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Schlagnitweit J, Steiner E, Karlsson H, Petzold K. Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach. Chemistry 2018; 24:6067-6070. [PMID: 29504639 PMCID: PMC5947647 DOI: 10.1002/chem.201800992] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 01/10/2023]
Abstract
The knowledge of structure and dynamics is crucial to explain the function of RNAs. While nuclear magnetic resonance (NMR) is well suited to probe these for complex biomolecules, it requires expensive, isotopically labeled samples, and long measurement times. Here we present SELOPE, a new robust, proton-only NMR method that allows us to obtain site-specific overview of structure and dynamics in an entire RNA molecule using an unlabeled sample. SELOPE simplifies assignment and allows for cost-effective screening of the response of nucleic acids to physiological changes (e.g. ion concentration) or screening of drugs in a high throughput fashion. This single technique allows us to probe an unprecedented range of exchange time scales (the whole μs to ms motion range) with increased sensitivity, surpassing all current experiments to detect chemical exchange. For the first time we could describe an RNA excited state using an unlabeled RNA.
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Affiliation(s)
- Judith Schlagnitweit
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Emilie Steiner
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Hampus Karlsson
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
| | - Katja Petzold
- Department of Medical Biochemistry and BiophysicsKarolinska Institute17177StockholmSweden
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The Dynamic Basis for Signal Propagation in Human Pin1-WW. Structure 2016; 24:1464-75. [PMID: 27499442 DOI: 10.1016/j.str.2016.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/11/2016] [Accepted: 06/14/2016] [Indexed: 12/23/2022]
Abstract
Allostery is the structural manifestation of information transduction in biomolecules. Its hallmark is conformational change induced by perturbations at a distal site. An increasing body of evidence demonstrates the presence of allostery in very flexible and even disordered proteins, encouraging a thermodynamic description of this phenomenon. Still, resolving such processes at atomic resolution is difficult. Here we establish a protocol to determine atomistic thermodynamic models of such systems using high-resolution solution state nuclear magnetic resonance data and extensive molecular simulations. Using this methodology, we study information transduction in the WW domain of a key cell-cycle regulator Pin1. Pin1 binds promiscuously to phospho-Ser/Thr-Pro motifs, however, disparate structural and dynamic responses have been reported upon binding different ligands. Our model consists of two topologically distinct states whose relative population may be specifically skewed by an incoming ligand. This model provides a canonical basis for the understanding of multi-functionality in Pin1.
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Pratihar S, Sabo TM, Ban D, Fenwick RB, Becker S, Salvatella X, Griesinger C, Lee D. Kinetics of the Antibody Recognition Site in the Third IgG-Binding Domain of Protein G. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Supriya Pratihar
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - T. Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
| | - R. Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Department of Integrative Structural and Computational Biology; Skaggs Institute for Chemical Biology, The Scripps Research Institute; 10550 N. Torrey Pines Rd. La Jolla CA 92037 USA
| | - Stefan Becker
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology; Baldiri Reixac 10 08028 Barcelona Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Barcelona Spain
| | - Christian Griesinger
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
| | - Donghan Lee
- Department for NMR-based Structural Biology; Max-Planck Institute for Biophysical Chemistry; Am Fassberg 11 37077 Göttingen Germany
- Department of Medicine, James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St Louisville KY 40202 USA
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Pratihar S, Sabo TM, Ban D, Fenwick RB, Becker S, Salvatella X, Griesinger C, Lee D. Kinetics of the Antibody Recognition Site in the Third IgG-Binding Domain of Protein G. Angew Chem Int Ed Engl 2016; 55:9567-70. [PMID: 27345359 DOI: 10.1002/anie.201603501] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 05/20/2016] [Indexed: 12/31/2022]
Abstract
Protein dynamics occurring on a wide range of timescales play a crucial role in governing protein function. Particularly, motions between the globular rotational correlation time (τc ) and 40 μs (supra-τc window), strongly influence molecular recognition. This supra-τc window was previously hidden, owing to a lack of experimental methods. Recently, we have developed a high-power relaxation dispersion (RD) experiment for measuring kinetics as fast as 4 μs. For the first time, this method, performed under super-cooled conditions, enabled us to detect a global motion in the first β-turn of the third IgG-binding domain of protein G (GB3), which was extrapolated to 371±115 ns at 310 K. Furthermore, the same residues show the plasticity in the model-free residual dipolar coupling (RDC) order parameters and in an ensemble encoding the supra-τc dynamics. This β-turn is involved in antibody binding, exhibiting the potential link of the observed supra-τc motion with molecular recognition.
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Affiliation(s)
- Supriya Pratihar
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - T Michael Sabo
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - David Ban
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA
| | - R Bryn Fenwick
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.,Department of Integrative Structural and Computational Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Christian Griesinger
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Donghan Lee
- Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany. .,Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St, Louisville, KY, 40202, USA.
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Carneiro MG, Koharudin LMI, Ban D, Sabo TM, Trigo-Mourino P, Mazur A, Griesinger C, Gronenborn AM, Lee D. Sampling of Glycan-Bound Conformers by the Anti-HIV Lectin Oscillatoria agardhiiagglutinin in the Absence of Sugar. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Carneiro MG, Koharudin LMI, Ban D, Sabo TM, Trigo-Mourino P, Mazur A, Griesinger C, Gronenborn AM, Lee D. Sampling of Glycan-Bound Conformers by the Anti-HIV Lectin Oscillatoria agardhii agglutinin in the Absence of Sugar. Angew Chem Int Ed Engl 2015; 54:6462-5. [PMID: 25873445 DOI: 10.1002/anie.201500213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/16/2015] [Indexed: 02/01/2023]
Abstract
Lectins from different sources have been shown to interfere with HIV infection by binding to the sugars of viral-envelope glycoproteins. Three-dimensional atomic structures of a number of HIV-inactivating lectins have been determined, both as free proteins and in glycan-bound forms. However, details on the mechanism of recognition and binding to sugars are elusive. Herein we focus on the anti-HIV lectin OAA from Oscillatoria agardhii: We show that in the absence of sugars in solution, both the sugar-free and sugar-bound protein conformations that were observed in the X-ray crystal structures exist as conformational substates. Our results suggest that glycan recognition occurs by conformational selection within the ground state; this model differs from the popular "excited-state" model. Our findings provide further insight into molecular recognition of the major receptor on the HIV virus by OAA. These details can potentially be used for the optimization and/or development of preventive anti-HIV therapeutics.
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Affiliation(s)
- Marta G Carneiro
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Leonardus M I Koharudin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1050 Biomedical Science Tower 3, 3501 5th Avenue, Pittsburgh, PA 15260 (USA)
| | - David Ban
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany).,Present address: St. Jude Children's Research Hospital, Department of Structural Biology, 262 Danny Thomas Place, Memphis, TN 38105 (USA)
| | - T Michael Sabo
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Pablo Trigo-Mourino
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Adam Mazur
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany).,Present address: Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel (Switzerland)
| | - Christian Griesinger
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany)
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1050 Biomedical Science Tower 3, 3501 5th Avenue, Pittsburgh, PA 15260 (USA)
| | - Donghan Lee
- Department for NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany).
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