1
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Beriashvili D, Zhou J, Liu Y, Folkers GE, Baldus M. Cellular Applications of DNP Solid-State NMR -State of the Art and a Look to the Future. Chemistry 2024:e202400323. [PMID: 38451060 DOI: 10.1002/chem.202400323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
Sensitivity enhanced dynamic nuclear polarization solid-state NMR is emerging as a powerful technique for probing the structural properties of conformationally homogenous and heterogenous biomolecular species irrespective of size at atomic resolution within native environments. Herein we detail advancements that have made acquiring such data, specifically within the confines of intact bacterial and eukaryotic cell a reality, and further discuss the type of structural information that can be presently garnered by the technique's exploitation. Subsequently, we discuss bottlenecks that have thus far curbed cellular DNP-ssNMR's broad adoption, namely a lack of sensitivity and spectral resolution, and explore possible solutions ranging from utilization of new pulse sequences, design of better performing polarizing agents, and application of additional biochemical/ cell biological methodologies.
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Affiliation(s)
| | - Jiaxin Zhou
- Tianjin Medical University, School of Pharmacy, CHINA
| | - Yangping Liu
- Tianjin Medical University, School of Pharmacy, CHINA
| | | | - Marc Baldus
- Utrecht University, Bijvoet Center for Biomolecular Research, Padualaan 8, 3584, Utrecht, NETHERLANDS
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2
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Romanuka J, Folkers GE, Gnida M, Kovačič L, Wienk H, Kaptein R, Boelens R. Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery. Proc Natl Acad Sci U S A 2023; 120:e2311240120. [PMID: 38019859 DOI: 10.1073/pnas.2311240120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.
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Affiliation(s)
- Julija Romanuka
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Manuel Gnida
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Robert Kaptein
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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3
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Beriashvili D, Yao R, D'Amico F, Krafčíková M, Gurinov A, Safeer A, Cai X, Mulder MPC, Liu Y, Folkers GE, Baldus M. A high-field cellular DNP-supported solid-state NMR approach to study proteins with sub-cellular specificity. Chem Sci 2023; 14:9892-9899. [PMID: 37736634 PMCID: PMC10510770 DOI: 10.1039/d3sc02117c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/24/2023] [Indexed: 09/23/2023] Open
Abstract
Studying the structural aspects of proteins within sub-cellular compartments is of growing interest. Dynamic nuclear polarization supported solid-state NMR (DNP-ssNMR) is uniquely suited to provide such information, but critically lacks the desired sensitivity and resolution. Here we utilize SNAPol-1, a novel biradical, to conduct DNP-ssNMR at high-magnetic fields (800 MHz/527 GHz) inside HeLa cells and isolated cell nuclei electroporated with [13C,15N] labeled ubiquitin. We report that SNAPol-1 passively diffuses and homogenously distributes within whole cells and cell nuclei providing ubiquitin spectra of high sensitivity and remarkably improved spectral resolution. For cell nuclei, physical enrichment facilitates a further 4-fold decrease in measurement time and provides an exclusive structural view of the nuclear ubiquitin pool. Taken together, these advancements enable atomic interrogation of protein conformational plasticity at atomic resolution and with sub-cellular specificity.
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Affiliation(s)
- David Beriashvili
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ru Yao
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Francesca D'Amico
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Michaela Krafčíková
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Andrei Gurinov
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Adil Safeer
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University Tianjin 300070 P. R. China
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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4
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Narasimhan S, Pinto C, Lucini Paioni A, van der Zwan J, Folkers GE, Baldus M. Characterizing proteins in a native bacterial environment using solid-state NMR spectroscopy. Nat Protoc 2021; 16:893-918. [PMID: 33442051 DOI: 10.1038/s41596-020-00439-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/09/2020] [Indexed: 01/29/2023]
Abstract
For a long time, solid-state nuclear magnetic resonance (ssNMR) has been employed to study complex biomolecular systems at the detailed chemical, structural, or dynamic level. Recent progress in high-resolution and high-sensitivity ssNMR, in combination with innovative sample preparation and labeling schemes, offers novel opportunities to study proteins in their native setting irrespective of the molecular tumbling rate. This protocol describes biochemical preparation schemes to obtain cellular samples of both soluble as well as insoluble or membrane-associated proteins in bacteria. To this end, the protocol is suitable for studying a protein of interest in both whole cells and in cell envelope or isolated membrane preparations. In the first stage of the procedure, an appropriate strain of Escherichia coli (DE3) is transformed with a plasmid of interest harboring the protein of interest under the control of an inducible T7 promoter. Next, the cells are adapted to grow in minimal (M9) medium. Before the growth enters stationary phase, protein expression is induced, and shortly thereafter, the native E. coli RNA polymerase is inhibited using rifampicin for targeted labeling of the protein of interest. The cells are harvested after expression and prepared for ssNMR rotor filling. In addition to conventional 13C/15N-detected ssNMR, we also outline how these preparations can be readily subjected to multidimensional ssNMR experiments using dynamic nuclear polarization (DNP) or proton (1H) detection schemes. We estimate that the entire preparative procedure until NMR experiments can be started takes 3-5 days.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Cecilia Pinto
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.,Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands.
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5
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le Paige UB, Xiang S, Hendrix MMRM, Zhang Y, Folkers GE, Weingarth M, Bonvin AMJJ, Kutateladze TG, Voets IK, Baldus M, van Ingen H. Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy. Magn Reson (Gott) 2021; 2:187-202. [PMID: 35647606 PMCID: PMC9135053 DOI: 10.5194/mr-2-187-2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins with the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ~ 200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein-binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle X-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low-affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.
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Affiliation(s)
- Ulric B. le Paige
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - ShengQi Xiang
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Marco M. R. M. Hendrix
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gert E. Folkers
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Alexandre M. J. J. Bonvin
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Marc Baldus
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Hugo van Ingen
- Utrecht NMR Group, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, the Netherlands
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6
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Narasimhan S, Folkers GE, Baldus M. When Small becomes Too Big: Expanding the Use of In‐Cell Solid‐State NMR Spectroscopy. Chempluschem 2020; 85:760-768. [DOI: 10.1002/cplu.202000167] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/31/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular ResearchUtrecht University Padualaan 8 3584 CH Utrecht (The Netherlands
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7
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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. Back Cover: DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells (Angew. Chem. Int. Ed. 37/2019). Angew Chem Int Ed Engl 2019. [DOI: 10.1002/anie.201908849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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8
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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. Rücktitelbild: DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells (Angew. Chem. 37/2019). Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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9
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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP-Supported Solid-State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019; 58:12969-12973. [PMID: 31233270 PMCID: PMC6772113 DOI: 10.1002/anie.201903246] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Indexed: 11/25/2022]
Abstract
Elucidating at atomic level how proteins interact and are chemically modified in cells represents a leading frontier in structural biology. We have developed a tailored solid‐state NMR spectroscopic approach that allows studying protein structure inside human cells at atomic level under high‐sensitivity dynamic nuclear polarization (DNP) conditions. We demonstrate the method using ubiquitin (Ub), which is critically involved in cellular functioning. Our results pave the way for structural studies of larger proteins or protein complexes inside human cells, which have remained elusive to in‐cell solution‐state NMR spectroscopy due to molecular size limitations.
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Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
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10
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Narasimhan S, Scherpe S, Lucini Paioni A, van der Zwan J, Folkers GE, Ovaa H, Baldus M. DNP‐Supported Solid‐State NMR Spectroscopy of Proteins Inside Mammalian Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903246] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Siddarth Narasimhan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Stephan Scherpe
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Alessandra Lucini Paioni
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Johan van der Zwan
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Gert E. Folkers
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Center (LUMC) Einthovenweg 20 2333 ZC Leiden The Netherlands
| | - Marc Baldus
- NMR Spectroscopy group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands
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11
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Geng C, Vangone A, Folkers GE, Xue LC, Bonvin AMJJ. iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations. Proteins 2018; 87:110-119. [PMID: 30417935 PMCID: PMC6587874 DOI: 10.1002/prot.25630] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 10/19/2018] [Accepted: 11/05/2018] [Indexed: 02/06/2023]
Abstract
Quantitative evaluation of binding affinity changes upon mutations is crucial for protein engineering and drug design. Machine learning‐based methods are gaining increasing momentum in this field. Due to the limited number of experimental data, using a small number of sensitive predictive features is vital to the generalization and robustness of such machine learning methods. Here we introduce a fast and reliable predictor of binding affinity changes upon single point mutation, based on a random forest approach. Our method, iSEE, uses a limited number of interface Structure, Evolution, and Energy‐based features for the prediction. iSEE achieves, using only 31 features, a high prediction performance with a Pearson correlation coefficient (PCC) of 0.80 and a root mean square error of 1.41 kcal/mol on a diverse training dataset consisting of 1102 mutations in 57 protein‐protein complexes. It competes with existing state‐of‐the‐art methods on two blind test datasets. Predictions for a new dataset of 487 mutations in 56 protein complexes from the recently published SKEMPI 2.0 database reveals that none of the current methods perform well (PCC < 0.42), although their combination does improve the predictions. Feature analysis for iSEE underlines the significance of evolutionary conservations for quantitative prediction of mutation effects. As an application example, we perform a full mutation scanning of the interface residues in the MDM2–p53 complex.
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Affiliation(s)
- Cunliang Geng
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Anna Vangone
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands.,Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg, Penzberg, Germany
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Li C Xue
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands
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12
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Cloin BMC, De Zitter E, Salas D, Gielen V, Folkers GE, Mikhaylova M, Bergeler M, Krajnik B, Harvey J, Hoogenraad CC, Van Meervelt L, Dedecker P, Kapitein LC. Efficient switching of mCherry fluorescence using chemical caging. Proc Natl Acad Sci U S A 2017; 114:7013-7018. [PMID: 28630286 PMCID: PMC5502588 DOI: 10.1073/pnas.1617280114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME). The molecules can be recovered to the red fluorescent state by washing out the βME or through irradiation with violet light, with up to 80% total recovery. We show that this can be used to perform single-molecule localization microscopy (SMLM) on cells expressing mCherry, which renders this approach applicable to a very wide range of existing constructs. We performed a detailed investigation of the mechanism underlying these dynamics, using X-ray crystallography, NMR spectroscopy, and ab initio quantum-mechanical calculations. We find that the βME-induced fluorescence quenching of mCherry occurs both via the direct addition of βME to the chromophore and through βME-mediated reduction of the chromophore. These results not only offer a strategy to expand SMLM imaging to a broad range of available biological models, but also present unique insights into the chemistry and functioning of a highly important class of fluorophores.
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Affiliation(s)
- Bas M C Cloin
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Elke De Zitter
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Desiree Salas
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Vincent Gielen
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Gert E Folkers
- NMR Spectroscopy, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Marina Mikhaylova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Maike Bergeler
- Quantum Chemistry and Physical Chemistry, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Bartosz Krajnik
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
- Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Jeremy Harvey
- Quantum Chemistry and Physical Chemistry, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Luc Van Meervelt
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Heverlee, Belgium;
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands;
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13
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Das D, Faridounnia M, Kovacic L, Kaptein R, Boelens R, Folkers GE. Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex. J Biol Chem 2016; 292:2842-2853. [PMID: 28028171 DOI: 10.1074/jbc.m116.747857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/24/2016] [Indexed: 11/06/2022] Open
Abstract
The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of DNA damage. Functional studies have provided insights into the binding of ERCC1-XPF to various DNA substrates. However, because no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the helix-hairpin-helix (HhH) domains of XPF and ERCC-XPF and show that the binding to single-stranded DNA (ssDNA)/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF. We reveal that the homodimeric XPF is able to bind various ssDNA sequences but with a clear preference for guanine-containing substrates. NMR titration experiments and in vitro DNA binding assays also show that, within the heterodimeric ERCC1-XPF complex, XPF specifically recognizes ssDNA. On the other hand, the HhH domain of ERCC1 preferentially binds dsDNA through the hairpin region. The two separate non-overlapping DNA binding domains in the ERCC1-XPF heterodimer jointly bind to an ssDNA/dsDNA substrate and, thereby, at least partially dictate the incision position during damage removal. Based on structural models, NMR titrations, DNA-binding studies, site-directed mutagenesis, charge distribution, and sequence conservation, we propose that the HhH domain of ERCC1 binds to dsDNA upstream of the damage, and XPF binds to the non-damaged strand within a repair bubble.
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Affiliation(s)
- Devashish Das
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Lidija Kovacic
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
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14
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Kaplan M, Narasimhan S, de Heus C, Mance D, van Doorn S, Houben K, Popov-Čeleketić D, Damman R, Katrukha EA, Jain P, Geerts WJC, Heck AJR, Folkers GE, Kapitein LC, Lemeer S, van Bergen En Henegouwen PMP, Baldus M. EGFR Dynamics Change during Activation in Native Membranes as Revealed by NMR. Cell 2016; 167:1241-1251.e11. [PMID: 27839865 DOI: 10.1016/j.cell.2016.10.038] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/08/2016] [Accepted: 10/20/2016] [Indexed: 10/20/2022]
Abstract
The epidermal growth factor receptor (EGFR) represents one of the most common target proteins in anti-cancer therapy. To directly examine the structural and dynamical properties of EGFR activation by the epidermal growth factor (EGF) in native membranes, we have developed a solid-state nuclear magnetic resonance (ssNMR)-based approach supported by dynamic nuclear polarization (DNP). In contrast to previous crystallographic results, our experiments show that the ligand-free state of the extracellular domain (ECD) is highly dynamic, while the intracellular kinase domain (KD) is rigid. Ligand binding restricts the overall and local motion of EGFR domains, including the ECD and the C-terminal region. We propose that the reduction in conformational entropy of the ECD by ligand binding favors the cooperative binding required for receptor dimerization, causing allosteric activation of the intracellular tyrosine kinase.
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Affiliation(s)
- Mohammed Kaplan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Siddarth Narasimhan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Cecilia de Heus
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Deni Mance
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Sander van Doorn
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Dušan Popov-Čeleketić
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Reinier Damman
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Eugene A Katrukha
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Purvi Jain
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Willie J C Geerts
- Biomolecular Imaging, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands
| | | | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
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15
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Dongre R, Folkers GE, Gualerzi CO, Boelens R, Wienk H. A model for the interaction of the G3-subdomain of Geobacillus stearothermophilus IF2 with the 30S ribosomal subunit. Protein Sci 2016; 25:1722-33. [PMID: 27364543 DOI: 10.1002/pro.2977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 11/10/2022]
Abstract
Bacterial translation initiation factor IF2 complexed with GTP binds to the 30S ribosomal subunit, promotes ribosomal binding of fMet-tRNA, and favors the joining of the small and large ribosomal subunits yielding a 70S initiation complex ready to enter the translation elongation phase. Within the IF2 molecule subdomain G3, which is believed to play an important role in the IF2-30S interaction, is positioned between the GTP-binding G2 and the fMet-tRNA binding C-terminal subdomains. In this study the solution structure of subdomain G3 of Geobacillus stearothermophilus IF2 has been elucidated. G3 forms a core structure consisting of two β-sheets with each four anti-parallel strands, followed by a C-terminal α-helix. In line with its role as linker between G3 and subdomain C1, this helix has no well-defined orientation but is endowed with a dynamic nature. The structure of the G3 core is that of a typical OB-fold module, similar to that of the corresponding subdomain of Thermus thermophilus IF2, and to that of other known RNA-binding modules such as IF2-C2, IF1 and subdomains II of elongation factors EF-Tu and EF-G. Structural comparisons have resulted in a model that describes the interaction between IF2-G3 and the 30S ribosomal subunit.
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Affiliation(s)
- Ramachandra Dongre
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Gert E Folkers
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Claudio O Gualerzi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, Italy
| | - Rolf Boelens
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Hans Wienk
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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16
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Nooren IM, Folkers GE, Kaptein R, Sauer RT, Boelens R. Structure and dynamics of the tetrameric mnt repressor and a model for its DNA complex. J Biomol Struct Dyn 2016; 17 Suppl 1:113-22. [PMID: 22607414 DOI: 10.1080/07391102.2000.10506611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Abstract The tetrameric Mnt repressor of bacteriophage P22 consists of two dimeric DNA-binding domains and a tetramerization domain. The NOE and chemical shift data demonstrate that the structures of the domains in the wild-type repressor protein are similar to those of the separate domains, the three-dimensional structures of which have been determined previously. (15)N relaxation measurements show that the linker that connects the anti-parallel four-helix bundle with the two β-sheet DNA-binding dimers is highly flexible. No evidence was found for interactions between the distinct modules. The (15)N relaxation properties of the two domains differ substantially, confirming their structural independence. A model in which one two-stranded coiled coil of the four-helix bundle is attached to one N-terminal dimer is most consistent with the biochemical data and (15)N relaxation data. For the Mnt-DNA complex this geometry fits with a model in which the two β-sheet DNA-binding domains are bound at two successive major grooves of the Mnt operator and the tetramerization domain is packed between these two DNA-bound dimers. In such a model the two-fold symmetry axis of the four-helix bundle coincides with that of the operator sequence and the two bound dimers. Bending of the Mnt operator of approximately 30° upon binding of the tetramer, as measured by gel-shift assays, is in agreement with this model of the Mnt-DNA complex.
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Affiliation(s)
- I M Nooren
- a Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research , Utrecht University , Padualaan 8 , 3584 , CH Utrecht , The Netherlands
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17
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Faridounnia M, Wienk H, Kovačič L, Folkers GE, Jaspers NGJ, Kaptein R, Hoeijmakers JHJ, Boelens R. The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex. J Biol Chem 2015; 290:20541-55. [PMID: 26085086 DOI: 10.1074/jbc.m114.635169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Indexed: 12/15/2022] Open
Abstract
The ERCC1-XPF heterodimer, a structure-specific DNA endonuclease, is best known for its function in the nucleotide excision repair (NER) pathway. The ERCC1 point mutation F231L, located at the hydrophobic interaction interface of ERCC1 (excision repair cross-complementation group 1) and XPF (xeroderma pigmentosum complementation group F), leads to severe NER pathway deficiencies. Here, we analyze biophysical properties and report the NMR structure of the complex of the C-terminal tandem helix-hairpin-helix domains of ERCC1-XPF that contains this mutation. The structures of wild type and the F231L mutant are very similar. The F231L mutation results in only a small disturbance of the ERCC1-XPF interface, where, in contrast to Phe(231), Leu(231) lacks interactions stabilizing the ERCC1-XPF complex. One of the two anchor points is severely distorted, and this results in a more dynamic complex, causing reduced stability and an increased dissociation rate of the mutant complex as compared with wild type. These data provide a biophysical explanation for the severe NER deficiencies caused by this mutation.
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Affiliation(s)
- Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia, and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nicolaas G J Jaspers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jan H J Hoeijmakers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands,
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18
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Baker LA, Daniëls M, van der Cruijsen EAW, Folkers GE, Baldus M. Efficient cellular solid-state NMR of membrane proteins by targeted protein labeling. J Biomol NMR 2015; 62:199-208. [PMID: 25956570 PMCID: PMC4451474 DOI: 10.1007/s10858-015-9936-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/23/2015] [Indexed: 05/20/2023]
Abstract
Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label a single protein by repressing endogenous protein expression with rifampicin. Our results demonstrate that treatment of E. coli with rifampicin during induction of recombinant membrane protein expression reduces background signals for different expression levels and improves sensitivity in cellular membrane samples. Further, the method reduces the amount of time and resources needed to produce membrane protein samples, enabling new strategies for studying challenging membrane proteins by ssNMR.
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Affiliation(s)
- Lindsay A. Baker
- />NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- />Oxford Particle Imaging Centre, The Wellcome Trust Centre for Human Genetics, Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Mark Daniëls
- />NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Elwin A. W. van der Cruijsen
- />NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gert E. Folkers
- />NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- />NMR Spectroscopy, Department of Chemistry, Faculty of Science, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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19
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Kaplan M, Cukkemane A, van Zundert GCP, Narasimhan S, Daniëls M, Mance D, Waksman G, Bonvin AMJJ, Fronzes R, Folkers GE, Baldus M. Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR. Nat Methods 2015; 12:649-52. [PMID: 25984698 DOI: 10.1038/nmeth.3406] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 03/25/2015] [Indexed: 12/24/2022]
Abstract
Studying biomolecules at atomic resolution in their native environment is the ultimate aim of structural biology. We investigated the bacterial type IV secretion system core complex (T4SScc) by cellular dynamic nuclear polarization-based solid-state nuclear magnetic resonance spectroscopy to validate a structural model previously generated by combining in vitro and in silico data. Our results indicate that T4SScc is well folded in the cellular setting, revealing protein regions that had been elusive when studied in vitro.
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Affiliation(s)
- Mohammed Kaplan
- NMR Spectroscopy, Utrecht University, Utrecht, the Netherlands
| | | | | | | | - Mark Daniëls
- NMR Spectroscopy, Utrecht University, Utrecht, the Netherlands
| | - Deni Mance
- NMR Spectroscopy, Utrecht University, Utrecht, the Netherlands
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, UK
| | | | - Rémi Fronzes
- Groupe à 5 ans, Biologie structurale de la secretion bacterienne, Unité mixte de recherche Centre National de la Recherche Scientifique-Institut Pasteur 3528, Institut Pasteur, Paris, France
| | - Gert E Folkers
- NMR Spectroscopy, Utrecht University, Utrecht, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Utrecht University, Utrecht, the Netherlands
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20
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Baker LA, Folkers GE, Sinnige T, Houben K, Kaplan M, van der Cruijsen EAW, Baldus M. Magic-angle-spinning solid-state NMR of membrane proteins. Methods Enzymol 2015; 557:307-28. [PMID: 25950971 DOI: 10.1016/bs.mie.2014.12.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Solid-state NMR spectroscopy (ssNMR) provides increasing possibilities to examine membrane proteins in different molecular settings, ranging from synthetic bilayers to whole cells. This flexibility often enables ssNMR experiments to be directly correlated with membrane protein function. In this contribution, we discuss experimental aspects of such studies starting with protein expression and labeling, leading to membrane protein isolation or to membrane proteins in a cellular environment. We show that optimized procedures can depend on aspects such as the achieved levels of expression, the stability of the protein during purification or proper refolding. Dealing with native membrane samples, such as isolated cellular membranes, can alleviate or entirely remove such biochemical challenges. Subsequently, we outline ssNMR experiments that involve the use of magic-angle-spinning and can be used to study membrane protein structure and their functional aspects. We pay specific attention to spectroscopic issues such as sensitivity and spectral resolution. The latter aspect can be controlled using a combination of tailored preparation procedures with solid-state NMR experiments that simplify the spectral analysis using specific filtering and correlation methods. Such approaches have already provided access to obtain structural views of membrane proteins and study their function in lipid bilayers. Ongoing developments in sample preparation and NMR methodology, in particular in using hyperpolarization or proton-detection schemes, offer additional opportunities to study membrane proteins close to their cellular function. These considerations suggest a further increase in the potential of using solid-state NMR in the context of prokaryotic or eukaryotic membrane protein systems in the near future.
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Affiliation(s)
- Lindsay A Baker
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Tessa Sinnige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Klaartje Houben
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mohammed Kaplan
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Elwin A W van der Cruijsen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
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21
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Khan F, Daniëls MA, Folkers GE, Boelens R, Saqlan Naqvi SM, van Ingen H. Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function. Nucleic Acids Res 2014; 42:8705-18. [PMID: 24957607 PMCID: PMC4117745 DOI: 10.1093/nar/gku468] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 04/30/2014] [Accepted: 05/12/2014] [Indexed: 12/30/2022] Open
Abstract
Glycine-rich RNA-binding proteins (GR-RBPs) are involved in cold shock response of plants as RNA chaperones facilitating mRNA transport, splicing and translation. GR-RBPs are bipartite proteins containing a RNA recognition motif (RRM) followed by a glycine-rich region. Here, we studied the structural basis of nucleic acid binding of full-length Nicotiana tabacum GR-RBP1. NMR studies of NtGR-RBP1 show that the glycine-rich domain, while intrinsically disordered, is responsible for mediating self-association by transient interactions with its RRM domain (NtRRM). Both NtGR-RBP1 and NtRRM bind specifically and with low micromolar affinity to RNA and single-stranded DNA. The solution structure of NtRRM shows that it is a canonical RRM domain. A HADDOCK model of the NtRRM-RNA complex, based on NMR chemical shift and NOE data, shows that nucleic acid binding results from a combination of stacking and electrostatic interactions with conserved RRM residues. Finally, DNA melting experiments demonstrate that NtGR-RBP1 is more efficient in melting CTG containing nucleic acids than isolated NtRRM. Together, our study supports the model that self-association of GR-RBPs by the glycine-rich region results in cooperative unfolding of non-native substrate structures, thereby enhancing its chaperone function.
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Affiliation(s)
- Fariha Khan
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Mark A Daniëls
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - S M Saqlan Naqvi
- Department of Biochemistry, PMAS Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Hugo van Ingen
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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22
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Wienk H, Slootweg JC, Speerstra S, Kaptein R, Boelens R, Folkers GE. The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition. Nucleic Acids Res 2013; 41:6739-49. [PMID: 23661679 PMCID: PMC3711432 DOI: 10.1093/nar/gkt354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition.
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Affiliation(s)
- Hans Wienk
- Bijvoet Center For Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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23
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Das D, Folkers GE, van Dijk M, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R. The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition. Structure 2012; 20:667-75. [PMID: 22483113 DOI: 10.1016/j.str.2012.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/22/2012] [Accepted: 02/17/2012] [Indexed: 11/26/2022]
Abstract
Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first HhH motif contacts the ssDNA phosphate backbone. One guanine base is flipped out of register and positioned in a pocket contacting residues from both HhH motifs of XPF. Comparison to other HhH-containing proteins indicates a one-residue deletion in the second HhH motif of XPF that has altered the hairpin conformation, thereby permitting ssDNA interactions. Previous nuclear magnetic resonance studies showed that ERCC1 in the XPF-ERCC1 heterodimer can bind dsDNA. Combining the two observations gives a model that underscores the asymmetry of the human XPF/ERCC1 heterodimer in binding at an ss/ds DNA junction.
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Affiliation(s)
- Devashish Das
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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24
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Wienk H, Tishchenko E, Belardinelli R, Tomaselli S, Dongre R, Spurio R, Folkers GE, Gualerzi CO, Boelens R. Structural dynamics of bacterial translation initiation factor IF2. J Biol Chem 2012; 287:10922-32. [PMID: 22308033 DOI: 10.1074/jbc.m111.333393] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial translation initiation factor IF2 promotes ribosomal subunit association, recruitment, and binding of fMet-tRNA to the ribosomal P-site and initiation dipeptide formation. Here, we present the solution structures of GDP-bound and apo-IF2-G2 of Bacillus stearothermophilus and provide evidence that this isolated domain binds the 50 S ribosomal subunit and hydrolyzes GTP. Differences between the free and GDP-bound structures of IF2-G2 suggest that domain reorganization within the G2-G3-C1 regions underlies the different structural requirements of IF2 during the initiation process. However, these structural signals are unlikely forwarded from IF2-G2 to the C-terminal fMet-tRNA binding domain (IF2-C2) because the connected IF2-C1 and IF2-C2 modules show completely independent mobility, indicating that the bacterial interdomain connector lacks the rigidity that was found in the archaeal IF2 homolog aIF5B.
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Affiliation(s)
- Hans Wienk
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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25
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Berger I, Blanco AG, Boelens R, Cavarelli J, Coll M, Folkers GE, Nie Y, Pogenberg V, Schultz P, Wilmanns M, Moras D, Poterszman A. Structural insights into transcription complexes. J Struct Biol 2011; 175:135-46. [DOI: 10.1016/j.jsb.2011.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 04/09/2011] [Accepted: 04/27/2011] [Indexed: 01/24/2023]
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26
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Huang A, de Jong RN, Folkers GE, Boelens R. NMR characterization of foldedness for the production of E3 RING domains. J Struct Biol 2010; 172:120-7. [PMID: 20682345 DOI: 10.1016/j.jsb.2010.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 07/23/2010] [Accepted: 07/28/2010] [Indexed: 01/17/2023]
Abstract
We summarize the use of NMR spectroscopy in the production and the screening of stability and foldedness of protein domains, and apply it to the RING domains of E3 ubiquitin-ligases. RING domains are involved in specific interactions with E2 ubiquitin-conjugating enzymes and thus play an essential role in the ubiquitination pathway. Protein production of the Zn(2+) containing and cysteine rich RING domains for molecular studies frequently turns out to be problematic. We compared the expression and solubility of 14 E3 RING/U-box domains fused to the N-terminal tags of His(6), His(6)-GB1, His(6)-Trx and His(6)-GST at small scale and analyzed, by NMR spectroscopy, their correct folding after purification. The addition of GST, Trx or GB1 to the N-terminal His(6) tag significantly improved both the expression and solubility of target proteins as compared to His(6) tag alone. More importantly most of the immobilized metal affinity chromatography (IMAC) purified proteins were largely unfolded as judged by analysis of the (1)H-(15)N HSQC spectra. We demonstrate that imidazole causes a concentration dependent decrease in stability of RING proteins ascribed to metal depletion and resulting in unfolding or precipitation. In contrast, using glutathione affinity chromatography, the His(6)-GST fused RING and U-box domains were purified as correctly folded proteins with high yields. Our data clearly demonstrate that IMAC should be avoided and that GST-fusion affinity chromatography is generally applicable for expression and purification of Zn(2+) containing proteins.
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Affiliation(s)
- Anding Huang
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, The Netherlands
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27
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Bird LE, Ren J, Nettleship JE, Folkers GE, Owens RJ, Stammers DK. Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains. BMC Struct Biol 2010; 10:13. [PMID: 20509910 PMCID: PMC2893186 DOI: 10.1186/1472-6807-10-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 05/28/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Zhx1 to 3 (zinc-fingers and homeoboxes) form a set of paralogous genes encoding multi-domain proteins. ZHX proteins consist of two zinc fingers followed by five homeodomains. ZHXs have biological roles in cell cycle control by acting as co-repressors of the transcriptional regulator Nuclear Factor Y. As part of a structural genomics project we have expressed single and multi-domain fragments of the different human ZHX genes for use in structure determination. RESULTS A total of 30 single and multiple domain ZHX1-3 constructs selected from bioinformatics protocols were screened for soluble expression in E. coli using high throughput methodologies. Two homeodomains were crystallized leading to structures for ZHX1 HD4 and ZHX2 HD2. ZHX1 HD4, although closest matched to homeodomains from 'homez' and 'engrailed', showed structural differences, notably an additional C-terminal helix (helix V) which wrapped over helix I thereby making extensive contacts. Although ZHX2 HD2-3 was successfully expressed and purified, proteolysis occurred during crystallization yielding crystals of just HD2. The structure of ZHX2 HD2 showed an unusual open conformation with helix I undergoing 'domain-swapping' to form a homodimer. CONCLUSIONS Although multiple-domain constructs of ZHX1 selected by bioinformatics studies could be expressed solubly, only single homeodomains yielded crystals. The crystal structure of ZHX1 HD4 showed additional hydrophobic interactions relative to many known homeodomains via extensive contacts formed by the novel C-terminal helix V with, in particular, helix I. Additionally, the replacement of some charged covariant residues (which are commonly observed to form salt bridges in non-homeotherms such as the Drosophila 'engrailed' homeodomain), by apolar residues further increases hydrophobic contacts within ZHX1 HD4, and potentially stability, relative to engrailed homeodomain. ZHX1 HD4 helix V points away from the normally observed DNA major groove binding site on homeodomains and thus would not obstruct the putative binding of nucleic acid. In contrast, for ZHX2 HD2 the observed altered conformation involving rearrangement of helix I, relative to the canonical homeodomain fold, disrupts the normal DNA binding site, although protein-protein binding is possible as observed in homodimer formation.
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28
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Dadvar P, Kovanich D, Folkers GE, Rumpel K, Raijmakers R, Heck AJR. Phosphatidylethanolamine-binding proteins, including RKIP, exhibit affinity for phosphodiesterase-5 inhibitors. Chembiochem 2010; 10:2654-62. [PMID: 19760692 DOI: 10.1002/cbic.200900452] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Identifying protein "interactors" of drugs is of great importance to understand their mode of action and possible cross-reactivity to off-target protein binders. In this study, we profile proteins that bind to PF-3717842, a high-affinity phosphodiesterase-5 (PDE5) inhibitor, by using a refined affinity pulldown approach with PF-3717842 immobilized beads. By performing these pulldowns in rat testis tissue lysate, we strongly and specifically enriched for PDE5 and a few other PDEs. In addition to these expected affinity-enriched proteins we also detect rodent-specific phosphatidylethanolamine-binding protein 2 (PEBP2), as a putative binder to the PDE5 inhibitor. By using recombinant forms of the related murine mPEBP2, mPEBP1 and human hPEBP1 (also known as Raf kinase inhibitor protein or RKIP) we confirm that they all can bind strongly to immobilized as well as soluble PF-3717842. As the phosphatidylethanolamine-binding proteins are involved in various important signal transduction pathways, the synthetic PDE5 inhibitor used here might form a platform to synthesize enhanced binders/inhibitors of the family of PEBP proteins. Our approach shows how chemical proteomics might be used to profile the biochemical space (interactome) of small molecule inhibitors.
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Affiliation(s)
- Poupak Dadvar
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, NL
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29
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Dadvar P, Kovanich D, Folkers GE, Rumpel K, Raijmakers R, Heck AJR. Cover Picture: Phosphatidylethanolamine-Binding Proteins, Including RKIP, Exhibit Affinity for Phosphodiesterase-5 Inhibitors (ChemBioChem 16/2009). Chembiochem 2009. [DOI: 10.1002/cbic.200990071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Wienk H, Lammers I, Hotze A, Wu J, Wechselberger RW, Owens R, Stammers DK, Stuart D, Kaptein R, Folkers GE. The Tandem Zinc-Finger Region of Human ZHX Adopts a Novel C2H2 Zinc Finger Structure with a C-Terminal Extension. Biochemistry 2009; 48:4431-9. [DOI: 10.1021/bi9001997] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Romanuka J, van den Bulke H, Kaptein R, Boelens R, Folkers GE. Novel strategies to overcome expression problems encountered with toxic proteins: application to the production of Lac repressor proteins for NMR studies. Protein Expr Purif 2009; 67:104-12. [PMID: 19460439 DOI: 10.1016/j.pep.2009.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Revised: 05/01/2009] [Accepted: 05/12/2009] [Indexed: 11/19/2022]
Abstract
NMR studies of structural aspects of allosteric regulation by the Lac repressor requires overexpression and isotope labeling of the protein. The size of the repressor makes it a challenging target, putting constraints on both expression conditions and sample preparation methods to overcome problems associated with studies of larger proteins by NMR. We optimized protocols for the production of deuterated functionally active thermostable dimeric Lac repressor and its core domain mutants. The Lac repressor core domain has never been obtained as a recombinant protein, possibly due to the observed toxicity to the host cells. We overcame the core domain induced toxicity by co-expression of this domain with the full length Lac repressor, combined with a stringent control of culture conditions. Significant overexpression was only obtained if during all stages of pre-culturing the bacteria were kept in their exponential growth phase at low density. The sensitivity of NMR measurements is dramatically affected by buffer conditions; we therefore used a thermofluor buffer optimization screen to determine the optimal buffer conditions. The combined thermofluor and NMR screening method yielded thermostable fully functional Lac repressor domain samples suitable for high-resolution NMR studies. The optimized procedures to adapt Escherichia coli to growth in D2O, to overcome toxicity, and to optimize protein sample conditions provides a broad range of universally applicable techniques for production of larger proteins for NMR spectroscopy.
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Affiliation(s)
- Julija Romanuka
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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32
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Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AMJJ, Kaptein R, Boelens R. Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. J Mol Biol 2009; 390:478-89. [PMID: 19450607 DOI: 10.1016/j.jmb.2009.05.022] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 05/08/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
Abstract
The structures of a dimeric mutant of the Lac repressor DNA-binding domain complexed with the auxiliary operators O2 and O3 have been determined using NMR spectroscopy and compared to the structures of the previously determined Lac-O1 and Lac-nonoperator complexes. Structural analysis of the Lac-O1 and Lac-O2 complexes shows highly similar structures with very similar numbers of specific and nonspecific contacts, in agreement with similar affinities for these two operators. The left monomer of the Lac repressor in the Lac-O3 complex retains most of these specific contacts. However, in the right half-site of the O3 operator, there is a significant loss of protein-DNA contacts, explaining the low affinity of the Lac repressor for the O3 operator. The binding mode in the right half-site resembles that of the nonspecific complex. In contrast to the Lac-nonoperator DNA complex where no hinge helices are formed, the stability of the hinge helices in the weak Lac-O3 complex is the same as in the Lac-O1 and Lac-O2 complexes, as judged from the results of hydrogen/deuterium experiments.
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Affiliation(s)
- Julija Romanuka
- Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands
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33
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Diercks T, AB E, Daniels MA, de Jong RN, Besseling R, Kaptein R, Folkers GE. Solution structure and characterization of the DNA-binding activity of the B3BP-Smr domain. J Mol Biol 2008; 383:1156-70. [PMID: 18804481 DOI: 10.1016/j.jmb.2008.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 09/01/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
Abstract
The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain.
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Affiliation(s)
- Tammo Diercks
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Faculty of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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34
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Das D, Tripsianes K, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R, Folkers GE. The HhH domain of the human DNA repair protein XPF forms stable homodimers. Proteins 2008; 70:1551-63. [PMID: 17912758 DOI: 10.1002/prot.21635] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human XPF-ERCC1 protein complex plays an essential role in nucleotide excision repair by catalysing positioned nicking of a DNA strand at the 5' side of the damage. We have recently solved the structure of the heterodimeric complex of the C-terminal domains of XPF and ERCC1 (Tripsianes et al., Structure 2005;13:1849-1858). We found that this complex comprises a pseudo twofold symmetry axis and that the helix-hairpin-helix motif of ERCC1 is required for DNA binding, whereas the corresponding domain of XPF is functioning as a scaffold for complex formation with ERCC1. Despite the functional importance of heterodimerization, the C-terminal domain of XPF can also form homodimers in vitro. We here compare the stabilities of homodimeric and heterodimeric complexes of the C-terminal domains of XPF and ERCC1. The higher stability of the XPF HhH complexes under various experimental conditions, determined using CD and NMR spectroscopy and mass spectrometry, is well explained by the structural differences that exist between the HhH domains of the two complexes. The XPF HhH homodimer has a larger interaction interface, aromatic stacking interactions, and additional hydrogen bond contacts as compared to the XPF/ERCC1 HhH complex, which accounts for its higher stability.
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Affiliation(s)
- Devashish Das
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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35
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de Jong RN, Truffault V, Diercks T, Ab E, Daniels MA, Kaptein R, Folkers GE. Structure and DNA binding of the human Rtf1 Plus3 domain. Structure 2008; 16:149-59. [PMID: 18184592 DOI: 10.1016/j.str.2007.10.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 09/17/2007] [Accepted: 10/16/2007] [Indexed: 11/30/2022]
Abstract
The yeast Paf1 complex consists of Paf1, Rtf1, Cdc73, Ctr9, and Leo1 and regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. We provide structural insight into the Paf1 complex with the NMR structure of the conserved and functionally important Plus3 domain of human Rtf1. A predominantly beta-stranded subdomain displays structural similarity to Dicer/Argonaute PAZ domains and to Tudor domains. We further demonstrate that the highly basic Rtf1 Plus3 domain can interact in vitro with single-stranded DNA via residues on the rim of the beta sheet, reminiscent of siRNA binding by PAZ domains, but did not detect binding to double-stranded DNA or RNA. We discuss the potential role of Rtf1 Plus3 ssDNA binding during transcription elongation.
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Affiliation(s)
- Rob N de Jong
- Bijvoet Centre for Biomolecular Research, Utrecht University, Faculty of Chemistry, Department NMR Spectroscopy, Padualaan 8, Utrecht, The Netherlands
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36
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Tripsianes K, Folkers GE, Zheng C, Das D, Grinstead JS, Kaptein R, Boelens R. Analysis of the XPA and ssDNA-binding surfaces on the central domain of human ERCC1 reveals evidence for subfunctionalization. Nucleic Acids Res 2007; 35:5789-98. [PMID: 17720715 PMCID: PMC2034474 DOI: 10.1093/nar/gkm503] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Human ERCC1/XPF is a structure-specific endonuclease involved in multiple DNA repair pathways. We present the solution structure of the non-catalytic ERCC1 central domain. Although this domain shows structural homology with the catalytically active XPF nuclease domain, functional investigation reveals a completely distinct function for the ERCC1 central domain by performing interactions with both XPA and single-stranded DNA. These interactions are non-competitive and can occur simultaneously through distinct interaction surfaces. Interestingly, the XPA binding by ERCC1 and the catalytic function of XPF are dependent on a structurally homologous region of the two proteins. Although these regions are strictly conserved in each protein family, amino acid composition and surface characteristics are distinct. We discuss the possibility that after XPF gene duplication, the redundant ERCC1 central domain acquired novel functions, thereby increasing the fidelity of eukaryotic DNA repair.
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Affiliation(s)
| | | | | | | | | | | | - Rolf Boelens
- *To whom correspondence should be addressed. +31 30 2534035+31 30 2537623
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37
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Kamphuis MB, Monti MC, van den Heuvel RHH, Santos-Sierra S, Folkers GE, Lemonnier M, Díaz-Orejas R, Heck AJR, Boelens R. Interactions between the toxin Kid of the bacterial parD system and the antitoxins Kis and MazE. Proteins 2007; 67:219-31. [PMID: 17206710 DOI: 10.1002/prot.21254] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The proteins Kid and Kis are the toxin and antitoxin, respectively, encoded by the parD operon of Escherichia coli plasmid R1. Kis prevents the inhibition of E. coli cell growth caused by the RNA cleavage activity of Kid. Overproduction of MazE, the chromosome-encoded homologue of Kis, has been demonstrated to neutralize Kid toxicity to a certain extent in the absence of native Kis. Here, we show that a high structural similarity exists between these antitoxins, using NMR spectroscopy. We report about the interactions between Kid and Kis that are responsible for neutralization of Kid toxicity and enhance autoregulation of parD transcription. Native macromolecular mass spectrometry data demonstrate that Kid and Kis form multiple complexes. At Kis:Kid ratios equal to or exceeding 1:1, as found in vivo in a plasmid-containing cell, various complexes are present, ranging from Kid(2)-Kis(2) tetramer up to Kis(2)-Kid(2)-Kis(2)-Kid(2)-Kis(2) decamer. When Kid is in excess of Kis, corresponding to an in vivo situation immediately after loss of the plasmid, the Kid(2)-Kis(2)-Kid(2) heterohexamer is the most abundant species. NMR chemical shift and intensity perturbations in the (1)H (15)N HSQC spectra of Kid and Kis, observed when titrating the partner protein, show that the interaction sites of Kid and Kis resemble those within the previously reported MazF(2)-MazE(2)-MazF(2) complex. Furthermore, we demonstrate that Kid(2)-MazE(2) tetramers can be formed via weak interactions involving a limited part of the Kis-binding residues of Kid. The functional roles of the identified Kid-Kis and Kid-MazE interaction sites and complexes in toxin neutralization and repression of transcription are discussed.
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Affiliation(s)
- Monique B Kamphuis
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Utrecht, The Netherlands
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38
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de Jong RN, Daniëls MA, Kaptein R, Folkers GE. Enzyme free cloning for high throughput gene cloning and expression. ACTA ACUST UNITED AC 2007; 7:109-18. [PMID: 17295099 DOI: 10.1007/s10969-006-9014-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 12/14/2006] [Indexed: 10/23/2022]
Abstract
Structural and functional genomics initiatives significantly improved cloning methods over the past few years. Although recombinational cloning is highly efficient, its costs urged us to search for an alternative high throughput (HTP) cloning method. We implemented a modified Enzyme Free Cloning (EFC) procedure, a PCR-only method that eliminates all variables other than PCR efficiency by circumventing enzymatic treatments. We compared the cloning efficiency of EFC with that of Ligation Independent Cloning (LIC). Both methods are well suited for HTP cloning, but EFC yields three times more transformants and a cloning efficiency of 91%, comparable with recombinational cloning methods and significantly better than LIC (79%). EFC requires only nanogram amounts of both vector and insert, does not require highly competent cells and is, in contrast to LIC, largely insensitive to variations in PCR product concentration. Automated protein expression screening of expression strains directly transformed with EFC reactions showed, that the traditional preceding step via a cloning strain can be circumvented. EFC proves an efficient and robust HTP cloning method, that is compatible with existing Ligation Independent Cloning vectors, and highly suitable for automation.
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Affiliation(s)
- Rob N de Jong
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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39
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Grenha R, Rzechorzek NJ, Brannigan JA, de Jong RN, Ab E, Diercks T, Truffault V, Ladds JC, Fogg MJ, Bongiorni C, Perego M, Kaptein R, Wilson KS, Folkers GE, Wilkinson AJ. Structural Characterization of Spo0E-like Protein-aspartic Acid Phosphatases That Regulate Sporulation in Bacilli. J Biol Chem 2006; 281:37993-8003. [PMID: 17001075 DOI: 10.1074/jbc.m607617200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Spore formation is an extreme response of many bacterial species to starvation. In the case of pathogenic species of Bacillus and Clostridium, it is also a component of disease transmission. Entry into the pathway of sporulation in Bacillus subtilis and its relatives is controlled by an expanded two-component system in which starvation signals lead to the activation of sensor kinases and phosphorylation of the master sporulation response regulator Spo0A. Accumulation of threshold concentrations of Spo0A approximately P heralds the commitment to sporulation. Countering the activities of the sensor kinases are phosphatases such as Spo0E, which dephosphorylate Spo0A approximately P and inhibit sporulation. Spo0E-like protein-aspartic acid-phosphate phosphatases, consisting of 50-90 residues, are conserved in sporeforming bacteria and unrelated in sequence to proteins of known structure. Here we determined the structures of the Spo0A approximately P phosphatases BA1655 and BA5174 from Bacillus anthracis using nuclear magnetic resonance spectroscopy. Each is composed of two anti-parallel alpha-helices flanked by flexible regions at the termini. The signature SQELD motif (SRDLD in BA1655) is situated in the middle of helix alpha2 with its polar residues projecting outward. BA5174 is a monomer, whereas BA1655 is a dimer. The four-helix bundle structure in the dimer is reminiscent of the phosphotransferase Spo0B and the chemotaxis phosphatase CheZ, although in contrast to these systems, the subunits in BA1655 are in head-to-tail rather than head-to-head apposition. The implications of the structures for interactions between the phosphatases and their substrate Spo0A approximately P are discussed.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Bacillus anthracis/enzymology
- Bacillus anthracis/genetics
- Bacillus anthracis/physiology
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Base Sequence
- DNA, Bacterial/genetics
- Dimerization
- Genes, Bacterial
- Models, Molecular
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Phosphoric Monoester Hydrolases/chemistry
- Phosphoric Monoester Hydrolases/genetics
- Phosphoric Monoester Hydrolases/physiology
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Sequence Homology, Amino Acid
- Spores, Bacterial/enzymology
- Spores, Bacterial/genetics
- Spores, Bacterial/physiology
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Affiliation(s)
- Rosa Grenha
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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40
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Ab E, Atkinson AR, Banci L, Bertini I, Ciofi-Baffoni S, Brunner K, Diercks T, Dötsch V, Engelke F, Folkers GE, Griesinger C, Gronwald W, Günther U, Habeck M, de Jong RN, Kalbitzer HR, Kieffer B, Leeflang BR, Loss S, Luchinat C, Marquardsen T, Moskau D, Neidig KP, Nilges M, Piccioli M, Pierattelli R, Rieping W, Schippmann T, Schwalbe H, Travé G, Trenner J, Wöhnert J, Zweckstetter M, Kaptein R. NMR in the SPINE Structural Proteomics project. Acta Crystallogr D Biol Crystallogr 2006; 62:1150-61. [PMID: 17001092 DOI: 10.1107/s0907444906032070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 08/14/2006] [Indexed: 11/10/2022]
Abstract
This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.
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Affiliation(s)
- E Ab
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
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41
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Berrow NS, Büssow K, Coutard B, Diprose J, Ekberg M, Folkers GE, Levy N, Lieu V, Owens RJ, Peleg Y, Pinaglia C, Quevillon-Cheruel S, Salim L, Scheich C, Vincentelli R, Busso D. Recombinant protein expression and solubility screening in Escherichia coli: a comparative study. Acta Crystallogr D Biol Crystallogr 2006; 62:1218-26. [PMID: 17001098 DOI: 10.1107/s0907444906031337] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Accepted: 08/09/2006] [Indexed: 11/10/2022]
Abstract
Producing soluble proteins in Escherichia coli is still a major bottleneck for structural proteomics. Therefore, screening for soluble expression on a small scale is an attractive way of identifying constructs that are likely to be amenable to structural analysis. A variety of expression-screening methods have been developed within the Structural Proteomics In Europe (SPINE) consortium and to assist the further refinement of such approaches, eight laboratories participating in the network have benchmarked their protocols. For this study, the solubility profiles of a common set of 96 His(6)-tagged proteins were assessed by expression screening in E. coli. The level of soluble expression for each target was scored according to estimated protein yield. By reference to a subset of the proteins, it is demonstrated that the small-scale result can provide a useful indicator of the amount of soluble protein likely to be produced on a large scale (i.e. sufficient for structural studies). In general, there was agreement between the different groups as to which targets were not soluble and which were the most soluble. However, for a large number of the targets there were wide discrepancies in the results reported from the different screening methods, which is correlated with variations in the procedures and the range of parameters explored. Given finite resources, it appears that the question of how to most effectively explore ;expression space' is similar to several other multi-parameter problems faced by crystallographers, such as crystallization.
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Affiliation(s)
- Nick S Berrow
- Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, Oxford, England
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42
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Abstract
The unstructured N-terminal domain of the transcriptional cofactor PC4 contains multiple phosphorylation sites that regulate activity. The phosphorylation status differentially influences the various biochemical functions performed by the structured core of PC4. Binding to ssDNA is slightly enhanced by phosphorylation of one serine residue, which is not augmented by further phosphorylation. The presence of at least two phosphoserines decreases DNA-unwinding activity and abrogates binding to the transcriptional activator VP16. Phosphorylation gradually decreases the binding affinity for dsDNA. These phosphorylation-dependent changes in PC4 activities correlate with the sequential functions PC4 fulfils throughout the transcription cycle. MS and NMR revealed that up to eight serines are progressively phosphorylated towards the N-terminus, resulting in gradual environmental changes in the C-terminal direction of the following lysine-rich region. Also within the structured core, primarily around the interaction surfaces, environmental changes are observed. We propose a model for co-ordinated changes in PC4 cofactor functions, mediated by phosphorylation status-dependent gradual masking of the lysine-rich region causing shielding or exposure of interaction surfaces.
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Affiliation(s)
- Hendrik R A Jonker
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands
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43
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Jonker HRA, Wechselberger RW, Boelens R, Kaptein R, Folkers GE. The Intrinsically Unstructured Domain of PC4 Modulates the Activity of the Structured Core through Inter- and Intramolecular Interactions. Biochemistry 2006; 45:5067-81. [PMID: 16605275 DOI: 10.1021/bi052531b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins frequently contain unstructured regions apart from a functionally important and well-conserved structured domain. Functional and structural aspects for these regions are frequently less clear. The general human positive cofactor 4 (PC4), has such a domain organization and can interact with various DNA substrates, transcriptional activators, and basal transcription factors. While essential for the cofactor function, structural and functional knowledge about these interactions is limited. Using biochemical, nuclear magnetic resonance (NMR), and docking experiments, we show that the carboxy-terminal structured core domain (PC4ctd) is required and sufficient for binding to single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and the herpes simplex virion protein 16 (VP16) activation domain (VP16ad). We determined the interaction surfaces within PC4 and showed that VP16 and DNA binding are mutually exclusive. Although the amino-terminal domain of PC4 (PC4ntd) alone is devoid of any bioactivity, it increases the interaction with VP16ad. While it decreases the ssDNA-binding and DNA-unwinding activity, it does not influence dsDNA binding. Structural characterization of this domain showed that it is highly flexible and mostly unstructured both in the free form and in the complex. NMR titration experiments using various protein and DNA substrates of the individual domains and the full-length PC4 revealed local conformational or environmental changes in both the structured and unstructured subdomains, which are interpreted to be caused by inter- and intramolecular interactions. We propose that the unstructured PC4ntd regulates the PC4 cofactor function by specific interactions with the activator and through modulation and/or shielding of the interaction surface in the structured core of PC4ctd.
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Affiliation(s)
- Hendrik R A Jonker
- Bijvoet Center for Biomolecular Research, Section NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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44
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de Jong RN, Ab E, Diercks T, Truffault V, Daniëls M, Kaptein R, Folkers GE. Solution Structure of the Human Ubiquitin-specific Protease 15 DUSP Domain. J Biol Chem 2006; 281:5026-31. [PMID: 16298993 DOI: 10.1074/jbc.m510993200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) can remove covalently attached ubiquitin moieties from target proteins and regulate both the stability and ubiquitin-signaling state of their substrates. All USPs contain a conserved catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. One such specific subdomain, the DUSP domain (domain present in ubiquitin-specific proteases), is present in at least seven different human USPs that regulate the stability of or interact with the hypoxia-inducible transcription factor HIF1-alpha, the Von Hippel-Lindau protein (pVHL), cullin E3 ligases, and BRCA2. We describe the NMR solution structure of the DUSP domain of human USP15, recently implicated in COP9 (constitutive photomorphogenic gene 9)-signalosome regulation. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet. The DUSP domain displays a novel fold, an alpha/beta tripod (AB3). DUSP domain surface properties and previously described work suggest a potential role in protein/protein interaction or substrate recognition.
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Affiliation(s)
- Rob N de Jong
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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45
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Kopke Salinas R, Folkers GE, Bonvin AMJJ, Das D, Boelens R, Kaptein R. Altered specificity in DNA binding by the lac repressor: a mutant lac headpiece that mimics the gal repressor. Chembiochem 2006; 6:1628-37. [PMID: 16094693 DOI: 10.1002/cbic.200500049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recognition of the lac operator by the lac repressor involves specific interactions between residues in the repressor's recognition helix and bases in the DNA major groove. Tyr17 and Gln18, at positions 1 and 2 in the lac repressor recognition helix, can be exchanged for other amino acids to generate mutant repressors that display altered specificity. We have solved the solution structure of a protein-DNA complex of an altered-specificity mutant lac headpiece in which Tyr17 and Gln18 were exchanged for valine and alanine, respectively, as found in the recognition helix of the gal repressor. As previously described by Lehming et al. (EMBO J. 1987, 6, 3145-3153), this altered-specificity mutant of the lac repressor recognizes a variant lac operator that is similar to the gal operator Oe. The mutant lac headpiece showed the predicted specificity and is also able to mimic the gal repressor by recognizing and bending the natural gal operator Oe. These structural data show that, while most of the anchoring points that help the lac headpiece to assemble on the lac operator were preserved, a different network of protein-DNA interactions connecting Ala17 and Val18 to bases in the DNA major groove drives the specificity towards the altered operator.
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Affiliation(s)
- Roberto Kopke Salinas
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.
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46
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Patterson HM, Brannigan JA, Cutting SM, Wilson KS, Wilkinson AJ, Ab E, Diercks T, de Jong RN, Truffault V, Folkers GE, Kaptein R. The Structure of Bypass of Forespore C, an Intercompartmental Signaling Factor during Sporulation in Bacillus. J Biol Chem 2005; 280:36214-20. [PMID: 16049010 DOI: 10.1074/jbc.m506910200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sporulation in Bacillus subtilis begins with an asymmetric cell division giving rise to smaller forespore and larger mother cell compartments. Different programs of gene expression are subsequently directed by compartment-specific RNA polymerase sigma-factors. In the final stages, spore coat proteins are synthesized in the mother cell under the control of RNA polymerase containing sigma(K), (Esigma(K)). sigma(K) is synthesized as an inactive zymogen, pro-sigma(K), which is activated by proteolytic cleavage. Processing of pro-sigma(K) is performed by SpoIVFB, a metalloprotease that resides in a complex with SpoIVFA and bypass of forespore (Bof)A in the outer forespore membrane. Ensuring coordination of events taking place in the two compartments, pro-sigma(K) processing in the mother cell is delayed until appropriate signals are received from the forespore. Cell-cell signaling is mediated by SpoIVB and BofC, which are expressed in the forespore and secreted to the intercompartmental space where they regulate pro-sigma(K) processing by mechanisms that are not yet fully understood. Here we present the three-dimensional structure of BofC determined by solution state NMR. BofC is a monomer made up of two domains. The N-terminal domain, containing a four-stranded beta-sheet onto one face of which an alpha-helix is packed, closely resembles the third immunoglobulin-binding domain of protein G from Streptococcus. The C-terminal domain contains a three-stranded beta-sheet and three alpha-helices in a novel domain topology. The sequence connecting the domains contains a conserved DISP motif to which mutations that affect BofC activity map. Possible roles for BofC in the sigma(K) checkpoint are discussed in the light of sequence and structure comparisons.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Bacillus subtilis/metabolism
- Bacterial Outer Membrane Proteins/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/physiology
- Cell Communication
- Cell Membrane/metabolism
- DNA-Directed RNA Polymerases/chemistry
- Electrophoresis, Polyacrylamide Gel
- Gene Deletion
- Gene Expression Regulation, Bacterial
- Magnetic Resonance Spectroscopy
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Phenotype
- Plasmids/metabolism
- Protein Conformation
- Protein Folding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Recombinant Proteins/chemistry
- Sequence Homology, Amino Acid
- Signal Transduction
- Spectrometry, Mass, Electrospray Ionization
- Spores, Bacterial/metabolism
- Spores, Bacterial/physiology
- Transcription Factors/chemistry
- Transcription Factors/physiology
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Affiliation(s)
- Hayley M Patterson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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Abstract
Herpes simplex virion protein 16 (VP16) contains two strong activation regions that can independently and cooperatively activate transcription in vivo. We have identified the regions and residues involved in the interaction with the human transcriptional coactivator positive cofactor 4 (PC4) and the general transcription factor TFIIB. NMR and biochemical experiments revealed that both VP16 activation regions are required for the interaction and undergo a conformational transition from random coil to alpha-helix upon binding to its target PC4. The interaction is strongly electrostatically driven and the binding to PC4 is enhanced by the presence of its amino-terminal domain. We propose models for binding of VP16 to the core domains of PC4 and TFIIB that are based on two independent docking approaches using NMR chemical shift changes observed in titration experiments. The models are consistent with results from site-directed mutagenesis and provide an explanation for the contribution of both acidic and hydrophobic residues for transcriptional activation by VP16. Both intrinsically unstructured activation domains are attracted to their interaction partner by electrostatic interactions, and adopt an alpha-helical conformation around the important hydrophobic residues. The models showed multiple distinct binding surfaces upon interaction with various partners, providing an explanation for the promiscuous properties, cooperativity, and the high activity of this activation domain.
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Affiliation(s)
- Hendrik R A Jonker
- Bijvoet Center for Biomolecular Research, section NMR spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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48
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Abstract
Structural genomics, the determination of protein structures on a genome-wide scale, is still in its infancy for eukaryotes due to the number and size of their genes. Low protein expression and solubility of eukaryotic geneproducts are the major bottlenecks in high-throughput (HTP) recombinant protein production with the E. coli expression systems. To circumvent this problem we decided to focus on separate protein domains. We describe here a fast microtiterplate based, expression and solubility screening procedure, using a combination of in vitro and in vivo expression, and purification with nickel-NTA magnetic beads. All steps are optimized for automatic HTP processing using a liquid handling station. Furthermore, large-scale expression and protein purification conditions are optimized, permitting the purification of 24 protein samples per week. We further show that results obtained from the expression screening can be extrapolated to the production of protein samples for NMR. Starting with 81 cloned human protein domains, in vivo expression was detected in 54 cases, and from 28 of those milligrams of protein were purified. An informative HSQC spectrum was recorded for 18 proteins (22%), half of which were indicative of a folded protein. The success rate and quality of the HSQC spectra suggest that the domain approach holds promise for human proteins.
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Affiliation(s)
- G E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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49
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Kalodimos CG, Folkers GE, Boelens R, Kaptein R. Strong DNA binding by covalently linked dimeric Lac headpiece: evidence for the crucial role of the hinge helices. Proc Natl Acad Sci U S A 2001; 98:6039-44. [PMID: 11353825 PMCID: PMC33418 DOI: 10.1073/pnas.101129898] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The combined structural and biochemical studies on Lac repressor bound to operator DNA have demonstrated the central role of the hinge helices in operator bending and the induction mechanism. We have constructed a covalently linked dimeric Lac-headpiece that binds DNA with four orders of magnitude higher affinity as compared with the monomeric form. This enabled a detailed biochemical and structural study of Lac binding to its cognate wild-type and selected DNA operators. The results indicate a profound contribution of hinge helices to the stability of the protein-DNA complex and highlight their central role in operator recognition. Furthermore, protein-DNA interactions in the minor groove appear to modulate hinge helix stability, thus accounting for affinity differences and protein-induced DNA bending among the various operator sites. Interestingly, the in vitro DNA-binding affinity of the reported dimeric Lac construct can de readily modulated by simple adjustment of redox conditions, thus rendering it a potential artificial gene regulator.
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Affiliation(s)
- C G Kalodimos
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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50
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van Tilborg PJ, Czisch M, Mulder FA, Folkers GE, Bonvin AM, Nair M, Boelens R, Kaptein R. Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site. Biochemistry 2000; 39:8747-57. [PMID: 10913286 DOI: 10.1021/bi991550g] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The retinoid X receptor (RXR) is a prominent member of the nuclear receptor family of ligand-inducible transcription factors. Many proteins of this family exert their function as heterodimers with RXR as a common upstream partner. Studies of the DNA-binding domains of several nuclear receptors reveal differences in structure and dynamics, both between the different proteins and between the free- and DNA-bound receptor DBDs. We investigated the differences in dynamics between RXR free in solution and in complex with a 14 base-pair oligonucleotide, using (1)H and (15)N relaxation studies. Nano- to picosecond dynamics were probed on (15)N, employing Lipari-Szabo analysis with an axially symmetric tumbling model to estimate the exchange contributions to the transverse relaxation rates. Furthermore, milli- to microsecond dynamics were estimated qualitatively for (1)H and (15)N, using CPMG-HSQC and CPMG-T(2) measurements with differential pulse spacing. RXR shows hardly any nano- to picosecond time-scale internal motion. Upon DNA binding, the order parameters show a tiny increase. Dynamics in the milli- to microsecond time scale is more prevalent. It is localized in the first and second zinc fingers of the free RXR. Upon DNA-binding, exchange associated with specific/aspecific DNA-binding of RXR is observed throughout the sequence, whereas conformational flexibility of the D-box and the second zinc finger of RXR is greatly reduced. Since this DNA-binding induced folding transition occurs remote from the DNA in a region which is involved in protein-protein interactions, it may very well be related to the cooperativity of dimeric DNA binding.
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Affiliation(s)
- P J van Tilborg
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy Department, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
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