1
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Belov AS, Belova SA, Efimov NN, Zlobina VV, Novikov VV, Nelyubina YV, Zubavichus YV, Voloshin YZ, Pavlov AA. Synthesis, X-ray structure and magnetic properties of the apically functionalized monocapped cobalt(II) tris-pyridineoximates possessing SMM behaviour. Dalton Trans 2023; 52:2928-2932. [PMID: 36811361 DOI: 10.1039/d2dt04073e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The title cobalt(II) pseudoclathrochelate complexes possess an intermediate trigonal prismatic-trigonal antiprismatic geometry. As follows from PPMS data, they exhibit an SMM behaviour with Orbach relaxation barriers of approximately 90 K. Paramagnetic NMR experiments confirmed a persistence of these magnetic characteristics in solution. Therefore, a straightforward apical functionalization of this 3D molecular platform for its targeted delivery to a given biosystem can be performed without substantial changes.
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Affiliation(s)
- Alexander S Belov
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia. .,Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Svetlana A Belova
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia. .,Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Nikolay N Efimov
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia.
| | - Veronika V Zlobina
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Valentin V Novikov
- Moscow Institute of Physics and Technology, National Research University, Institutsliy per. 9, Dolgoprudny, 141700 Moscow Region, Russia.,BMSTU Center of National Technological Initiative "Digital Material Science: New Material and Substances", Bauman Moscow State Technical University, 2nd Baumanskaya st. 5, 105005, Moscow, Russia
| | - Yulya V Nelyubina
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia.,BMSTU Center of National Technological Initiative "Digital Material Science: New Material and Substances", Bauman Moscow State Technical University, 2nd Baumanskaya st. 5, 105005, Moscow, Russia
| | - Yan V Zubavichus
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis of the Siberian Branch of the Russian Academy of Sciences, 1 Nikolskii pr., 630559 Koltsovo, Russia
| | - Yan Z Voloshin
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia. .,Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Alexander A Pavlov
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia.,BMSTU Center of National Technological Initiative "Digital Material Science: New Material and Substances", Bauman Moscow State Technical University, 2nd Baumanskaya st. 5, 105005, Moscow, Russia.,National Research University Higher School of Economics, 101000 Moscow, Russia
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2
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Karschin N, Becker S, Griesinger C. Interdomain Dynamics via Paramagnetic NMR on the Highly Flexible Complex Calmodulin/Munc13-1. J Am Chem Soc 2022; 144:17041-17053. [PMID: 36082939 PMCID: PMC9501808 DOI: 10.1021/jacs.2c06611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paramagnetic NMR constraints are very useful to study protein interdomain motion, but their interpretation is not always straightforward. On the example of the particularly flexible complex Calmodulin/Munc13-1, we present a new approach to characterize this motion with pseudocontact shifts and residual dipolar couplings. Using molecular mechanics, we sampled the conformational space of the complex and used a genetic algorithm to find ensembles that are in agreement with the data. We used the Bayesian information criterion to determine the ideal ensemble size. This way, we were able to make an accurate, unambiguous, reproducible model of the interdomain motion of Calmodulin/Munc13-1 without prior knowledge about the domain orientation from crystallography.
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Affiliation(s)
- Niels Karschin
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Niedersachsen D-37077, Germany
| | - Stefan Becker
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Niedersachsen D-37077, Germany
| | - Christian Griesinger
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, Göttingen, Niedersachsen D-37077, Germany.,Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen D-37075, Germany
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3
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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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4
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- 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
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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5
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Abstract
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We report the preparation of enantiomerically
enriched β-thio-α-hydroxy
and α-chloro carboxylic acid and ester building blocks by diazotization
of S-sulfonyl-cysteines. The thiosulfonate protecting
group demonstrated resistance to oxidation and attenuation of sulfur’s
nucleophilicity by the anomeric effect. The key transformation was
optimized by a 22 factorial design of experiment, highlighting
the unique reactivity of cysteine derivatives in comparison with aliphatic
amino acids.
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Affiliation(s)
- Sarah Jane Mear
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Timothy F Jamison
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
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6
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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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7
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Muhl C, Schäfer O, Bauer T, Räder HJ, Barz M. Poly(S-ethylsulfonyl-l-homocysteine): An α-Helical Polypeptide for Chemoselective Disulfide Formation. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01442] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Christian Muhl
- Institute of Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Olga Schäfer
- Institute of Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Tobias Bauer
- Institute of Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
- Graduate School MAterials Science IN mainZ (MAINZ), Staudingerweg 9, 55128 Mainz, Germany
| | - Hans-Joachim Räder
- Max-Planck-Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Matthias Barz
- Institute of Organic Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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8
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Chen JL, Zhao Y, Gong YJ, Pan BB, Wang X, Su XC. Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis. JOURNAL OF BIOMOLECULAR NMR 2018; 70:77-92. [PMID: 29224182 DOI: 10.1007/s10858-017-0160-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/05/2017] [Indexed: 06/07/2023]
Abstract
Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yu Zhao
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin-Bin Pan
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin, 300071, China.
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9
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Mulla RS, Pitarch-Jarque J, García-España E, Desa T, Lurie-Luke E, Williams JAG. Monoamide Derivatives of EDTA Incorporating Pendent Carboxylates or Pyridyls: Synthesis, Metal Binding, and Crystal Structure of a Dinuclear Ca2+
Complex Featuring Bridging Na+
Ions. ChemistrySelect 2017. [DOI: 10.1002/slct.201700995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Javier Pitarch-Jarque
- Instituto de Ciencia Molecular (ICMol); Universidad de Valencia; C/ Catedrático José Beltrán, 2 46980, Paterna Valencia Spain
| | - Enrique García-España
- Instituto de Ciencia Molecular (ICMol); Universidad de Valencia; C/ Catedrático José Beltrán, 2 46980, Paterna Valencia Spain
| | - Tanya Desa
- Procter and Gamble Technical Centres Limited, Rusham Park; Whitehall Lane, Egham Surrey TW20 9NW
| | - Elena Lurie-Luke
- Procter and Gamble Technical Centres Limited, Rusham Park; Whitehall Lane, Egham Surrey TW20 9NW
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10
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Pilla KB, Gaalswyk K, MacCallum JL. Molecular modeling of biomolecules by paramagnetic NMR and computational hybrid methods. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28648524 DOI: 10.1016/j.bbapap.2017.06.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The 3D atomic structures of biomolecules and their complexes are key to our understanding of biomolecular function, recognition, and mechanism. However, it is often difficult to obtain structures, particularly for systems that are complex, dynamic, disordered, or exist in environments like cell membranes. In such cases sparse data from a variety of paramagnetic NMR experiments offers one possible source of structural information. These restraints can be incorporated in computer modeling algorithms that can accurately translate the sparse experimental data into full 3D atomic structures. In this review, we discuss various types of paramagnetic NMR/computational hybrid modeling techniques that can be applied to successful modeling of not only the atomic structure of proteins but also their interacting partners. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
| | - Kari Gaalswyk
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
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11
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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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12
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Zhang MN, Zhao MN, Chen M, Ren ZH, Wang YY, Guan ZH. Copper-catalyzed radical coupling of 1,3-dicarbonyl compounds with terminal alkenes for the synthesis of tetracarbonyl compounds. Chem Commun (Camb) 2016; 52:6127-30. [PMID: 27071461 DOI: 10.1039/c6cc01942k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel and efficient copper-catalyzed radical cross-coupling of 1,3-dicarbonyl compounds with terminal alkenes for the synthesis of tetracarbonyl compounds with a quaternary carbon atom has been developed. Mechanistically, this transformation involves the construction of two C-C bonds and two C[double bond, length as m-dash]O bonds in a one-pot process. The reaction tolerates a wide range of functional groups and proceeds under mild conditions.
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Affiliation(s)
- Mei-Na Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, Department of Chemistry & Materials Science, Northwest University, Xi'an, 710127, P. R. China.
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13
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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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14
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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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15
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Carniato F, Tei L, Phadngam S, Isidoro C, Botta M. NaGdF4Nanoparticles Coated with Functionalised Ethylenediaminetetraacetic Acid as Versatile Probes for Dual Optical and Magnetic Resonance Imaging. Chempluschem 2014; 80:503-510. [DOI: 10.1002/cplu.201402245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/29/2014] [Indexed: 11/07/2022]
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16
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17
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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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18
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Canales Á, Mallagaray Á, Berbís MÁ, Navarro-Vázquez A, Domínguez G, Cañada FJ, André S, Gabius HJ, Pérez-Castells J, Jiménez-Barbero J. Lanthanide-Chelating Carbohydrate Conjugates Are Useful Tools To Characterize Carbohydrate Conformation in Solution and Sensitive Sensors to Detect Carbohydrate–Protein Interactions. J Am Chem Soc 2014; 136:8011-7. [DOI: 10.1021/ja502406x] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ángeles Canales
- Department
of Química Orgánica I, Fac. C.C. Químicas, Universidad Complutense de Madrid, Avd. Complutense s/n 28040, Madrid, Spain
| | - Álvaro Mallagaray
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - M. Álvaro Berbís
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Armando Navarro-Vázquez
- Department
of Química Orgánica, Universidade de Vigo, Campus Universitario
Vigo, 36310, Pontevedra, Spain
| | - Gema Domínguez
- Faculty
of De Farmacia, Department of Química, Universidad CEU San Pablo, Urb. Montepríncipe, ctra. Boadilla del Monte, 28668, Madrid, Spain
| | - F. Javier Cañada
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Sabine André
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539, Munich, Germany
| | - Hans-Joachim Gabius
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians University, 80539, Munich, Germany
| | - Javier Pérez-Castells
- Faculty
of De Farmacia, Department of Química, Universidad CEU San Pablo, Urb. Montepríncipe, ctra. Boadilla del Monte, 28668, Madrid, Spain
| | - Jesús Jiménez-Barbero
- Department
of De Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
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19
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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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20
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del Carmen Fernández-Alonso M, Díaz D, Berbis MÁ, Marcelo F, Cañada J, Jiménez-Barbero J. Protein-carbohydrate interactions studied by NMR: from molecular recognition to drug design. Curr Protein Pept Sci 2013; 13:816-30. [PMID: 23305367 PMCID: PMC3706953 DOI: 10.2174/138920312804871175] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/12/2012] [Accepted: 07/25/2012] [Indexed: 02/04/2023]
Abstract
Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications.
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21
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Shishmarev D, Otting G. How reliable are pseudocontact shifts induced in proteins and ligands by mobile paramagnetic metal tags? A modelling study. JOURNAL OF BIOMOLECULAR NMR 2013; 56:203-16. [PMID: 23652856 DOI: 10.1007/s10858-013-9738-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/27/2013] [Indexed: 05/20/2023]
Abstract
The anisotropic component of the magnetic susceptibility tensor (Δχ tensor) associated with various paramagnetic metal ions can induce pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) in proteins, yielding valuable restraints in structural studies. In particular, PCSs have successfully been used to study ligands that bind to proteins tagged with a paramagnetic metal ion, which is of great interest in fragment-based drug design. To create easy-to-interpret PCSs, the metal ion must be attached to the protein in a rigid manner. Most of the existing methods for site-specific attachment of a metal tag, however, result in tethers with residual flexibility. Here we present model calculations to quantify the extent, to which mobility of the metal-binding tag can compromise the quality of the Δχ tensor that can be determined from the PCSs observed in the protein. Assuming that the protein can be approximated by a sphere and the tag is attached by a single tether, the results show that a single effective ∆χ tensor can describe the PCSs and RDCs of the protein spins very well even in the presence of substantial tag mobility, implying that PCSs of ligands in binding pockets of the protein can be predicted with similar accuracy. In contrast, the quality of the PCS prediction for nuclear spins positioned above the surface of the protein is significantly poorer, with implications for studies of protein-protein complexes. The simulations probed the sensitivity of the effective Δχ tensor to different parameters, including length of the tether between protein and metal ion, protein size, type and amplitude of tag motion, tensor orientation relative to the protein and direction of tag motion. Tether length and amplitude of motion were identified as two key parameters. It is shown that the amplitude of tag motions cannot be quantified by simple comparisons of the effective Δχ tensor with the alignment tensor determined from RDCs.
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Affiliation(s)
- Dmitry Shishmarev
- Research School of Chemistry, Australian National University, Canberra, ACT, 0200, Australia
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22
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El-Yazbi AF, Loppnow GR. Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids. Anal Chim Acta 2013; 786:116-23. [PMID: 23790300 DOI: 10.1016/j.aca.2013.04.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/23/2013] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)). Single-stranded oligonucleotides greatly enhance the Tb(3+) emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb(3+)/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb(3+), producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb(3+)/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb(3+)/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36±1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.
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Affiliation(s)
- Amira F El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
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23
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Skinner SP, Moshev M, Hass MAS, Keizers PHJ, Ubbink M. PARAssign--paramagnetic NMR assignments of protein nuclei on the basis of pseudocontact shifts. JOURNAL OF BIOMOLECULAR NMR 2013; 55:379-89. [PMID: 23526169 DOI: 10.1007/s10858-013-9722-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/14/2013] [Indexed: 05/07/2023]
Abstract
The use of paramagnetic NMR data for the refinement of structures of proteins and protein complexes is widespread. However, the power of paramagnetism for protein assignment has not yet been fully exploited. PARAssign is software that uses pseudocontact shift data derived from several paramagnetic centers attached to the protein to obtain amide and methyl assignments. The ability of PARAssign to perform assignment when the positions of the paramagnetic centers are known and unknown is demonstrated. PARAssign has been tested using synthetic data for methyl assignment of a 47 kDa protein, and using both synthetic and experimental data for amide assignment of a 14 kDa protein. The complex fitting space involved in such an assignment procedure necessitates that good starting conditions are found, both regarding placement and strength of paramagnetic centers. These starting conditions are obtained through automated tensor placement and user-defined tensor parameters. The results presented herein demonstrate that PARAssign is able to successfully perform resonance assignment in large systems with a high degree of reliability. This software provides a method for obtaining the assignments of large systems, which may previously have been unassignable, by using 2D NMR spectral data and a known protein structure.
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Affiliation(s)
- Simon P Skinner
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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24
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Loh CT, Ozawa K, Tuck KL, Barlow N, Huber T, Otting G, Graham B. Lanthanide Tags for Site-Specific Ligation to an Unnatural Amino Acid and Generation of Pseudocontact Shifts in Proteins. Bioconjug Chem 2013; 24:260-8. [DOI: 10.1021/bc300631z] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Choy Theng Loh
- Research School of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Kiyoshi Ozawa
- School of Chemistry, University of Wollongong, NSW 2522, Australia
| | - Kellie L. Tuck
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Nicholas Barlow
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville,
VIC 3052, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Bim Graham
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville,
VIC 3052, Australia
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25
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Kobashigawa Y, Saio T, Ushio M, Sekiguchi M, Yokochi M, Ogura K, Inagaki F. Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination. JOURNAL OF BIOMOLECULAR NMR 2012; 53:53-63. [PMID: 22487935 PMCID: PMC3351616 DOI: 10.1007/s10858-012-9623-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 03/27/2012] [Indexed: 05/14/2023]
Abstract
Pseudo contact shifts (PCSs) induced by paramagnetic lanthanide ions fixed in a protein frame provide long-range distance and angular information, and are valuable for the structure determination of protein-protein and protein-ligand complexes. We have been developing a lanthanide-binding peptide tag (hereafter LBT) anchored at two points via a peptide bond and a disulfide bond to the target proteins. However, the magnetic susceptibility tensor displays symmetry, which can cause multiple degenerated solutions in a structure calculation based solely on PCSs. Here we show a convenient method for resolving this degeneracy by changing the spacer length between the LBT and target protein. We applied this approach to PCS-based rigid body docking between the FKBP12-rapamycin complex and the mTOR FRB domain, and demonstrated that degeneracy could be resolved using the PCS restraints obtained from two-point anchored LBT with two different spacer lengths. The present strategy will markedly increase the usefulness of two-point anchored LBT for protein complex structure determination.
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Affiliation(s)
- Yoshihiro Kobashigawa
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Tomohide Saio
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Masahiro Ushio
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Mitsuhiro Sekiguchi
- Analysis and Pharmacokinetics Research Labs, Department of Drug Discovery, Astellas Pharma Inc., Tokyo, Japan
| | - Masashi Yokochi
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Kenji Ogura
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
| | - Fuyuhiko Inagaki
- Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, N-21, W-11, Kita-ku, Sapporo, 001-0021 Japan
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26
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Peters F, Maestre-Martinez M, Leonov A, Kovačič L, Becker S, Boelens R, Griesinger C. Cys-Ph-TAHA: a lanthanide binding tag for RDC and PCS enhanced protein NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:329-37. [PMID: 21892794 PMCID: PMC3193991 DOI: 10.1007/s10858-011-9560-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 08/11/2011] [Indexed: 05/16/2023]
Abstract
Here we present Cys-Ph-TAHA, a new nonadentate lanthanide tag for the paramagnetic labelling of proteins. The tag can be easily synthesized and is stereochemically homogenous over a wide range of temperatures, yielding NMR spectra with a single set of peaks. Bound to ubiquitin, it induced large residual dipolar couplings and pseudocontact shifts that could be measured easily and agreed very well with the protein structure. We show that Cys-Ph-TAHA can be used to label large proteins that are biochemically challenging such as the Lac repressor in a 90 kDa ternary complex with DNA and inducer.
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Affiliation(s)
- Fabian Peters
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mitcheell Maestre-Martinez
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrei Leonov
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lidija Kovačič
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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27
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Koehler J, Meiler J. Expanding the utility of NMR restraints with paramagnetic compounds: background and practical aspects. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 59:360-89. [PMID: 22027343 PMCID: PMC3202700 DOI: 10.1016/j.pnmrs.2011.05.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2011] [Accepted: 05/06/2011] [Indexed: 05/05/2023]
Affiliation(s)
- Julia Koehler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-8725, USA.
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28
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Erdélyi M, d'Auvergne E, Navarro-Vázquez A, Leonov A, Griesinger C. Dynamics of the glycosidic bond: conformational space of lactose. Chemistry 2011; 17:9368-76. [PMID: 21755545 DOI: 10.1002/chem.201100854] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Indexed: 11/11/2022]
Abstract
The dynamics of the glycosidic bond of lactose was studied by a paramagnetic tagging-based NMR technique, which allowed the collection of an unusually large series of NMR data for a single compound. By the use of distance- and orientation-dependent residual dipolar couplings and pseudocontact shifts, the simultaneous fitting of the probabilities of computed conformations and the orientation of the magnetic susceptibility tensor of a series of lanthanide complexes of lactose show that its glycosidic bond samples syn/syn, anti/syn and syn/anti ϕ/ψ regions of the conformational space in water. The analysis indicates a higher reliability of pseudocontact shift data as compared to residual dipolar couplings with the presently available weakly orienting paramagnetic tagging technique. The method presented herein allows for an improved understanding of the dynamic behaviour of oligosaccharides.
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Affiliation(s)
- Máté Erdélyi
- NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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29
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Jia X, Maleckis A, Huber T, Otting G. 4,4′-Dithiobisdipicolinic Acid: A Small and Convenient Lanthanide Binding Tag for Protein NMR Spectroscopy. Chemistry 2011; 17:6830-6. [DOI: 10.1002/chem.201003573] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Indexed: 11/09/2022]
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30
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Giovenzana GB, Imperio D, Lattuada L, Uggeri F. Stevens rearrangement as a tool for the structural modification of polyaminopolycarboxylic ligands. Org Biomol Chem 2011; 9:679-81. [PMID: 21249235 DOI: 10.1039/c0ob00909a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyaminopolycarboxylic acids are a well known class of ligands employed for metal ion complexation. Despite the large commercial availability, reports of their use as substrates for direct structural modifications are rare. Herein we report a simple and efficient protocol for the preparation of substituted polyaminopolycarboxylic ligands relying on a one-pot N-alkylation-Stevens rearrangement cascade.
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31
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Keizers PHJ, Ubbink M. Paramagnetic tagging for protein structure and dynamics analysis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:88-96. [PMID: 21241885 DOI: 10.1016/j.pnmrs.2010.08.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 08/05/2010] [Indexed: 05/18/2023]
Affiliation(s)
- Peter H J Keizers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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32
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Gruene T, Cho MK, Karyagina I, Kim HY, Grosse C, Giller K, Zweckstetter M, Becker S. Integrated analysis of the conformation of a protein-linked spin label by crystallography, EPR and NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2011; 49:111-9. [PMID: 21271275 PMCID: PMC3042103 DOI: 10.1007/s10858-011-9471-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 12/22/2010] [Indexed: 05/11/2023]
Abstract
Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as protein-protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron paramagnetic resonance (EPR) and NMR spectroscopy. Close agreement was found between the conformation of the spin label observed in the crystal structure with interspin distances measured by EPR and signal broadening in NMR spectra, suggesting that the conformation seen in the crystal structure is also preferred in solution. In contrast, conformations of the spin label observed in crystal structures of T4 lysozyme are not in agreement with the paramagnetic relaxation enhancement observed for spin-labeled CylR2 in solution. Our data demonstrate that accurate positioning of the paramagnetic center is essential for high-resolution structure determination.
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Affiliation(s)
- Tim Gruene
- Department of Structural Chemistry, University of Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Min-Kyu Cho
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Irina Karyagina
- Max Planck Institute for Biophysical Chemistry, AG Electron Spin Resonance Spectroscopy, Am Faßberg 11, 37077 Göttingen, Germany
| | - Hai-Young Kim
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Christian Grosse
- Department of Structural Chemistry, University of Göttingen, Tammannstraße 4, 37077 Göttingen, Germany
| | - Karin Giller
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Markus Zweckstetter
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany
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33
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Lattuada L, Barge A, Cravotto G, Giovenzana GB, Tei L. The synthesis and application of polyamino polycarboxylic bifunctional chelating agents. Chem Soc Rev 2011; 40:3019-49. [DOI: 10.1039/c0cs00199f] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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34
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Ming Yang C. Biometal binding-site mimicry with modular, hetero-bifunctionally modified architecture encompassing a Trp/His motif: Insights into spatiotemporal noncovalent interactions from a comparative spectroscopic study. Dalton Trans 2011; 40:3008-27. [DOI: 10.1039/c0dt00237b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Mallagaray A, Canales A, Domínguez G, Jiménez-Barbero J, Pérez-Castells J. A rigid lanthanide binding tag for NMR structural analysis of carbohydrates. Chem Commun (Camb) 2011; 47:7179-81. [DOI: 10.1039/c1cc11860a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Saio T, Yokochi M, Kumeta H, Inagaki F. PCS-based structure determination of protein-protein complexes. JOURNAL OF BIOMOLECULAR NMR 2010; 46:271-80. [PMID: 20300805 PMCID: PMC2844537 DOI: 10.1007/s10858-010-9401-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 02/17/2010] [Indexed: 05/03/2023]
Abstract
A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and (1)H(N)/(15)N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (approximately 40 A) distance and angular restraints between the lanthanide ion and the observed nuclei, while the (1)H(N)/(15)N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure determination of the p62 PB1-PB1 complex, which forms a front-to-back 20 kDa homo-oligomer. As p62 PB1 does not intrinsically bind metal ions, the lanthanide binding peptide tag was attached to one subunit of the dimer at two anchoring points. Each monomer was treated as a rigid body and was docked based on the backbone PCS and backbone chemical shift perturbation data. Unlike NOE-based structural determination, this method only requires resonance assignments of the backbone (1)H(N)/(15)N signals and the PCS data obtained from several sets of two-dimensional (15)N-heteronuclear single quantum coherence spectra, thus facilitating rapid structure determination of the protein-protein complex.
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Affiliation(s)
- Tomohide Saio
- Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021 Japan
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 001-0021 Japan
| | - Masashi Yokochi
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 001-0021 Japan
| | - Hiroyuki Kumeta
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 001-0021 Japan
| | - Fuyuhiko Inagaki
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 001-0021 Japan
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37
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Man B, Su XC, Liang H, Simonsen S, Huber T, Messerle B, Otting G. 3-Mercapto-2,6-Pyridinedicarboxylic Acid: A Small Lanthanide-Binding Tag for Protein Studies by NMR Spectroscopy. Chemistry 2010; 16:3827-32. [DOI: 10.1002/chem.200902904] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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38
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Su XC, Otting G. Paramagnetic labelling of proteins and oligonucleotides for NMR. JOURNAL OF BIOMOLECULAR NMR 2010; 46:101-112. [PMID: 19529883 DOI: 10.1007/s10858-009-9331-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2009] [Accepted: 05/20/2009] [Indexed: 05/26/2023]
Abstract
Paramagnetic effects offer a rich source of long-range structural restraints. Here we review current methods for site-specific tagging of proteins and oligonucleotides with paramagnetic molecules. The paramagnetic tags include nitroxide radicals and metal chelators. Particular emphasis is placed on tags suitable for site-specific and rigid attachment of lanthanide ions to macromolecules.
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Affiliation(s)
- Xun-Cheng Su
- The Australian National University, Canberra, Australia
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39
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Saio T, Ogura K, Yokochi M, Kobashigawa Y, Inagaki F. Two-point anchoring of a lanthanide-binding peptide to a target protein enhances the paramagnetic anisotropic effect. JOURNAL OF BIOMOLECULAR NMR 2009; 44:157-66. [PMID: 19468839 DOI: 10.1007/s10858-009-9325-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 05/01/2009] [Indexed: 05/15/2023]
Abstract
Paramagnetic lanthanide ions fixed in a protein frame induce several paramagnetic effects such as pseudo-contact shifts and residual dipolar couplings. These effects provide long-range distance and angular information for proteins and, therefore, are valuable in protein structural analysis. However, until recently this approach had been restricted to metal-binding proteins, but now it has become applicable to non-metalloproteins through the use of a lanthanide-binding tag. Here we report a lanthanide-binding peptide tag anchored via two points to the target proteins. Compared to conventional single-point attached tags, the two-point linked tag provides two to threefold stronger anisotropic effects. Though there is slight residual mobility of the lanthanide-binding tag, the present tag provides a higher anisotropic paramagnetic effect.
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Affiliation(s)
- Tomohide Saio
- Graduate School of Life Science, Hokkaido University, Sapporo, 001-0021, Japan
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40
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Keizers PHJ, Saragliadis A, Hiruma Y, Overhand M, Ubbink M. Design, synthesis, and evaluation of a lanthanide chelating protein probe: CLaNP-5 yields predictable paramagnetic effects independent of environment. J Am Chem Soc 2008; 130:14802-12. [PMID: 18826316 DOI: 10.1021/ja8054832] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Immobilized lanthanide ions offer the opportunity to refine structures of proteins and the complexes they form by using restraints obtained from paramagnetic NMR experiments. We report the design, synthesis, and spectroscopic evaluation of the lanthanide chelator, Caged Lanthanide NMR Probe 5 (CLaNP-5) readily attachable to a protein surface via two cysteine residues. The probe causes tunable pseudocontact shifts, alignment, paramagnetic relaxation enhancement, and luminescence, by chelating it to the appropriate lanthanide ion. The observation of single shifts and the finding that the magnetic susceptibility tensors obtained from shifts and alignment analyses are highly similar strongly indicate that the probe is rigid with respect to the protein backbone. By placing the probe at various positions on a model protein it is demonstrated that the size and orientation of the magnetic susceptibility tensor of the probe are independent of the local protein environment. Consequently, the effects of the probe are readily predictable using a protein structure only. These findings designate CLaNP-5 as a protein probe to deliver unambiguous high quality structural restraints in studies on protein-protein and protein-ligand interactions.
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Affiliation(s)
- Peter H J Keizers
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands
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41
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Otting G. Prospects for lanthanides in structural biology by NMR. JOURNAL OF BIOMOLECULAR NMR 2008; 42:1-9. [PMID: 18688728 DOI: 10.1007/s10858-008-9256-0] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 07/05/2008] [Indexed: 05/21/2023]
Abstract
The advent of different lanthanide-binding reagents has made site-specific labelling of proteins with paramagnetic lanthanides a viable proposition. This brings many powerful techniques originally established and demonstrated for paramagnetic metalloproteins into the mainstream of structural biology. The promise is that, by exploiting the long-range effects of paramagnetism, lanthanide labelling will allow the study of larger proteins and protein-ligand complexes with greater ease and accuracy than hitherto possible. In particular, lanthanide-induced pseudocontact shifts (PCS) provide powerful restraints and 3D structure determination using PCS as the only source of experimental restraints will probably be possible with data obtained from samples with different lanthanide-tagging sites. Cell-free protein synthesis is positioned to play an important role in this strategy, as an inexpensive source of selectively labelled protein samples and for easy site-specific incorporation of unnatural lanthanide-binding amino acids.
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Affiliation(s)
- Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia.
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42
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Su XC, McAndrew K, Huber T, Otting G. Lanthanide-binding peptides for NMR measurements of residual dipolar couplings and paramagnetic effects from multiple angles. J Am Chem Soc 2008; 130:1681-7. [PMID: 18189393 DOI: 10.1021/ja076564l] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lanthanide-binding peptide tags (LBTs) containing a single cysteine residue can be attached to proteins via a disulfide bond, presenting a flexible means of tagging proteins site-specifically with a lanthanide ion. Here we show that cysteine residues placed in different positions of the LBT can be used to expose the protein to different orientations of the magnetic susceptibility anisotropy (delta chi) tensor and to generate different molecular alignments in a magnetic field. Delta chi tensors determined by nuclear magnetic resonance (NMR) spectroscopy for LBT complexes with Yb3+, Tm3+, and Er3+ suggest a rational way of producing alignment tensors with different orientations. In addition, knowledge of the delta chi tensor of LBT allows modeling of the protein-LBT structures. Despite evidence for residual mobility of the LBTs with respect to the protein, the pseudocontact shifts and residual dipolar couplings displayed by proteins disulfide-bonded to LBTs are greater than those achievable with most other lanthanide binding tags.
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Affiliation(s)
- Xun-Cheng Su
- Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
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43
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Rumpel S, Becker S, Zweckstetter M. High-resolution structure determination of the CylR2 homodimer using paramagnetic relaxation enhancement and structure-based prediction of molecular alignment. JOURNAL OF BIOMOLECULAR NMR 2008; 40:1-13. [PMID: 18026911 PMCID: PMC2758389 DOI: 10.1007/s10858-007-9204-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 09/14/2007] [Indexed: 05/25/2023]
Abstract
Structure determination of homooligomeric proteins by NMR spectroscopy is difficult due to the lack of chemical shift perturbation data, which is very effective in restricting the binding interface in heterooligomeric systems, and the difficulty of obtaining a sufficient number of intermonomer distance restraints. Here we solved the high-resolution solution structure of the 15.4 kDa homodimer CylR2, the regulator of cytolysin production from Enterococcus faecalis, which deviates by 1.1 angstroms from the previously determined X-ray structure. We studied the influence of different experimental information such as long-range distances derived from paramagnetic relaxation enhancement, residual dipolar couplings, symmetry restraints and intermonomer Nuclear Overhauser Effect restraints on the accuracy of the derived structure. In addition, we show that it is useful to combine experimental information with methods of ab initio docking when the available experimental data are not sufficient to obtain convergence to the correct homodimeric structure. In particular, intermonomer distances may not be required when residual dipolar couplings are compared to values predicted on the basis of the charge distribution and the shape of ab initio docking solutions.
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Affiliation(s)
- Sigrun Rumpel
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
| | - Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany
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44
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John M, Schmitz C, Park AY, Dixon NE, Huber T, Otting G. Sequence-Specific and Stereospecific Assignment of Methyl Groups Using Paramagnetic Lanthanides. J Am Chem Soc 2007; 129:13749-57. [DOI: 10.1021/ja0744753] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael John
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Christophe Schmitz
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Ah Young Park
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Nicholas E. Dixon
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Huber
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
| | - Gottfried Otting
- Contribution from the Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia, and School of Molecular and Microbial Sciences and Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD 4072, Australia
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45
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John M, Pintacuda G, Park AY, Dixon NE, Otting G. Structure determination of protein-ligand complexes by transferred paramagnetic shifts. J Am Chem Soc 2007; 128:12910-6. [PMID: 17002387 DOI: 10.1021/ja063584z] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent (1)H and (13)C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the epsilon exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit theta, and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.
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Affiliation(s)
- Michael John
- Australian National University, Research School of Chemistry, Canberra, ACT 0200, Australia
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46
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Pintacuda G, John M, Su XC, Otting G. NMR structure determination of protein-ligand complexes by lanthanide labeling. Acc Chem Res 2007; 40:206-12. [PMID: 17370992 DOI: 10.1021/ar050087z] [Citation(s) in RCA: 235] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The paramagnetism of lanthanide ions offers outstanding opportunities for fast determinations of the three-dimensional (3D) structures of protein-ligand complexes by nuclear magnetic resonance (NMR) spectroscopy. It is shown how the combination of pseudocontact shifts (PCSs) induced by a site-specifically bound lanthanide ion and prior knowledge of the 3D structure of the lanthanide-labeled protein can be used to achieve (i) rapid assignments of NMR spectra, (ii) structure determinations of protein-protein complexes, and (iii) identification of the binding mode of low-molecular weight compounds in complexes with proteins. Strategies for site-specific incorporation of lanthanide ions into proteins are summarized.
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Affiliation(s)
- Guido Pintacuda
- Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
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47
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Vlasie MD, Comuzzi C, van den Nieuwendijk AMCH, Prudêncio M, Overhand M, Ubbink M. Long-Range-Distance NMR Effects in a Protein Labeled with a Lanthanide–DOTA Chelate. Chemistry 2007; 13:1715-23. [PMID: 17115462 DOI: 10.1002/chem.200600916] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A two-thiol reactive lanthanide-DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) chelate, CLaNP-3 (CLaNP=caged lanthanide NMR probe), was synthesized for the rigid attachment to cysteine groups on a protein surface, and used to obtain long-range-distance information from the {15N,1H} HSQC spectra of the protein-lanthanide complex. The DOTA ring exhibits several isomers that are in exchange; however, single resonances were observed for most amide groups in the protein, allowing determination of a single, apparent magnetic-susceptibility tensor. Pseudocontact shifts caused by Yb-containing CLaNP-3 were observed for atoms at 15-35 A from the metal. By using Gd-containing CLaNP-3, relaxation effects were observed, allowing distances up to 30 A from the paramagnetic center to be determined accurately. Similar results were obtained with a Gd-DTPA (diethylene-triaminepentaacetic acid) chelate, CLaNP-1, bound in the same bidentate manner to the protein. This study demonstrates that bidentate attachment of a paramagnetic probe enables determination of long-range distances.
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Affiliation(s)
- Monica D Vlasie
- Leiden Institute of Chemistry, Gorlaeus Laboratories Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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48
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Haberz P, Rodriguez-Castañeda F, Junker J, Becker S, Leonov A, Griesinger C. Two new chiral EDTA-based metal chelates for weak alignment of proteins in solution. Org Lett 2006; 8:1275-8. [PMID: 16562870 DOI: 10.1021/ol053049o] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text] A short synthesis of EDTA-based metal chelates that can be attached to the cysteine residue of a protein via a disulfide bond is described. The complexes were used after coordination of lanthanides to align trigger factor and apo-calmodulin in solution to yield residual dipolar couplings and pseudocontact shifts. Alignment tensors for the new tags are linearly independent compared to those of previously published tags.
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Affiliation(s)
- Peter Haberz
- Max-Planck Institute for Biophysical Chemistry, Department of NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
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49
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Rodriguez-Castañeda F, Haberz P, Leonov A, Griesinger C. Paramagnetic tagging of diamagnetic proteins for solution NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S10-6. [PMID: 16921533 DOI: 10.1002/mrc.1811] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this article, approaches towards the paramagnetic tagging of diamagnetic proteins are reviewed. Alignment can be achieved by adding paramagnetic fusion proteins or peptides to the C- or the N-terminus or by attaching paramagnetic tags to Cystein residues. Applications for the study of homodimer structures and protein/ligand interactions, as well as protein domain dynamics, are reviewed.
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50
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Schmitz C, John M, Park AY, Dixon NE, Otting G, Pintacuda G, Huber T. Efficient chi-tensor determination and NH assignment of paramagnetic proteins. JOURNAL OF BIOMOLECULAR NMR 2006; 35:79-87. [PMID: 16767502 DOI: 10.1007/s10858-006-9002-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 02/08/2006] [Indexed: 05/10/2023]
Abstract
Anisotropic magnetic susceptibility tensors chi of paramagnetic metal ions are manifested in pseudocontact shifts, residual dipolar couplings, and other paramagnetic observables that present valuable long-range information for structure determinations of protein-ligand complexes. A program was developed for automatic determination of the chi-tensor anisotropy parameters and amide resonance assignments in proteins labeled with paramagnetic metal ions. The program requires knowledge of the three-dimensional structure of the protein, the backbone resonance assignments of the diamagnetic protein, and a pair of 2D 15N-HSQC or 3D HNCO spectra recorded with and without paramagnetic metal ion. It allows the determination of reliable chi-tensor anisotropy parameters from 2D spectra of uniformly 15N-labeled proteins of fairly high molecular weight. Examples are shown for the 185-residue N-terminal domain of the subunit epsilon from E. coli DNA polymerase III in complex with the subunit theta and La3+ in its diamagnetic and Dy3+, Tb3+, and Er3+ in its paramagnetic form.
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Affiliation(s)
- Christophe Schmitz
- Department of Mathematics, University of Queensland, Brisbane, QLD, 4072, Australia
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