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Vandermarliere E, Maddelein D, Hulstaert N, Stes E, Di Michele M, Gevaert K, Jacoby E, Brehmer D, Martens L. PepShell: Visualization of Conformational Proteomics Data. J Proteome Res 2015; 14:1987-90. [DOI: 10.1021/pr5012125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Elien Vandermarliere
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Davy Maddelein
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Niels Hulstaert
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Elisabeth Stes
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Michela Di Michele
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Kris Gevaert
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Edgar Jacoby
- Oncology
Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Dirk Brehmer
- Oncology
Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Lennart Martens
- Department
of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Department
of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
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Hennig J, Wang I, Sonntag M, Gabel F, Sattler M. Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex. JOURNAL OF BIOMOLECULAR NMR 2013; 56:17-30. [PMID: 23456097 DOI: 10.1007/s10858-013-9719-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 02/19/2013] [Indexed: 05/12/2023]
Abstract
Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic acid interactions are typically connected by flexible linkers, which contribute to conformational dynamics and enable the formation of complexes with distinct binding partners. Solution techniques are therefore required for structural analysis and to characterize potential conformational dynamics. Nuclear magnetic resonance spectroscopy (NMR) provides such information but often only sparse data are obtained with increasing molecular weight of the complexes. It is therefore beneficial to combine NMR data with additional structural restraints from complementary solution techniques. Small angle X-ray/neutron scattering (SAXS/SANS) data can be efficiently combined with NMR-derived information, either for validation or by providing additional restraints for structural analysis. Here, we show that the combination of SAXS and SANS data can help to refine structural models obtained from data-driven docking using HADDOCK based on sparse NMR data. The approach is demonstrated with the ternary protein-protein-RNA complex involving two RNA recognition motif (RRM) domains of Sex-lethal, the N-terminal cold shock domain of Upstream-to-N-Ras, and msl-2 mRNA. Based on chemical shift perturbations we have mapped protein-protein and protein-RNA interfaces and complemented this NMR-derived information with SAXS data, as well as SANS measurements on subunit-selectively deuterated samples of the ternary complex. Our results show that, while the use of SAXS data is beneficial, the additional combination with contrast variation in SANS data resolves remaining ambiguities and improves the docking based on chemical shift perturbations of the ternary protein-RNA complex.
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Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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Hennig J, de Vries SJ, Hennig KD, Randles L, Walters KJ, Sunnerhagen M, Bonvin AMJJ. MTMDAT-HADDOCK: high-throughput, protein complex structure modeling based on limited proteolysis and mass spectrometry. BMC STRUCTURAL BIOLOGY 2012; 12:29. [PMID: 23153250 PMCID: PMC3557227 DOI: 10.1186/1472-6807-12-29] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/06/2012] [Indexed: 01/27/2023]
Abstract
BACKGROUND MTMDAT is a program designed to facilitate analysis of mass spectrometry data of proteins and biomolecular complexes that are probed structurally by limited proteolysis. This approach can provide information about stable fragments of multidomain proteins, yield tertiary and quaternary structure data, and help determine the origin of stability changes at the amino acid residue level. Here, we introduce a pipeline between MTMDAT and HADDOCK, that facilitates protein-protein complex structure probing in a high-throughput and highly automated fashion. RESULTS A new feature of MTMDAT allows for the direct identification of residues that are involved in complex formation by comparing the mass spectra of bound and unbound proteins after proteolysis. If 3D structures of the unbound components are available, this data can be used to define restraints for data-driven docking to calculate a model of the complex. We describe here a new implementation of MTMDAT, which includes a pipeline to the data-driven docking program HADDOCK, thus streamlining the entire procedure. This addition, together with usability improvements in MTMDAT, enables high-throughput modeling of protein complexes from mass spectrometry data. The algorithm has been validated by using the protein-protein interaction between the ubiquitin-binding domain of proteasome component Rpn13 and ubiquitin. The resulting structural model, based on restraints extracted by MTMDAT from limited proteolysis and modeled by HADDOCK, was compared to the published NMR structure, which relied on twelve unambiguous intermolecular NOE interactions. The MTMDAT-HADDOCK structure was of similar quality to structures generated using only chemical shift perturbation data derived by NMR titration experiments. CONCLUSIONS The new MTMDAT-HADDOCK pipeline enables direct high-throughput modeling of protein complexes from mass spectrometry data. MTMDAT-HADDOCK can be downloaded from http://www.ifm.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat/together with the manual and example files. The program is free for academic/non-commercial purposes.
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Affiliation(s)
- Janosch Hennig
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden.
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Wennerstrand P, Dametto P, Hennig J, Klingstedt T, Skoglund K, Lindqvist Appell M, Mårtensson LG. Structural Characteristics Determine the Cause of the Low Enzyme Activity of Two Thiopurine S-Methyltransferase Allelic Variants: A Biophysical Characterization of TPMT*2 and TPMT*5. Biochemistry 2012; 51:5912-20. [DOI: 10.1021/bi300377d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Patricia Wennerstrand
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Paolo Dametto
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Janosch Hennig
- Division of Molecular Biotechnology, Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Therése Klingstedt
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Karin Skoglund
- Division of Drug Research/Clinical Pharmacology, Department of Medical
and Health Sciences, Faculty of Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Malin Lindqvist Appell
- Division of Drug Research/Clinical Pharmacology, Department of Medical
and Health Sciences, Faculty of Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Lars-Göran Mårtensson
- Department of Physics, Chemistry,
and Biology, Linköping University, SE-581 83 Linköping, Sweden
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Espinosa A, Hennig J, Ambrosi A, Anandapadmanaban M, Abelius MS, Sheng Y, Nyberg F, Arrowsmith CH, Sunnerhagen M, Wahren-Herlenius M. Anti-Ro52 autoantibodies from patients with Sjögren's syndrome inhibit the Ro52 E3 ligase activity by blocking the E3/E2 interface. J Biol Chem 2011; 286:36478-91. [PMID: 21862588 DOI: 10.1074/jbc.m111.241786] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Ro52 (TRIM21) is an E3 ligase of the tripartite motif family that negatively regulates proinflammatory cytokine production by ubiquitinating transcription factors of the interferon regulatory factor family. Autoantibodies to Ro52 are present in patients with lupus and Sjögren's syndrome, but it is not known if these autoantibodies affect the function of Ro52. To address this question, the requirements for Ro52 E3 ligase activity were first analyzed in detail. Scanning a panel of E2 ubiquitin-conjugating enzymes, we found that UBE2D1-4 and UBE2E1-2 supported the E3 ligase activity of Ro52 and that the E3 ligase activity of Ro52 was dependent on its RING domain. We also found that the N-terminal extensions in the class III E2 enzymes affected their interaction with Ro52. Although the N-terminal extension in UBE2E3 made this E2 enzyme unable to function together with Ro52, the N-terminal extensions in UBE2E1 and UBE2E2 allowed for a functional interaction with Ro52. Anti-Ro52-positive patient sera and affinity-purified anti-RING domain autoantibodies inhibited the E3 activity of Ro52 in ubiquitination assays. Using NMR, limited proteolysis, ELISA, and Ro52 mutants, we mapped the interactions between Ro52, UBE2E1, and anti-Ro52 autoantibodies. We found that anti-Ro52 autoantibodies inhibited the E3 ligase activity of Ro52 by sterically blocking the E2/E3 interaction between Ro52 and UBE2E1. Our data suggest that anti-Ro52 autoantibodies binding the RING domain of Ro52 may be actively involved in the pathogenesis of rheumatic autoimmune disease by inhibiting Ro52-mediated ubiquitination.
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Affiliation(s)
- Alexander Espinosa
- Rheumatology Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
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de Vries SJ, van Dijk M, Bonvin AMJJ. The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 2010; 5:883-97. [DOI: 10.1038/nprot.2010.32] [Citation(s) in RCA: 977] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Karaca E, Melquiond ASJ, de Vries SJ, Kastritis PL, Bonvin AMJJ. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Mol Cell Proteomics 2010; 9:1784-94. [PMID: 20305088 PMCID: PMC2938057 DOI: 10.1074/mcp.m000051-mcp201] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Over the last years, large scale proteomics studies have generated a wealth of information of biomolecular complexes. Adding the structural dimension to the resulting interactomes represents a major challenge that classical structural experimental methods alone will have difficulties to confront. To meet this challenge, complementary modeling techniques such as docking are thus needed. Among the current docking methods, HADDOCK (High Ambiguity-Driven DOCKing) distinguishes itself from others by the use of experimental and/or bioinformatics data to drive the modeling process and has shown a strong performance in the critical assessment of prediction of interactions (CAPRI), a blind experiment for the prediction of interactions. Although most docking programs are limited to binary complexes, HADDOCK can deal with multiple molecules (up to six), a capability that will be required to build large macromolecular assemblies. We present here a novel web interface of HADDOCK that allows the user to dock up to six biomolecules simultaneously. This interface allows the inclusion of a large variety of both experimental and/or bioinformatics data and supports several types of cyclic and dihedral symmetries in the docking of multibody assemblies. The server was tested on a benchmark of six cases, containing five symmetric homo-oligomeric protein complexes and one symmetric protein-DNA complex. Our results reveal that, in the presence of either bioinformatics and/or experimental data, HADDOCK shows an excellent performance: in all cases, HADDOCK was able to generate good to high quality solutions and ranked them at the top, demonstrating its ability to model symmetric multicomponent assemblies. Docking methods can thus play an important role in adding the structural dimension to interactomes. However, although the current docking methodologies were successful for a vast range of cases, considering the variety and complexity of macromolecular assemblies, inclusion of some kind of experimental information (e.g. from mass spectrometry, nuclear magnetic resonance, cryoelectron microscopy, etc.) will remain highly desirable to obtain reliable results.
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Affiliation(s)
- Ezgi Karaca
- Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Utrecht, The Netherlands
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