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2. A round‐robin approach provides a detailed assessment of biomolecular small‐angle scattering data reproducibility and yields consensus curves for benchmarking

Author

Trewhella, Jill, Vachette, Patrice, Bierma, Jan, Blanchet, Clement, Brookes, Emre, Chakravarthy, Srinivas, Chatzimagas, Leonie, Cleveland, Thomas E, Cowieson, Nathan, Crossett, Ben, Duff, Anthony P, Franke, Daniel, Gabel, Frank, Gillilan, Richard E, Graewert, Melissa, Grishaev, Alexander, Guss, J Mitchell, Hammel, Michal, Hopkins, Jesse, Huang, Qingqui, Hub, Jochen S, Hura, Greg L, Irving, Thomas C, Jeffries, Cy Michael, Jeong, Cheol, Kirby, Nigel, Krueger, Susan, Martel, Anne, Matsui, Tsutomu, Li, Na, Pérez, Javier, Porcar, Lionel, Prangé, Thierry, Rajkovic, Ivan, Rocco, Mattia, Rosenberg, Daniel J, Ryan, Timothy M, Seifert, Soenke, Sekiguchi, Hiroshi, Svergun, Dmitri, Teixeira, Susana, Thureau, Aurelien, Weiss, Thomas M, Whitten, Andrew E, Wood, Kathleen, and Zuo, Xiaobing

Subjects
Biochemistry and Cell Biology, Physical Sciences, Biological Sciences, Bioengineering, Scattering, Small Angle, X-Ray Diffraction, Benchmarking, Consensus, Reproducibility of Results, Proteins, Solvents, X-ray scattering, benchmarking standards, biomolecular small-angle scattering, neutron scattering, scattering-profile calculation, standards, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences, Physical sciences
Abstract

Through an expansive international effort that involved data collection on 12 small-angle X-ray scattering (SAXS) and four small-angle neutron scattering (SANS) instruments, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were acquired. From these data, the solvent-subtracted protein scattering profiles were shown to be reproducible, with the caveat that an additive constant adjustment was required to account for small errors in solvent subtraction. Further, the major features of the obtained consensus SAXS data over the q measurement range 0-1 Å-1 are consistent with theoretical prediction. The inherently lower statistical precision for SANS limited the reliably measured q-range to 2.2 Å-1 showed good mutual agreement, affirming that this region has interpretable features for structural modelling. SAS measurements with inline size-exclusion chromatography (SEC) proved to be generally superior for eliminating sample heterogeneity, but with unavoidable sample dilution during column elution, while batch SAS data collected at higher concentrations and for longer times provided superior statistical precision. Careful merging of data measured using inline SEC and batch modes, or low- and high-concentration data from batch measurements, was successful in eliminating small amounts of aggregate or interparticle interference from the scattering while providing improved statistical precision overall for the benchmarking data set.

Published
2022

3. Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS)

Author

Blanchet, Clement E., Round, Adam, Mertens, Haydyn D. T., Ayyer, Kartik, Graewert, Melissa, Awel, Salah, Franke, Daniel, Dörner, Katerina, Bajt, Saša, Bean, Richard, Custódio, Tânia F., de Wijn, Raphael, Juncheng, E., Henkel, Alessandra, Gruzinov, Andrey, Jeffries, Cy M., Kim, Yoonhee, Kirkwood, Henry, Kloos, Marco, Knoška, Juraj, Koliyadu, Jayanath, Letrun, Romain, Löw, Christian, Makroczyova, Jana, Mall, Abhishek, Meijers, Rob, Pena Murillo, Gisel Esperanza, Oberthür, Dominik, Round, Ekaterina, Seuring, Carolin, Sikorski, Marcin, Vagovic, Patrik, Valerio, Joana, Wollweber, Tamme, Zhuang, Yulong, Schulz, Joachim, Haas, Heinrich, Chapman, Henry N., Mancuso, Adrian P., and Svergun, Dmitri

Published
2023
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7. Structural and biochemical characterization of the C‐terminal region of the human RTEL1 helicase.

Author

Cortone, Giuseppe, Graewert, Melissa A., Kanade, Manil, Longo, Antonio, Hegde, Raghurama, González‐Magaña, Amaia, Chaves‐Arquero, Belén, Blanco, Francisco J., Napolitano, Luisa M. R., and Onesti, Silvia

Abstract

RTEL1 is an essential DNA helicase which plays an important role in various aspects of genome stability, from telomere metabolism to DNA replication, repair and recombination. RTEL1 has been implicated in a number of genetic diseases and cancer development, including glioma, breast, lung and gastrointestinal tumors. RTEL1 is a FeS helicase but, in addition to the helicase core, it comprises a long C‐terminal region which includes a number of folded domains connected by intrinsically disordered loops and mediates RTEL1 interaction with factors involved in pivotal cellular pathways. However, information on the architecture and the function of this region is still limited. We expressed and purified a variety of fragments encompassing the folded domains and the unstructured regions. We determined the crystal structure of the second repeat, confirming that it has a fold similar to the harmonin homology domains. SAXS data provide low‐resolution information on all the fragments and suggest that the presence of the RING domain affects the overall architecture of the C‐terminal region, making the structure significantly more compact. NMR data provide experimental information on the interaction between PCNA and the RTEL1 C‐terminal region, revealing a putative low‐affinity additional site of interaction. A biochemical analysis shows that the C‐terminal region, in addition to a preference for telomeric RNA and DNA G‐quadruplexes, has a high affinity for R‐loops and D‐loops, consistent with the role played by the RTEL1 helicase in homologous recombination, telomere maintenance and preventing replication‐transcription conflicts. We further dissected the contribution of each domain in binding different substrates. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Sample and Buffer Preparation for SAXS

Author

Graewert, Melissa A., Jeffries, Cy M., COHEN, IRUN R., Series editor, LAJTHA, ABEL, Series editor, LAMBRIS, JOHN D., Series editor, PAOLETTI, RODOLFO, Series editor, REZAEI, NIMA, Series editor, Chaudhuri, Barnali, editor, Muñoz, Inés G., editor, Qian, Shuo, editor, and Urban, Volker S., editor

Published
2017
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12. Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Author

Custódio, Tânia F., Das, Hrishikesh, Sheward, Daniel J., Hanke, Leo, Pazicky, Samuel, Pieprzyk, Joanna, Sorgenfrei, Michèle, Schroer, Martin A., Gruzinov, Andrey Yu., Jeffries, Cy M., Graewert, Melissa A., Svergun, Dmitri I., Dobrev, Nikolay, Remans, Kim, Seeger, Markus A., McInerney, Gerald M., Murrell, Ben, Hällberg, B. Martin, and Löw, Christian

Published
2020
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13. Quantitative size-resolved characterization of mRNA nanoparticles by in-line coupling of asymmetrical-flow field-flow fractionation with small angle X-ray scattering

Author

Haas, Heinrich, primary, Graewert, Melissa, additional, Wilhelmy, Christoph, additional, Bacic, Tijana, additional, Schumacher, Jens, additional, Blanchet, Clement, additional, Meier, Florian, additional, Drexel, Roland, additional, Welz, Roland, additional, Kolb, Bastian, additional, Bartels, Kim, additional, Nawroth, Thomas, additional, Klein, Thorsten, additional, Svergun, Dmitri, additional, and Langguth, Peter, additional

Published
2023
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15. Structural and functional analysis of a plant nucleolar RNA chaperone-like protein.

Author

Fernandes, Rita, Ostendorp, Anna, Ostendorp, Steffen, Mehrmann, Judith, Falke, Sven, Graewert, Melissa Ann, Weingartner, Magdalena, Kehr, Julia, and Hoth, Stefan

Subjects
PLANT RNA, ORGANELLE formation, FUNCTIONAL analysis, CELL nuclei, NUCLEOLUS, RIBOSOMES, NUCLEOPHOSMIN
Abstract

Ribosome biogenesis is a key process in all eukaryotic cells that requires hundreds of ribosome biogenesis factors (RBFs), which are essential to build the mature ribosomes consisting of proteins and rRNAs. The processing of the required rRNAs has been studied extensively in yeast and mammals, but in plants much is still unknown. In this study, we focused on a RBF from A. thaliana that we named NUCLEOLAR RNA CHAPERONE-LIKE 1 (NURC1). NURC1 was localized in the nucleolus of plant cell nuclei, and other plant RBF candidates shared the same localization. SEC-SAXS experiments revealed that NURC1 has an elongated and flexible structure. In addition, SEC-MALLS experiments confirmed that NURC1 was present in its monomeric form with a molecular weight of around 28 kDa. RNA binding was assessed by performing microscale thermophoresis with the Arabidopsis internal transcribed spacer 2 (ITS2) of the polycistronic pre-rRNA precursor, which contains the 5.8S, 18S, and 25S rRNA. NURC1 showed binding activity to the ITS2 with a dissociation constant of 228 nM and exhibited RNA chaperone-like activity. Our data suggested that NURC1 may have a function in pre-rRNA processing and thus ribosome biogenesis. [ABSTRACT FROM AUTHOR]

Published
2023
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16. Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF

Author

Corbeski, Ivan, Guo, Xiaohu, Eckhardt, Bruna V, Fasci, Domenico, Wiegant, Wouter, Graewert, Melissa A, Vreeken, Kees, Wienk, Hans, Svergun, Dmitri I, Heck, Albert J R, van Attikum, Haico, Boelens, Rolf, Sixma, Titia K, Mattiroli, Francesca, van Ingen, Hugo, Sub NMR Spectroscopy, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, NMR Spectroscopy, Biomolecular Mass Spectrometry and Proteomics, Hubrecht Institute for Developmental Biology and Stem Cell Research, Sub NMR Spectroscopy, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, NMR Spectroscopy, and Biomolecular Mass Spectrometry and Proteomics

Subjects
Histones, Histone Chaperones/genetics, Multidisciplinary, DNA Repair, Histones/metabolism, Histone Chaperones, ddc:500, DNA, Molecular Chaperones/genetics, DNA/chemistry, Molecular Chaperones, Nucleosomes
Abstract

Science advances 8(30), eabo0517 (2022). doi:10.1126/sciadv.abo0517, Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLF$^{AD}$) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLF$^{AD}$-histone octamer complex shows that APLF$^{AD}$ tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLF$^{AD}$ affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted., Published by Assoc., Washington, DC [u.a.]

Published
2022

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

Author

Sub NMR Spectroscopy, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, NMR Spectroscopy, Biomolecular Mass Spectrometry and Proteomics, Corbeski, Ivan, Guo, Xiaohu, Eckhardt, Bruna V, Fasci, Domenico, Wiegant, Wouter, Graewert, Melissa A, Vreeken, Kees, Wienk, Hans, Svergun, Dmitri I, Heck, Albert J R, van Attikum, Haico, Boelens, Rolf, Sixma, Titia K, Mattiroli, Francesca, van Ingen, Hugo, Sub NMR Spectroscopy, Sub Biomol.Mass Spectrometry & Proteom., Afd Biomol.Mass Spect. and Proteomics, NMR Spectroscopy, Biomolecular Mass Spectrometry and Proteomics, Corbeski, Ivan, Guo, Xiaohu, Eckhardt, Bruna V, Fasci, Domenico, Wiegant, Wouter, Graewert, Melissa A, Vreeken, Kees, Wienk, Hans, Svergun, Dmitri I, Heck, Albert J R, van Attikum, Haico, Boelens, Rolf, Sixma, Titia K, Mattiroli, Francesca, and van Ingen, Hugo

Published
2022

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

Author

Hubrecht Institute with UMC, Corbeski, Ivan, Guo, Xiaohu, Eckhardt, Bruna V., Fasci, Domenico, Wiegant, Wouter, Graewert, Melissa A., Vreeken, Kees, Wienk, Hans, Svergun, Dmitri I., Heck, Albert J.R., van Attikum, Haico, Boelens, Rolf, Sixma, Titia K., Mattiroli, Francesca, van Ingen, Hugo, Hubrecht Institute with UMC, Corbeski, Ivan, Guo, Xiaohu, Eckhardt, Bruna V., Fasci, Domenico, Wiegant, Wouter, Graewert, Melissa A., Vreeken, Kees, Wienk, Hans, Svergun, Dmitri I., Heck, Albert J.R., van Attikum, Haico, Boelens, Rolf, Sixma, Titia K., Mattiroli, Francesca, and van Ingen, Hugo

Published
2022

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

Author

Corbeski, Ivan, primary, Guo, Xiaohu, additional, Eckhardt, Bruna V., additional, Fasci, Domenico, additional, Wiegant, Wouter, additional, Graewert, Melissa A., additional, Vreeken, Kees, additional, Wienk, Hans, additional, Svergun, Dmitri I., additional, Heck, Albert J.R., additional, van Attikum, Haico, additional, Boelens, Rolf, additional, Sixma, Titia K., additional, Mattiroli, Francesca, additional, and van Ingen, Hugo, additional

Published
2021
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21. The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding

Author

Bernardini, Andrea, primary, Lorenzo, Mariangela, additional, Chaves-Sanjuan, Antonio, additional, Swuec, Paolo, additional, Pigni, Matteo, additional, Saad, Dana, additional, Konarev, Petr V., additional, Graewert, Melissa Ann, additional, Valentini, Erica, additional, Svergun, Dmitri I., additional, Nardini, Marco, additional, Mantovani, Roberto, additional, and Gnesutta, Nerina, additional

Published
2021
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24. The allosteric modulation of complement C5 by knob domain peptides

Author

Macpherson, Alex, Laabei, Maisem, Ahdash, Zainab, Graewert, Melissa A., Birtley, James R., Schulze, Monika-Sarah E. D., Crennell, Susan, Robinson, Sarah A., Holmes, Ben, Oleinikovas, Vladas, Nilsson, Per H., Snowden, James, Ellis, Victoria, Mollnes, Tom Eirik, Deane, Charlotte M., Svergun, Dmitri, Lawson, Alastair D. G., van den Elsen, Jean M. H., Macpherson, Alex, Laabei, Maisem, Ahdash, Zainab, Graewert, Melissa A., Birtley, James R., Schulze, Monika-Sarah E. D., Crennell, Susan, Robinson, Sarah A., Holmes, Ben, Oleinikovas, Vladas, Nilsson, Per H., Snowden, James, Ellis, Victoria, Mollnes, Tom Eirik, Deane, Charlotte M., Svergun, Dmitri, Lawson, Alastair D. G., and van den Elsen, Jean M. H.

Abstract

Bovines have evolved a subset of antibodies with ultra-long heavy chain complementarity determining regions that harbour cysteine-rich knob domains. To produce high-affinity peptides, we previously isolated autonomous 3-6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 angstrom from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors, and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential.

Published
2021
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25. Molecular basis of F-actin regulation and sarcomere assembly via myotilin

Author

Kostan, Julius, primary, Pavšič, Miha, additional, Puž, Vid, additional, Schwarz, Thomas C., additional, Drepper, Friedel, additional, Molt, Sibylle, additional, Graewert, Melissa Ann, additional, Schreiner, Claudia, additional, Sajko, Sara, additional, van der Ven, Peter F. M., additional, Onipe, Adekunle, additional, Svergun, Dmitri I., additional, Warscheid, Bettina, additional, Konrat, Robert, additional, Fürst, Dieter O., additional, Lenarčič, Brigita, additional, and Djinović-Carugo, Kristina, additional

Published
2021
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26. The allosteric modulation of complement C5 by knob domain peptides

Author

Macpherson, Alex, primary, Laabei, Maisem, additional, Ahdash, Zainab, additional, Graewert, Melissa A, additional, Birtley, James R, additional, Schulze, Monika-Sarah ED, additional, Crennell, Susan, additional, Robinson, Sarah A, additional, Holmes, Ben, additional, Oleinikovas, Vladas, additional, Nilsson, Per H, additional, Snowden, James, additional, Ellis, Victoria, additional, Mollnes, Tom Eirik, additional, Deane, Charlotte M, additional, Svergun, Dmitri, additional, Lawson, Alastair DG, additional, and van den Elsen, Jean MH, additional

Published
2021
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27. Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Author

Custódio, Tânia F, Das, Hrishikesh; https://orcid.org/0000-0001-7495-7065, Sheward, Daniel J, Hanke, Leo; https://orcid.org/0000-0001-5514-2418, Pazicky, Samuel; https://orcid.org/0000-0002-4674-9784, Pieprzyk, Joanna, Sorgenfrei, Michèle, Schroer, Martin A; https://orcid.org/0000-0002-0747-3965, Gruzinov, Andrey Yu, Jeffries, Cy M, Graewert, Melissa A; https://orcid.org/0000-0001-7547-636X, Svergun, Dmitri I, Dobrev, Nikolay, Remans, Kim, Seeger, Markus A; https://orcid.org/0000-0003-1761-8571, McInerney, Gerald M; https://orcid.org/0000-0003-2257-7241, Murrell, Ben; https://orcid.org/0000-0002-0393-4445, Hällberg, B Martin; https://orcid.org/0000-0002-6781-0345, Löw, Christian; https://orcid.org/0000-0003-0764-7483, Custódio, Tânia F, Das, Hrishikesh; https://orcid.org/0000-0001-7495-7065, Sheward, Daniel J, Hanke, Leo; https://orcid.org/0000-0001-5514-2418, Pazicky, Samuel; https://orcid.org/0000-0002-4674-9784, Pieprzyk, Joanna, Sorgenfrei, Michèle, Schroer, Martin A; https://orcid.org/0000-0002-0747-3965, Gruzinov, Andrey Yu, Jeffries, Cy M, Graewert, Melissa A; https://orcid.org/0000-0001-7547-636X, Svergun, Dmitri I, Dobrev, Nikolay, Remans, Kim, Seeger, Markus A; https://orcid.org/0000-0003-1761-8571, McInerney, Gerald M; https://orcid.org/0000-0003-2257-7241, Murrell, Ben; https://orcid.org/0000-0002-0393-4445, Hällberg, B Martin; https://orcid.org/0000-0002-6781-0345, and Löw, Christian; https://orcid.org/0000-0003-0764-7483

Abstract

The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC$_{50}$ of 0.6 µg/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed an unusual conformation of the spike where two RBDs are in the 'up' ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.

Published
2020

28. Author response: The allosteric modulation of complement C5 by knob domain peptides

Author

Macpherson, Alex, primary, Laabei, Maisem, additional, Ahdash, Zainab, additional, Graewert, Melissa A, additional, Birtley, James R, additional, Schulze, Monika-Sarah ED, additional, Crennell, Susan, additional, Robinson, Sarah A, additional, Holmes, Ben, additional, Oleinikovas, Vladas, additional, Nilsson, Per H, additional, Snowden, James, additional, Ellis, Victoria, additional, Mollnes, Tom Eirik, additional, Deane, Charlotte M, additional, Svergun, Dmitri, additional, Lawson, Alastair DG, additional, and van den Elsen, Jean MH, additional

Published
2020
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29. Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats

Author

Sajko, Sara, primary, Grishkovskaya, Irina, additional, Kostan, Julius, additional, Graewert, Melissa, additional, Setiawan, Kim, additional, Trübestein, Linda, additional, Niedermüller, Korbinian, additional, Gehin, Charlotte, additional, Sponga, Antonio, additional, Puchinger, Martin, additional, Gavin, Anne-Claude, additional, Leonard, Thomas A., additional, Svergun, Dimitri I., additional, Smith, Terry K., additional, Morriswood, Brooke, additional, and Djinovic-Carugo, Kristina, additional

Published
2020
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31. The allosteric modulation of Complement C5 by knob domain peptides

Author

Macpherson, Alex, primary, Laabei, Maisem, additional, Ahdash, Zainab, additional, Graewert, Melissa, additional, Birtley, James R., additional, Schulze, Sarah, additional, Crennell, Susan, additional, Robinson, Sarah A., additional, Holmes, Ben, additional, Oleinikovas, Vladas, additional, Nilsson, Per H., additional, Snowden, James, additional, Ellis, Victoria, additional, Mollnes, Tom Eirik, additional, Deane, Charlotte M., additional, Svergun, Dmitri, additional, Lawson, Alastair D.G., additional, and van den Elsen, Jean, additional

Published
2020
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32. Molecular basis of F-actin regulation and sarcomere assembly via myotilin

Author

Kostan, Julius, primary, Pavšič, Miha, additional, Puž, Vid, additional, Schwarz, Thomas C., additional, Drepper, Friedel, additional, Molt, Sibylle, additional, Graewert, Melissa Ann, additional, Schreiner, Claudia, additional, Sajko, Sara, additional, van der Ven, Peter F.M., additional, Svergun, Dmitri I., additional, Warscheid, Bettina, additional, Konrat, Robert, additional, Fürst, Dieter O., additional, Lenarčič, Brigita, additional, and Djinović-Carugo, Kristina, additional

Published
2020
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35. Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2

Author

Custódio, Tânia F., primary, Das, Hrishikesh, additional, Sheward, Daniel J, additional, Hanke, Leo, additional, Pazicky, Samuel, additional, Pieprzyk, Joanna, additional, Sorgenfrei, Michèle, additional, Schroer, Martin, additional, Gruzinov, Andrey, additional, Jeffries, Cy, additional, Graewert, Melissa, additional, Svergun, Dmitri, additional, Dobrev, Nikolay, additional, Remans, Kim, additional, Seeger, Markus A., additional, McInerney, Gerald M, additional, Murrell, Ben, additional, Hällberg, B. Martin, additional, and Löw, Christian, additional

Published
2020
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36. Author Reply to Peer Reviews of Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats

Author

Djinovic-Carugo, Kristina, primary, Morriswood, Brooke, additional, Smith, Terry K., additional, Svergun, Dimitri, additional, Leonard, Thomas, additional, Gavin, Anne-Claude, additional, Puchinger, Martin, additional, Sponga, Antonio, additional, Gehin, Charlotte, additional, Niedermüller, Korbinian, additional, Trübestein, Linda, additional, Setiawan, Kim, additional, Graewert, Melissa, additional, Kostan, Julius, additional, Grishkovskaya, Irina, additional, and Sajko, Sara, additional

Published
2020
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38. EFAMIX, a tool to decompose inline chromatography SAXS data from partially overlapping components.

Author

Konarev, Petr V., Graewert, Melissa A., Jeffries, Cy M., Fukuda, Masakazu, Cheremnykh, Taisiia A., Volkov, Vladimir V., and Svergun, Dmitri I.

Abstract

Small‐angle X‐ray scattering (SAXS) is an established technique for structural analysis of biological macromolecules in solution. During the last decade, inline chromatography setups coupling SAXS with size exclusion (SEC‐SAXS) or ion exchange (IEC‐SAXS) have become popular in the community. These setups allow one to separate individual components in the sample and to record SAXS data from isolated fractions, which is extremely important for subsequent data interpretation, analysis, and structural modeling. However, in case of partially overlapping elution peaks, inline chromatography SAXS may still yield scattering profiles from mixtures of components. The deconvolution of these scattering data into the individual fractions is nontrivial and potentially ambiguous. We describe a cross‐platform computer program, EFAMIX, for restoring the scattering and concentration profiles of the components based on the evolving factor analysis (EFA). The efficiency of the program is demonstrated in a number of simulated and experimental SEC‐SAXS data sets. Sensitivity and limitations of the method are explored, and its applicability to IEC‐SAXS data is discussed. EFAMIX requires minimal user intervention and is available to academic users through the program package ATSAS as from release 3.1. [ABSTRACT FROM AUTHOR]

Published
2022
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39. Structures of three MORN repeat proteins and a re-evaluation of the proposed lipid-binding properties of MORN repeats

Author

Sajko, Sara, primary, Grishkovskaya, Irina, additional, Kostan, Julius, additional, Graewert, Melissa, additional, Setiawan, Kim, additional, Trübestein, Linda, additional, Niedermüller, Korbinian, additional, Gehin, Charlotte, additional, Sponga, Antonio, additional, Puchinger, Martin, additional, Gavin, Anne-Claude, additional, Leonard, Thomas, additional, Svergun, Dimitri, additional, Smith, Terry K., additional, Morriswood, Brooke, additional, and Djinovic-Carugo, Kristina, additional

Published
2019
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43. Status of the EMBL BioSAXS beamline P12 at PETRA III

Author

Blanchet, Clement Emmanuel, primary, Schroer, Martin A., additional, Gruzinov, Andrey Yu., additional, Spilotros, Alessandro, additional, Graewert, Melissa A., additional, Franke, Daniel, additional, Hajizadeh, Nelly R., additional, Jeffries, Cy M., additional, Fiedler, Stefan, additional, and Svergun, Dmitri I., additional

Published
2017
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49. Characterization of mAb dimers reveals predominant dimer forms common in therapeutic mAbs

Author

Plath, Friederike, primary, Ringler, Philippe, additional, Graff-Meyer, Alexandra, additional, Stahlberg, Henning, additional, Lauer, Matthias E., additional, Rufer, Arne C., additional, Graewert, Melissa A., additional, Svergun, Dmitri, additional, Gellermann, Gerald, additional, Finkler, Christof, additional, Stracke, Jan O., additional, Koulov, Atanas, additional, and Schnaible, Volker, additional

Published
2016
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50. Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research

Author

Sousa, Bruno L., primary, Silva-Filho, José C., additional, Kumar, Prashant, additional, Graewert, Melissa A., additional, Pereira, Ronniery I., additional, Cunha, Rodrigo M.S., additional, Nascimento, Kyria S., additional, Bezerra, Gustavo A., additional, Delatorre, Plínio, additional, Djinovic-Carugo, Kristina, additional, Nagano, Celso S., additional, Gruber, Karl, additional, and Cavada, Benildo S., additional

Published
2016
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