152 results on '"Blackledge M"'
Search Results
2. 162P A CT radiomics model to predict overall survival following curative-intent radiotherapy for stage I-III non-small cell lung cancer
- Author
-
Hindocha, S., primary, Charlton, T.G., additional, Linton-Reid, K., additional, Hunter, B., additional, Chan, C., additional, Ahmed, M., additional, Robinson, E., additional, Orton, M., additional, Lunn, J., additional, Ahmad, S., additional, McDonald, F., additional, Locke, I., additional, Power, D., additional, Doran, S., additional, Blackledge, M., additional, Lee, R.W., additional, and Aboagye, E., additional
- Published
- 2022
- Full Text
- View/download PDF
3. Lack of clinically meaningful anatomical variations in bone marrow apparent diffusion coefficient in diffuse pattern myeloma allows untargeted sampling to confirm disease burden
- Author
-
Blackledge M, Kaiser M, O’Connor S, Koh Dm, Keeling A, Boyd K, and Messiou C
- Subjects
medicine.medical_specialty ,Diffuse Pattern ,medicine.anatomical_structure ,business.industry ,medicine ,Sampling (statistics) ,Effective diffusion coefficient ,Radiology ,Bone marrow ,business ,Disease burden - Published
- 2020
4. Dynamic complexes and complex cynamics - visualising molecular recognition trajectories of intrinsically disordered viral and signalling proteins using NMR spectroscopy
- Author
-
Blackledge, M.
- Published
- 2015
5. An intrinsically disordered proteins community for ELIXIR [version 1; peer review: 2 approved]
- Author
-
Davey, N. E., Babu, M. M., Blackledge, M., Bridge, A., Capella-Gutierrez, S., Dosztanyi, Z., Drysdale, R., Edwards, R. J., Elofsson, A., Felli, I. C., Gibson, T. J., Gutmanas, A., Hancock, J. M., Harrow, J., Higgins, D., Jeffries, C. M., Le Mercier, P., Meszaros, B., Necci, M., Notredame, C., Orchard, S., Ouzounis, C. A., Pancsa, R., Papaleo, E., Pierattelli, R., Piovesan, D., Promponas, V. J., Ruch, P., Rustici, G., Romero, P., Sarntivijai, S., Saunders, G., Schuler, B., Sharan, M., Shields, D. C., Sussman, J. L., Tedds, J. A., Tompa, P., Turewicz, M., Vondrasek, J., Vranken, W. F., Wallace, B. A., Wichapong, K., and Tosatto, S. C. E.
- Subjects
Cellular regulation ,Databases ,Intrinsically disordered proteins ,Community standards ,Protein-protein interactions ,lcsh:R ,Protein function ,lcsh:Medicine ,lcsh:Q ,ELIXIR ,Protein dynamics ,lcsh:Science - Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.
- Published
- 2019
6. Mapping hidden residual structure within the Myc bHLH-LZ domain using chemical denaturant titration
- Author
-
Panova, S., Cliff, M.J., Macek, P., Blackledge, M., Jensen, M.R., Nissink, J.W.M., Embrey, K.J., Davies, R., and Waltho, J.P.
- Abstract
Intrinsically disordered proteins (IDPs) underpin biological regulation and hence are highly desirable drug-development targets. NMR is normally the tool of choice for studying the conformational preferences of IDPs, but the association of regions with residual structure into partially collapsed states can lead to poor spectral quality. The bHLH-LZ domain of the oncoprotein Myc is an archetypal example of such behavior. To circumvent spectral limitations, we apply chemical denaturant titration (CDT)-NMR, which exploits the predictable manner in which chemical denaturants disrupt residual structure and the rapid exchange between conformers in IDP ensembles. The secondary structure propensities and tertiary interactions of Myc are determined for all bHLH-LZ residues, including those with poor NMR properties under native conditions. This reveals conformations that are not predictable using existing crystal structures. The CDT-NMR method also maps sites perturbed by the prototype Myc inhibitor, 10058-F4, to areas of residual structure.
- Published
- 2019
7. Bio-NMR Structural disorder and induced folding within proteins of the replicative complex of paramyxoviruses: P00-6
- Author
-
Longhi, S., Habchi, J., Blocquel, D., Blangy, S., Blackledge, M., and Ringkjobing-Jensen, M.
- Published
- 2012
8. 672P Fracture risk in men with metastatic castration-resistant prostate cancer (mCRPC) treated with radium-223 (Ra 223)
- Author
-
Hijab, A., primary, Tunariu, N., additional, Tovey, H., additional, Alonzi, R., additional, Tree, A., additional, Staffurth, J., additional, Blackledge, M., additional, Padhani, A.R., additional, Stidwill, H., additional, Finch, J., additional, Chatfield, P., additional, Perry, S., additional, Koh, D-M., additional, Hall, E., additional, and Parker, C., additional
- Published
- 2020
- Full Text
- View/download PDF
9. Spatial localisation of '3'1P NMR spectroscopy in human and animal tissue in vivo
- Author
-
Blackledge, M. J.
- Subjects
539.7 ,Biological NMR spectrocopy - Published
- 1987
10. NMR structures of the C-terminal end of human complement serine protease C1s
- Author
-
Gans, P., Rossi, V., Gaboriaud, C., Bally, I., Hernandez, J.-F., Blackledge, M. J., and Arlaud, G. J.
- Published
- 1998
- Full Text
- View/download PDF
11. Multi-conformational peptide dynamics derived from NMR data: A new search algorithm and its application to antamanide
- Author
-
Brüschweiler, R., Blackledge, M., and Ernst, R. R.
- Published
- 1991
- Full Text
- View/download PDF
12. ePS6.01 Prevalence and clinical significance of Staphylococcus aureus smallcolony variants: a prospective longitudinal, multicentre study
- Author
-
Wolter, D., primary, Onchiri, F., additional, Emerson, J., additional, Precit, M., additional, Lee, M., additional, McNamara, S., additional, Nay, L., additional, Blackledge, M., additional, Uluer, A., additional, Mann, M., additional, Orenstein, D., additional, Hoover, W., additional, Burns, J., additional, and Hoffman, L., additional
- Published
- 2019
- Full Text
- View/download PDF
13. Structural characterization of α-synuclein in an aggregation prone state
- Author
-
Cho, M., Nodet, G., Kim, H., Jensen, M., Bernado, P., Fernandez, C., Becker, S., Blackledge, M., and Zweckstetter, M.
- Published
- 2009
14. Testing the validity of ensemble descriptions of intrinsically disordered proteins
- Author
-
Jensen, M. R., primary and Blackledge, M., additional
- Published
- 2014
- Full Text
- View/download PDF
15. 150 Staphylococcus aureus small-colony variants are independently associated with worse lung disease in children with cystic fibrosis
- Author
-
Wolter, D., primary, Emerson, J.C., additional, McNamara, S., additional, Buccat, A.M., additional, Qin, X., additional, Cochrane, E., additional, Houston, L.S., additional, Rogers, G.B., additional, Marsh, P., additional, Prehar, K., additional, Pope, C.E., additional, Blackledge, M., additional, Déziel, E., additional, Bruce, K.D., additional, Ramsey, B.W., additional, Gibson, R.L., additional, Burns, J.L., additional, and Hoffman, L., additional
- Published
- 2013
- Full Text
- View/download PDF
16. Human primary brain tumour metabolism in vivo: a phosphorus magnetic resonance spectroscopy study.
- Author
-
Cadoux-Hudson, TAD, Blackledge, MJ, Rajagopalan, B, Taylor, DJ, Radda, GK, Cadoux-Hudson, T A, Blackledge, M J, Taylor, D J, and Radda, G K
- Published
- 1989
- Full Text
- View/download PDF
17. Investigation of oxidation state-dependent conformational changes in Desulfovibrio vulgaris Hildenborough cytochrome c~5~5~3 by two-dimensional ^1H-NMR spectra
- Author
-
Blanchard, L., Blackledge, M. J., Marion, D., and Guerlesquin, F.
- Published
- 1996
- Full Text
- View/download PDF
18. Quantitative studies of human cardiac metabolism by 31P rotating-frame NMR.
- Author
-
Blackledge, M J, Rajagopalan, B, Oberhaensli, R D, Bolas, N M, Styles, P, and Radda, G K
- Abstract
We have developed 31P NMR spectroscopic methods to determine quantitatively relative levels of phosphorous-containing metabolites in the human myocardium. We have used localization techniques based on the rotating-frame imaging experiment and carried out with a double-surface coil probe. Information is obtained from selected slices by rotating-frame depth selection and from a complete one-dimensional spectroscopic image using phase-modulated rotating-frame imaging. The methods collect biochemical information from metabolites in human heart, and we use the fact that the phosphocreatine/ATP molar ratio in skeletal muscle at rest is higher than that in working heart to demonstrate that localization has been achieved for each investigation. The phosphocreatine/ATP molar ratio in normal human heart has been measured as 1.55 +/- 0.20 (mean +/- SD) (3.5-sec interpulse delay) in six subjects using depth selection and as 1.53 +/- 0.25 (mean +/- SD) in four subjects using spectroscopic imaging. Measurement of this ratio is expected to give a useful and reproducible index of myocardial energetics in normal and pathological states.
- Published
- 1987
- Full Text
- View/download PDF
19. P-31 MAGNETIC-RESONANCE SPECTROSCOPY IN RENAL ISCHEMIA
- Author
-
Ratcliffe, P. J., Zoltan Endre, Blackledge, M. J., Ledingham, J. G. G., and Radda, G. K.
- Published
- 1986
20. 31P nuclear magnetic resonance in the investigation of renal ischemia during hypotension
- Author
-
Peter Ratcliffe, Moonen, C. T., Endre, Z. H., Blackledge, M. J., Ledingham, J. G., and Radda, G. K.
- Published
- 1987
21. Rydberg-Klein-Rees (RKR) Franck-Condon factors for the O2 Schumann-Runge system including high vibrational quantum numbers
- Author
-
Harris, R., primary, Blackledge, M., additional, and Generosa, J., additional
- Published
- 1969
- Full Text
- View/download PDF
22. ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble
- Author
-
Blackledge Martin, Bernadó Pau, Estrada Jorge, and Sancho Javier
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background The stability of proteins is governed by the heat capacity, enthalpy and entropy changes of folding, which are strongly correlated to the change in solvent accessible surface area experienced by the polypeptide. While the surface exposed in the folded state can be easily determined, accessibilities for the unfolded state at the atomic level cannot be obtained experimentally and are typically estimated using simplistic models of the unfolded ensemble. A web application providing realistic accessibilities of the unfolded ensemble of a given protein at the atomic level will prove useful. Results ProtSA, a web application that calculates sequence-specific solvent accessibilities of the unfolded state ensembles of proteins has been developed and made freely available to the scientific community. The input is the amino acid sequence of the protein of interest. ProtSA follows a previously published calculation protocol which uses the Flexible-Meccano algorithm to generate unfolded conformations representative of the unfolded ensemble of the protein, and uses the exact analytical software ALPHASURF to calculate atom solvent accessibilities, which are averaged on the ensemble. Conclusion ProtSA is a novel tool for the researcher investigating protein folding energetics. The sequence specific atom accessibilities provided by ProtSA will allow obtaining better estimates of the contribution of the hydrophobic effect to the free energy of folding, will help to refine existing parameterizations of protein folding energetics, and will be useful to understand the influence of point mutations on protein stability.
- Published
- 2009
- Full Text
- View/download PDF
23. Rydberg-Klein-Rees (RKR) Franck-Condon factors for the O 2 Schumann-Runge system including high vibrational quantum numbers
- Author
-
Harris, R., Blackledge, M., and Generosa, J.
- Published
- 1969
- Full Text
- View/download PDF
24. NMR structures of ferredoxin chloroplastic transit peptide from Chlamydomonas reinhardtii promoted by trifluoroethanol in aqueous solution
- Author
-
Lancelin, J.-M., Bally, I., Arlaud, G. J., and Blackledge, M.
- Published
- 1994
- Full Text
- View/download PDF
25. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications
- Author
-
Altincekic, Nadide, Korn, Sophie Marianne, Qureshi, Nusrat Shahin, Dujardin, Marie, Ninot-Pedrosa, Martí, Abele, Rupert, Abi Saad, Marie Jose, Alfano, Caterina, Almeida, Fabio, Alshamleh, Islam, de Amorim, Gisele Cardoso, Anderson, Thomas, Anobom, Cristiane, Anorma, Chelsea, Bains, Jasleen Kaur, Bax, Adriaan, Blackledge, Martin, Blechar, Julius, Böckmann, Anja, Brigandat, Louis, Bula, Anna, Bütikofer, Matthias, Camacho-Zarco, Aldo, Carlomagno, Teresa, Caruso, Icaro Putinhon, Ceylan, Betül, Chaikuad, Apirat, Chu, Feixia, Cole, Laura, Crosby, Marquise, de Jesus, Vanessa, Dhamotharan, Karthikeyan, Felli, Isabella, Ferner, Jan, Fleischmann, Yanick, Fogeron, Marie-Laure, Fourkiotis, Nikolaos, Fuks, Christin, Fürtig, Boris, Gallo, Angelo, Gande, Santosh, Gerez, Juan Atilio, Ghosh, Dhiman, GOMES-NETO, Francisco, Gorbatyuk, Oksana, Guseva, Serafima, Hacker, Carolin, Häfner, Sabine, Hao, Bing, Hargittay, Bruno, Henzler-Wildman, K., Hoch, Jeffrey, Hohmann, Katharina, Hutchison, Marie, Jaudzems, Kristaps, Jović, Katarina, Kaderli, Janina, Kalniņš, Gints, Kaņepe, Iveta, Kirchdoerfer, Robert, Kirkpatrick, John, Knapp, Stefan, Krishnathas, Robin, Kutz, Felicitas, zur Lage, Susanne, Lambertz, Roderick, Lang, Andras, Laurents, Douglas, Lecoq, Lauriane, Linhard, Verena, Löhr, Frank, Malki, Anas, Bessa, Luiza Mamigonian, Martin, Rachel, Matzel, Tobias, Maurin, Damien, McNutt, Seth, Mebus-Antunes, Nathane Cunha, Meier, Beat, Meiser, Nathalie, Mompeán, Miguel, Monaca, Elisa, Montserret, Roland, Mariño Perez, Laura, Moser, Celine, Muhle-Goll, Claudia, Neves-Martins, Thais Cristtina, Ni, Xiamonin, Norton-Baker, Brenna, Pierattelli, Roberta, Pontoriero, Letizia, Pustovalova, Yulia, Ohlenschläger, Oliver, Orts, Julien, Da Poian, Andrea, Pyper, Dennis, Richter, Christian, Riek, Roland, Rienstra, Chad, Robertson, Angus, Pinheiro, Anderson, Sabbatella, Raffaele, Salvi, Nicola, Saxena, Krishna, Schulte, Linda, Schiavina, Marco, Schwalbe, Harald, Silber, Mara, Almeida, Marcius da Silva, Sprague-Piercy, Marc, Spyroulias, Georgios, Sreeramulu, Sridhar, Tants, Jan-Niklas, Tārs, Kaspars, Torres, Felix, Töws, Sabrina, Treviño, Miguel, Trucks, Sven, Tsika, Aikaterini, Varga, Krisztina, Wang, Ying, Weber, Marco, Weigand, Julia, Wiedemann, Christoph, Wirmer-Bartoschek, Julia, Wirtz Martin, Maria Alexandra, Zehnder, Johannes, Hengesbach, Martin, Schlundt, Andreas, Treviño, Miguel Á., Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Goethe University Frankfurt am Main, German Research Foundation, Cassa di Risparmio di Firenze, European Commission, University of New Hampshire, The Free State of Thuringia, National Institutes of Health (US), National Science Foundation (US), Howard Hughes Medical Institute, Latvian Council of Science, Ministry of Development and Investments (Greece), Helmholtz Association, Centre National de la Recherche Scientifique (France), Agence Nationale de la Recherche (France), Fondation pour la Recherche Médicale, Swiss National Science Foundation, Fonds National Suisse de la Recherche Scientifique, ETH Zurich, European Research Council, Université Grenoble Alpes, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Fundación 'la Caixa', Instituto de Salud Carlos III, Boehringer Ingelheim Fonds, Ministero dell'Istruzione, dell'Università e della Ricerca, Polytechnic Foundation of Frankfurt am Main, Goethe University Frankfurt, CNRS/Lyon University, Fondazione Ri.MED, Federal University of Rio de Janeiro, Caxias Federal University of Rio de Janeiro, University of Wisconsin-Madison, University of California, NIDDK, IBS, Latvian Institute of Organic Synthesis, Leibniz University Hannover, Helmholtz Centre for Infection Research, Universidade Estadual Paulista (Unesp), Buchmann Institute for Molecular Life Sciences, University of Florence, University of Patras, Oswaldo Cruz Foundation (FIOCRUZ), UConn Health, Signals GmbH Co. KG, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Latvian Biomedical Research and Study Centre, Spanish National Research Council (CSIC), Karlsruhe Institute of Technology, Technical University of Darmstadt, Martin Luther University Halle-Wittenberg, Altincekic N., Korn S.M., Qureshi N.S., Dujardin M., Ninot-Pedrosa M., Abele R., Abi Saad M.J., Alfano C., Almeida F.C.L., Alshamleh I., de Amorim G.C., Anderson T.K., Anobom C.D., Anorma C., Bains J.K., Bax A., Blackledge M., Blechar J., Bockmann A., Brigandat L., Bula A., Butikofer M., Camacho-Zarco A.R., Carlomagno T., Caruso I.P., Ceylan B., Chaikuad A., Chu F., Cole L., Crosby M.G., de Jesus V., Dhamotharan K., Felli I.C., Ferner J., Fleischmann Y., Fogeron M.-L., Fourkiotis N.K., Fuks C., Furtig B., Gallo A., Gande S.L., Gerez J.A., Ghosh D., Gomes-Neto F., Gorbatyuk O., Guseva S., Hacker C., Hafner S., Hao B., Hargittay B., Henzler-Wildman K., Hoch J.C., Hohmann K.F., Hutchison M.T., Jaudzems K., Jovic K., Kaderli J., Kalnins G., Kanepe I., Kirchdoerfer R.N., Kirkpatrick J., Knapp S., Krishnathas R., Kutz F., zur Lage S., Lambertz R., Lang A., Laurents D., Lecoq L., Linhard V., Lohr F., Malki A., Bessa L.M., Martin R.W., Matzel T., Maurin D., McNutt S.W., Mebus-Antunes N.C., Meier B.H., Meiser N., Mompean M., Monaca E., Montserret R., Marino Perez L., Moser C., Muhle-Goll C., Neves-Martins T.C., Ni X., Norton-Baker B., Pierattelli R., Pontoriero L., Pustovalova Y., Ohlenschlager O., Orts J., Da Poian A.T., Pyper D.J., Richter C., Riek R., Rienstra C.M., Robertson A., Pinheiro A.S., Sabbatella R., Salvi N., Saxena K., Schulte L., Schiavina M., Schwalbe H., Silber M., Almeida M.D.S., Sprague-Piercy M.A., Spyroulias G.A., Sreeramulu S., Tants J.-N., Tars K., Torres F., Tows S., Trevino M.A., Trucks S., Tsika A.C., Varga K., Wang Y., Weber M.E., Weigand J.E., Wiedemann C., Wirmer-Bartoschek J., Wirtz Martin M.A., Zehnder J., Hengesbach M., Schlundt A., HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., and Obra Social la Caixa
- Subjects
Life sciences ,biology ,SARS-COV-2 ,COVID-19 ,protein production ,structural biology, NMR ,[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Biochemistry ,Accessory proteins ,NMR spectroscopy ,ddc:570 ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Molecular Biosciences ,ddc:610 ,Nonstructural proteins ,Molecular Biology ,Original Research ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,SARS-CoV-2 ,Intrinsically disordered region ,nonstructural proteins ,structural proteins ,Cell-free protein synthesis ,intrinsically disordered region ,cell-free protein synthesis ,accessory proteins ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Structural proteins - Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form., This work was supported by Goethe University (Corona funds), the DFG-funded CRC: “Molecular Principles of RNA-Based Regulation,” DFG infrastructure funds (project numbers: 277478796, 277479031, 392682309, 452632086, 70653611), the state of Hesse (BMRZ), the Fondazione CR Firenze (CERM), and the IWB-EFRE-program 20007375. This project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 871037. AS is supported by DFG Grant SCHL 2062/2-1 and by the JQYA at Goethe through project number 2019/AS01. Work in the lab of KV was supported by a CoRE grant from the University of New Hampshire. The FLI is a member of the Leibniz Association (WGL) and financially supported by the Federal Government of Germany and the State of Thuringia. Work in the lab of RM was supported by NIH (2R01EY021514) and NSF (DMR-2002837). BN-B was supported by theNSF GRFP.MCwas supported byNIH (R25 GM055246 MBRS IMSD), and MS-P was supported by the HHMI Gilliam Fellowship. Work in the labs of KJ and KT was supported by Latvian Council of Science Grant No. VPP-COVID 2020/1-0014. Work in the UPAT’s lab was supported by the INSPIRED (MIS 5002550) project, which is implemented under the Action “Reinforcement of the Research and Innovation Infrastructure,” funded by the Operational Program “Competitiveness, Entrepreneurship and Innovation” (NSRF 2014–2020) and cofinanced by Greece and the EU (European Regional Development Fund) and the FP7 REGPOT CT-2011- 285950–“SEE-DRUG” project (purchase of UPAT’s 700MHz NMR equipment). Work in the CM-G lab was supported by the Helmholtz society. Work in the lab of ABö was supported by the CNRS, the French National Research Agency (ANR, NMRSCoV2- ORF8), the Fondation de la Recherche Médicale (FRM, NMR-SCoV2-ORF8), and the IR-RMN-THC Fr3050 CNRS. Work in the lab of BM was supported by the Swiss National Science Foundation (Grant number 200020_188711), the Günthard Stiftung für Physikalische Chemie, and the ETH Zurich. Work in the labs of ABö and BM was supported by a common grant from SNF (grant 31CA30_196256). This work was supported by the ETHZurich, the grant ETH40 18 1, and the grant Krebsliga KFS 4903 08 2019. Work in the lab of the IBS Grenoble was supported by the Agence Nationale de Recherche (France) RA-COVID SARS2NUCLEOPROTEIN and European Research Council Advanced Grant DynamicAssemblies. Work in the CA lab was supported by Patto per il Sud della Regione Siciliana–CheMISt grant (CUP G77B17000110001). Part of this work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-05-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE- 0003). Work at the UW-Madison was supported by grant numbers NSF MCB2031269 and NIH/NIAID AI123498. MM is a Ramón y Cajal Fellow of the Spanish AEI-Ministry of Science and Innovation (RYC2019-026574-I), and a “La Caixa” Foundation (ID 100010434) Junior Leader Fellow (LCR/BQ/PR19/11700003). Funded by project COV20/00764 fromthe Carlos III Institute of Health and the SpanishMinistry of Science and Innovation to MMand DVL. VDJ was supported by the Boehringer Ingelheim Fonds. Part of this work used the resources of the Italian Center of Instruct-ERIC at the CERM/ CIRMMP infrastructure, supported by the Italian Ministry for University and Research (FOE funding). CF was supported by the Stiftung Polytechnische Gesellschaft. Work in the lab of JH was supported by NSF (RAPID 2030601) and NIH (R01GM123249).
- Published
- 2021
26. Structures of influenza A and B replication complexes give insight into avian to human host adaptation and reveal a role of ANP32 as an electrostatic chaperone for the apo-polymerase.
- Author
-
Arragain B, Krischuns T, Pelosse M, Drncova P, Blackledge M, Naffakh N, and Cusack S
- Subjects
- Humans, Animals, Nuclear Proteins metabolism, Nuclear Proteins chemistry, RNA, Viral metabolism, RNA, Viral chemistry, RNA, Viral genetics, Birds virology, RNA-Dependent RNA Polymerase metabolism, RNA-Dependent RNA Polymerase chemistry, RNA-Dependent RNA Polymerase genetics, Influenza in Birds virology, Influenza in Birds metabolism, Models, Molecular, Influenza, Human virology, Virus Replication, Molecular Chaperones metabolism, Molecular Chaperones chemistry, Molecular Chaperones genetics, Influenza A virus metabolism, Influenza A virus genetics, RNA-Binding Proteins metabolism, RNA-Binding Proteins chemistry, RNA-Binding Proteins genetics, Cryoelectron Microscopy, Static Electricity
- Abstract
Replication of influenza viral RNA depends on at least two viral polymerases, a parental replicase and an encapsidase, and cellular factor ANP32. ANP32 comprises an LRR domain and a long C-terminal low complexity acidic region (LCAR). Here we present evidence suggesting that ANP32 is recruited to the replication complex as an electrostatic chaperone that stabilises the encapsidase moiety within apo-polymerase symmetric dimers that are distinct for influenza A and B polymerases. The ANP32 bound encapsidase, then forms the asymmetric replication complex with the replicase, which is embedded in a parental ribonucleoprotein particle (RNP). Cryo-EM structures reveal the architecture of the influenza A and B replication complexes and the likely trajectory of the nascent RNA product into the encapsidase. The cryo-EM map of the FluB replication complex shows extra density attributable to the ANP32 LCAR wrapping around and stabilising the apo-encapsidase conformation. These structures give new insight into the various mutations that adapt avian strain polymerases to use the distinct ANP32 in mammalian cells., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
27. A specific phosphorylation-dependent conformational switch in SARS-CoV-2 nucleocapsid protein inhibits RNA binding.
- Author
-
Botova M, Camacho-Zarco AR, Tognetti J, Bessa LM, Guseva S, Mikkola E, Salvi N, Maurin D, Herrmann T, and Blackledge M
- Subjects
- Phosphorylation, Humans, Protein Conformation, COVID-19 virology, COVID-19 metabolism, Nucleocapsid Proteins metabolism, Nucleocapsid Proteins chemistry, Models, Molecular, Binding Sites, Phosphoproteins, SARS-CoV-2 metabolism, Coronavirus Nucleocapsid Proteins metabolism, Coronavirus Nucleocapsid Proteins chemistry, Protein Binding, RNA, Viral metabolism, RNA, Viral chemistry
- Abstract
The nucleocapsid protein of severe acute respiratory syndrome coronavirus 2 encapsidates the viral genome and is essential for viral function. The central disordered domain comprises a serine-arginine-rich (SR) region that is hyperphosphorylated in infected cells. This modification regulates function, although mechanistic details remain unknown. We use nuclear magnetic resonance to follow structural changes occurring during hyperphosphorylation by serine arginine protein kinase 1, glycogen synthase kinase 3, and casein kinase 1, that abolishes interaction with RNA. When eight approximately uniformly distributed sites have been phosphorylated, the SR domain binds the same interface as single-stranded RNA, resulting in complete inhibition of RNA binding. Phosphorylation by protein kinase A does not prevent RNA binding, indicating that the pattern resulting from physiologically relevant kinases is specific for inhibition. Long-range contacts between the RNA binding, linker, and dimerization domains are abrogated, phenomena possibly related to genome packaging and unpackaging. This study provides insight into the recruitment of specific host kinases to regulate viral function.
- Published
- 2024
- Full Text
- View/download PDF
28. Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro.
- Author
-
Vu DD, Bonucci A, Brenière M, Cisneros-Aguirre M, Pelupessy P, Wang Z, Carlier L, Bouvignies G, Cortes P, Aggarwal AK, Blackledge M, Gueroui Z, Belle V, Stark JM, Modesti M, and Ferrage F
- Abstract
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70-Ku80 heterodimer (Ku), X-ray repair cross complementing 4 (XRCC4) in complex with DNA ligase 4 (X4L4) and XRCC4-like factor (XLF) form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) were recently obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at residue resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs lead to the formation of XLF and X4L4 condensates in vitro, which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome-editing strategies., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
- Published
- 2024
- Full Text
- View/download PDF
29. Revisiting the interaction between complement lectin pathway protease MASP-2 and SARS-CoV-2 nucleoprotein.
- Author
-
Bally I, Drumont G, Rossi V, Guseva S, Botova M, Reiser JB, Thépaut M, Dergan Dylon S, Dumestre-Pérard C, Gaboriaud C, Fieschi F, Blackledge M, Poignard P, and Thielens NM
- Subjects
- Humans, Protein Binding, Coronavirus Nucleocapsid Proteins immunology, Coronavirus Nucleocapsid Proteins metabolism, Complement Activation immunology, Mannose-Binding Lectin metabolism, Mannose-Binding Lectin immunology, Phosphoproteins, Mannose-Binding Protein-Associated Serine Proteases metabolism, Mannose-Binding Protein-Associated Serine Proteases immunology, SARS-CoV-2 immunology, Complement Pathway, Mannose-Binding Lectin immunology, COVID-19 immunology, COVID-19 virology
- Abstract
Complement activation is considered to contribute to the pathogenesis of severe SARS-CoV-2 infection, mainly by generating potent immune effector mechanisms including a strong inflammatory response. Involvement of the lectin complement pathway, a major actor of the innate immune anti-viral defense, has been reported previously. It is initiated by recognition of the viral surface Spike glycoprotein by mannose-binding lectin (MBL), which induces activation of the MBL-associated protease MASP-2 and triggers the proteolytic complement cascade. A role for the viral nucleoprotein (N) has also been reported, through binding to MASP-2, leading to protease overactivation and potentiation of the lectin pathway. In the present study, we reinvestigated the interactions of the SARS-CoV-2 N protein, produced either in bacteria or secreted by mammalian cells, with full-length MASP-2 or its catalytic domain, in either active or proenzyme form. We could not confirm the interaction of the N protein with the catalytic domain of MASP-2 but observed N protein binding to proenzyme MASP-2. We did not find a role of the N protein in MBL-mediated activation of the lectin pathway. Finally, we showed that incubation of the N protein with MASP-2 results in proteolysis of the viral protein, an observation that requires further investigation to understand a potential functional significance in infected patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Bally, Drumont, Rossi, Guseva, Botova, Reiser, Thépaut, Dergan Dylon, Dumestre-Pérard, Gaboriaud, Fieschi, Blackledge, Poignard and Thielens.)
- Published
- 2024
- Full Text
- View/download PDF
30. Predicting cervical cancer target motion using a multivariate regression model to enable patient selection for adaptive external beam radiotherapy.
- Author
-
Wang L, McQuaid D, Blackledge M, McNair H, Harris E, and Lalondrelle S
- Abstract
Background and Purpose: Interfraction motion during cervical cancer radiotherapy is substantial in some patients, minimal in others. Non-adaptive plans may miss the target and/or unnecessarily irradiate normal tissue. Adaptive radiotherapy leads to superior dose-volume metrics but is resource-intensive. The aim of this study was to predict target motion, enabling patient selection and efficient resource allocation., Materials and Methods: Forty cervical cancer patients had CT with full-bladder (CT-FB) and empty-bladder (CT-EB) at planning, and daily cone-beam CTs (CBCTs). The low-risk clinical target volume (CTV
LR ) was contoured. Mean coverage of the daily CTVLR by the CT-FB CTVLR was calculated for each patient. Eighty-three investigated variables included measures of organ geometry, patient, tumour and treatment characteristics. Models were trained on 29 patients (171 fractions). The Two-CT multivariate model could use all available data. The Single-CT multivariate model excluded data from the CT-EB. A univariate model was trained using the distance moved by the uterine fundus tip between CTs, the only method of patient selection found in published cervix plan-of-the-day studies. Models were tested on 11 patients (68 fractions). Accuracy in predicting mean coverage was reported as mean absolute error (MAE), mean squared error (MSE) and R2 ., Results: The Two-CT model was based upon rectal volume, dice similarity coefficient between CT-FB and CT-EB CTVLR , and uterine thickness. The Single-CT model was based upon rectal volume, uterine thickness and tumour size. Both performed better than the univariate model in predicting mean coverage (MAE 7 %, 7 % and 8 %; MSE 82 %2 , 65 %2 , 110 %2 ; R2 0.2, 0.4, -0.1)., Conclusion: Uterocervix motion is complex and multifactorial. We present two multivariate models which predicted motion with reasonable accuracy using pre-treatment information, and outperformed the only published method., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Lei Wang is part-funded by the National Institute for Health Research (NIHR) Biomedical Research Centre at The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London; and part-funded by Elekta Ltd. Helen McNair is funded by a National Institute for Health Research and Health Education England (HEE/NIHR) Senior Clinical Lectureship (ICA-SCL-2018–04-ST2-002). Emma Harris has received research funding from Elekta Ltd and Cancer Research UK Programme Foundation Award A23557. Susan Lalondrelle has received research funding and speaking fees from Elekta Ltd., (© 2024 The Author(s).)- Published
- 2024
- Full Text
- View/download PDF
31. Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties.
- Author
-
Li XH, Yu CWH, Gomez-Navarro N, Stancheva V, Zhu H, Murthy A, Wozny M, Malhotra K, Johnson CM, Blackledge M, Santhanam B, Liu W, Huang J, Freund SMV, Miller EA, and Babu MM
- Abstract
A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life., (© The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences.)
- Published
- 2024
- Full Text
- View/download PDF
32. Image quality in whole-body MRI using the MY-RADS protocol in a prospective multi-centre multiple myeloma study.
- Author
-
Keaveney S, Dragan A, Rata M, Blackledge M, Scurr E, Winfield JM, Shur J, Koh DM, Porta N, Candito A, King A, Rennie W, Gaba S, Suresh P, Malcolm P, Davis A, Nilak A, Shah A, Gandhi S, Albrizio M, Drury A, Pratt G, Cook G, Roberts S, Jenner M, Brown S, Kaiser M, and Messiou C
- Abstract
Background: The Myeloma Response Assessment and Diagnosis System (MY-RADS) guidelines establish a standardised acquisition and analysis pipeline for whole-body MRI (WB-MRI) in patients with myeloma. This is the first study to assess image quality in a multi-centre prospective trial using MY-RADS., Methods: The cohort consisted of 121 examinations acquired across ten sites with a range of prior WB-MRI experience, three scanner manufacturers and two field strengths. Image quality was evaluated qualitatively by a radiologist and quantitatively using a semi-automated pipeline to quantify common artefacts and image quality issues. The intra- and inter-rater repeatability of qualitative and quantitative scoring was also assessed., Results: Qualitative radiological scoring found that the image quality was generally good, with 94% of examinations rated as good or excellent and only one examination rated as non-diagnostic. There was a significant correlation between radiological and quantitative scoring for most measures, and intra- and inter-rater repeatability were generally good. When the quality of an overall examination was low, this was often due to low quality diffusion-weighted imaging (DWI), where signal to noise ratio (SNR), anterior thoracic signal loss and brain geometric distortion were found as significant predictors of examination quality., Conclusions: It is possible to successfully deliver a multi-centre WB-MRI study using the MY-RADS protocol involving scanners with a range of manufacturers, models and field strengths. Quantitative measures of image quality were developed and shown to be significantly correlated with radiological assessment. The SNR of DW images was identified as a significant factor affecting overall examination quality., Trial Registration: ClinicalTrials.gov, NCT03188172 , Registered on 15 June 2017., Critical Relevance Statement: Good overall image quality, assessed both qualitatively and quantitatively, can be achieved in a multi-centre whole-body MRI study using the MY-RADS guidelines., Key Points: • A prospective multi-centre WB-MRI study using MY-RADS can be successfully delivered. • Quantitative image quality metrics were developed and correlated with radiological assessment. • SNR in DWI was identified as a significant predictor of quality, allowing for rapid quality adjustment., (© 2023. European Society of Radiology (ESR).)
- Published
- 2023
- Full Text
- View/download PDF
33. Intrinsically disordered regions in TRPV2 mediate protein-protein interactions.
- Author
-
Sanganna Gari RR, Tagiltsev G, Pumroy RA, Jiang Y, Blackledge M, Moiseenkova-Bell VY, and Scheuring S
- Subjects
- Microscopy, Atomic Force, Single Molecule Imaging, Intrinsically Disordered Proteins, TRPV Cation Channels
- Abstract
Transient receptor potential (TRP) ion channels are gated by diverse intra- and extracellular stimuli leading to cation inflow (Na
+ , Ca2+ ) regulating many cellular processes and initiating organismic somatosensation. Structures of most TRP channels have been solved. However, structural and sequence analysis showed that ~30% of the TRP channel sequences, mainly the N- and C-termini, are intrinsically disordered regions (IDRs). Unfortunately, very little is known about IDR 'structure', dynamics and function, though it has been shown that they are essential for native channel function. Here, we imaged TRPV2 channels in membranes using high-speed atomic force microscopy (HS-AFM). The dynamic single molecule imaging capability of HS-AFM allowed us to visualize IDRs and revealed that N-terminal IDRs were involved in intermolecular interactions. Our work provides evidence about the 'structure' of the TRPV2 IDRs, and that the IDRs may mediate protein-protein interactions., (© 2023. Springer Nature Limited.)- Published
- 2023
- Full Text
- View/download PDF
34. Response to A. Eleuteri regarding "A radiomics-based decision support tool improves lung cancer diagnosis in combination with the Herder score in large lung nodules".
- Author
-
Hunter B, Bunce C, Blackledge M, Aboagye E, and Lee R
- Subjects
- Humans, Tomography, X-Ray Computed, Lung, Lung Neoplasms diagnostic imaging
- Abstract
Competing Interests: Declaration of interests Dr Lee is funded by the Royal Marsden NIHR BRC and Royal Marsden Cancer Charity. RL's institution receives compensation for time spent in a secondment role for the lung health check program and as a national specialty lead for the National Institute of Health and Care Research. He has received research funding from CRUK, Innovate UK (co-funded by GE Healthcare, Roche and Optellum), SBRI (co-applicant in grants with QURE.AI), RM Partners Care Alliance and NIHR (co-applicant in grants with Optellum). He has received honoraria from CRUK. The other authors have no conflict of interest to report.
- Published
- 2023
- Full Text
- View/download PDF
35. Multivalent interactions of the disordered regions of XLF and XRCC4 foster robust cellular NHEJ and drive the formation of ligation-boosting condensates in vitro .
- Author
-
Vu DD, Bonucci A, Brenière M, Cisneros-Aguirre M, Pelupessy P, Wang Z, Carlier L, Bouvignies G, Cortes P, Aggarwal AK, Blackledge M, Gueroui Z, Belle V, Stark JM, Modesti M, and Ferrage F
- Abstract
In mammalian cells, DNA double-strand breaks are predominantly repaired by non-homologous end joining (NHEJ). During repair, the Ku70/80 heterodimer (Ku), XRCC4 in complex with DNA Ligase 4 (X4L4), and XLF form a flexible scaffold that holds the broken DNA ends together. Insights into the architectural organization of the NHEJ scaffold and its regulation by the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) have recently been obtained by single-particle cryo-electron microscopy analysis. However, several regions, especially the C-terminal regions (CTRs) of the XRCC4 and XLF scaffolding proteins, have largely remained unresolved in experimental structures, which hampers the understanding of their functions. Here, we used magnetic resonance techniques and biochemical assays to comprehensively characterize the interactions and dynamics of the XRCC4 and XLF CTRs at atomic resolution. We show that the CTRs of XRCC4 and XLF are intrinsically disordered and form a network of multivalent heterotypic and homotypic interactions that promotes robust cellular NHEJ activity. Importantly, we demonstrate that the multivalent interactions of these CTRs led to the formation of XLF and X4L4 condensates in vitro which can recruit relevant effectors and critically stimulate DNA end ligation. Our work highlights the role of disordered regions in the mechanism and dynamics of NHEJ and lays the groundwork for the investigation of NHEJ protein disorder and its associated condensates inside cells with implications in cancer biology, immunology and the development of genome editing strategies.
- Published
- 2023
- Full Text
- View/download PDF
36. Phase separation and molecular ordering of the prion-like domain of the Arabidopsis thermosensory protein EARLY FLOWERING 3.
- Author
-
Hutin S, Kumita JR, Strotmann VI, Dolata A, Ling WL, Louafi N, Popov A, Milhiet PE, Blackledge M, Nanao MH, Wigge PA, Stahl Y, Costa L, Tully MD, and Zubieta C
- Subjects
- Prions, Temperature, Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism, Transcription Factors genetics, Transcription Factors metabolism
- Abstract
Liquid-liquid phase separation (LLPS) is an important mechanism enabling the dynamic compartmentalization of macromolecules, including complex polymers such as proteins and nucleic acids, and occurs as a function of the physicochemical environment. In the model plant, Arabidopsis thaliana , LLPS by the protein EARLY FLOWERING3 (ELF3) occurs in a temperature-sensitive manner and controls thermoresponsive growth. ELF3 contains a largely unstructured prion-like domain (PrLD) that acts as a driver of LLPS in vivo and in vitro. The PrLD contains a poly-glutamine (polyQ) tract, whose length varies across natural Arabidopsis accessions. Here, we use a combination of biochemical, biophysical, and structural techniques to investigate the dilute and condensed phases of the ELF3 PrLD with varying polyQ lengths. We demonstrate that the dilute phase of the ELF3 PrLD forms a monodisperse higher-order oligomer that does not depend on the presence of the polyQ sequence. This species undergoes LLPS in a pH- and temperature-sensitive manner and the polyQ region of the protein tunes the initial stages of phase separation. The liquid phase rapidly undergoes aging and forms a hydrogel as shown by fluorescence and atomic force microscopies. Furthermore, we demonstrate that the hydrogel assumes a semiordered structure as determined by small-angle X-ray scattering, electron microscopy, and X-ray diffraction. These experiments demonstrate a rich structural landscape for a PrLD protein and provide a framework to describe the structural and biophysical properties of biomolecular condensates.
- Published
- 2023
- Full Text
- View/download PDF
37. Structural insights into p300 regulation and acetylation-dependent genome organisation.
- Author
-
Ibrahim Z, Wang T, Destaing O, Salvi N, Hoghoughi N, Chabert C, Rusu A, Gao J, Feletto L, Reynoird N, Schalch T, Zhao Y, Blackledge M, Khochbin S, and Panne D
- Subjects
- Acetylation, Transcription Factors genetics, Transcription Factors metabolism, Chromatin, Nuclear Proteins metabolism, Lysine metabolism
- Abstract
Histone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
38. A radiomics-based decision support tool improves lung cancer diagnosis in combination with the Herder score in large lung nodules.
- Author
-
Hunter B, Chen M, Ratnakumar P, Alemu E, Logan A, Linton-Reid K, Tong D, Senthivel N, Bhamani A, Bloch S, Kemp SV, Boddy L, Jain S, Gareeboo S, Rawal B, Doran S, Navani N, Nair A, Bunce C, Kaye S, Blackledge M, Aboagye EO, Devaraj A, and Lee RW
- Subjects
- Male, Humans, Female, Retrospective Studies, Tomography, X-Ray Computed, Lung pathology, Lung Neoplasms diagnostic imaging, Lung Neoplasms pathology, Precancerous Conditions
- Abstract
Background: Large lung nodules (≥15 mm) have the highest risk of malignancy, and may exhibit important differences in phenotypic or clinical characteristics to their smaller counterparts. Existing risk models do not stratify large nodules well. We aimed to develop and validate an integrated segmentation and classification pipeline, incorporating deep-learning and traditional radiomics, to classify large lung nodules according to cancer risk., Methods: 502 patients from five U.K. centres were recruited to the large-nodule arm of the retrospective LIBRA study between July 2020 and April 2022. 838 CT scans were used for model development, split into training and test sets (70% and 30% respectively). An nnUNet model was trained to automate lung nodule segmentation. A radiomics signature was developed to classify nodules according to malignancy risk. Performance of the radiomics model, termed the large-nodule radiomics predictive vector (LN-RPV), was compared to three radiologists and the Brock and Herder scores., Findings: 499 patients had technically evaluable scans (mean age 69 ± 11, 257 men, 242 women). In the test set of 252 scans, the nnUNet achieved a DICE score of 0.86, and the LN-RPV achieved an AUC of 0.83 (95% CI 0.77-0.88) for malignancy classification. Performance was higher than the median radiologist (AUC 0.75 [95% CI 0.70-0.81], DeLong p = 0.03). LN-RPV was robust to auto-segmentation (ICC 0.94). For baseline solid nodules in the test set (117 patients), LN-RPV had an AUC of 0.87 (95% CI 0.80-0.93) compared to 0.67 (95% CI 0.55-0.76, DeLong p = 0.002) for the Brock score and 0.83 (95% CI 0.75-0.90, DeLong p = 0.4) for the Herder score. In the international external test set (n = 151), LN-RPV maintained an AUC of 0.75 (95% CI 0.63-0.85). 18 out of 22 (82%) malignant nodules in the Herder 10-70% category in the test set were identified as high risk by the decision-support tool, and may have been referred for earlier intervention., Interpretation: The model accurately segments and classifies large lung nodules, and may improve upon existing clinical models., Funding: This project represents independent research funded by: 1) Royal Marsden Partners Cancer Alliance, 2) the Royal Marsden Cancer Charity, 3) the National Institute for Health Research (NIHR) Biomedical Research Centre at the Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London, 4) the National Institute for Health Research (NIHR) Biomedical Research Centre at Imperial College London, 5) Cancer Research UK (C309/A31316)., Competing Interests: Declaration of interests Dr Navani is supported by a Medical Research Council Clinical Academic Research Partnership (MR/T02481X/1). This work was partly undertaken at the University College London Hospitals/University College London that received a proportion of funding from the Department of Health’s National Institute for Health Research (NIHR) Biomedical Research Centre’s funding scheme (NN). Dr Navani reports honoraria for educational talks or advisory boards from Amgen, Astra Zeneca, Boehringer Ingelheim, Bristol Myers Squibb, Guardant Health, Janssen, Lilly, Merck Sharp & Dohme, Olympus, OncLive, PeerVoice, Pfizer, and Takeda. Dr Nair receives research grants from the Department of Health’s NIHR Biomedical Research Centre and GRAIL. He has received consulting fees from Aidence BV, Faculty Science Limited and MSD. He has received a travel bursary from Takeda. He participates on advisory boards for Aidence BV and Faculty Science Limited. He has leadership roles within the British Society of Thoracic Imaging, the British Lung Foundation and the NHS England Targeted Lung Health Checks Programme. Dr Lee is funded by the Royal Marsden NIHR BRC, and Royal Marsden Cancer charity. RL's institution receives compensation for time spent in a secondment role for the lung health check program and as a National Specialty Lead for the National Institute of Health and Care Research. He has received research funding from CRUK, Innovate UK (co-funded by GE Healthcare, Roche and Optellum), SBRI (co-applicant in grants with QURE.AI), RM Partners Cancer Alliance and NIHR (co-applicant in grants with Optellum). He has received honoraria from CRUK. Professor Devaraj is employed by and has stocks in Brainomix. He receives consulting fees from Roche and Boehringer Ingelheim. The other authors report no potential conflict of interest., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
39. Author Correction: Gross tumour volume radiomics for prognostication of recurrence & death following radical radiotherapy for NSCLC.
- Author
-
Hindocha S, Charlton TG, Linton-Reid K, Hunter B, Chan C, Ahmed M, Greenlay EJ, Orton M, Bunce C, Lunn J, Doran SJ, Ahmad S, McDonald F, Locke I, Power D, Blackledge M, Lee RW, and Aboagye EO
- Published
- 2022
- Full Text
- View/download PDF
40. Gross tumour volume radiomics for prognostication of recurrence & death following radical radiotherapy for NSCLC.
- Author
-
Hindocha S, Charlton TG, Linton-Reid K, Hunter B, Chan C, Ahmed M, Greenlay EJ, Orton M, Bunce C, Lunn J, Doran SJ, Ahmad S, McDonald F, Locke I, Power D, Blackledge M, Lee RW, and Aboagye EO
- Abstract
Recurrence occurs in up to 36% of patients treated with curative-intent radiotherapy for NSCLC. Identifying patients at higher risk of recurrence for more intensive surveillance may facilitate the earlier introduction of the next line of treatment. We aimed to use radiotherapy planning CT scans to develop radiomic classification models that predict overall survival (OS), recurrence-free survival (RFS) and recurrence two years post-treatment for risk-stratification. A retrospective multi-centre study of >900 patients receiving curative-intent radiotherapy for stage I-III NSCLC was undertaken. Models using radiomic and/or clinical features were developed, compared with 10-fold cross-validation and an external test set, and benchmarked against TNM-stage. Respective validation and test set AUCs (with 95% confidence intervals) for the radiomic-only models were: (1) OS: 0.712 (0.592-0.832) and 0.685 (0.585-0.784), (2) RFS: 0.825 (0.733-0.916) and 0.750 (0.665-0.835), (3) Recurrence: 0.678 (0.554-0.801) and 0.673 (0.577-0.77). For the combined models: (1) OS: 0.702 (0.583-0.822) and 0.683 (0.586-0.78), (2) RFS: 0.805 (0.707-0.903) and 0·755 (0.672-0.838), (3) Recurrence: 0·637 (0.51-0.·765) and 0·738 (0.649-0.826). Kaplan-Meier analyses demonstrate OS and RFS difference of >300 and >400 days respectively between low and high-risk groups. We have developed validated and externally tested radiomic-based prediction models. Such models could be integrated into the routine radiotherapy workflow, thus informing a personalised surveillance strategy at the point of treatment. Our work lays the foundations for future prospective clinical trials for quantitative personalised risk-stratification for surveillance following curative-intent radiotherapy for NSCLC., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
41. Convergent views on disordered protein dynamics from NMR and computational approaches.
- Author
-
Salvi N, Zapletal V, Jaseňáková Z, Zachrdla M, Padrta P, Narasimhan S, Marquardsen T, Tyburn JM, Žídek L, Blackledge M, Ferrage F, and Kadeřávek P
- Subjects
- Protein Conformation, Magnetic Resonance Spectroscopy, Molecular Dynamics Simulation, DNA-Directed RNA Polymerases chemistry, Amides, Intrinsically Disordered Proteins chemistry
- Abstract
Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) is a class of biologically important proteins exhibiting specific biophysical characteristics. They lack a hydrophobic core, and their conformational behavior is strongly influenced by electrostatic interactions. IDPs and IDRs are highly dynamic, and a characterization of the motions of IDPs and IDRs is essential for their physically correct description. NMR together with molecular dynamics simulations are the methods best suited to such a task because they provide information about dynamics of proteins with atomistic resolution. Here, we present a study of motions of a disordered C-terminal domain of the delta subunit of RNA polymerase from Bacillus subtilis. Positively and negatively charged residues in the studied domain form transient electrostatic contacts critical for the biological function. Our study is focused on investigation of ps-ns dynamics of backbone of the delta subunit based on analysis of amide
15 N NMR relaxation data and molecular dynamics simulations. In order to extend an informational content of NMR data to lower frequencies, which are more sensitive to slower motions, we combined standard (high-field) NMR relaxation experiments with high-resolution relaxometry. Altogether, we collected data reporting the relaxation at 12 different magnetic fields, resulting in an unprecedented data set. Our results document that the analysis of such data provides a consistent description of dynamics and confirms the validity of so far used protocols of the analysis of dynamics of IDPs also for a partially folded protein. In addition, the potential to access detailed description of motions at the timescale of tens of ns with the help of relaxometry data is discussed. Interestingly, in our case, it appears to be mostly relevant for a region involved in the formation of temporary contacts within the disordered region, which was previously proven to be biologically important., Competing Interests: Declaration of interests T.M. and J.-M.T. were employees of the Bruker BioSpin. The other authors declare no other conflict of interest., (Copyright © 2022 Biophysical Society. Published by Elsevier Inc. All rights reserved.)- Published
- 2022
- Full Text
- View/download PDF
42. Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex.
- Author
-
Spittler D, Indorato RL, Boeri Erba E, Delaforge E, Signor L, Harris SJ, Garcia-Saez I, Palencia A, Gabel F, Blackledge M, Noirclerc-Savoye M, and Petosa C
- Subjects
- Models, Structural, Molecular Docking Simulation, RNA, Viral metabolism, HIV-1 metabolism, beta Karyopherins genetics, beta Karyopherins metabolism
- Abstract
HIV-1 Rev mediates the nuclear export of intron-containing viral RNA transcripts and is essential for viral replication. Rev is imported into the nucleus by the host protein importin β (Impβ), but how Rev associates with Impβ is poorly understood. Here, we report biochemical, mutational, and biophysical studies of the Impβ/Rev complex. We show that Impβ binds two Rev monomers through independent binding sites, in contrast to the 1:1 binding stoichiometry observed for most Impβ cargos. Peptide scanning data and charge-reversal mutations identify the N-terminal tip of Rev helix α2 within Rev's arginine-rich motif (ARM) as a primary Impβ-binding epitope. Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos., (© 2022 Spittler et al.)
- Published
- 2022
- Full Text
- View/download PDF
43. Implementation of Whole-Body MRI (MY-RADS) within the OPTIMUM/MUKnine multi-centre clinical trial for patients with myeloma.
- Author
-
Rata M, Blackledge M, Scurr E, Winfield J, Koh DM, Dragan A, Candito A, King A, Rennie W, Gaba S, Suresh P, Malcolm P, Davis A, Nilak A, Shah A, Gandhi S, Albrizio M, Drury A, Roberts S, Jenner M, Brown S, Kaiser M, and Messiou C
- Abstract
Background: Whole-body (WB) MRI, which includes diffusion-weighted imaging (DWI) and T
1 -w Dixon, permits sensitive detection of marrow disease in addition to qualitative and quantitative measurements of disease and response to treatment of bone marrow. We report on the first study to embed standardised WB-MRI within a prospective, multi-centre myeloma clinical trial (IMAGIMM trial, sub-study of OPTIMUM/MUKnine) to explore the use of WB-MRI to detect minimal residual disease after treatment., Methods: The standardised MY-RADS WB-MRI protocol was set up on a local 1.5 T scanner. An imaging manual describing the MR protocol, quality assurance/control procedures and data transfer was produced and provided to sites. For non-identical scanners (different vendor or magnet strength), site visits from our physics team were organised to support protocol optimisation. The site qualification process included review of phantom and volunteer data acquired at each site and a teleconference to brief the multidisciplinary team. Image quality of initial patients at each site was assessed., Results: WB-MRI was successfully set up at 12 UK sites involving 3 vendor systems and two field strengths. Four main protocols (1.5 T Siemens, 3 T Siemens, 1.5 T Philips and 3 T GE scanners) were generated. Scanner limitations (hardware and software) and scanning time constraint required protocol modifications for 4 sites. Nevertheless, shared methodology and imaging protocols enabled other centres to obtain images suitable for qualitative and quantitative analysis., Conclusions: Standardised WB-MRI protocols can be implemented and supported in prospective multi-centre clinical trials. Trial registration NCT03188172 clinicaltrials.gov; registration date 15th June 2017 https://clinicaltrials.gov/ct2/show/study/NCT03188172., (© 2022. The Author(s).)- Published
- 2022
- Full Text
- View/download PDF
44. Quantitative analysis of diffusion weighted imaging in rectal cancer during radiotherapy using a magnetic resonance imaging integrated linear accelerator.
- Author
-
Ingle M, Blackledge M, White I, Wetscherek A, Lalondrelle S, Hafeez S, and Bhide S
- Abstract
Background and Purpose: Magnetic resonance imaging integrated linear accelerator (MR-Linac) platforms enable acquisition of diffusion weighted imaging (DWI) during treatment providing potential information about treatment response. Obtaining DWI on these platforms is technically different from diagnostic magnetic resonance imaging (MRI) scanners. The aim of this project was to determine feasibility of obtaining DWI and calculating apparent diffusion coefficient (ADC) parameters longitudinally in rectal cancer patients on the MR-Linac., Materials and Methods: Nine patients undergoing treatment on MR-Linac had DWI acquired using b-values 0, 30, 150, 500 s/mm
2 . Gross tumour volume (GTV) and normal tissue was delineated on DWI throughout treatment and median ADC was calculated using an in-house tool (pyOsirix ®)., Results: Seven out of nine patients were included in the analysis; all demonstrated downstaging at follow-up. A total of 63 out of 70 DWI were analysed (7 excluded due to poor image quality). An increasing trend of ADC median for GTV (1.15 × 10-3 mm2 /s interquartile range (IQ): 1.05-1.17 vs 1.59 × 10-3 mm2 /s IQ: 1.37 - 1.64; p = 0.0156 ), correlating to treatment response. In comparison ADC median for normal tissue remained the same between first and last fraction (1.61 × 10-3 mm2 /s IQ: 1.56-1.71 vs 1.67 × 10-3 mm2 /s IQ: 1.37-2.00; p = 0.9375)., Conclusions: DWI assessment in rectal cancer patients on MR-Linac is feasible. Initial results provide foundations for further studies to determine DWI use for treatment adaptation in rectal cancer., Competing Interests: The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: SL reports travel and educational grants from Elekta (Elekta AB, Stockholm, Sweden). SH reports non-financial support from Elekta (Elekta AB, Stockholm, Sweden), non-financial support from Merck Sharp & Dohme (MSD), personal fees and non-financial support from Roche outside the submitted work. SB reports travel and educational grants from Elekta (Elekta AB, Stockholm, Sweden).., (© 2022 The Author(s).)- Published
- 2022
- Full Text
- View/download PDF
45. A thermodynamic switch modulates abscisic acid receptor sensitivity.
- Author
-
Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodriguez PL, and Márquez JA
- Published
- 2022
- Full Text
- View/download PDF
46. A comparison of machine learning methods for predicting recurrence and death after curative-intent radiotherapy for non-small cell lung cancer: Development and validation of multivariable clinical prediction models.
- Author
-
Hindocha S, Charlton TG, Linton-Reid K, Hunter B, Chan C, Ahmed M, Robinson EJ, Orton M, Ahmad S, McDonald F, Locke I, Power D, Blackledge M, Lee RW, and Aboagye EO
- Subjects
- Humans, Machine Learning, Models, Statistical, Neoplasm Staging, Prognosis, Retrospective Studies, Carcinoma, Non-Small-Cell Lung diagnosis, Carcinoma, Non-Small-Cell Lung drug therapy, Carcinoma, Non-Small-Cell Lung radiotherapy, Lung Neoplasms diagnosis, Lung Neoplasms drug therapy, Lung Neoplasms radiotherapy
- Abstract
Background: Surveillance is universally recommended for non-small cell lung cancer (NSCLC) patients treated with curative-intent radiotherapy. High-quality evidence to inform optimal surveillance strategies is lacking. Machine learning demonstrates promise in accurate outcome prediction for a variety of health conditions. The purpose of this study was to utilise readily available patient, tumour, and treatment data to develop, validate and externally test machine learning models for predicting recurrence, recurrence-free survival (RFS) and overall survival (OS) at 2 years from treatment., Methods: A retrospective, multicentre study of patients receiving curative-intent radiotherapy for NSCLC was undertaken. A total of 657 patients from 5 hospitals were eligible for inclusion. Data pre-processing derived 34 features for predictive modelling. Combinations of 8 feature reduction methods and 10 machine learning classification algorithms were compared, producing risk-stratification models for predicting recurrence, RFS and OS. Models were compared with 10-fold cross validation and an external test set and benchmarked against TNM-stage and performance status. Youden Index was derived from validation set ROC curves to distinguish high and low risk groups and Kaplan-Meier analyses performed., Findings: Median follow-up time was 852 days. Parameters were well matched across training-validation and external test sets: Mean age was 73 and 71 respectively, and recurrence, RFS and OS rates at 2 years were 43% vs 34%, 54% vs 47% and 54% vs 47% respectively. The respective validation and test set AUCs were as follows: 1) RFS: 0·682 (0·575-0·788) and 0·681 (0·597-0·766), 2) Recurrence: 0·687 (0·582-0·793) and 0·722 (0·635-0·81), and 3) OS: 0·759 (0·663-0·855) and 0·717 (0·634-0·8). Our models were superior to TNM stage and performance status in predicting recurrence and OS., Interpretation: This robust and ready to use machine learning method, validated and externally tested, sets the stage for future clinical trials entailing quantitative personalised risk-stratification and surveillance following curative-intent radiotherapy for NSCLC., Funding: A full list of funding bodies that contributed to this study can be found in the Acknowledgements section., Competing Interests: Declaration of interests Richard Lee receives funding from Cancer Research UK, Innovate UK (co-funded with Roche and Optellum), NIHR and RM Partners outside of this work. He is Joint Clinical Lead for the NHS England Lung Health Checks programme and a National Specialty Lead for the NIHR, and receives funding directly to his institution, outside of this work for these roles. He receives consulting fees from the Royal Marsden Private Care, and honoraria from Cancer Research UK as a member of the Early Diagnosis grants peer review panel, not related to this work., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
47. Visualizing protein breathing motions associated with aromatic ring flipping.
- Author
-
Mariño Pérez L, Ielasi FS, Bessa LM, Maurin D, Kragelj J, Blackledge M, Salvi N, Bouvignies G, Palencia A, and Jensen MR
- Subjects
- Crystallography, X-Ray, Motion, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, src Homology Domains, Proteins chemistry, Proteins genetics, Proteins metabolism, Tyrosine chemistry, Tyrosine metabolism
- Abstract
Aromatic residues cluster in the core of folded proteins, where they stabilize the structure through multiple interactions. Nuclear magnetic resonance (NMR) studies in the 1970s showed that aromatic side chains can undergo ring flips-that is, 180° rotations-despite their role in maintaining the protein fold
1-3 . It was suggested that large-scale 'breathing' motions of the surrounding protein environment would be necessary to accommodate these ring flipping events1 . However, the structural details of these motions have remained unclear. Here we uncover the structural rearrangements that accompany ring flipping of a buried tyrosine residue in an SH3 domain. Using NMR, we show that the tyrosine side chain flips to a low-populated, minor state and, through a proteome-wide sequence analysis, we design mutants that stabilize this state, which allows us to capture its high-resolution structure by X-ray crystallography. A void volume is generated around the tyrosine ring during the structural transition between the major and minor state, and this allows fast flipping to take place. Our results provide structural insights into the protein breathing motions that are associated with ring flipping. More generally, our study has implications for protein design and structure prediction by showing how the local protein environment influences amino acid side chain conformations and vice versa., (© 2022. The Author(s).)- Published
- 2022
- Full Text
- View/download PDF
48. The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a.
- Author
-
Bessa LM, Guseva S, Camacho-Zarco AR, Salvi N, Maurin D, Perez LM, Botova M, Malki A, Nanao M, Jensen MR, Ruigrok RWH, and Blackledge M
- Abstract
The processes of genome replication and transcription of SARS-CoV-2 represent important targets for viral inhibition. Betacoronaviral nucleoprotein (N) is a highly dynamic cofactor of the replication-transcription complex (RTC), whose function depends on an essential interaction with the amino-terminal ubiquitin-like domain of nsp3 (Ubl1). Here, we describe this complex (dissociation constant - 30 to 200 nM) at atomic resolution. The interaction implicates two linear motifs in the intrinsically disordered linker domain (N3), a hydrophobic helix (
219 LALLLLDRLNQL230 ) and a disordered polar strand (243 GQTVTKKSAAEAS255 ), that mutually engage to form a bipartite interaction, folding N3 around Ubl1. This results in substantial collapse in the dimensions of dimeric N, forming a highly compact molecular chaperone, that regulates binding to RNA, suggesting a key role of nsp3 in the association of N to the RTC. The identification of distinct linear motifs that mediate an important interaction between essential viral factors provides future targets for development of innovative strategies against COVID-19.- Published
- 2022
- Full Text
- View/download PDF
49. Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins.
- Author
-
Naudi-Fabra S, Blackledge M, and Milles S
- Subjects
- Fluorescence Resonance Energy Transfer methods, Nuclear Magnetic Resonance, Biomolecular, Protein Conformation, Intrinsically Disordered Proteins chemistry
- Abstract
Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on how these two techniques were employed synergistically for multidomain proteins harboring intrinsically disordered linkers, for veritable IDPs, but also for liquid-liquid phase separated systems. Additionally, we provide insights into the first approaches to use single molecule Förster resonance energy transfer (FRET) and NMR for the description of multiconformational models of IDPs.
- Published
- 2021
- Full Text
- View/download PDF
50. Sendai Virus and a Unified Model of Mononegavirus RNA Synthesis.
- Author
-
Kolakofsky D, Le Mercier P, Nishio M, Blackledge M, Crépin T, and Ruigrok RWH
- Subjects
- Animals, Genome, Viral, Humans, Mononegavirales metabolism, RNA, Viral metabolism, Respirovirus Infections virology, Sendai virus metabolism, Mononegavirales genetics, Mononegavirales Infections virology, RNA, Viral genetics, Sendai virus genetics
- Abstract
Vesicular stomatitis virus (VSV), the founding member of the mononegavirus order ( Mononegavirales ), was found to be a negative strand RNA virus in the 1960s, and since then the number of such viruses has continually increased with no end in sight. Sendai virus (SeV) was noted soon afterwards due to an outbreak of newborn pneumonitis in Japan whose putative agent was passed in mice, and nowadays this mouse virus is mainly the bane of animal houses and immunologists. However, SeV was important in the study of this class of viruses because, like flu, it grows to high titers in embryonated chicken eggs, facilitating the biochemical characterization of its infection and that of its nucleocapsid, which is very close to that of measles virus (MeV). This review and opinion piece follow SeV as more is known about how various mononegaviruses express their genetic information and carry out their RNA synthesis, and proposes a unified model based on what all MNV have in common.
- Published
- 2021
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.