci
Published in: ACS Chemical Biology, 2020, ISSN 1554-8929
Publisher: American Chemical Society
DOI: 10.1021/acschembio.0c00590

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

Author(s): 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
Published in: Angewandte Chemie International Edition, 2021, ISSN 1433-7851
Publisher: 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

Author(s): Weinhäupl K, Gragera M, Bueno-Carrasco MT, Arranz R, Krandor O, Akopian T, Soares R, Rubin E, Felix J, Fraga H
Published in: Journal of Biological Chemistry, Issue 00219258, 2022, ISSN 0021-9258
Publisher: 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

Author(s): E. Fernández-Giménez, M. Martínez, R. Sánchez-García, R. Marabini, E. Ramírez-Aportela, P. Conesa, J.M. Carazo, C.O.S. Sorzano
Published in: Journal of Structural Biology, Issue 213/4, 2021, Page(s) 107780, ISSN 1047-8477
Publisher: 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

Author(s): Enrico Luchinat, Letizia Barbieri, Timothy F. Campbell, Lucia Banci
Published in: Analytical Chemistry, Issue 92/14, 2020, Page(s) 9997-10006, ISSN 0003-2700
Publisher: 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

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

Molecular mechanisms and evolutionary robustness of a color switch in proteorhodopsins

Author(s): Mao J, Jin X, Shi M, Heidenreich D, Brown LJ, Brown RCD, Lelli M, He X, Glaubitz C.
Published in: Science Advances, 2024, ISSN 2375-2548
Publisher: AAAS
DOI: 10.1126/sciadv.adj0384

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

Author(s): Dzurov M, Pospíšilová Š, Krafčíková M, Trantírek L, Vojtová L, Ryneš J
Published in: J Biomol NMR, 2023, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-023-00422-7

Rapid protein delivery to living cells for biomolecular investigation

Author(s): Francesco Torricella, Alessio Bonucci, Panagis Polykretis, Francesca Cencetti, Lucia Banci
Published in: Biochemical and Biophysical Research Communications, Issue 570, 2021, Page(s) 82-88, ISSN 0006-291X
Publisher: Academic Press
DOI: 10.1016/j.bbrc.2021.07.006

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

Author(s): Brunetti F, Ghiglione B, Gudeta DD, Gutkind G, Guardabassi L, Klinke S, Power P.
Published in: Antimicrobial Agents and Chemotherapy, 2024, ISSN 1098-6596
Publisher: ASM Journals
DOI: 10.1128/aac.00061-23

Modulation of the substrate specificity of the kinase PDK1 by distinct conformations of the full-length protein

Author(s): 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.
Published in: Science Signaling, 2023, ISSN 1937-9145
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scisignal.add3184

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

Author(s): Bauda E, Gallet B, Moravcova J, Effantin G, Chan H, Novacek J, Jouneau PH, Rodrigues CDA, Schoehn G, Moriscot C, Morlot C
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-45770-6

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

Author(s): Wehlin A, Cornaciu I, Marquez JM, Perrakis A, von Castelmur E.
Published in: Journal of Structural Biology, Issue 10478477, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2022.107903

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

Author(s): 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
Published in: Acta Crystallographica Section D Structural Biology, Issue 77/8, 2021, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798321008196

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

Author(s): 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.
Published in: Biomedicines, 2023, ISSN 2227-9059
Publisher: MDPI
DOI: 10.3390/biomedicines11051421

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

Author(s): Kosinas C, Zerva A, Topakas E, Dimarogona M.
Published in: Acta Crystallogr D Struct Biol, 2023, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798323004175

A modular platform for automated cryo-FIB workflows

Author(s): Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoelz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J
Published in: Elife, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.70506

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Author(s): Joshua B.R. White, Daniel P. Maskell, Andrew Howe, Martin Harrow, Daniel K. Clare, C. Alistair Siebert, Emma L. Hesketh, Rebecca F. Thompson
Published in: Journal of Visualized Experiments, Issue 171, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62415

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

Author(s): Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Matteo Pennestri, Alessio Nocentini, Claudiu T. Supuran, Lucia Banci
Published in: Acta Crystallographica Section D Structural Biology, Issue 77/10, 2021, Page(s) 1270-1281, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798321009037

Updated restraint dictionaries for carbohydrates in the pyranose form

Author(s): Atanasova M, Nicholls RA, Joosten RP, Agirre J.
Published in: Acta Crystallogr D Struct Biol, 2022, ISSN 2059-7983
Publisher: IUCr/Wiley
DOI: 10.1107/s2059798322001103

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

Author(s): Premetis GE, Stathi A, Papageorgiou AC, Labrou NE.
Published in: Scientific Reports, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-34309-2

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

Author(s): Hallier DC, Smales GJ, Seitz H, Hahn MB.
Published in: Phys Chem Chem Phys, 2023, ISSN 1463-9076
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2cp05053f

Image processing tools for the validation of CryoEM maps

Author(s): 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
Published in: Faraday Discussions, 2022, ISSN 1364-5498
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2fd00059h

The Coming of Age of In-Cell Solution NMR

Author(s): Luchinat E, Cremonini M, Banci L
Published in: Chemical Reviews, 2022, ISSN 0009-2665
Publisher: American Chemical Society
DOI: 10.1021/acs.chemrev.1c00790

Staphylococcus aureus sacculus mediates activities of M23 hydrolases

Author(s): Razew A, Laguri C, Vallet A, Bougault C, Kaus-Drobek M, Sabala I, Simorre JP.
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-42506-w

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

Author(s): Steinebrei M, Baur J, Pradhan A, Kupfer N, Wiese S, Hegenbart U, Schönland SO, Schmidt M, Fändrich M.
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-43301-3

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

Author(s): Tatjana Barthel, Franziska U. Huschmann, Dirk Wallacher, Christian G. Feiler, Gerhard Klebe, Manfred S. Weiss, Jan Wollenhaupt
Published in: Journal of Applied Crystallography, Issue 54/1, 2021, Page(s) 376-382, ISSN 1600-5767
Publisher: IUCr
DOI: 10.1107/s1600576720016477

Protocol for image registration of correlative soft X-ray tomography and super-resolution structured illumination microscopy images

Author(s): Nina Vyas, Stephan Kunne, Thomas M. Fish, Ian M. Dobbie, Maria Harkiolaki, Perrine Paul-Gilloteaux
Published in: STAR Protocols, Issue 2/2, 2021, Page(s) 100529, ISSN 2666-1667
Publisher: Cell Press
DOI: 10.1016/j.xpro.2021.100529

Cryo-EM and Single-Particle Analysis with Scipion

Author(s): 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
Published in: Journal of Visualized Experiments, Issue 171, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62261

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

Author(s): 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
Published in: Molecules, 2021, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26206224

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

Author(s): Niesteruk A,Sreeramulu S, Jonker HRA, Richter C, Schwalbe H.
Published in: FEBS letters, 2022, ISSN 1873-3468
Publisher: Wiley
DOI: 10.1002/1873-3468.14348

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

Author(s): György Pintér, Katharina F. Hohmann, J. Tassilo Grün, Julia Wirmer-Bartoschek, Clemens Glaubitz, Boris Fürtig, Harald Schwalbe
Published in: Magnetic Resonance Discussions, 2021, ISSN 2699-0059
Publisher: Copernicus Publications
DOI: 10.5194/mr-2021-16

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

Author(s): 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.
Published in: Biomolecules, 2022, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12070922

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

Author(s): Joosten RP, Nicholls RA, Agirre J.
Published in: Curr Med Chem., 2022, ISSN 1875-533X
Publisher: Bentham Science Publishers
DOI: 10.2174/0929867328666210902140754

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

Author(s): 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.
Published in: Pharmaceuticals, 2022, ISSN 1424-8247
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ph15040477

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

Author(s): Gustavo M. A. Lima, Elmir Jagudin, Vladimir O. Talibov, Laila S. Benz, Costantino Marullo, Tatjana Barthel, Jan Wollenhaupt, Manfred S. Weiss, Uwe Mueller
Published in: Acta Crystallographica Section D Structural Biology, Issue 77/6, 2021, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798321003818

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

Author(s): 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.
Published in: Chemistry, 2023, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.202203967

The missing link: covalent linkages in structural models

Author(s): Robert A. Nicholls, Marcin Wojdyr, Robbie P. Joosten, Lucrezia Catapano, Fei Long, Marcus Fischer, Paul Emsley, Garib N. Murshudov
Published in: Acta Crystallographica Section D Structural Biology, Issue 77/6, 2021, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798321003934

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

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

Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties

Author(s): Maity A, Wulffelé J, Ayala I, Favier A, Adam V, Bourgeois D, Brutscher B
Published in: Advanced Science, 2023, ISSN 2198-3844
Publisher: WIley
DOI: 10.1002/advs.202306272

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

Author(s): 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
Published in: Frontiers in Oncology, 2022, ISSN 2234-943X
Publisher: Frontiers Media S. A.
DOI: 10.3389/fonc.2022.933446

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

Author(s): Fréchin L, Holvec S, von Loeffelholz O, Hazemann I, Klaholz BP
Published in: Journal of Structural BIology, 2022, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2022.107905

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

Author(s): 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.
Published in: Nature, 2023, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-023-06506-6

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

Author(s): 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
Published in: Nucleic Acids Research, 2021, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab184

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

Author(s): 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.
Published in: Science Advances, 2023, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.ade5417

Evasion of cGAS and TRIM5 defines pandemic HIV

Author(s): 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.
Published in: nature microbiology, Issue 20585276, 2022, ISSN 2058-5276
Publisher: Nature Portfolio
DOI: 10.1038/s41564-022-01247-0

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

Author(s): Deborah Grifagni, Vito Calderone, Stefano Giuntini, Francesca Cantini, Marco Fragai, Lucia Banci
Published in: Chemical Communications, Issue 57/64, 2021, Page(s) 7910-7913, ISSN 1359-7345
Publisher: 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

Author(s): 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
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-26584-2

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

Author(s): Fiorillo A, Colotti G, Exertier C, Liuzzi A, Seghetti F, Salerno A, Caciolla J, Ilari A.
Published in: Frontiers in molecular biosciences, 2022, ISSN 2296-889X
Publisher: Frontiers Media S.A.
DOI: 10.3389/fmolb.2022.900882

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

Author(s): Giastas P, Papakyriakou A, Tsafaras G, Tzartos SJ, Zouridakis M.
Published in: Molecules, 2022, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules27144642

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy

Author(s): 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
Published in: Nucleic Acids Research, Issue 48/22, 2020, Page(s) 12415-12435, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1013

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

Author(s): Carlos Oscar S. Sorzano, Jose Maria Carazo
Published in: Acta Crystallographica Section D Structural Biology, Issue 77/6, 2021, Page(s) 835-839, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798321002291

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

Author(s): Cerofolini L, Ramberg KO, Padilla LC, Antonik P, Ravera E, Luchinat C, Fragai M, Crowley PB.
Published in: Chemical Communications, 2023, ISSN 1364-548X
Publisher: Royal Society of Chemistry
DOI: 10.1039/d2cc05725e

Targeting EPHA2 with Kinase Inhibitors in Colorectal Cancer

Author(s): Tröster A, Jores N, Mineev KS, Sreeramulu S, DiPrima M, Tosato G, Schwalbe H.
Published in: ChemMedChem, 2023, ISSN 1860-7179
Publisher: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/cmdc.202300420

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

Author(s): Johannes Groen, Andrea Sorrentino, Lucía Aballe, Robert Oliete, Ricardo Valcárcel, Chidinma Okolo, Ilias Kounatidis, Maria Harkiolaki, Ana Joaquina Pérez-Berná, Eva Pereiro
Published in: Journal of Visualized Experiments, Issue 169, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62190

Strategies for Optimization of Cryogenic Electron Tomography Data Acquisition

Author(s): Felix Weis, Wim J. H. Hagen, Martin Schorb, Simone Mattei
Published in: Journal of Visualized Experiments, Issue 169, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62383

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

Author(s): Domenico Rizzo, Linda Cerofolini, Stefano Giuntini, Luisa Iozzino, Carlo Pergola, Francesca Sacco, Angelo Palmese, Enrico Ravera, Claudio Luchinat, Fabio Baroni, Marco Fragai
Published in: Journal of the American Chemical Society, 2022, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.2c03232

Structure of the Borrelia bacteriophage φBB1 procapsid

Author(s): Rūmnieks J, Füzik T, Tārs K.
Published in: Journal of Molecular Biology, 2023, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2023.168323

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

Author(s): Wan Z, Shi M, Gong Y, Lucci M, Li J, Zhou J, Yang X-L, Lelli M, He X, Mao J.
Published in: Molecules, 2024, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules29020376

The COVID19-NMR Consortium: A Public Report on the Impact of this New Global Collaboration

Author(s): Duchardt-Ferner E, Ferner J, Fürtig B, Hengesbach M, Richter C, Schlundt A, Sreeramulu S, Wacker A, Weigand JE, Wirmer-Bartoschek J, Schwalbe H.
Published in: Angewandte Chemie, 2023, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/ange.202217171

Protein in-cell NMR spectroscopy at 1.2 GHz

Author(s): Enrico Luchinat, Letizia Barbieri, Matteo Cremonini, Lucia Banci
Published in: Journal of Biomolecular NMR, 2021, ISSN 0925-2738
Publisher: 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

Author(s): Riboni N, Bianchi F, Mattarozzi M, Caldara M, Gullì M, Graziano S, Maestri E, Marmiroli N, Careri M.
Published in: J Agric Food Chem, 2023, ISSN 0021-8561
Publisher: American Chemical Society
DOI: 10.1021/acs.jafc.3c04532

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

Author(s): Wiedemann C, Obika KB, Liebscher S, Jirschitzka J, Ohlenschläger O, Bordusa F.
Published in: Biomol NMR Assign., 2022, ISSN 1874-2718
Publisher: Springer Verlag
DOI: 10.1007/s12104-022-10086-3

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

Author(s): 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
Published in: Frontiers in Molecular Biosciences, Issue 8, 2021, ISSN 2296-889X
Publisher: Frontiers Media SA
DOI: 10.3389/fmolb.2021.653148

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

Author(s): 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
Published in: IUCrJ, Issue 8/6, 2021, ISSN 2052-2525
Publisher: IUCrJ
DOI: 10.1107/s2052252521008903

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

Author(s): 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.
Published in: Biological Imaging, 2023, ISSN 2633-903X
Publisher: Cambridge University Press
DOI: 10.1017/s2633903x23000132

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

Author(s): 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
Published in: Molecular Psychiatry, 2022, ISSN 1359-4184
Publisher: Nature Publishing Group
DOI: 10.1038/s41380-022-01882-3

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

Author(s): Ioannou E, Papageorgiou AC, Labrou NE.
Published in: International Journal of Molecular Sciences, 2022, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23137469

Analysis and validation of overall N-glycan conformation in Privateer

Author(s): Dialpuri JS, Bagdonas H, Atanasova M, Schofield LC, Hekkelman ML, Joosten RP, Agirre J.
Published in: Acta Crystallogr D Struct Biol, 2023, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798323003510

Teixobactin kills bacteria by a two-pronged attack on the cell envelope

Author(s): 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.
Published in: Nature, 2022, ISSN 1476-4687
Publisher: Nature Research (subsidiary of Springer Nature)
DOI: 10.1038/s41586-022-05019-y

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

Author(s): Saridakis E, Vishwakarma R, Lai-Kee-Him J, Martin K, Simon I, Cohen-Gonsaud M, Coste F, Bron P, Margeat E, Boudvillain M
Published in: Commun Biol., Issue 5(1):120, 2022, ISSN 2399-3642
Publisher: Springer Nature Limited
DOI: 10.1038/s42003-022-03069-6

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

Author(s): 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.
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-34636-4

AlphaFill: enriching AlphaFold models with ligands and cofactors

Author(s): Hekkelman ML, De Vries I, Joosten RP, Perrakis A
Published in: Nature Methods, Issue 15487091, 2022, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-022-01685-y

The structured organization of Deinococcus radiodurans' cell envelope

Author(s): Farci D, Haniewicz P, Piano D.
Published in: Proc Natl Acad Sci U S A., 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2209111119

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

Author(s): Andronov L, Genthial R, Hentsch D, Klaholz BP.
Published in: Communications Biology, Issue 23993642, 2022, ISSN 2399-3642
Publisher: Nature Portfolio
DOI: 10.1038/s42003-022-04040-1

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

Author(s): Farci D, Graça AT, Iesu L, de Sanctis D, Piano D.
Published in: Journal of Biological Chemistry, 2022, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2022.102784

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

Author(s): Weishuai Yu, Imran Mohsin, Anastassios C. Papageorgiou and Duochuan Li
Published in: Catalysts, 2022, ISSN 2073-4344
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/catal12020139

PAXX binding to the NHEJ machinery explains functional redundancy with XLF

Author(s): 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
Published in: Science Advances, 2023, ISSN 2375-2548
Publisher: American Association for the Advancement of Science
DOI: 10.1126/sciadv.adg2834

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

Author(s): Tobias Lieblein, Rene Zangl, Janosch Martin, Jan Hoffmann, Marie J Hutchison, Tina Stark, Elke Stirnal, Thomas Schrader, Harald Schwalbe, Nina Morgner
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.59306

NMR quality control of fragment libraries for screening

Author(s): 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
Published in: Journal of Biomolecular NMR, 2020, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-020-00327-9

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

Author(s): Reinier Damman, Alessandra Lucini Paioni, Katerina T. Xenaki, Irati Beltrán Hernández, Paul M. P. van Bergen en Henegouwen, Marc Baldus
Published in: Journal of Biomolecular NMR, Issue June 19 2020, 2020, ISSN 0925-2738
Publisher: Kluwer Academic Publishers
DOI: 10.1007/s10858-020-00328-8

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

Author(s): Cy M. Jeffries, Zuzanna Pietras, Dmitri I. Svergun
Published in: EPJ Web of Conferences, Issue 236, 2020, Page(s) 03001, ISSN 2100-014X
Publisher: EDP Sciences
DOI: 10.1051/epjconf/202023603001

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

Author(s): 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
Published in: Cell Reports, Issue 31/12, 2020, Page(s) 107817, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2020.107817

Anomeric Selectivity of Trehalose Transferase with Rare l -Sugars

Author(s): 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
Published in: ACS Catalysis, Issue 10/15, 2020, Page(s) 8835-8839, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.0c02117

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

Author(s): 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
Published in: ChemBioChem, Issue Aug 14 2020, 2020, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202000476

Cryo-Structured Illumination Microscopic Data Collection from Cryogenically Preserved Cells

Author(s): 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
Published in: Journal of Visualized Experiments, Issue 171, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62274

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

Author(s): 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
Published in: Acta Crystallogr D Struct Biol, 2023, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798323004497

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

Author(s): 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
Published in: Journal of the American Chemical Society, 2021, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.1c01914

Heteronuclear decoupling with Rotor-Synchronized Phase-Alternated Cycles

Author(s): Simion A, Schubeis T, Tanguy Le Marchand T, Vasilescu M, Pintacuda G, Lesage A, Filip C
Published in: The Journal of Chemical Physics, 2022, ISSN 0021-9606
Publisher: American Institute of Physics
DOI: 10.1063/5.0098135

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

Author(s): de Freitas Fernandes A, Leonardo DA, Cavini IA, Rosa HVD, Vargas JA, D'Muniz Pereira H, Nascimento AS, Garratt RC
Published in: Cytoskeleton (Hoboken), 2022, ISSN 1949-3584
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cm.21740

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

Author(s): Irina Cornaciu, Raphael Bourgeas, Guillaume Hoffmann, Florine Dupeux, Anne-Sophie Humm, Vincent Mariaule, Andrea Pica, Damien Clavel, Gael Seroul, Peter Murphy, José Antonio Márquez
Published in: Journal of Visualized Experiments, Issue 172, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62491

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

Author(s): Robert D. Healey, Shibom Basu, Anne-Sophie Humm, Cedric Leyrat, Xiaojing Cong, Jérome Golebiowski, Florine Dupeux, Andrea Pica, Sébastien Granier, José Antonio Márquez
Published in: bioRxiv, Issue June 3, 2021, 2021, ISSN 0362-4331
Publisher: New York Times Company
DOI: 10.1101/2021.06.03.446146

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

Author(s): Pham LBT, Costantino A, Barbieri L, Calderone V, Luchinat E, Banci L.
Published in: J Am Chem Soc, 2023, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.2c12086

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

Author(s): 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
Published in: International Journal of Molecular Sciences, 2023, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms24108559

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

Author(s): 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
Published in: Journal of Visualized Experiments, Issue 169, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62208

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

Author(s): 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
Published in: Computational and Structural Biotechnology Journal, Issue 19, 2021, Page(s) 632-646, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.12.044

In‐cell NMR of functional riboswitch aptamers in eukaryotic cells

Author(s): P. Broft, S. Dzatko, M. Krafcikova, Robert Hansel-Hertsch, A. Wacker, Volker Doetsch, L. Trantirek, Harald Schwalbe
Published in: Angewandte Chemie International Edition, 2020, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202007184

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

Author(s): Melissa A. Graewert, Stefano Da Vela, Tobias W. Gräwert, Dmitry S. Molodenskiy, Clément E. Blanchet, Dmitri I. Svergun, Cy M. Jeffries
Published in: Crystals, Issue 10/11, 2020, Page(s) 975, ISSN 2073-4352
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cryst10110975

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

Author(s): Mihajlo Novakovic, Eriks Kupce, Tali Scherf, Andreas Oxenfarth, Robbin Schnieders, Tassilo Grün, Julia Wirmer-Bartoschek, Christian Richter, Harald Schwalbe, Lucio Frydman
Published in: Angewandte Chemie International Edition, 2021, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202015948

Cryo-EM structure of the fully assembled Elongator complex.

Author(s): 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.
Published in: Nucleic Acid Research, 2023, ISSN 1362-4962
Publisher: Oxford Academic
DOI: 10.1093/nar/gkac1232

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

Author(s): Cuéllar J, Vallin J, Svanström A, Maestro-López M, Bueno-Carrasco MT, Ludlam WG, Willardson BM, Valpuesta JM, Grantham J
Published in: J Mol Biol, 2021, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2021.167399

Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

Author(s): 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
Published in: Journal of Visualized Experiments, Issue 171, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62414

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

Author(s): Vitali V, Torricella F, Massai L, Messori L, Banci L.
Published in: Scientific reports, 2023, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-49247-2

Engineered Nonviral Protein Cages Modified for MR Imaging

Author(s): Kaster MA, Levasseur MD, Edwardson TGW, Caldwell MA, Hofmann D, Licciardi G, Parigi G, Luchinat C, Hilvert D, Meade TJ
Published in: ACS Applied Bio Materials, 2023, ISSN 2576-6422
Publisher: American Chemical Society
DOI: 10.1021/acsabm.2c00892

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

Author(s): Gárdonyi M, Hasewinkel C, Wallbaum J, Wollenhaupt J, Weiss MS, Klebe G, Reuter K, Heine A
Published in: ACS Omega, 2023, ISSN 2470-1343
Publisher: American Chemical Society
DOI: 10.1021/acsomega.3c07058

Emerging Themes in CryoEM─Single Particle Analysis Image Processing

Author(s): Vilas JL, Carazo JM, Sorzano COS
Published in: Chemical Reviews, 2022, ISSN 0009-2665
Publisher: 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

Author(s): Cavini IA, Winter AJ, D'Muniz Pereira H, Woolfson DN, Crump MP, Garratt RC
Published in: Acta Crystallogr D Struct Biol, 2023, ISSN 2059-7983
Publisher: IUCr
DOI: 10.1107/s2059798323006514

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

Author(s): 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.
Published in: Elife, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.71887

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

Author(s): Juliana Goncalves, A. Margarida Juliano, Nadia Charepe, Marta Alenquer, Diogo Athayde, Filipe Ferreira, Margarida Archer, Maria Joao Amorim, Fatima Serrano, Helena Soares
Published in: Cell Reports Medicine, 2021, ISSN 2666-3791
Publisher: 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

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

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

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

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

Author(s): Hans Wienk, Lucia Banci, Susan Daenke, Eva Pereiro, Harald Schwalbe, David Ian Stuart, Manfred S. Weiss, Anastassis Perrakis
Published in: Journal of Visualized Experiments, Issue 177, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/63435

Modelling covalent linkages in CCP 4

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

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

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

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

Author(s): 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.
Published in: RSC Medicinal Chemistry, 2024, ISSN 2632-8682
Publisher: Royal Society of Chemistry
DOI: 10.1039/d3md00724c

AI revolutions in biology: The joys and perils of AlphaFold

Author(s): Anastassis Perrakis, Titia K. Sixma
Published in: EMBO Reports, 2021, ISSN 1469-3178
Publisher: EMBO Press
DOI: 10.15252/embr.202154046

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

Author(s): Hyjek-Składanowska M, Anderson BA, Mykhaylyk V, Orr C, Wagner A, Poznański JT, Skowronek K, Seth P, Nowotny M
Published in: Nucleic Acid Research, 2022, ISSN 0305-1048
Publisher: 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

Author(s): 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
Published in: Nature Protocols, Issue 16/6, 2021, Page(s) 2851-2885, ISSN 1754-2189
Publisher: Nature Publishing Group
DOI: 10.1038/s41596-021-00522-4

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

Author(s): Jana Moravcová, Matyáš Pinkas, Radka Holbová, Jiří Nováček
Published in: Journal of Visualized Experiments, Issue 177, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62351

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

Author(s): Miglė Kišonaitė, Klemens Wild, Karine Lapouge, Thomas Ruppert, Irmgard Sinning
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-27967-9

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

Author(s): 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.
Published in: European Journal of Medicinal Chemistry, Issue 02235234, 2022, ISSN 0223-5234
Publisher: Elsevier BV
DOI: 10.1016/j.ejmech.2022.114857

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

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

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

Author(s): Polimeni M, Zaccarelli E, Gulotta A, Lund M, Stradner A, Schurtenberger P
Published in: APL Bioengineering, 2024, ISSN 2473-2877
Publisher: American Institute of Physics
DOI: 10.1063/5.0186642

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

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

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

Author(s): Hannes Berg, M. A. Wirtz Martin, A. Niesteruk, C. Richter, S. Sreeramulu, H. Schwalbe
Published in: Journal of Visualized Experiments, Issue 172, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62262

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

Author(s): Misbha Ud Din Ahmad, Alexander Fish, Jeroen Molenaar, Sridhar Sreeramulu, Christian Richter, Nadide Altincekic, Harald Schwalbe, Hans Wienk, Anastassis Perrakis
Published in: Journal of Visualized Experiments, Issue 171, 2021, ISSN 1940-087X
Publisher: MYJoVE Corporation
DOI: 10.3791/62469

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

Author(s): Ramirez-Aportela E, Carazo JM, Sorzano COS
Published in: IUCrJ, 2022, ISSN 2052-2525
Publisher: IUCr
DOI: 10.1107/s2052252522006959

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

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

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

Author(s): 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
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: 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

Author(s): 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.
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.01.03.522595

Phase distortion-free pNMR spectra

Author(s): Enrico Ravera
Published in: arXiv.org, 2021, ISSN 2331-8422
Publisher: arXiv.org / Cornell University

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

Author(s): Düring J, Wolter M, Toplak J, Torres C, Dybkov O, Fokkens TJ, Urlaub H, Steinchen W, Dienemann C, Lorenz S.
Published in: Research Square, 2023, ISSN 2693-5015
Publisher: 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

Author(s): Krieger JM, Sorzano COS, Carazo JM.
Published in: Preprints 2023, 2023080828, 2023, ISSN 2310-287X
Publisher: Preprints
DOI: 10.20944/preprints202308.0828.v1

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

Author(s): Sadet A, Ianc O, Teleanu F, Ciumeică A, Lupulescu A, Vasos P.
Published in: Research Square, 2024, ISSN 2693-5015
Publisher: Springer Nature
DOI: 10.21203/rs.3.rs-3694602/v1

A Modular Platform for Streamlining Automated Cryo-FIB Workflows

Author(s): Klumpe S, Fung HKH, Goetz SK, Zagoriy I, Hampoetz B, Zhang X, Erdmann PS, Baumbach J, Müller CW, Beck M, Plitzko JM, Mahamid J.
Published in: bioRxiv, 2021, ISSN 0362-4331
Publisher: 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

Author(s): Talachia Rosa L, Vernhes E, Soulet AL, Polard P, Fronzes R.
Published in: BioRxiv, 2024, ISSN 2692-8205
Publisher: 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

Author(s): Oberdick S, Jordanova K, Lundstrom J, Parigi G, Poorman M, Poorman G, Keenan K.
Published in: Research Square, 2023, ISSN 2693-5015
Publisher: Research Square Company
DOI: 10.21203/rs.3.rs-2485292/v1

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

Author(s): 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.
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: 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

Author(s): Arroyo-Urea S, Nazarova AL, Carrión-Antolí A, Bonifazi A, Battiti FO, Homing Lam J, Hauck Newman A, Katritch V, García-Nafría J.
Published in: Research Square, 2023, ISSN 2693-5015
Publisher: 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

Author(s): Kravikass M, Koren G, Saleh OA, Beck R.
Published in: arXiv, 2023, ISSN 2331-8422
Publisher: Cornell University

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

Author(s): 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.
Published in: Research Square, 2023, ISSN 2693-5015
Publisher: Springer Nature
DOI: 10.21203/rs.3.rs-3734993/v1

Improvements on marker-free images alignment for electron tomography

Author(s): Sorzano COS, De Isidro-Gomez F, Fernandez-Gimenez E, Herreros D, Marco S, Carazo JM, Messaoudi C.
Published in: BioRxiv, Issue May 24 2020, 2020, ISSN 0362-4331
Publisher: New York Times Company
DOI: 10.1101/2020.05.22.110445

Multitarget Virtual Screening for Drug Repurposing in COVID19

Author(s): CO Sorzano, E Crisman, JM Carazo, R leon
Published in: ChemRxiv, Issue July 17 2020, 2020, ISSN 2573-2293
Publisher: 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.

Author(s): Janssen AFJ, Marcelot A, Breusegem SY, Legrand P, Zinn-Justin S, Larrieu D
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.02.25.481780

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

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

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

Author(s): 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.
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: 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

Author(s): Barret L, Schubeis T, Kugler V, Guyot L, Pintacuda G, Wagner R.
Published in: Methods Mol Biol. 2022, Issue 2507, 2022, Page(s) 201-221, ISBN 978-1-0716-2367-1
Publisher: Springer
DOI: 10.1007/978-1-0716-2368-8_11

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

Author(s): Jana Moravcová, Radka Dopitová, Matyáš Pinkas, Jiří Nováček
Published in: Methods in Molecular Biology, Issue Vol. 2305, Ch. 15, 2021
Publisher: Springer
DOI: 10.1007/978-1-0716-1406-8

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

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

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

Author(s): 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.
Published in: Methods. Methods Mol Biol. 2021; 2305, 2021, Page(s) 257-289, ISBN 978-1-0716-1405-1
Publisher: Springer
DOI: 10.1007/978-1-0716-1406-8_13

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

Author(s): Andrei Gurinov, Benedikt Sieland, Andrei Kuzhelev, Hossam Elgabarty, Thomas D. Kuhne, Thomas Prisner, Jan Paradies, Marc Baldus, Konstantin L. Ivanov, and Svetlana Pylaeva
Published in: Condensed Matter - arXiv.org, 2021
Publisher: Cornell University

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

Author(s): Gulotta A, Polimeni M, Lenton S, Starr CG, Kingsbury JS, Stradner A, Zaccarelli E, Schurtenberger P.
Published in: arXiv, 2023, ISSN 2331-8422
Publisher: arXiv

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

Author(s): Banerjee S
Published in: 2023
Publisher: Banerjee S

Searching for OpenAIRE data...

Deliverables

Publications

Share this page

Download