1
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Nouri S, Boudet J, Dreher-Teo H, Allain FHT, Glockshuber R, Salmon L, Giese C. Elongated Bacterial Pili as a Versatile Alignment Medium for NMR Spectroscopy. Angew Chem Int Ed Engl 2023; 62:e202305120. [PMID: 37248171 DOI: 10.1002/anie.202305120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
In NMR spectroscopy, residual dipolar couplings (RDCs) have emerged as one of the most exquisite probes of biological structure and dynamics. The measurement of RDCs relies on the partial alignment of the molecule of interest, for example by using a liquid crystal as a solvent. Here, we establish bacterial type 1 pili as an alternative liquid-crystalline alignment medium for the measurement of RDCs. To achieve alignment at pilus concentrations that allow for efficient NMR sample preparation, we elongated wild-type pili by recombinant overproduction of the main structural pilus subunit. Building on the extraordinary stability of type 1 pili against spontaneous dissociation and unfolding, we show that the medium is compatible with challenging experimental conditions such as high temperature, the presence of detergents, organic solvents or very acidic pH, setting it apart from most established alignment media. Using human ubiquitin, HIV-1 TAR RNA and camphor as spectroscopic probes, we demonstrate the applicability of the medium for the determination of RDCs of proteins, nucleic acids and small molecules. Our results show that type 1 pili represent a very useful alternative to existing alignment media and may readily assist the characterization of molecular structure and dynamics by NMR.
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Affiliation(s)
- Sirine Nouri
- Centre de RMN à Très Hauts Champs, CNRS, ENSL, UCBL, Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Julien Boudet
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Hiang Dreher-Teo
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Loïc Salmon
- Centre de RMN à Très Hauts Champs, CNRS, ENSL, UCBL, Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Christoph Giese
- Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
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2
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Zhu W, Yang DT, Gronenborn AM. Ligand-Capped Cobalt(II) Multiplies the Value of the Double-Histidine Motif for PCS NMR Studies. J Am Chem Soc 2023; 145:4564-4569. [PMID: 36786809 PMCID: PMC10032564 DOI: 10.1021/jacs.2c12021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 02/15/2023]
Abstract
In structural studies by NMR, pseudocontact shifts (PCSs) provide both angular and distance information. For proteins, incorporation of a di-histidine (diHis) motif, coordinated to Co2+, has emerged as an important tool to measure PCS. Here, we show that using different Co(II)-chelating ligands, such as nitrilotriacetic acid (NTA) and iminodiacetic acid (IDA), resolves the isosurface ambiguity of Co2+-diHis and yields orthogonal PCS data sets with different Δχ-tensors for the same diHis-bearing protein. Importantly, such capping ligands effectively eliminate undesired intermolecular interactions, which can be detrimental to PCS studies. Devising and employing ligand-capping strategies afford versatile and powerful means to obtain multiple orthogonal PCS data sets, significantly extending the use of the diHis motif for structural studies by NMR.
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Affiliation(s)
- Wenkai Zhu
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Darian T. Yang
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department
of Chemistry, University of Pittsburgh,
Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M. Gronenborn
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department
of Chemistry, University of Pittsburgh,
Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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3
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Andrałojć W, Wieruszewska J, Pasternak K, Gdaniec Z. Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints. Chemistry 2022; 28:e202202114. [PMID: 36043489 PMCID: PMC9828363 DOI: 10.1002/chem.202202114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 01/12/2023]
Abstract
In this contribution we report the high-resolution NMR structure of a recently identified lanthanide-binding aptamer (LnA). We demonstrate that the rigid lanthanide binding by LnA allows for the measurement of anisotropic paramagnetic NMR restraints which to date remain largely inaccessible for nucleic acids. One type of such restraints - pseudocontact shifts (PCS) induced by four different paramagnetic lanthanides - was extensively used throughout the current structure determination study and the measured PCS turned out to be exceptionally well reproduced by the final aptamer structure. This finding opens the perspective for a broader application of paramagnetic effects in NMR studies of nucleic acids through the transplantation of the binding site found in LnA into other DNA/RNA systems.
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Affiliation(s)
- Witold Andrałojć
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Julia Wieruszewska
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Karol Pasternak
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Zofia Gdaniec
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
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4
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Trindade IB, Coelho A, Cantini F, Piccioli M, Louro RO. NMR of paramagnetic metalloproteins in solution: Ubi venire, quo vadis? J Inorg Biochem 2022; 234:111871. [DOI: 10.1016/j.jinorgbio.2022.111871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
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5
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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6
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Chiliveri SC, Robertson AJ, Shen Y, Torchia DA, Bax A. Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems. Chem Rev 2021; 122:9307-9330. [PMID: 34766756 DOI: 10.1021/acs.chemrev.1c00730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide 15N-1H RDCs, to 1H-1H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Angus J Robertson
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Dennis A Torchia
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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7
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Giannoulis A, Ben-Ishay Y, Goldfarb D. Characteristics of Gd(III) spin labels for the study of protein conformations. Methods Enzymol 2021; 651:235-290. [PMID: 33888206 DOI: 10.1016/bs.mie.2021.01.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gd(III) complexes are currently established as spin labels for structural studies of biomolecules using pulse dipolar electron paramagnetic resonance (PD-EPR) techniques. This has been achieved by the availability of medium- and high-field spectrometers, understanding the spin physics underlying the spectroscopic properties of high spin Gd(III) (S=7/2) pairs and their dipolar interaction, the design of well-defined model compounds and optimization of measurement techniques. In addition, a variety of Gd(III) chelates and labeling schemes have allowed a broad scope of applications. In this review, we provide a brief background of the spectroscopic properties of Gd(III) pertinent for effective PD-EPR measurements and focus on the various labels available to date. We report on their use in PD-EPR applications and highlight their pros and cons for particular applications. We also devote a section to recent in-cell structural studies of proteins using Gd(III), which is an exciting new direction for Gd(III) spin labeling.
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Affiliation(s)
- Angeliki Giannoulis
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Yasmin Ben-Ishay
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel.
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8
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Wang Y, An L, Yang Y, Yao L. Generating Five Independent Molecular Alignments for Simultaneous Protein Structure and Dynamics Determination Using Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2020; 92:15263-15269. [PMID: 33166130 DOI: 10.1021/acs.analchem.0c02882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are commonly used in NMR for protein structure and dynamics studies, but it is challenging to generate five independent RDC data sets (required for simultaneous structure and dynamics determination) for most protein molecules in the magnetic field. In this work, a reporter protein with a lanthanide tag is introduced to create five independent alignments. This reporter protein is then attached to target proteins where five independent sets of RDCs are also obtained for the target proteins. The fitting of RDCs provides important information about the structure and dynamics of the target proteins. The method is simple and effective and, in principle, can be used to generate complete sets of RDCs for different protein molecules.
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Affiliation(s)
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Hatanaka T, Kikkawa N, Matsugami A, Hosokawa Y, Hayashi F, Ishida N. The origins of binding specificity of a lanthanide ion binding peptide. Sci Rep 2020; 10:19468. [PMID: 33173124 PMCID: PMC7656248 DOI: 10.1038/s41598-020-76527-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/23/2020] [Indexed: 11/09/2022] Open
Abstract
Lanthanide ions (Ln3+) show similar physicochemical properties in aqueous solutions, wherein they exist as + 3 cations and exhibit ionic radii differences of less than 0.26 Å. A flexible linear peptide lanthanide binding tag (LBT), which recognizes a series of 15 Ln3+, shows an interesting characteristic in binding specificity, i.e., binding affinity biphasically changes with an increase in the atomic number, and shows a greater than 60-fold affinity difference between the highest and lowest values. Herein, by combining experimental and computational investigations, we gain deep insight into the reaction mechanism underlying the specificity of LBT3, an LBT mutant, toward Ln3+. Our results clearly show that LBT3-Ln3+ binding can be divided into three, and the large affinity difference is based on the ability of Ln3+ in a complex to be directly coordinated with a water molecule. When the LBT3 recognizes a Ln3+ with a larger ionic radius (La3+ to Sm3+), a water molecule can interact with Ln3+ directly. This extra water molecule infiltrates the complex and induces dissociation of the Asn5 sidechain (one of the coordinates) from Ln3+, resulting in a destabilizing complex and low affinity. Conversely, with recognition of smaller Ln3+ (Sm3+ to Yb3+), the LBT3 completely surrounds the ions and constructs a stable high affinity complex. Moreover, when the LBT3 recognizes the smallest Ln3+, namely Lu3+, although it completely surrounds Lu3+, an entropically unfavorable phenomenon specifically occurs, resulting in lower affinity than that of Yb3+. Our findings will be useful for the design of molecules that enable the distinction of sub-angstrom size differences.
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Affiliation(s)
- Takaaki Hatanaka
- Toyota Central R&D Labs., Inc., 41-1, Nagakute, Aichi, 480-1192, Japan.
| | - Nobuaki Kikkawa
- Toyota Central R&D Labs., Inc., 41-1, Nagakute, Aichi, 480-1192, Japan
| | - Akimasa Matsugami
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoichi Hosokawa
- Toyota Central R&D Labs., Inc., 41-1, Nagakute, Aichi, 480-1192, Japan
| | - Fumiaki Hayashi
- Advanced NMR Application and Platform Team, NMR Research and Collaboration Group, NMR Science and Development Division, RIKEN SPring-8 Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Nobuhiro Ishida
- Toyota Central R&D Labs., Inc., 41-1, Nagakute, Aichi, 480-1192, Japan
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10
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Giassa IC, Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Boelens R, Fiala R, Trantírek L. HERMES - A Software Tool for the Prediction and Analysis of Magnetic-Field-Induced Residual Dipolar Couplings in Nucleic Acids. Chempluschem 2020; 85:2177-2185. [PMID: 32986260 DOI: 10.1002/cplu.202000505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Indexed: 11/06/2022]
Abstract
Field-Induced Residual Dipolar Couplings (fiRDC) are a valuable source of long-range information on structure of nucleic acids (NA) in solution. A web application (HERMES) was developed for structure-based prediction and analysis of the (fiRDCs) in NA. fiRDC prediction is based on input 3D model structure(s) of NA and a built-in library of nucleobase-specific magnetic susceptibility tensors and reference geometries. HERMES allows three basic applications: (i) the prediction of fiRDCs for a given structural model of NAs, (ii) the validation of experimental or modeled NA structures using experimentally derived fiRDCs, and (iii) assessment of the oligomeric state of the NA fragment and/or the identification of a molecular NA model that is consistent with experimentally derived fiRDC data. Additionally, the program's built-in routine for rigid body modeling allows the evaluation of relative orientation of domains within NA that is in agreement with experimental fiRDCs.
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Affiliation(s)
| | - Andrea Vavrinská
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Jiří Zelinka
- Department of Mathematics and Statistics, Faculty of Science, Masaryk University, Brno, 611 37, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 166 10, Czech Republic
| | - Rolf Boelens
- Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, 3584 CH, The Netherlands
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Brno
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Brno
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11
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Täubert S, Zhang YH, Martinez MM, Siepel F, Wöltjen E, Leonov A, Griesinger C. Lanthanide Tagging of Oligonucleotides to Nucleobase for Paramagnetic NMR. Chembiochem 2020; 21:3333-3337. [PMID: 32687667 PMCID: PMC7754328 DOI: 10.1002/cbic.202000417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/19/2020] [Indexed: 12/03/2022]
Abstract
Although lanthanide tags, which have large anisotropic magnetic susceptibilities, have already been introduced to enrich NMR parameters by long‐range pseudoconact shifts (PCSs) and residual dipolar couplings (RDCs) of proteins, their application to nucleotides has so far been limited to one previous report, due to the high affinities of lanthanides for the phosphodiester backbone of nucleotides and difficult organic synthesis. Herein, we report successful attachment of a lanthanide tag to a chemically synthesized oligonucleotide via a disulfide bond. NMR experiments reveal PCSs of up to 1 ppm and H−H RDCs of up to 8 Hz at 950 MHz. Although weaker magnetic alignment was achieved than with proteins, the paramagnetic data could be fitted to the known structure of the DNA, taking the mobility of the tag into account. While further rigidification of the tag is desirable, this tag could also be used to measure heteronuclear RDCs of 13C,15N‐labeled chemically synthesized DNA and RNA.
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Affiliation(s)
- Sebastian Täubert
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Yong-Hui Zhang
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Mitcheell Maestre Martinez
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Florian Siepel
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Edith Wöltjen
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Andrei Leonov
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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12
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Cho U, Chen JK. Lanthanide-Based Optical Probes of Biological Systems. Cell Chem Biol 2020; 27:921-936. [PMID: 32735780 DOI: 10.1016/j.chembiol.2020.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/28/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
The unique photophysical properties of lanthanides, such as europium, terbium, and ytterbium, make them versatile molecular probes of biological systems. In particular, their long-lived photoluminescence, narrow bandwidth emissions, and large Stokes shifts enable experiments that are infeasible with organic fluorophores and fluorescent proteins. The ability of these metal ions to undergo luminescence resonance energy transfer, and photon upconversion further expands the capabilities of lanthanide probes. In this review, we describe recent advances in the design of lanthanide luminophores and their application in biological research. We also summarize the latest detection systems that have been developed to fully exploit the optical properties of lanthanide luminophores. We conclude with a discussion of remaining challenges and new frontiers in lanthanide technologies. The unprecedented levels of sensitivity and multiplexing afforded by rare-earth elements illustrate how chemistry can enable new approaches in biology.
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Affiliation(s)
- Ukrae Cho
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
| | - James K Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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13
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Urmey AR, Zondlo NJ. Cysteine oxidation to the sulfinic acid induces oxoform-specific lanthanide binding and fluorescence in a designed peptide. Free Radic Biol Med 2020; 152:166-174. [PMID: 32097680 DOI: 10.1016/j.freeradbiomed.2020.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/30/2020] [Accepted: 02/19/2020] [Indexed: 10/24/2022]
Abstract
Cysteine sulfinic acid (Cys-SO2-) is a protein post-translational modification that is formed reversibly under oxidative conditions. A short, encodable peptide was developed whose metal binding and terbium luminescence are dependent on cysteine (Cys) oxidation to the sulfinic acid. The protein design is based on the modification of a key metal-binding aspartate (Asp) in a canonical EF-Hand motif (DKDADGWISPAEAK) to Cys. In this design, Cys in the thiol oxidation state does not mimic the native Asp, and thus the peptide binds terbium(III) (Tb3+) poorly and exhibits weak terbium luminescence (fluorescence). In contrast, when Cys is oxidized to the Cys sulfinic acid oxoform, the Cys sulfinate effectively mimics Asp, resulting in a significant increase in terbium affinity and luminescence. Asp residues at positions 1, 3, and 5 of the EF-Hand motif were examined as potential sites for Cys oxidation-responsive metal binding. The peptide with Cys at residue 1 exhibited the highest Tb3+ affinity in both oxidation states. The peptide with Cys at residue 3 exhibited a 4.2-fold distinction in affinity between the oxidation states. Most significantly, the peptide with Cys at residue 5 had only modest Tb3+ affinity as the Cys thiol, but exhibited a 30-fold increase in Tb3+ affinity and an 18-fold increase in Tb3+ luminescence on Cys oxidation to the sulfinic acid. This peptide (Ac-DKDACGWISPAEAK-NH2) exhibited selective Tb3+ binding via Cys-SO2- over the thiol, S-glutathionyl, S-nitrosyl, and sulfonic acid oxoforms, indicating substantially greater Lewis basicity of the sulfinate than the sulfonate. NMR spectroscopy and quantum homology modeling indicated that the designed peptide binds metal with an overall geometry similar to that of an EF-Hand motif, with the Cys sulfinate effectively replacing Asp as a metal-binding ligand. This peptide was applied to detect Cys oxidation to the sulfinic acid by fluorescence spectroscopy, suggesting its broader application in understanding Cys sulfinic acid biology.
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Affiliation(s)
- Andrew R Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States.
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14
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Joss D, Häussinger D. Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:284-312. [PMID: 31779884 DOI: 10.1016/j.pnmrs.2019.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 05/14/2023]
Abstract
In this review, lanthanide chelating tags and their applications to pseudocontact shift NMR spectroscopy as well as analysis of residual dipolar couplings are covered. A complete overview is presented of DOTA-derived and non-DOTA-derived lanthanide chelating tags, critical points in the design of lanthanide chelating tags as appropriate linker moieties, their stability under reductive conditions, e.g., for in-cell applications, the magnitude of the anisotropy transferred from the lanthanide chelating tag to the biomacromolecule under investigation and structural properties, as well as conformational bias of the lanthanide chelating tags are discussed. Furthermore, all DOTA-derived lanthanide chelating tags used for PCS NMR spectroscopy published to date are displayed in tabular form, including their anisotropy parameters, with all employed lanthanide ions, CB-Ln distances and tagging reaction conditions, i.e., the stoichiometry of lanthanide chelating tags, pH, buffer composition, temperature and reaction time. Additionally, applications of lanthanide chelating tags for pseudocontact shifts and residual dipolar couplings that have been reported for proteins, protein-protein and protein-ligand complexes, carbohydrates, carbohydrate-protein complexes, nucleic acids and nucleic acid-protein complexes are presented and critically reviewed. The vast and impressive range of applications of lanthanide chelating tags to structural investigations of biomacromolecules in solution clearly illustrates the significance of this particular field of research. The extension of the repertoire of lanthanide chelating tags from proteins to nucleic acids holds great promise for the determination of valuable structural parameters and further developments in characterizing intermolecular interactions.
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Affiliation(s)
- Daniel Joss
- University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
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15
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Joss D, Bertrams M, Häussinger D. A Sterically Overcrowded, Isopropyl‐Substituted, Lanthanide‐Chelating Tag for Protein Pseudocontact Shift NMR Spectroscopy: Synthesis of its Macrocyclic Scaffold and Benchmarking on Ubiquitin S57 C and hCA II S166 C. Chemistry 2019; 25:11910-11917. [DOI: 10.1002/chem.201901692] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/27/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Daniel Joss
- Department of ChemistryUniversity of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Maria‐Sophie Bertrams
- Department of ChemistryUniversity of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Daniel Häussinger
- Department of ChemistryUniversity of Basel St. Johanns-Ring 19 4056 Basel Switzerland
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16
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Zimmermann K, Joss D, Müntener T, Nogueira ES, Schäfer M, Knörr L, Monnard FW, Häussinger D. Localization of ligands within human carbonic anhydrase II using 19F pseudocontact shift analysis. Chem Sci 2019; 10:5064-5072. [PMID: 31183057 PMCID: PMC6530540 DOI: 10.1039/c8sc05683h] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/09/2019] [Indexed: 12/17/2022] Open
Abstract
Unraveling the native structure of protein-ligand complexes in solution enables rational drug design. We report here the use of 19F pseudocontact shift (PCS) NMR as a method to determine fluorine positions of high affinity ligands bound within the drug target human carbonic anhydrase II with high accuracy. Three different ligands were localized within the protein by analysis of the obtained PCS from simple one-dimensional 19F spectra with an accuracy of up to 0.8 Å. In order to validate the PCS, four to five independent magnetic susceptibility tensors induced by lanthanide chelating tags bound site-specifically to single cysteine mutants were refined. Least-squares minimization and a Monte-Carlo approach allowed the assessment of experimental errors on the intersection of the corresponding four to five PCS isosurfaces. By defining an angle score that reflects the relative isosurface orientation for different tensor combinations, it was established that the ligand can be localized accurately using only three tensors, if the isosurfaces are close to orthogonal. For two out of three ligands, the determined position closely matched the X-ray coordinates. Our results for the third ligand suggest, in accordance with previously reported ab initio calculations, a rotated position for the difluorophenyl substituent, enabling a favorable interaction with Phe-131. The lanthanide-fluorine distance varied between 22 and 38 Å and induced 19F PCS ranged from 0.078 to 0.409 ppm, averaging to 0.213 ppm. Accordingly, even longer metal-fluorine distances will lead to meaningful PCS, rendering the investigation of protein-ligand complexes significantly larger than 30 kDa feasible.
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Affiliation(s)
- Kaspar Zimmermann
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Daniel Joss
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Thomas Müntener
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Elisa S Nogueira
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Marc Schäfer
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Livia Knörr
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Fabien W Monnard
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
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17
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Joss D, Häussinger D. P4T-DOTA – a lanthanide chelating tag combining a sterically highly overcrowded backbone with a reductively stable linker. Chem Commun (Camb) 2019; 55:10543-10546. [DOI: 10.1039/c9cc04676c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A highly rigidified lanthanide complex induces strong pseudocontact shifts and residual dipolar couplings for structural analysis of proteins in solution.
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Affiliation(s)
- Daniel Joss
- Department of Chemistry
- University of Basel
- 4056 Basel
- Switzerland
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18
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Joss D, Walliser RM, Zimmermann K, Häussinger D. Conformationally locked lanthanide chelating tags for convenient pseudocontact shift protein nuclear magnetic resonance spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2018; 72:29-38. [PMID: 30117038 DOI: 10.1007/s10858-018-0203-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
Pseudocontact shifts (PCS) generated by lanthanide chelating tags yield valuable restraints for investigating protein structures, dynamics and interactions in solution. In this work, dysprosium-, thulium- and terbium-complexes of eight-fold methylated 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid tags [DOTA-M8-(4R4S)-SSPy] are presented that induce large pseudocontact shifts up to 5.5 ppm and adopt exclusively the square antiprismatic conformation. This is in contrast to our earlier findings on complexes of the stereoisomeric DOTA-M8-(8S)-SSPy, where significant amounts of the twisted square antiprismatic conformer for the Dy tag were observed. The Dy-, Tm-, Tb- and Lu-complexes of DOTA-M8-(4R4S)-SSPy were conjugated to ubiquitin S57C and selectively 15N leucine labeled human carbonic anhydrase II S50C, resulting in only one set of signals. Furthermore, we investigated the conformation of the thulium- and dysprosium-complexes in vacuo and with implicit water solvent using density functional theory calculations. The calculated energy differences between the two different conformations (7.0-50.5 kJ/mol) and experimental evidence from the corresponding ytterbium- and yttrium-complexes clearly suggest a SAP [Λ(δδδδ)] geometry for the complexes presented in this study. The lanthanide chelating tag studied in this work offer insights into the solution structure of proteins by inducing strong pseudocontact shifts, show different tensor properties compared to its predecessor, enables a convenient assignment procedure, is accessed by a more economic synthesis than its predecessor and constitutes a highly promising starting point for further developments of lanthanide chelating tags.
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Affiliation(s)
- Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Roché M Walliser
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Kaspar Zimmermann
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland.
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Calisti L, Trabuco MC, Boffi A, Testi C, Montemiglio LC, des Georges A, Benni I, Ilari A, Taciak B, Białasek M, Rygiel T, Król M, Baiocco P, Bonamore A. Engineered ferritin for lanthanide binding. PLoS One 2018; 13:e0201859. [PMID: 30102720 PMCID: PMC6089422 DOI: 10.1371/journal.pone.0201859] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/23/2018] [Indexed: 11/18/2022] Open
Abstract
Ferritin H-homopolymers have been extensively used as nanocarriers for diverse applications in the targeted delivery of drugs and imaging agents, due to their unique ability to bind the transferrin receptor (CD71), highly overexpressed in most tumor cells. In order to incorporate novel fluorescence imaging properties, we have fused a lanthanide binding tag (LBT) to the C-terminal end of mouse H-chain ferritin, HFt. The HFt-LBT possesses one high affinity Terbium binding site per each of the 24 subunits provided by six coordinating aminoacid side chains and a tryptophan residue in its close proximity and is thus endowed with strong FRET sensitization properties. Accordingly, the characteristic Terbium emission band at 544 nm for the HFt-LBT Tb(III) complex was detectable upon excitation of the tag enclosed at two order of magnitude higher intensity with respect to the wtHFt protein. X-ray data at 2.9 Å and cryo-EM at 7 Å resolution demonstrated that HFt-LBT is correctly assembled as a 24-mer both in crystal and in solution. On the basis of the intrinsic Tb(III) binding properties of the wt protein, 32 additional Tb(III) binding sites, located within the natural iron binding sites of the protein, were identified besides the 24 Tb(III) ions coordinated to the LBTs. HFt-LBT Tb(III) was demonstrated to be actively uptaken by selected tumor cell lines by confocal microscopy and FACS analysis of their FITC derivatives, although direct fluorescence from Terbium emission could not be singled out with conventional, 295-375 nm, fluorescence excitation.
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Affiliation(s)
- Lorenzo Calisti
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | | | - Alberto Boffi
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Claudia Testi
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Linda Celeste Montemiglio
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Amédée des Georges
- The City University of New York Advanced Science Research Center, New York, NY
| | - Irene Benni
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Bartłomiej Taciak
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Maciej Białasek
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
| | - Tomasz Rygiel
- Cellis Ltd., Warsaw, Poland
- Department of Immunology, Center for Biostructure Research, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Król
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, ul. Nowoursynowska, Warszawa, Poland
- Cellis Ltd., Warsaw, Poland
| | - Paola Baiocco
- Center for Life Nano Science @ Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
- * E-mail:
| | - Alessandra Bonamore
- Department of Biochemical Sciences "Alessandro Rossi Fanelli", Sapienza University of Rome, Rome Italy
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20
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Pan BB, Yang F, Ye Y, Wu Q, Li C, Huber T, Su XC. 3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy. Chem Commun (Camb) 2018; 52:10237-40. [PMID: 27470136 DOI: 10.1039/c6cc05490k] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Determining the three-dimensional structure of a protein in living cells remains particularly challenging. We demonstrated that the integration of site-specific tagging proteins and GPS-Rosetta calculations provides a fast and effective way of determining the structures of proteins in living cells, and in principle the interactions and dynamics of protein-ligand complexes.
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Affiliation(s)
- Bin-Bin Pan
- State Key Laboratory and Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China.
| | - Feng Yang
- State Key Laboratory and Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China.
| | - Yansheng Ye
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Qiong Wu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
| | - Xun-Cheng Su
- State Key Laboratory and Research Institute of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin 300071, China.
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21
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Harner MJ, Mueller L, Robbins KJ, Reily MD. NMR in drug design. Arch Biochem Biophys 2017; 628:132-147. [DOI: 10.1016/j.abb.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 02/09/2023]
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22
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Barthelmes D, Barthelmes K, Schnorr K, Jonker HRA, Bodmer B, Allen KN, Imperiali B, Schwalbe H. Conformational dynamics and alignment properties of loop lanthanide-binding-tags (LBTs) studied in interleukin-1β. JOURNAL OF BIOMOLECULAR NMR 2017; 68:187-194. [PMID: 28534082 DOI: 10.1007/s10858-017-0118-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
Encodable lanthanide binding tags (LBTs) have become an attractive tool in modern structural biology as they can be expressed as fusion proteins of targets of choice. Previously, we have demonstrated the feasibility of inserting encodable LBTs into loop positions of interleukin-1β (Barthelmes et al. in J Am Chem Soc 133:808-819, 2011). Here, we investigate the differences in fast dynamics of selected loop-LBT interleukin-1β constructs by measuring 15N nuclear spin relaxation experiments. We show that the loop-LBT does not significantly alter the dynamic motions of the host protein in the sub-τc-timescale and that the loop-LBT adopts a rigid conformation with significantly reduced dynamics compared to the terminally attached encodable LBT leading to increased paramagnetic alignment strength. We further analyze residual dipolar couplings (RDCs) obtained by loop-LBTs and additional liquid crystalline media to assess the applicability of the loop-LBT approach for RDC-based methods to determine structure and dynamics of proteins, including supra-τc dynamics. Using orthogonalized linear combinations (OLCs) of RDCs and Saupe matrices, we show that the combined use of encodable LBTs and external alignment media yields up to five linear independent alignments.
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Affiliation(s)
- Dominic Barthelmes
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Katja Barthelmes
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Kai Schnorr
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Hendrik R A Jonker
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Bianca Bodmer
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany
| | - Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Barbara Imperiali
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University of Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt, Germany.
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23
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Schnorr KA, Gophane DB, Helmling C, Cetiner E, Pasemann K, Fürtig B, Wacker A, Qureshi NS, Gränz M, Barthelmes D, Jonker HRA, Stirnal E, Sigurdsson ST, Schwalbe H. Impact of spin label rigidity on extent and accuracy of distance information from PRE data. JOURNAL OF BIOMOLECULAR NMR 2017; 68:53-63. [PMID: 28500543 DOI: 10.1007/s10858-017-0114-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, UreidoU-TEMPO was incorporated into the 3' terminal end of helix P1 while, the recently developed rigid spin-label Çm was incorporated in the 5' terminal end of helix P1. We determined PRE rates obtained from aromatic 13C bound proton intensities and compared these rates to PREs derived from imino proton intensities in this sizeable RNA (~78 nt). PRE restraints derived from both imino and aromatic protons yielded similar data quality, and hence can both be reliably used for PRE determination. For NMR, the data quality derived from the rigid spin label Çm is slightly better than the data quality for the flexible UreidoTEMPO as judged by comparison of the structural agreement with the I-A aptamer crystal structure (3SKI).
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Affiliation(s)
- K A Schnorr
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D B Gophane
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - C Helmling
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Cetiner
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - K Pasemann
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - B Fürtig
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - A Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - N S Qureshi
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - M Gränz
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D Barthelmes
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - H R A Jonker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Stirnal
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - S Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - H Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany.
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24
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Chiliveri SC, Deshmukh MV. Recent excitements in protein NMR: Large proteins and biologically relevant dynamics. J Biosci 2017; 41:787-803. [PMID: 27966496 DOI: 10.1007/s12038-016-9640-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The advent of Transverse Relaxation Optimized SpectroscopY (TROSY) and perdeuteration allowed biomolecular NMR spectroscopists to overcome the size limitation barrier (approx. 20 kDa) in de novo structure determination of proteins. The utility of these techniques was immediately demonstrated on large proteins and protein complexes (e.g. GroELGroES, ClpP protease, Hsp90-p53, 20S proteasome, etc.). Further, recent methodological developments such as Residual Dipolar Couplings and Paramagnetic Relaxation Enhancement allowed accurate measurement of long-range structural restraints. Additionally, Carr-Purcell-Meiboom-Gill (CPMG), rotating frame relaxation experiments (R1(rho)) and saturation transfer experiments (CEST and DEST) created never-before accessibility to the (mu)s-ms timescale dynamic parameters that led to the deeper understanding of biological processes. Meanwhile, the excitement in the field continued with a series of developments in the fast data acquisition methods allowing rapid structural studies on less stable proteins. This review aims to discuss important developments in the field of biomolecular NMR spectroscopy in the recent past, i.e., in the post TROSY era. These developments not only gave access to the structural studies of large protein assemblies, but also revolutionized tools in the arsenal of today's biomolecular NMR and point to a bright future of biomolecular NMR spectroscopy.
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25
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Nitsche C, Otting G. Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 98-99:20-49. [PMID: 28283085 DOI: 10.1016/j.pnmrs.2016.11.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 05/14/2023]
Affiliation(s)
- Christoph Nitsche
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia. http://www.rsc.anu.edu.au/~go/index.html
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26
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Hammoud H, de Bettencourt-Dias A, Schmitt M, Monteiro JHSK, Rossini JS, Lecointre A, Gallet S, Bourguignon JJ, Mameri S. Unusual O-Bridged Symmetric Quinoline-Based Ligand for the Formation of Luminescent Mono-Aqua Lanthanide Complexes. ChemistrySelect 2016. [DOI: 10.1002/slct.201601223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hassan Hammoud
- Laboratoire d'Innovation Thérapeutique; UMR 7200-CNRS/Unistra; Faculté de Pharmacie, 74, route du Rhin; Illkirch 67401 FRANCE
| | | | - Martine Schmitt
- Laboratoire d'Innovation Thérapeutique; UMR 7200-CNRS/Unistra; Faculté de Pharmacie, 74, route du Rhin; Illkirch 67401 FRANCE
| | | | | | - Alexandre Lecointre
- Laboratoire d'Ingénierie Moléculaire Appliquée à l'Analyse; Institut Pluridisciplinaire Hubert Curien; 23 rue du Loess Strasbourg 67037 FRANCE
| | - Sébastien Gallet
- Institut Universitaire de Technologie Robert Schuman; Département Chimie; Université de Strasbourg; 72 route du Rhin Illkirch 67411 FRANCE
| | - Jean-Jacques Bourguignon
- Laboratoire d'Innovation Thérapeutique; UMR 7200-CNRS/Unistra; Faculté de Pharmacie, 74, route du Rhin; Illkirch 67401 FRANCE
| | - Samir Mameri
- Laboratoire d'Innovation Thérapeutique; UMR 7200-CNRS/Unistra; Faculté de Pharmacie, 74, route du Rhin; Illkirch 67401 FRANCE
- Institut Universitaire de Technologie Robert Schuman; Département Chimie; Université de Strasbourg; 72 route du Rhin Illkirch 67411 FRANCE
- Laboratoire de Chimie Moléculaire; UMR CNRS 7509; Université de Strasbourg; 25 rue Becquerel Strasbourg 67087 FRANCE
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Mascali FC, Ching HYV, Rasia RM, Un S, Tabares LC. Using Genetically Encodable Self-Assembling GdIIISpin Labels To Make In-Cell Nanometric Distance Measurements. Angew Chem Int Ed Engl 2016; 55:11041-3. [DOI: 10.1002/anie.201603653] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/20/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Florencia C. Mascali
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, Ocampo y Esmeralda; Rosario 2000 Argentina
| | - H. Y. Vincent Ching
- Institut de Biologie Intégrative de la Cellule (I2BC); IBITECS, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette France
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, Ocampo y Esmeralda; Rosario 2000 Argentina
| | - Sun Un
- Institut de Biologie Intégrative de la Cellule (I2BC); IBITECS, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette France
| | - Leandro C. Tabares
- Institut de Biologie Intégrative de la Cellule (I2BC); IBITECS, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette France
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28
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Mascali FC, Ching HYV, Rasia RM, Un S, Tabares LC. Using Genetically Encodable Self-Assembling GdIIISpin Labels To Make In-Cell Nanometric Distance Measurements. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Florencia C. Mascali
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, Ocampo y Esmeralda; Rosario 2000 Argentina
| | - H. Y. Vincent Ching
- Institut de Biologie Intégrative de la Cellule (I2BC); IBITECS, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette France
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario; Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas; Universidad Nacional de Rosario, Ocampo y Esmeralda; Rosario 2000 Argentina
| | - Sun Un
- Institut de Biologie Intégrative de la Cellule (I2BC); IBITECS, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette France
| | - Leandro C. Tabares
- Institut de Biologie Intégrative de la Cellule (I2BC); IBITECS, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay; F-91198 Gif-sur-Yvette France
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29
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Carlon A, Ravera E, Andrałojć W, Parigi G, Murshudov GN, Luchinat C. How to tackle protein structural data from solution and solid state: An integrated approach. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:54-70. [PMID: 26952192 DOI: 10.1016/j.pnmrs.2016.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 05/17/2023]
Abstract
Long-range NMR restraints, such as diamagnetic residual dipolar couplings and paramagnetic data, can be used to determine 3D structures of macromolecules. They are also used to monitor, and potentially to improve, the accuracy of a macromolecular structure in solution by validating or "correcting" a crystal model. Since crystal structures suffer from crystal packing forces they may not be accurate models for the macromolecular structures in solution. However, the presence of real differences should be tested for by simultaneous refinement of the structure using both crystal and solution NMR data. To achieve this, the program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic and paramagnetic NMR data and/or diamagnetic residual dipolar couplings. Inconsistencies between crystal structures and solution NMR data, if any, may be due either to structural rearrangements occurring on passing from the solution to solid state, or to a greater degree of conformational heterogeneity in solution with respect to the crystal. In the case of multidomain proteins, paramagnetic restraints can provide the correct mutual orientations and positions of domains in solution, as well as information on the conformational variability experienced by the macromolecule.
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Affiliation(s)
- Azzurra Carlon
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Witold Andrałojć
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
| | - Garib N Murshudov
- MRC Laboratory for Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, UK.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry "Ugo Schiff", University of Florence, Italy(1).
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Vavrinská A, Zelinka J, Šebera J, Sychrovský V, Fiala R, Boelens R, Sklenář V, Trantírek L. Impact of nucleic acid self-alignment in a strong magnetic field on the interpretation of indirect spin-spin interactions. JOURNAL OF BIOMOLECULAR NMR 2016; 64:53-62. [PMID: 26685997 PMCID: PMC4742510 DOI: 10.1007/s10858-015-0005-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
Heteronuclear and homonuclear direct (D) and indirect (J) spin-spin interactions are important sources of structural information about nucleic acids (NAs). The Hamiltonians for the D and J interactions have the same functional form; thus, the experimentally measured apparent spin-spin coupling constant corresponds to a sum of J and D. In biomolecular NMR studies, it is commonly presumed that the dipolar contributions to Js are effectively canceled due to random molecular tumbling. However, in strong magnetic fields, such as those employed for NMR analysis, the tumbling of NA fragments is anisotropic because the inherent magnetic susceptibility of NAs causes an interaction with the external magnetic field. This motional anisotropy is responsible for non-zero D contributions to Js. Here, we calculated the field-induced D contributions to 33 structurally relevant scalar coupling constants as a function of magnetic field strength, temperature and NA fragment size. We identified two classes of Js, namely (1)JCH and (3)JHH couplings, whose quantitative interpretation is notably biased by NA motional anisotropy. For these couplings, the magnetic field-induced dipolar contributions were found to exceed the typical experimental error in J-coupling determinations by a factor of two or more and to produce considerable over- or under-estimations of the J coupling-related torsion angles, especially at magnetic field strengths >12 T and for NA fragments longer than 12 bp. We show that if the non-zero D contributions to J are not properly accounted for, they might cause structural artifacts/bias in NA studies that use solution NMR spectroscopy.
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Affiliation(s)
- Andrea Vavrinská
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Jiří Zelinka
- Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
- Institute of Physics, Academy of Sciences of the Czech Republic, v.v.i, Na Slovance 2, 182 21, Prague 8, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo náměstí 542/2, 166 10, Praha 6, Czech Republic
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Vladimír Sklenář
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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Barthelmes D, Gränz M, Barthelmes K, Allen KN, Imperiali B, Prisner T, Schwalbe H. Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2015; 63:275-282. [PMID: 26341230 DOI: 10.1007/s10858-015-9984-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
We recently engineered encodable lanthanide binding tags (LBTs) into proteins and demonstrated their applicability in Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography and luminescence studies. Here, we engineered two-loop-LBTs into the model protein interleukin-1β (IL1β) and measured (1)H, (15)N-pseudocontact shifts (PCSs) by NMR spectroscopy. We determined the Δχ-tensors associated with each Tm(3+)-loaded loop-LBT and show that the experimental PCSs yield structural information at the interface between the two metal ion centers at atomic resolution. Such information is very valuable for the determination of the sites of interfaces in protein-protein-complexes. Combining the experimental PCSs of the two-loop-LBT construct IL1β-S2R2 and the respective single-loop-LBT constructs IL1β-S2, IL1β-R2 we additionally determined the distance between the metal ion centers. Further, we explore the use of two-loop LBTs loaded with Gd(3+) as a novel tool for distance determination by Electron Paramagnetic Resonance spectroscopy and show the NMR-derived distances to be remarkably consistent with distances derived from Pulsed Electron-Electron Dipolar Resonance.
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Affiliation(s)
- Dominic Barthelmes
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany
| | - Markus Gränz
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany
| | - Katja Barthelmes
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany
- Department of Chemistry, Munich Center for Integrated Protein Science and Chair Biomolecular NMR, Technical University Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Karen N Allen
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Barbara Imperiali
- Departments of Chemistry and Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany.
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438, Frankfurt Am Main, Germany.
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The best and the brightest: exploiting tryptophan-sensitized Tb(3+) luminescence to engineer lanthanide-binding tags. Methods Mol Biol 2015; 1248:201-20. [PMID: 25616335 DOI: 10.1007/978-1-4939-2020-4_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Consider the lanthanide metals, comprising lanthanum through lutetium. Lanthanides form stable cations with a +3 charge, and these ions exhibit a variety of useful physical properties (long-lifetime luminescence, paramagnetism, anomalous X-ray scattering) that are amenable to studies of biomolecules. The absence of lanthanide ions in living systems means that background signals are generally a nonissue; however, to exploit the advantageous properties it is necessary to engineer a robust lanthanide-binding sequence that can be appended to any macromolecules of interest. To this end, the luminescence produced by tryptophan-sensitized Tb(3+) has been used as a selection marker for peptide sequences that avidly chelate these ions. A combinatorial split-and-pool library that uses two orthogonal linkers-one that is cleaved for selection and one that is cleaved for sequencing and characterization-has been used to develop lanthanide-binding tags (LBTs): peptides of 15-20 amino acids with low-nM affinity for Tb(3+). Further validating the success of this screen, knowledge about LBTs has enabled the introduction of a lanthanide-binding loop in place of one of the four native calcium-binding loops within the protein calcineurin B.
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34
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Brath U, Swamy SI, Veiga AX, Tung CC, Van Petegem F, Erdélyi M. Paramagnetic Ligand Tagging To Identify Protein Binding Sites. J Am Chem Soc 2015; 137:11391-8. [PMID: 26289584 PMCID: PMC4583072 DOI: 10.1021/jacs.5b06220] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Transient
biomolecular interactions are the cornerstones of the
cellular machinery. The identification of the binding sites for low
affinity molecular encounters is essential for the development of
high affinity pharmaceuticals from weakly binding leads but is hindered
by the lack of robust methodologies for characterization of weakly
binding complexes. We introduce a paramagnetic ligand tagging approach
that enables localization of low affinity protein–ligand binding
clefts by detection and analysis of intermolecular protein NMR pseudocontact
shifts, which are invoked by the covalent attachment of a paramagnetic
lanthanoid chelating tag to the ligand of interest. The methodology
is corroborated by identification of the low millimolar volatile anesthetic
interaction site of the calcium sensor protein calmodulin. It presents
an efficient route to binding site localization for low affinity complexes
and is applicable to rapid screening of protein–ligand systems
with varying binding affinity.
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Affiliation(s)
- Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Shashikala I Swamy
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Alberte X Veiga
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
| | - Ching-Chieh Tung
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, BC V6T 1Z3, Canada
| | - Máté Erdélyi
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg , SE-412 96 Gothenburg, Sweden
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35
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Andrałojć W, Berlin K, Fushman D, Luchinat C, Parigi G, Ravera E, Sgheri L. Information content of long-range NMR data for the characterization of conformational heterogeneity. JOURNAL OF BIOMOLECULAR NMR 2015; 62:353-71. [PMID: 26044033 PMCID: PMC4782772 DOI: 10.1007/s10858-015-9951-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/25/2015] [Indexed: 05/16/2023]
Abstract
Long-range NMR data, namely residual dipolar couplings (RDCs) from external alignment and paramagnetic data, are becoming increasingly popular for the characterization of conformational heterogeneity of multidomain biomacromolecules and protein complexes. The question addressed here is how much information is contained in these averaged data. We have analyzed and compared the information content of conformationally averaged RDCs caused by steric alignment and of both RDCs and pseudocontact shifts caused by paramagnetic alignment, and found that, despite the substantial differences, they contain a similar amount of information. Furthermore, using several synthetic tests we find that both sets of data are equally good towards recovering the major state(s) in conformational distributions.
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Affiliation(s)
- Witold Andrałojć
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Konstantin Berlin
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular
Structure and Organization, University of Maryland, College Park, MD 20742, USA
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Corresponding authors: David Fushman, ,
Claudio Luchinat,
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via
L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University
of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Luca Sgheri
- Istituto per le Applicazioni del Calcolo, Sezione di Firenze,
CNR, Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
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36
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Kato K, Yamaguchi T. Paramagnetic NMR probes for characterization of the dynamic conformations and interactions of oligosaccharides. Glycoconj J 2015; 32:505-13. [PMID: 26050258 DOI: 10.1007/s10719-015-9599-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 12/21/2022]
Abstract
Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques have recently been applied to a wide variety of biomolecular systems, using sophisticated immobilization methods to attach paramagnetic probes, such as spin labels and lanthanide-chelating groups, at specific sites of the target biomolecules. This is also true in the field of carbohydrate NMR spectroscopy. NMR analysis of oligosaccharides is often precluded by peak overlap resulting from the lack of variability of local chemical structures, by the insufficiency of conformational restraints from nuclear Overhauser effect (NOE) data due to low proton density, and moreover, by the inherently flexible nature of carbohydrate chains. Paramagnetic probes attached to the reducing ends of oligosaccharides cause paramagnetic relaxation enhancements (PREs) and/or pseudocontact shifts (PCSs) resolve the peak overlap problem. These spectral perturbations can be sources of long-range atomic distance information, which complements the local conformational information derived from J couplings and NOEs. Furthermore, paramagnetic NMR approaches, in conjunction with computational methods, have opened up possibilities for the description of dynamic conformational ensembles of oligosaccharides in solution. Several applications of paramagnetic NMR techniques are presented to demonstrate their utility for characterizing the conformational dynamics of oligosaccharides and for probing the carbohydrate-recognition modes of proteins. These techniques can be applied to the characterization of transient, non-stoichiometric interactions and will contribute to the visualization of dynamic biomolecular processes involving sugar chains.
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Affiliation(s)
- Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tababe-dori, Mizuho-ku, Nagoya, 467-8603, Japan.
- The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo, 112-8610, Japan.
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tababe-dori, Mizuho-ku, Nagoya, 467-8603, Japan
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37
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Park SH, Wang V, Radoicic J, De Angelis AA, Berkamp S, Opella SJ. Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA). JOURNAL OF BIOMOLECULAR NMR 2015; 61:185-96. [PMID: 25430059 PMCID: PMC4398598 DOI: 10.1007/s10858-014-9884-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/20/2014] [Indexed: 05/16/2023]
Abstract
The use of paramagnetic constraints in protein NMR is an active area of research because of the benefits of long-range distance measurements (>10 Å). One of the main issues in successful execution is the incorporation of a paramagnetic metal ion into diamagnetic proteins. The most common metal ion tags are relatively long aliphatic chains attached to the side chain of a selected cysteine residue with a chelating group at the end where it can undergo substantial internal motions, decreasing the accuracy of the method. An attractive alternative approach is to incorporate an unnatural amino acid that binds metal ions at a specific site on the protein using the methods of molecular biology. Here we describe the successful incorporation of the unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA) into two different membrane proteins by heterologous expression in E. coli. Fluorescence and NMR experiments demonstrate complete replacement of the natural amino acid with HQA and stable metal chelation by the mutated proteins. Evidence of site-specific intra- and inter-molecular PREs by NMR in micelle solutions sets the stage for the use of HQA incorporation in solid-state NMR structure determinations of membrane proteins in phospholipid bilayers.
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38
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Hennig J, Warner LR, Simon B, Geerlof A, Mackereth CD, Sattler M. Structural Analysis of Protein-RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements. Methods Enzymol 2015; 558:333-362. [PMID: 26068746 DOI: 10.1016/bs.mie.2015.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biological activity in the cell is predominantly mediated by large multiprotein and protein-nucleic acid complexes that act together to ensure functional fidelity. Nuclear magnetic resonance (NMR) spectroscopy is the only method that can provide information for high-resolution three-dimensional structures and the conformational dynamics of these complexes in solution. Mapping of binding interfaces and molecular interactions along with the characterization of conformational dynamics is possible for very large protein complexes. In contrast, de novo structure determination by NMR becomes very time consuming and difficult for protein complexes larger than 30 kDa as data are noisy and sparse. Fortunately, high-resolution structures are often available for individual domains or subunits of a protein complex and thus sparse data can be used to define their arrangement and dynamics within the assembled complex. In these cases, NMR can therefore be efficiently combined with complementary solution techniques, such as small-angle X-ray or neutron scattering, to provide a comprehensive description of the structure and dynamics of protein complexes in solution. Particularly useful are NMR-derived paramagnetic relaxation enhancements (PREs), which provide long-range distance restraints (ca. 20Å) for structural analysis of large complexes and also report on conformational dynamics in solution. Here, we describe the use of PREs from sample production to structure calculation, focusing on protein-RNA complexes. On the basis of recent examples from our own research, we demonstrate the utility, present protocols, and discuss potential pitfalls when using PREs for studying the structure and dynamic features of protein-RNA complexes.
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Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Oberschleißheim, Germany; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Lisa R Warner
- Institute of Structural Biology, Helmholtz Zentrum München, Oberschleißheim, Germany; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, Oberschleißheim, Germany; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Cameron D Mackereth
- Institut Européen de Chimie et Biologie, IECB, Univ. Bordeaux, Pessac, France; Inserm, U869, ARNA Laboratory, Bordeaux, France
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Oberschleißheim, Germany; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany.
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39
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Loh CT, Graham B, Abdelkader EH, Tuck KL, Otting G. Generation of pseudocontact shifts in proteins with lanthanides using small "clickable" nitrilotriacetic acid and iminodiacetic acid tags. Chemistry 2015; 21:5084-92. [PMID: 25676727 DOI: 10.1002/chem.201406274] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Indexed: 01/07/2023]
Abstract
Pseudocontact shifts (PCS) induced by paramagnetic lanthanide ions provide unique long-range structural information in nuclear magnetic resonance (NMR) spectra, but the site-specific attachment of lanthanide tags to proteins remains a challenge. Here we incorporated p-azido-phenylalanine (AzF) site-specifically into the proteins ubiquitin and GB1, and ligated the AzF residue with alkyne derivatives of small nitrilotriacetic acid and iminodiacetic acid tags using the Cu(I) -catalysed "click" reaction. These tags form lanthanide complexes with no or only a small net charge and produced sizeable PCSs with paramagnetic lanthanide ions in all mutants tested. The PCSs were readily fitted by single magnetic susceptibility anisotropy tensors. Protein precipitation during the click reaction was greatly alleviated by the presence of 150 mM NaCl.
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Affiliation(s)
- Choy-Theng Loh
- Research School of Chemistry, Australian National University, Canberra ACT 2601 (Australia)
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40
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Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
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Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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Rinaldelli M, Carlon A, Ravera E, Parigi G, Luchinat C. FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data. JOURNAL OF BIOMOLECULAR NMR 2015; 61:21-34. [PMID: 25416616 DOI: 10.1007/s10858-014-9877-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 11/15/2014] [Indexed: 05/17/2023]
Abstract
Pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) arising from the presence of paramagnetic metal ions in proteins as well as RDCs due to partial orientation induced by external orienting media are nowadays routinely measured as a part of the NMR characterization of biologically relevant systems. PCSs and RDCs are becoming more and more popular as restraints (1) to determine and/or refine protein structures in solution, (2) to monitor the extent of conformational heterogeneity in systems composed of rigid domains which can reorient with respect to one another, and (3) to obtain structural information in protein-protein complexes. The use of both PCSs and RDCs proceeds through the determination of the anisotropy tensors which are at the origin of these NMR observables. A new user-friendly web tool, called FANTEN (Finding ANisotropy TENsors), has been developed for the determination of the anisotropy tensors related to PCSs and RDCs and has been made freely available through the WeNMR ( http://fanten-enmr.cerm.unifi.it:8080 ) gateway. The program has many new features not available in other existing programs, among which the possibility of a joint analysis of several sets of PCS and RDC data and the possibility to perform rigid body minimizations.
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Affiliation(s)
- Mauro Rinaldelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, Sesto Fiorentino, Florence, Italy
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Ravera E, Salmon L, Fragai M, Parigi G, Al-Hashimi H, Luchinat C. Insights into domain-domain motions in proteins and RNA from solution NMR. Acc Chem Res 2014; 47:3118-26. [PMID: 25148413 PMCID: PMC4204921 DOI: 10.1021/ar5002318] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Many multidomain proteins and ribonucleic acids consist of domains
that autonomously fold and that are linked together by flexible junctions.
This architectural design allows domains to sample a wide range of
positions with respect to one another, yet do so in a way that retains
structural specificity, since the number of sampled conformations
remains extremely small compared to the total conformations that would
be sampled if the domains were connected by an infinitely long linker.
This “tuned” flexibility in interdomain conformation
is in turn used in many biochemical processes. There is great
interest in characterizing the dynamic properties
of multidomain systems, and moving beyond conventional descriptions
in terms of static structures, toward the characterization of population-weighted
ensembles describing a distribution of many conformations sampled
in solution. There is also great interest in understanding the design
principles and underlying physical and chemical interactions that
specify the nature of interdomain flexibility. NMR spectroscopy is
one of the most powerful techniques for characterizing motions in
complex biomolecules and has contributed greatly toward our basic
understanding of dynamics in proteins and nucleic acids and its role
in folding, recognition, and signaling. Here, we review methods
that have been developed in our laboratories
to address these challenges. Our approaches are based on the ability
of one domain of the molecule to self-align in a magnetic field, or
to dominate the overall orientation of the molecule, so that the conformational
freedom of other domains can be assessed by their degree of alignment
induced by the aligned part. In turn, this self-alignment ability
can be intrinsic or can be caused by tagging appropriate constructs
to the molecule of interest. In general, self-alignment is due to
magnetic susceptibility anisotropy. Nucleic acids with elongated helices
have this feature, as well as several paramagnetic metal centers that
can be found in, or attached to, a protein domain.
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Affiliation(s)
- Enrico Ravera
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Loïc Salmon
- Department
of Biophysics, University of Michigan, 830 N. University, Ann Arbor, Michigan 48109, United States
| | - Marco Fragai
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Hashim Al-Hashimi
- Department
of Biochemistry and Department of Chemistry, Duke University School of Medicine, 307 Research Drive, Durham, North Carolina 27710, United States
| | - Claudio Luchinat
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry “U. Schiff”, University of Florence, via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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43
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Camacho-Zarco AR, Munari F, Wegstroth M, Liu WM, Ubbink M, Becker S, Zweckstetter M. Multiple paramagnetic effects through a tagged reporter protein. Angew Chem Int Ed Engl 2014; 54:336-9. [PMID: 25293958 DOI: 10.1002/anie.201408615] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Indexed: 11/12/2022]
Abstract
Paramagnetic effects provide unique information about the structure and dynamics of biomolecules. We developed a method in which the lanthanoid tag is not directly attached to the protein of interest, but instead to a "reporter" protein, which binds and then transmits paramagnetic information to the target. The designed method allows access to a large number of paramagnetic restraints and residual dipolar couplings produced from independent molecular alignments in high-molecular-weight proteins with unknown 3D structure.
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Affiliation(s)
- Aldo R Camacho-Zarco
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); German Center for Neurodegenerative Diseases (DZNE), Göttingen (Germany); Center for the Molecular Physiology of the Brain, University Medical Center, Göttingen (Germany)
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44
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Camacho‐Zarco AR, Munari F, Wegstroth M, Liu W, Ubbink M, Becker S, Zweckstetter M. Paramagnetische Effekte mittels eines markierten Reporterproteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Aldo R. Camacho‐Zarco
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Francesca Munari
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Melanie Wegstroth
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Wei‐Min Liu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Niederlande)
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Niederlande)
| | - Stefan Becker
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Markus Zweckstetter
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
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45
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Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
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Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
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46
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Helmling C, Bessi I, Wacker A, Schnorr KA, Jonker HRA, Richter C, Wagner D, Kreibich M, Schwalbe H. Noncovalent spin labeling of riboswitch RNAs to obtain long-range structural NMR restraints. ACS Chem Biol 2014; 9:1330-9. [PMID: 24673892 DOI: 10.1021/cb500050t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Paramagnetic relaxation enhancement (PRE) NMR is a powerful method to study structure, dynamics and function of proteins. Up to now, the application of PRE NMR on RNAs is a significant challenge due to the limited size of chemically synthesized RNA. Here, we present a noncovalent spin labeling strategy to spin label RNAs in high yields required for NMR studies. The approach requires the presence of a helix segment composed of about 10 nucleotides (nt) but is not restricted by the size of the RNA. We show successful application of this strategy on the 2'dG sensing aptamer domain of Mesoplasma florum (78 nt). The aptamer domain was prepared in two fragments. A larger fragment was obtained by biochemical means, while a short spin labeled fragment was prepared by chemical solid-phase synthesis. The two fragments were annealed noncovalently by hybridization. We performed NMR, cw-EPR experiments and gel shift assays to investigate the stability of the two-fragment complex. NMR analysis in (15)N-TROSY and (1)H,(1)H-NOESY spectra of both unmodified and spin labeled aptamer domain show that the fragmented system forms a stable hybridization product, is in structural agreement with the full length aptamer domain and maintains its function. Together with structure modeling, experimentally determined (1)H-Γ2 rates are in agreement with reported crystal structure data and show that distance restraints up to 25 Å can be obtained from NMR PRE data of RNA.
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Affiliation(s)
- Christina Helmling
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Irene Bessi
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Anna Wacker
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Kai A. Schnorr
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Hendrik R. A. Jonker
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Christian Richter
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Dominic Wagner
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Michael Kreibich
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
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47
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Mills BJ, Mu Q, Krause ME, Laurence JS. claMP Tag: a versatile inline metal-binding platform based on the metal abstraction peptide. Bioconjug Chem 2014; 25:1103-11. [PMID: 24807049 PMCID: PMC4215913 DOI: 10.1021/bc500115h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Molecularly
targeted research and diagnostic tools are essential
to advancing understanding and detection of many diseases. Metals
often impart the desired functionality to these tools, and conjugation
of high-affinity chelators to proteins is carried out to enable targeted
delivery of the metal. This approach has been much more effective
with large lanthanide series metals than smaller transition metals.
Because chemical conjugation requires additional processing and purification
steps and yields a heterogeneous mixture of products, inline incorporation
of a peptide tag capable of metal binding is a highly preferable alternative.
Development of a transition metal binding tag would provide opportunity
to greatly expand metal-based analyses. The metal abstraction peptide
(MAP) sequence was genetically engineered into recombinant protein
to generate the claMP Tag. The effects of this tag
on recombinant epidermal growth factor (EGF) protein expression, disulfide
bond formation, tertiary structural integrity, and transition metal
incorporation using nickel were examined to confirm the viability
of utilizing the MAP sequence to generate linker-less metal conjugates.
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Affiliation(s)
- Brittney J Mills
- Department of Chemistry, The University of Kansas , Lawrence, Kansas 66045, United States
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48
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Hennig J, Sattler M. The dynamic duo: combining NMR and small angle scattering in structural biology. Protein Sci 2014; 23:669-82. [PMID: 24687405 DOI: 10.1002/pro.2467] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 12/12/2022]
Abstract
Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of complementary aspects provided by different structural biology techniques. Although X-ray crystallography remains the method of choice for structural analysis of large complexes, crystallization of flexible systems is often difficult and does typically not provide insights into conformational dynamics present in solution. Nuclear magnetic resonance spectroscopy (NMR) is well-suited to study dynamics at picosecond to second time scales, and to map binding interfaces even of large systems at residue resolution but suffers from poor sensitivity with increasing molecular weight. Small angle scattering (SAS) methods provide low resolution information in solution and can characterize dynamics and conformational equilibria complementary to crystallography and NMR. The combination of NMR, crystallography, and SAS is, thus, very useful for analysis of the structure and conformational dynamics of (large) protein complexes in solution. In high molecular weight systems, where NMR data are often sparse, SAS provides additional structural information and can differentiate between NMR-derived models. Scattering data can also validate the solution conformation of a crystal structure and indicate the presence of conformational equilibria. Here, we review current state-of-the-art approaches for combining NMR, crystallography, and SAS data to characterize protein complexes in solution.
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Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr.1, D-85764, Neuherberg, Germany; Center for Integrated Protein Science Munich at Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747, Garching, Germany
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49
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Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:958-67. [PMID: 24699641 PMCID: PMC4306559 DOI: 10.1107/s1399004713034160] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/18/2013] [Indexed: 11/12/2022]
Abstract
The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.
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Affiliation(s)
- Mauro Rinaldelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Vito Calderone
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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50
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Russo L, Maestre-Martinez M, Wolff S, Becker S, Griesinger C. Interdomain dynamics explored by paramagnetic NMR. J Am Chem Soc 2013; 135:17111-20. [PMID: 24111622 DOI: 10.1021/ja408143f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
An ensemble-based approach is presented to explore the conformational space sampled by a multidomain protein showing moderate interdomain dynamics in terms of translational and rotational motions. The strategy was applied on a complex of calmodulin (CaM) with the IQ-recognition motif from the voltage-gated calcium channel Ca(v)1.2 (IQ), which adopts three different interdomain orientations in the crystal. The N60D mutant of calmodulin was used to collect pseudocontact shifts and paramagnetically induced residual dipolar couplings for six different lanthanide ions. Then, starting from the crystal structure, pools of conformations were generated by free MD. We found the three crystal conformations in solution, but four additional MD-derived conformations had to be included into the ensemble to fulfill all the paramagnetic data and cross-validate optimally against unused paramagnetic data. Alternative approaches led to similar ensembles. Our "ensemble" approach is a simple and efficient tool to probe and describe the interdomain dynamics and represents a general method that can be used to provide a proper ensemble description of multidomain proteins.
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Affiliation(s)
- Luigi Russo
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 37077 Göttingen, Germany
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