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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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2
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Spitz AZ, Zacharioudakis E, Reyna DE, Garner TP, Gavathiotis E. Eltrombopag directly inhibits BAX and prevents cell death. Nat Commun 2021; 12:1134. [PMID: 33602934 PMCID: PMC7892824 DOI: 10.1038/s41467-021-21224-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/14/2021] [Indexed: 01/08/2023] Open
Abstract
The BCL-2 family protein BAX has essential activity in mitochondrial regulation of cell death. While BAX activity ensures tissue homeostasis, when dysregulated it contributes to aberrant cell death in several diseases. During cellular stress BAX is transformed from an inactive cytosolic conformation to a toxic mitochondrial oligomer. Although the BAX transformation process is not well understood, drugs that interfere with this process are useful research tools and potential therapeutics. Here, we show that Eltrombopag, an FDA-approved drug, is a direct inhibitor of BAX. Eltrombopag binds the BAX trigger site distinctly from BAX activators, preventing them from triggering BAX conformational transformation and simultaneously promoting stabilization of the inactive BAX structure. Accordingly, Eltrombopag is capable of inhibiting BAX-mediated apoptosis induced by cytotoxic stimuli. Our data demonstrate structure-function insights into a mechanism of BAX inhibition and reveal a mechanism for Eltrombopag that may expand its use in diseases of uncontrolled cell death.
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Affiliation(s)
- Adam Z Spitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Emmanouil Zacharioudakis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Denis E Reyna
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Thomas P Garner
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
- Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.
- Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA.
- Institute of Aging Research, Albert Einstein College of Medicine, Bronx, NY, USA.
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3
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Garner TP, Amgalan D, Reyna DE, Li S, Kitsis RN, Gavathiotis E. Small-molecule allosteric inhibitors of BAX. Nat Chem Biol 2019; 15:322-330. [PMID: 30718816 PMCID: PMC6430685 DOI: 10.1038/s41589-018-0223-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/18/2018] [Indexed: 01/06/2023]
Abstract
BAX is a critical effector of the mitochondrial cell death pathway in response to a diverse range of stimuli in physiological and disease contexts. Upon binding by BH3-only proteins, cytosolic BAX undergoes conformational activation and translocation, resulting in mitochondrial outer membrane permeabilization. Efforts to rationally target BAX and develop inhibitors have been elusive, despite the clear therapeutic potential of inhibiting BAX-mediated cell death in a host of diseases. Here, we describe a class of small molecule BAX inhibitors, termed BAIs, which bind directly to a previously unrecognized pocket and allosterically inhibit BAX activation. BAI-binding around the hydrophobic helix α5 using hydrophobic and hydrogen bonding interactions stabilizes key areas of the hydrophobic core. BAIs inhibit conformational events in BAX activation that prevent BAX mitochondrial translocation and oligomerization. Our data highlight a novel paradigm for effective and selective pharmacological targeting of BAX to enable rational development of inhibitors of BAX-mediated cell death.
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Affiliation(s)
- Thomas P Garner
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA.,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Dulguun Amgalan
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA.,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Denis E Reyna
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA.,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sheng Li
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Richard N Kitsis
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.,Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA.,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA. .,Wilf Family Cardiovascular Research Institute, Albert Einstein College of Medicine, Bronx, NY, USA. .,Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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4
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Sasmal S, Lincoff J, Head-Gordon T. Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-β. Biophys J 2017; 113:1002-1011. [PMID: 28877484 DOI: 10.1016/j.bpj.2017.06.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/16/2017] [Accepted: 06/30/2017] [Indexed: 10/18/2022] Open
Abstract
Paramagnetic relaxation enhancement is an NMR technique that has yielded important insight into the structure of folded proteins, although the perturbation introduced by the large spin probe might be thought to diminish its usefulness when applied to characterizing the structural ensembles of intrinsically disordered proteins (IDPs). We compare the computationally generated structural ensembles of the IDP amyloid-β42 (Aβ42) to an alternative sequence in which a nitroxide spin label attached to cysteine has been introduced at its N-terminus. Based on this internally consistent computational comparison, we find that the spin label does not perturb the signature population of the β-hairpin formed by residues 16-21 and 29-36 that is dominant in the Aβ42 reference ensemble. However, the presence of the tag induces a strong population shift in a subset of the original Aβ42 structural sub-populations, including a sevenfold enhancement of the β-hairpin formed by residues 27-31 and 33-38. Through back-calculation of NMR observables from the computational structural ensembles, we show that the structural differences between the labeled and unlabeled peptide would be evident in local residual dipolar couplings, and possibly differences in homonuclear 1H-1H nuclear Overhauser effects (NOEs) and heteronuclear 1H-15N NOEs if the paramagnetic contribution to the longitudinal relaxation does not suppress the NOE intensities in the real experiment. This work shows that molecular simulation provides a complementary approach to resolving the potential structural perturbations introduced by reporter tags that can aid in the interpretation of paramagnetic relaxation enhancement, double electron-electron resonance, and fluorescence resonance energy transfer experiments applied to IDPs.
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Affiliation(s)
- Sukanya Sasmal
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
| | - James Lincoff
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California; Department of Chemistry, University of California, Berkeley, Berkeley, California; Department of Bioengineering, University of California, Berkeley, Berkeley, California; Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California.
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Hocking HG, Zangger K, Madl T. Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes. Chemphyschem 2013; 14:3082-94. [PMID: 23836693 PMCID: PMC4171756 DOI: 10.1002/cphc.201300219] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 12/20/2022]
Abstract
Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes.
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Affiliation(s)
- Henry G Hocking
- Chair of Biomolecular NMR, Department Chemie, Technische Universität München, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg (Germany)
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Abstract
This review will highlight the most commonly used methods to discover small molecule Type III/IV kinase inhibitors.
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Affiliation(s)
- Lori Krim Gavrin
- Pfizer Research
- Rare Disease Chemistry and Chemical Biology
- BioTherapeutics Chemistry
- Cambridge
- USA
| | - Eddine Saiah
- Pfizer Research
- Rare Disease Chemistry and Chemical Biology
- BioTherapeutics Chemistry
- Cambridge
- USA
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7
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Ratera I, Veciana J. Playing with organic radicals as building blocks for functional molecular materials. Chem Soc Rev 2012; 41:303-49. [DOI: 10.1039/c1cs15165g] [Citation(s) in RCA: 600] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements. J Struct Biol 2011; 174:434-42. [PMID: 21501688 DOI: 10.1016/j.jsb.2011.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 04/02/2011] [Accepted: 04/04/2011] [Indexed: 11/21/2022]
Abstract
Protein-protein interactions are necessary for various cellular processes, and therefore, information related to protein-protein interactions and structural information of complexes is invaluable. To identify protein-protein interfaces using NMR, resonance assignments are generally necessary to analyze the data; however, they are time consuming to collect, especially for large proteins. In this paper, we present a rapid, effective, and unbiased approach for the identification of a protein-protein interface without resonance assignments. This approach requires only a single set of 2D titration experiments of a single protein sample, labeled with a unique combination of an (15)N-labeled amino acid and several amino acids (13)C-labeled on specific atoms. To rapidly obtain high resolution data, we applied a new pulse sequence for time-shared NMR measurements that allowed simultaneous detection of a ω(1)-TROSY-type backbone (1)H-(15)N and aromatic (1)H-(13)C shift correlations together with single quantum methyl (1)H-(13)C shift correlations. We developed a structure-based computational approach, that uses our experimental data to search the protein surfaces in an unbiased manner to identify the residues involved in the protein-protein interface. Finally, we demonstrated that the obtained information of the molecular interface could be directly leveraged to support protein-protein docking studies. Such rapid construction of a complex model provides valuable information and enables more efficient biochemical characterization of a protein-protein complex, for instance, as the first step in structure-guided drug development.
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Calle LP, Cañada FJ, Jiménez-Barbero J. Application of NMR methods to the study of the interaction of natural products with biomolecular receptors. Nat Prod Rep 2011; 28:1118-25. [DOI: 10.1039/c0np00071j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Moy FJ, Lee A, Gavrin LK, Xu ZB, Sievers A, Kieras E, Stochaj W, Mosyak L, McKew J, Tsao DHH. Novel synthesis and structural characterization of a high-affinity paramagnetic kinase probe for the identification of non-ATP site binders by nuclear magnetic resonance. J Med Chem 2010; 53:1238-49. [PMID: 20038108 DOI: 10.1021/jm901525b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To aid in the pursuit of selective kinase inhibitors, we have developed a unique ATP site binder tool for the detection of binders outside the ATP site by nuclear magnetic resonance (NMR). We report here the novel synthesis that led to this paramagnetic spin-labeled pyrazolopyrimidine probe (1), which exhibits nanomolar inhibitory activity against multiple kinases. We demonstrate the application of this probe by performing NMR binding experiments with Lck and Src kinases and utilize it to detect the binding of two compounds proximal to the ATP site. The complex structure of the probe with Lck is also presented, revealing how the probe fits in the ATP site and the specific interactions it has with the protein. We believe that this spin-labeled probe is a valuable tool that holds broad applicability in a screen for non-ATP site binders.
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Affiliation(s)
- Franklin J Moy
- Structural Biology and Computational Chemistry, Wyeth Research, 200 CambridgePark Drive, Cambridge, Massachusetts 02140, USA
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An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations. Biochim Biophys Acta Gen Subj 2009; 1790:1368-76. [PMID: 19520148 DOI: 10.1016/j.bbagen.2009.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/28/2009] [Accepted: 06/01/2009] [Indexed: 11/20/2022]
Abstract
BACKGROUND The determination of protein-protein interfaces is of crucial importance to understand protein function and to guide the design of compounds. To identify protein-protein interface by NMR spectroscopy, 13C NMR paramagnetic shifts induced by freely diffusing 4-hydroxy-2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPOL) are promising, because TEMPOL affects distinct 13C NMR chemical shifts of the solvent accessible nuclei belonging to proteins of interest, while 13C nuclei within the interior of the proteins may be distinguished by a lack of such shifts. METHOD We measured the 13C NMR paramagnetic shifts induced by TEMPOL by recording 13C-(13)C TOCSY spectra for ubiquitin in the free state and the complex state with yeast ubiquitin hydrolase1 (YUH1). RESULTS Upon complexation of ubiquitin with YUH1, 13C NMR paramagnetic shifts associated with the protein binding interface were reduced by 0.05 ppm or more. The identified interfacial atoms agreed with the prior X-ray crystallographic data. CONCLUSIONS The TEMPOL-induced 13C chemical shift perturbation is useful to determine precise protein-protein interfaces. GENERAL SIGNIFICANCE The present method is a useful method to determine protein-protein interface by NMR, because it has advantages in easy sample preparations, simple data analyses, and wide applicabilities.
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12
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Mascioni A, Bentley BE, Camarda R, Dilts DA, Fink P, Gusarova V, Hoiseth SK, Jacob J, Lin SL, Malakian K, McNeil LK, Mininni T, Moy F, Murphy E, Novikova E, Sigethy S, Wen Y, Zlotnick GW, Tsao DHH. Structural Basis for the Immunogenic Properties of the Meningococcal Vaccine Candidate LP2086. J Biol Chem 2009; 284:8738-46. [PMID: 19103601 PMCID: PMC2659232 DOI: 10.1074/jbc.m808831200] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Indexed: 11/06/2022] Open
Abstract
LP2086 is a family of outer membrane lipoproteins from Neisseria meningitidis, which elicits bactericidal antibodies and are currently undergoing human clinical trials in a bivalent formulation where each antigen represents one of the two known LP2086 subfamilies. Here we report the NMR structure of the recombinant LP2086 variant B01, a representative of the LP2086 subfamily B. The structure reveals a novel fold composed of two domains: a "taco-shaped" N-terminal beta-sheet and a C-terminal beta-barrel connected by a linker. The structure in micellar solution is consistent with a model of LP2086 anchored to the outer membrane bilayer through its lipidated N terminus. A long flexible chain connects the folded part of the protein to the lipid anchor and acts as spacer, making both domains accessible to the host immune system. Antibodies broadly reactive against members from both subfamilies have been mapped to the N terminus. A surface of subfamily-defining residues was identified on one face of the protein, offering an explanation for the induction of subfamily-specific bactericidal antibodies.
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Affiliation(s)
- Alessandro Mascioni
- Wyeth Research, Structural Biology and Computational Chemistry, Cambridge, Massachusetts 02140 and Wyeth Vaccines Research, Pearl River, New York 10965, USA
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13
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Xu X, Reinle W, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M. Dynamics in a Pure Encounter Complex of Two Proteins Studied by Solution Scattering and Paramagnetic NMR Spectroscopy. J Am Chem Soc 2008; 130:6395-403. [DOI: 10.1021/ja7101357] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xingfu Xu
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Wolfgang Reinle
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Frank Hannemann
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Peter V. Konarev
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Dmitri I. Svergun
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Rita Bernhardt
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Marcellus Ubbink
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
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14
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Showalter SA, Bruschweiler-Li L, Johnson E, Zhang F, Brüschweiler R. Quantitative lid dynamics of MDM2 reveals differential ligand binding modes of the p53-binding cleft. J Am Chem Soc 2008; 130:6472-8. [PMID: 18435534 DOI: 10.1021/ja800201j] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The oncoprotein MDM2 regulates the activity and stability of the tumor suppressor p53 through protein-protein interaction involving their N-terminal domains. The N-terminal lid of MDM2 has been implicated in p53 regulation; however, due to its flexible nature, limited data are available concerning its role in ligand binding. The quantitative dynamics study using NMR reported here shows, for the first time, that the lid in apo-MDM2 slowly interconverts between a "closed" state that is associated with the p53-binding cleft and an "open" state that is highly flexible. Our results reveal that apo-MDM2 predominantly populates the closed state, whereas the p53-bound MDM2 exclusively populates the open state. Unlike p53 binding, the small molecule MDM2 antagonist nutlin-3 binds to the cleft essentially without perturbing the closed lid state. The lid dynamics thereby represents a signature for the experimental and virtual screening of therapeutic antagonists that target the p53-MDM2 interaction.
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Affiliation(s)
- Scott A Showalter
- Department of Chemistry and Biochemistry, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32306, USA
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15
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Vlasie MD, Comuzzi C, van den Nieuwendijk AMCH, Prudêncio M, Overhand M, Ubbink M. Long-Range-Distance NMR Effects in a Protein Labeled with a Lanthanide–DOTA Chelate. Chemistry 2007; 13:1715-23. [PMID: 17115462 DOI: 10.1002/chem.200600916] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A two-thiol reactive lanthanide-DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) chelate, CLaNP-3 (CLaNP=caged lanthanide NMR probe), was synthesized for the rigid attachment to cysteine groups on a protein surface, and used to obtain long-range-distance information from the {15N,1H} HSQC spectra of the protein-lanthanide complex. The DOTA ring exhibits several isomers that are in exchange; however, single resonances were observed for most amide groups in the protein, allowing determination of a single, apparent magnetic-susceptibility tensor. Pseudocontact shifts caused by Yb-containing CLaNP-3 were observed for atoms at 15-35 A from the metal. By using Gd-containing CLaNP-3, relaxation effects were observed, allowing distances up to 30 A from the paramagnetic center to be determined accurately. Similar results were obtained with a Gd-DTPA (diethylene-triaminepentaacetic acid) chelate, CLaNP-1, bound in the same bidentate manner to the protein. This study demonstrates that bidentate attachment of a paramagnetic probe enables determination of long-range distances.
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Affiliation(s)
- Monica D Vlasie
- Leiden Institute of Chemistry, Gorlaeus Laboratories Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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