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Dos Santos K, Bartocci A, Gillet N, Denis-Quanquin S, Roux A, Lin E, Xu Z, Finizola R, Chedozeau P, Chen X, Caradeuc C, Baudin M, Bertho G, Riobé F, Maury O, Dumont E, Giraud N. One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics. Phys Chem Chem Phys 2024; 26:14573-14581. [PMID: 38722087 DOI: 10.1039/d4cp00463a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin. As the interaction process is dynamic, the acquired NMR data only reflect the time average of the different steps. We have used molecular dynamics (MD) simulations to get a deeper insight into the detailed interaction scenario at the microsecond scale. This NMR/MD approach enabled us to establish that the tris-dipicolinate complex interacts specifically with arginines and lysines, while the crystallophore explores the protein surface through weak interactions with carboxylates. These observations shed new light on the dynamic interaction properties of these complexes, which will ultimately enable us to propose a crystallization mechanism.
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Affiliation(s)
- Karen Dos Santos
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Sandrine Denis-Quanquin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Amandine Roux
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
- Polyvalan SAS, Lyon, France
| | - Eugene Lin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Zeren Xu
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Raphael Finizola
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Pauline Chedozeau
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Xi Chen
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Cédric Caradeuc
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Mathieu Baudin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université 45 Rue d'Ulm, 75005 Paris, France
| | - Gildas Bertho
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - François Riobé
- Univ. Bordeaux CNRS, Bordeaux INP, ICMCB UMR 5026, F-33600 Pessac, France
| | - Olivier Maury
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France.
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Nicolas Giraud
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
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Angelova S, Kircheva N, Nikolova V, Dobrev S, Dudev T. Electrostatic interactions - key determinants of the metal selectivity in La 3+ and Ca 2+ binding proteins. Phys Chem Chem Phys 2023. [PMID: 37386862 DOI: 10.1039/d3cp01978k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Nearly half of all known proteins contain metal co-factors. In the course of evolution two dozen metal cations (mostly monovalent and divalent species) have been selected to participate in processes of vital importance for living organisms. Trivalent metal cations have also been selected, although to a lesser extent as compared with their mono- and divalent counterparts. Notably, factors governing the metal selectivity in trivalent metal centers in proteins are less well understood than those in the respective divalent metal centers. Thus, the source of high La3+/Ca2+ selectivity in lanthanum-binding proteins, as compared with that of calcium-binding proteins (i.e., calmodulin), is still shrouded in mystery. The well-calibrated thermochemical calculations, performed here, reveal the dominating role of electrostatic interactions in shaping the metal selectivity in La3+-binding centers. The calculations also disclose other (second-order) determinants of metal selectivity in these systems, such as the rigidity and extent of solvent exposure of the binding site. All these factors are also implicated in shaping the metal selectivity in Ca2+-binding proteins.
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Affiliation(s)
- Silvia Angelova
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | - Nikoleta Kircheva
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria.
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies "Acad. J. Malinowski", Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria.
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", 1164 Sofia, Bulgaria.
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3
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Martynov AG, Birin KP, Kirakosyan GA, Gorbunova YG, Tsivadze AY. Site-Selective Solvation-Induced Conformational Switching of Heteroleptic Heteronuclear Tb(III) and Y(III) Trisphthalocyaninates for the Control of Their Magnetic Anisotropy. Molecules 2023; 28:molecules28114474. [PMID: 37298954 DOI: 10.3390/molecules28114474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
In the present work, we report the synthesis of isomeric heteronuclear terbium(III) and yttrium(III) triple-decker phthalocyaninates [(BuO)8Pc]M[(BuO)8Pc]M*[(15C5)4Pc] (M = Tb, M* = Y or M = Y, M* = Tb, [(BuO)8Pc]2--octa-n-butoxyphthalocyaninato-ligand, [(15C5)4Pc]2--tetra-15-crown-5-phthalocyaninato-ligand). We show that these complexes undergo solvation-induced switching: the conformers in which both metal centers are in square-antiprismatic environments are stabilized in toluene, whereas in dichloromethane, the metal centers M and M* are in distorted prismatic and antiprismatic environments, respectively. This conclusion follows from the detailed analysis of lanthanide-induced shifts in 1H NMR spectra, which makes it possible to extract the axial component of the magnetic susceptibility tensor χaxTb and to show that this term is particularly sensitive to conformational switching when terbium(III) ion is placed in the switchable "M" site. This result provides a new tool for controlling the magnetic properties of lanthanide complexes with phthalocyanine ligands.
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Affiliation(s)
- Alexander G Martynov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia
| | - Kirill P Birin
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia
| | - Gayane A Kirakosyan
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky pr., 31, 119991 Moscow, Russia
| | - Yulia G Gorbunova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky pr., 31, 119991 Moscow, Russia
| | - Aslan Yu Tsivadze
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky pr., 31, 119991 Moscow, Russia
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Koehler Leman J, Künze G. Recent Advances in NMR Protein Structure Prediction with ROSETTA. Int J Mol Sci 2023; 24:ijms24097835. [PMID: 37175539 PMCID: PMC10178863 DOI: 10.3390/ijms24097835] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for studying the structure and dynamics of proteins in their native state. For high-resolution NMR structure determination, the collection of a rich restraint dataset is necessary. This can be difficult to achieve for proteins with high molecular weight or a complex architecture. Computational modeling techniques can complement sparse NMR datasets (<1 restraint per residue) with additional structural information to elucidate protein structures in these difficult cases. The Rosetta software for protein structure modeling and design is used by structural biologists for structure determination tasks in which limited experimental data is available. This review gives an overview of the computational protocols available in the Rosetta framework for modeling protein structures from NMR data. We explain the computational algorithms used for the integration of different NMR data types in Rosetta. We also highlight new developments, including modeling tools for data from paramagnetic NMR and hydrogen-deuterium exchange, as well as chemical shifts in CS-Rosetta. Furthermore, strategies are discussed to complement and improve structure predictions made by the current state-of-the-art AlphaFold2 program using NMR-guided Rosetta modeling.
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
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5
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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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6
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Chen JL, Li B, Ma B, Su XC. Distinct stereospecific effect of chiral tether between a tag and protein on the rigidity of paramagnetic tag. JOURNAL OF BIOMOLECULAR NMR 2022; 76:107-119. [PMID: 35841475 DOI: 10.1007/s10858-022-00399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Flexibility between the paramagnetic tag and its protein conjugates is a common yet unresolved issue in the applications of paramagnetic NMR spectroscopy in biological systems. The flexibility greatly attenuates the magnetic anisotropy and compromises paramagnetic effects especially for pseudocontact shift and residual dipolar couplings. Great efforts have been made to improve the rigidity of paramagnetic tag in the protein conjugates, however, the effect of local environment vicinal to the protein ligation site on the paramagnetic effects remains poorly understood. In the present work, the stereospecific effect of chiral tether between the protein and a tag on the paramagnetic effects produced by the tag attached via a D- and L-type linker between the protein and paramagnetic metal chelating moiety was assessed. The remarkable chiral effect of the D- and L-type tether between the tag and the protein on the rigidity of paramagnetic tag is disclosed in a number of protein-tag-Ln complexes. The chiral tether formed between the D-type tag and L-type protein surface minimizes the effect of the local environment surrounding the ligation site on the averaging of paramagnetic tag, which is helpful to preserve the rigidity of a paramagnetic tag in the protein conjugates.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bo Ma
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.
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7
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Jaworski A, Hedin N. Electron correlation and vibrational effects in predictions of paramagnetic NMR shifts. Phys Chem Chem Phys 2022; 24:15230-15244. [PMID: 35703010 DOI: 10.1039/d2cp01206e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure calculations are fundamentally important for the interpretation of nuclear magnetic resonance (NMR) spectra from paramagnetic systems that include organometallic and inorganic compounds, catalysts, or metal-binding sites in proteins. Prediction of induced paramagnetic NMR shifts requires knowledge of electron paramagnetic resonance (EPR) parameters: the electronic g tensor, zero-field splitting D tensor, and hyperfine A tensor. The isotropic part of A, called the hyperfine coupling constant (HFCC), is one of the most troublesome properties for quantum chemistry calculations. Yet, even relatively small errors in calculations of HFCC tend to propagate into large errors in the predicted NMR shifts. The poor quality of A tensors that are currently calculated using density functional theory (DFT) constitutes a bottleneck in improving the reliability of interpretation of the NMR spectra from paramagnetic systems. In this work, electron correlation effects in calculations of HFCCs with a hierarchy of ab initio methods were assessed, and the applicability of different levels of DFT approximations and the coupled cluster singles and doubles (CCSD) method was tested. These assessments were performed for the set of selected test systems comprising an organic radical, and complexes with transition metal and rare-earth ions, for which experimental data are available. Severe deficiencies of DFT were revealed but the CCSD method was able to deliver good agreement with experimental data for all systems considered, however, at substantial computational costs. We proposed a more computationally tractable alternative, where the A was computed with the coupled cluster theory exploiting locality of electron correlation. This alternative is based on the domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) method. In this way the robustness and reliability of the coupled cluster theory were incorporated into the modern formalism for the prediction of induced paramagnetic NMR shifts, and became applicable to systems of chemical interest. This approach was verified for the bis(cyclopentadienyl)vanadium(II) complex (Cp2V; vanadocene), and the metal-binding site of the Zn2+ → Co2+ substituted superoxide dismutase (SOD) metalloprotein. Excellent agreement with experimental NMR shifts was achieved, which represented a substantial improvement over previous theoretical attempts. The effects of vibrational corrections to orbital shielding and hyperfine tensor were evaluated and discussed within the second-order vibrational perturbation theory (VPT2) framework.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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8
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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: 21] [Impact Index Per Article: 10.5] [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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9
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Zapolotsky EN, Qu Y, Babailov SP. Lanthanide complexes with polyaminopolycarboxylates as prospective NMR/MRI diagnostic probes: peculiarities of molecular structure, dynamics and paramagnetic properties. J INCL PHENOM MACRO 2021; 102:1-33. [PMID: 34785985 PMCID: PMC8582344 DOI: 10.1007/s10847-021-01112-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022]
Abstract
The paramagnetic lanthanide complexes with polyaminopolycarboxylate (PAPC) ligands attract considerable attention from the standpoint of potential applications thereof as relaxation agents used in medical magnetic resonance imaging (MRI) and in luminescent materials, as well as owing to promising use thereof as paramagnetic labels for studying the properties of biopolymers since they exhibit thermodynamic stability, good solubility in aqueous media and moderate toxicity. For the last decades, the NMR methods have been used to determine the physical and chemical properties of paramagnetic Ln compounds. The studies concerning paramagnetic NMR lanthanide-induced shifts (LISs) in dissolved Ln complexes, as well as the analysis of band shape as a function of temperature make it possible to obtain valuable information on the structure, intra- and intermolecular dynamics and paramagnetic properties thereof. This review is devoted solely to the following features: firstly, the processes of intramolecular dynamics of lanthanide complexes with polyamino-polycarboxylate ligands such as DOTA, EDTA and DTPA and their derivatives studied by NMR; secondly, the LISs of lanthanide complexes with EDTA, DOTA, DTPA and some of their derivatives depending on temperature and pH. Moreover, in this review, for the first time, the dependence of the activation energy of molecular dynamics in complexes with polydentate ligands on the atomic number of the lanthanide cation is analyzed and a monotonic change in energy is detected, which is due to the effect of lanthanide contraction. It should be noted that this phenomenon is quite general and may also appear in the future in many other series of lanthanide complexes with both other multidentate ligands and with bidentate and monodentate ligands. In the future, it is possible to predict the dependence of the properties of certain lanthanide complexes on the ionic radius of the lanthanide cation based on the approaches presented in the review. In this review, we have also presented the dynamic NMR as the main research method widely used to analyze the processes of molecular dynamics, and the structural studies based on the NMR relaxation spectroscopy and LIS analysis.
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Affiliation(s)
- Eugeny N. Zapolotsky
- A.V. Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Av. Lavrentyev 3, Novosibirsk, Russia 630090
| | - Yanyang Qu
- Institute of Chemical Materials, CAEP, P. O. Box 919-311, Mianyang, 621900 Sichun China
| | - Sergey P. Babailov
- A.V. Nikolaev Institute of Inorganic Chemistry, Siberian Branch of the Russian Academy of Sciences, Av. Lavrentyev 3, Novosibirsk, Russia 630090
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10
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Herath ID, Breen C, Hewitt SH, Berki TR, Kassir AF, Dodson C, Judd M, Jabar S, Cox N, Otting G, Butler SJ. A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time-Resolved Luminescence Studies. Chemistry 2021; 27:13009-13023. [PMID: 34152643 PMCID: PMC8518945 DOI: 10.1002/chem.202101143] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A lanthanide-binding tag site-specifically attached to a protein presents a tool to probe the protein by multiple spectroscopic techniques, including nuclear magnetic resonance, electron paramagnetic resonance and time-resolved luminescence spectroscopy. Here a new stable chiral LnIII tag, referred to as C12, is presented for spontaneous and quantitative reaction with a cysteine residue to generate a stable thioether bond. The synthetic protocol of the tag is relatively straightforward, and the tag is stable for storage and shipping. It displays greatly enhanced reactivity towards selenocysteine, opening a route towards selective tagging of selenocysteine in proteins containing cysteine residues. Loaded with TbIII or TmIII ions, the C12 tag readily generates pseudocontact shifts (PCS) in protein NMR spectra. It produces a relatively rigid tether between lanthanide and protein, which is beneficial for interpretation of the PCSs by single magnetic susceptibility anisotropy tensors, and it is suitable for measuring distance distributions in double electron-electron resonance experiments. Upon reaction with cysteine or other thiol compounds, the TbIII complex exhibits a 100-fold enhancement in luminescence quantum yield, affording a highly sensitive turn-on luminescence probe for time-resolved FRET assays and enzyme reaction monitoring.
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Affiliation(s)
- Iresha D. Herath
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Colum Breen
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Sarah H. Hewitt
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Thomas R. Berki
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Ahmad F. Kassir
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Charlotte Dodson
- Department of Pharmacy & PharmacologyUniversity of Bath Claverton DownBathBA2 7AYUK
| | - Martyna Judd
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Shereen Jabar
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Nicholas Cox
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Gottfried Otting
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Stephen J. Butler
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
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11
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Denis-Quanquin S, Bartocci A, Szczepaniak F, Riobé F, Maury O, Dumont E, Giraud N. Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration. Phys Chem Chem Phys 2021; 23:11224-11232. [PMID: 34010374 DOI: 10.1039/d0cp06570f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy. This study highlights the importance of a large conformational sampling to reconcile characteristic time in NMR with molecular dynamics simulations, where sampling in the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complex-peptide or lanthanide complex-protein interaction or self-assembly processes.
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Affiliation(s)
- Sandrine Denis-Quanquin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Alessio Bartocci
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Florence Szczepaniak
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Francois Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Elise Dumont
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France. and Institut Universitaire de France, 5 rue Descartes, 75005, Paris, France
| | - Nicolas Giraud
- Université de Paris, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
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12
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Ma Z, Lu C, Chen J, Rokicińska A, Kuśtrowski P, Coridan R, Dronskowski R, Slabon A, Jaworski A. CeTiO 2N oxynitride perovskite: paramagnetic 14N MAS NMR without paramagnetic shifts. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2021. [DOI: 10.1515/znb-2021-0031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
14N magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of diamagnetic LaTiO2N perovskite oxynitride and its paramagnetic counterpart CeTiO2N are presented. The latter, to the best of our knowledge, constitutes the first high-resolution 14N MAS NMR spectrum collected from a paramagnetic solid material. The unpaired 4f-electrons in CeTiO2N do not induce a paramagnetic 14N NMR shift. This is remarkable given the direct Ce−N contacts in the structure for which ab initio calculations predict substantial Ce→14N contact shift interaction. The same effect is revealed with 14N MAS NMR for SrWO2N (unpaired 5d-electrons).
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Affiliation(s)
- Zili Ma
- Chair of Solid-State and Quantum Chemistry, Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen , Germany
| | - Can Lu
- Chair of Solid-State and Quantum Chemistry, Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen , Germany
| | - Jianhong Chen
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 , Stockholm , Sweden
| | - Anna Rokicińska
- Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, 30-387 Kraków , Poland
| | - Piotr Kuśtrowski
- Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, 30-387 Kraków , Poland
| | - Robert Coridan
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , AR 72701 , USA
| | - Richard Dronskowski
- Chair of Solid-State and Quantum Chemistry, Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen , Germany
| | - Adam Slabon
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 , Stockholm , Sweden
| | - Aleksander Jaworski
- Department of Materials and Environmental Chemistry , Stockholm University , SE-106 91 , Stockholm , Sweden
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13
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Abstract
The variety of magnetic properties exhibited by paramagnetic lanthanoids provides outstanding information in NMR-based structural biology and therefore can be a very useful tool for characterizing lanthanoid-binding proteins. Because of their dependence on the relative positions of the protein nuclei and of the lanthanoid ion, the paramagnetic restraints (PCS, PRDC and PRE) provide information on structure and dynamics of proteins. In this Chapter, we cover the use of lanthanoids in structural biology including protein sample preparation, NMR experiments and data interpretation.
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14
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Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6040046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The study of cellular machineries responsible for the iron–sulfur (Fe–S) cluster biogenesis has led to the identification of a large number of proteins, whose importance for life is documented by an increasing number of diseases linked to them. The labile nature of Fe–S clusters and the transient protein–protein interactions, occurring during the various steps of the maturation process, make their structural characterization in solution particularly difficult. Paramagnetic nuclear magnetic resonance (NMR) has been used for decades to characterize chemical composition, magnetic coupling, and the electronic structure of Fe–S clusters in proteins; it represents, therefore, a powerful tool to study the protein–protein interaction networks of proteins involving into iron–sulfur cluster biogenesis. The optimization of the various NMR experiments with respect to the hyperfine interaction will be summarized here in the form of a protocol; recently developed experiments for measuring longitudinal and transverse nuclear relaxation rates in highly paramagnetic systems will be also reviewed. Finally, we will address the use of extrinsic paramagnetic centers covalently bound to diamagnetic proteins, which contributed over the last twenty years to promote the applications of paramagnetic NMR well beyond the structural biology of metalloproteins.
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15
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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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16
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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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17
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Babailov SP, Zapolotsky EN. A new approach to determining the structure of lanthanide complexes in solution according to the Curie-spin contribution to the paramagnetic spin-spin relaxation rate enhancements: Ho-DOTA. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114487] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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18
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Peters JA, Djanashvili K, Geraldes CF, Platas-Iglesias C. The chemical consequences of the gradual decrease of the ionic radius along the Ln-series. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213146] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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19
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Tang M, Lam D. Paramagnetic solid-state NMR of proteins. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 103:9-16. [PMID: 31585788 DOI: 10.1016/j.ssnmr.2019.101621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
The paramagnetic properties of metal ions and stable radicals can affect NMR spectra, which can lead to changes in peak intensities, relaxation times and chemical shifts. The changes from paramagnetic effects provide intriguing opportunities for solid-state NMR studies of proteins. In this review, we summarized the trends and progress of paramagnetic solid-state NMR of proteins in the past decade, and showed that paramagnetic effects have great potential applications for sensitivity enhancement, structure determination and topological analysis for microcrystalline proteins, protein complexes, protein aggregates and membrane proteins.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Dennis Lam
- Department of Chemistry, College of Staten Island - Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
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20
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Bahramzadeh A, Huber T, Otting G. Three-Dimensional Protein Structure Determination Using Pseudocontact Shifts of Backbone Amide Protons Generated by Double-Histidine Co 2+-Binding Motifs at Multiple Sites. Biochemistry 2019; 58:3243-3250. [PMID: 31282649 DOI: 10.1021/acs.biochem.9b00404] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pseudocontact shifts (PCSs) generated by paramagnetic metal ions contribute highly informative long-range structure restraints that can be measured in solution and are ideally suited to guide structure prediction algorithms in determining global protein folds. We recently demonstrated that PCSs, which are relatively small but of high quality, can be generated by a double-histidine (dHis) motif in an α-helix, which provides a well-defined binding site for a single Co2+ ion. Here we show that PCSs of backbone amide protons generated by dHis-Co2+ motifs positioned in four different α-helices of a protein deliver excellent restraints to determine the three-dimensional (3D) structure of a protein in a way akin to the global positioning system (GPS). We demonstrate the approach with GPS-Rosetta calculations of the 3D structure of the C-terminal domain of the chaperone ERp29 (ERp29-C). Despite the relatively small size of the PCSs generated by the dHis-Co2+ motifs, the structure calculations converged readily. Generating PCSs by the dHis-Co2+ motif thus presents an excellent alternative to the use of lanthanide tags.
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Affiliation(s)
- Alireza Bahramzadeh
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Thomas Huber
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
| | - Gottfried Otting
- Research School of Chemistry , Australian National University , Canberra , ACT 2601 , Australia
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21
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Urmey AR, Zondlo NJ. Design of a Protein Motif Responsive to Tyrosine Nitration and an Encoded Turn-Off Sensor of Tyrosine Nitration. Biochemistry 2019; 58:2822-2833. [PMID: 31140788 PMCID: PMC6688601 DOI: 10.1021/acs.biochem.9b00334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine nitration is a protein post-translational modification that is predominantly non-enzymatic and is observed to be increased under conditions of nitrosative stress and in numerous disease states. A small protein motif (14-18 amino acids) responsive to tyrosine nitration has been developed. In this design, nitrotyrosine replaced the conserved Glu12 of an EF-hand metal-binding motif. Thus, the non-nitrated peptide bound terbium weakly. In contrast, tyrosine nitration resulted in a 45-fold increase in terbium affinity. Nuclear magnetic resonance spectroscopy indicated direct binding of nitrotyrosine to the metal and EF-hand-like metal contacts in this designed peptide. Nitrotyrosine is an efficient quencher of fluorescence. To develop a sensor of tyrosine nitration, the initial design was modified to incorporate Glu residues at EF-hand positions 9 and 16 as additional metal-binding residues, to increase the terbium affinity of the peptide with unmodified tyrosine. This peptide with a tyrosine at residue 12 bound terbium and effectively sensitized terbium luminescence. Tyrosine nitration resulted in a 180-fold increase in terbium affinity ( Kd = 1.6 μM) and quenching of terbium luminescence. This sequence was incorporated as an encoded protein tag and applied as a turn-off fluorescent protein sensor of tyrosine nitration. The sensor was responsive to nitration by peroxynitrite, with fluorescence quenched upon nitration. The greater terbium affinity upon tyrosine nitration resulted in a large dynamic range and sensitivity to substoichiometric nitration. An improved approach for the synthesis of peptides containing nitrotyrosine was also developed, via the in situ silyl protection of nitrotyrosine. This work represents the first designed, encodable protein motif that is responsive to tyrosine nitration.
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Affiliation(s)
- Andrew R. Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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22
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Ravera E, Takis PG, Fragai M, Parigi G, Luchinat C. NMR Spectroscopy and Metal Ions in Life Sciences. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800875] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Panteleimon G. Takis
- Giotto Biotech S.R.L.; Via Madonna del Piano 6 50019 Sesto Fiorentino (FI) Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP); Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry “Ugo Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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23
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Lam D, Zhuang J, Cohen LS, Arshava B, Naider FR, Tang M. Effects of chelator lipids, paramagnetic metal ions and trehalose on liposomes by solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2018; 94:1-6. [PMID: 30096558 DOI: 10.1016/j.ssnmr.2018.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
The effects of various lipid bound paramagnetic metal ions on liposomes prepared in the presence of trehalose and chelator lipids are evaluated to observe site-specific signal changes on liposome samples with optimal resolution in solid-state NMR spectroscopy. We found that Mn2+, Gd3+ and Dy3+ have different influences on the lipid 13C sites depending on their penetration depths into the bilayer, which can be extracted as distance information. The trehalose-liposome mixture is efficiently packed into solid-state NMR rotors and provides optimal resolution at reasonable instrument temperatures (10-50 °C). The effectiveness and convenience of the trehalose preparation for studying a membrane protein in liposomes are demonstrated by a membrane sample with a model membrane peptide to show that trehalose is useful to prepare consistent and stable membrane protein liposome samples for solid-state NMR.
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Affiliation(s)
- Dennis Lam
- Department of Chemistry, College of Staten Island - Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Jianqin Zhuang
- Department of Chemistry, College of Staten Island, Staten Island, NY, 10314, USA
| | - Leah S Cohen
- Department of Chemistry, College of Staten Island, Staten Island, NY, 10314, USA
| | - Boris Arshava
- Department of Chemistry, College of Staten Island, Staten Island, NY, 10314, USA
| | - Fred R Naider
- Department of Chemistry, College of Staten Island - Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Ming Tang
- Department of Chemistry, College of Staten Island - Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
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24
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Spronk CAEM, Żerko S, Górka M, Koźmiński W, Bardiaux B, Zambelli B, Musiani F, Piccioli M, Basak P, Blum FC, Johnson RC, Hu H, Merrell DS, Maroney M, Ciurli S. Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools. J Biol Inorg Chem 2018; 23:1309-1330. [PMID: 30264175 DOI: 10.1007/s00775-018-1616-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/05/2018] [Indexed: 01/03/2023]
Abstract
Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3-7.2 range. The structure of the Ni(II) binding site was probed using 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.
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Affiliation(s)
- Chris A E M Spronk
- JSC Spronk, Vilnius, Lithuania.,Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Mario Piccioli
- Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy
| | - Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Faith C Blum
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ryan C Johnson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Heidi Hu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Michael Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. .,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.
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25
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Sala D, Musiani F, Rosato A. Application of Molecular Dynamics to the Investigation of Metalloproteins Involved in Metal Homeostasis. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Davide Sala
- Magnetic Resonance Center (CERM); University of Florence; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry; Department of Pharmacy and Biotechnology; University of Bologna; Viale Giuseppe Fanin 40, I 40127 Bologna Italy
| | - Antonio Rosato
- Magnetic Resonance Center (CERM); University of Florence; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine; Via Luigi Sacconi 6 50019 Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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26
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Peterson KL, Srivastava K, Pierre VC. Fluorinated Paramagnetic Complexes: Sensitive and Responsive Probes for Magnetic Resonance Spectroscopy and Imaging. Front Chem 2018; 6:160. [PMID: 29876342 PMCID: PMC5974164 DOI: 10.3389/fchem.2018.00160] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/20/2018] [Indexed: 12/11/2022] Open
Abstract
Fluorine magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) of chemical and physiological processes is becoming more widespread. The strength of this technique comes from the negligible background signal in in vivo19F MRI and the large chemical shift window of 19F that enables it to image concomitantly more than one marker. These same advantages have also been successfully exploited in the design of responsive 19F probes. Part of the recent growth of this technique can be attributed to novel designs of 19F probes with improved imaging parameters due to the incorporation of paramagnetic metal ions. In this review, we provide a description of the theories and strategies that have been employed successfully to improve the sensitivity of 19F probes with paramagnetic metal ions. The Bloch-Wangsness-Redfield theory accurately predicts how molecular parameters such as internuclear distance, geometry, rotational correlation times, as well as the nature, oxidation state, and spin state of the metal ion affect the sensitivity of the fluorine-based probes. The principles governing the design of responsive 19F probes are subsequently described in a "how to" guide format. Examples of such probes and their advantages and disadvantages are highlighted through a synopsis of the literature.
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Affiliation(s)
- Katie L Peterson
- Department of Chemistry, Bemidji State University, Bemidji, MN, United States
| | - Kriti Srivastava
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Valérie C Pierre
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
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27
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Gao J, Liang E, Ma R, Li F, Liu Y, Liu J, Jiang L, Li C, Dai H, Wu J, Su X, He W, Ruan K. Fluorine Pseudocontact Shifts Used for Characterizing the Protein-Ligand Interaction Mode in the Limit of NMR Intermediate Exchange. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jia Gao
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - E Liang
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Fudong Li
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Yixiang Liu
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Jiuyang Liu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Ling Jiang
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Conggang Li
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Haiming Dai
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - Jihui Wu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collatorative Innovation Center of Chemical Science and Engineering(Tianjin); Nankai University; Tianjin 300071 P. R. China
| | - Wei He
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Ke Ruan
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
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Gao J, Liang E, Ma R, Li F, Liu Y, Liu J, Jiang L, Li C, Dai H, Wu J, Su X, He W, Ruan K. Fluorine Pseudocontact Shifts Used for Characterizing the Protein-Ligand Interaction Mode in the Limit of NMR Intermediate Exchange. Angew Chem Int Ed Engl 2017; 56:12982-12986. [DOI: 10.1002/anie.201707114] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/15/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jia Gao
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - E Liang
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Fudong Li
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Yixiang Liu
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Jiuyang Liu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Ling Jiang
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Conggang Li
- Key Laboratory of Magnet Resonance in Biological Systems; State Key Laboratory of Magnet Resonance and Atomic and Molecular Physics; Wuhan Center for Magnet Resonance Department; Wuhan Institute of Physics and Mathematics; Chinese Academy of Science; Wuhan Hubei 430071 P. R. China
| | - Haiming Dai
- Center of Medical Physics and Technology; Hefei Institute of Physical Science, Cancer Hospital; Chinese Academy of Science; Hefei Anhui 230031 P. R. China
| | - Jihui Wu
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic Chemistry; Collatorative Innovation Center of Chemical Science and Engineering(Tianjin); Nankai University; Tianjin 300071 P. R. China
| | - Wei He
- Department of pharmacology and Pharmaceutical Sciences; School of Medicine, Tsinghua-Peking Joint centers for Lifer Sciences; Tsinghua University; Beijing 100084 P. R. China
| | - Ke Ruan
- Hefei National Laboratory for Physical Science at the Microscale; School of Life Science; University of Science and Technology of China; Huangshan Road Hefei Anhui 230027 P. R. China
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29
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Modulation of RNA primer formation by Mn(II)-substituted T7 DNA primase. Sci Rep 2017; 7:5797. [PMID: 28724886 PMCID: PMC5517523 DOI: 10.1038/s41598-017-05534-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/19/2017] [Indexed: 12/22/2022] Open
Abstract
Lagging strand DNA synthesis by DNA polymerase requires RNA primers produced by DNA primase. The N-terminal primase domain of the gene 4 protein of phage T7 comprises a zinc-binding domain that recognizes a specific DNA sequence and an RNA polymerase domain that catalyzes RNA polymerization. Based on its crystal structure, the RNA polymerase domain contains two Mg(II) ions. Mn(II) substitution leads to elevated RNA primer synthesis by T7 DNA primase. NMR analysis revealed that upon binding Mn(II), T7 DNA primase undergoes conformational changes near the metal cofactor binding site that are not observed when the enzyme binds Mg(II). A machine-learning algorithm called linear discriminant analysis (LDA) was trained by using the large collection of Mn(II) and Mg(II) binding sites available in the protein data bank (PDB). Application of the model to DNA primase revealed a preference in the enzyme's second metal binding site for Mn(II) over Mg(II), suggesting that T7 DNA primase activity modulation when bound to Mn(II) is based on structural changes in the enzyme.
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Pederson K, Chalmers GR, Gao Q, Elnatan D, Ramelot TA, Ma LC, Montelione GT, Kennedy MA, Agard DA, Prestegard JH. NMR characterization of HtpG, the E. coli Hsp90, using sparse labeling with 13C-methyl alanine. JOURNAL OF BIOMOLECULAR NMR 2017; 68:225-236. [PMID: 28653216 PMCID: PMC5546222 DOI: 10.1007/s10858-017-0123-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/22/2017] [Indexed: 05/03/2023]
Abstract
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses 13C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-TROSY spectra, as well as the backbone-centered structural information from 1H-13C residual dipolar couplings (RDCs) of alanine methyl groups. In all, 40 of the 47 expected crosspeaks were resolved and 36 gave RDC data. Assignments of crosspeaks were partially achieved by transferring assignments from those made on individual domains using triple resonance methods. However, these were incomplete and in many cases the transfer was ambiguous. A genetic algorithm search for consistency between predictions based on domain structures and measurements for chemical shifts and RDCs allowed 60% of the 40 resolved crosspeaks to be assigned with confidence. Chemical shift changes of these crosspeaks on adding an ATP analog to the apo-protein are shown to be consistent with structural changes expected on comparing previous crystal structures for apo- and complex- structures. RDCs collected on the assigned alanine methyl peaks are used to generate a new solution model for the apo-protein structure.
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Affiliation(s)
- Kari Pederson
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Gordon R Chalmers
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
- Department of Computer Science, University of Georgia, Athens, USA
| | - Qi Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - Theresa A Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - Li-Chung Ma
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, USA.
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31
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Schubert M. Insights into Carbohydrate Recognition by 3D Structure Determination of Protein–Carbohydrate Complexes Using NMR. NMR IN GLYCOSCIENCE AND GLYCOTECHNOLOGY 2017:101-122. [DOI: 10.1039/9781782623946-00101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
This chapter provides an overview of protein–carbohydrate complex structures determined with NMR spectroscopy and deposited in the Protein Data Bank (PDB). These 14 structures include protein–carbohydrate interactions ranging from nanomolar to millimolar affinities. Two complexes are discussed in detail, one representing a tightly bound complex and one a weak but specific interaction. This review illustrates that NMR spectroscopy is a competitive method for three-dimensional structure determination of protein–carbohydrate complexes, especially in the case of weak interactions. The number of biological functions in which protein–carbohydrate interactions are involved is steadily growing. Essential functions of the immune system such as the distinction between self and non-self, or the resolution of inflammation, involve critical protein–carbohydrate recognition events. It is therefore expected that by providing atomic details, NMR spectroscopy can make a significant contribution in the near future to unexplored pathways of the immune system and of many other biological processes.
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Affiliation(s)
- Mario Schubert
- Department of Molecular Biology, University of Salzburg 5020 Salzburg Austria
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32
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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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33
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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: 84] [Impact Index Per Article: 12.0] [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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34
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Suturina EA, Häussinger D, Zimmermann K, Garbuio L, Yulikov M, Jeschke G, Kuprov I. Model-free extraction of spin label position distributions from pseudocontact shift data. Chem Sci 2017; 8:2751-2757. [PMID: 28553510 PMCID: PMC5426344 DOI: 10.1039/c6sc03736d] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Not a point, but a cloud: advanced PCS data analysis using 3D probability density reconstruction provides more information.
A significant problem with paramagnetic tags attached to proteins and nucleic acids is their conformational mobility. Each tag is statistically distributed within a volume between 5 and 10 Angstroms across; structural biology conclusions from NMR and EPR work are necessarily diluted by this uncertainty. The problem is solved in electron spin resonance, but remains open in the other major branch of paramagnetic resonance – pseudocontact shift (PCS) NMR spectroscopy, where structural biologists have so far been reluctantly using the point paramagnetic centre approximation. Here we describe a new method for extracting probability densities of lanthanide tags from PCS data. The method relies on Tikhonov-regularised 3D reconstruction and opens a new window into biomolecular structure and dynamics because it explores a very different range of conditions from those accessible to double electron resonance work on paramagnetic tags: a room-temperature solution rather than a glass at cryogenic temperatures. The method is illustrated using four different Tm3+ DOTA-M8 tagged mutants of human carbonic anhydrase II; the results are in good agreement with rotamer library and DEER data. The wealth of high-quality pseudocontact shift data accumulated by the biological magnetic resonance community over the last 30 years, and so far only processed using point models, could now become a major source of useful information on conformational distributions of paramagnetic tags in biomolecules.
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Affiliation(s)
- Elizaveta A Suturina
- School of Chemistry , University of Southampton , Highfield Campus , Southampton , SO17 1BJ , UK .
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns Ring 19 , CH-4056 Basel , Switzerland
| | - Kaspar Zimmermann
- Department of Chemistry , University of Basel , St. Johanns Ring 19 , CH-4056 Basel , Switzerland
| | - Luca Garbuio
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology in Zurich , Vladimir Prelog Weg 1-5/10 , CH-8093 Zürich , Switzerland
| | - Maxim Yulikov
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology in Zurich , Vladimir Prelog Weg 1-5/10 , CH-8093 Zürich , Switzerland
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology in Zurich , Vladimir Prelog Weg 1-5/10 , CH-8093 Zürich , Switzerland
| | - Ilya Kuprov
- School of Chemistry , University of Southampton , Highfield Campus , Southampton , SO17 1BJ , UK .
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Abstract
Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. A computational/experimental hybrid approach incorporating sparse experimental restraints in computational modeling algorithms drastically improves reliability and accuracy of 3D models. This chapter discusses the use of structural information obtained from various paramagnetic NMR measurements and demonstrates computational algorithms implementing pseudocontact shifts as restraints to determine the structure of proteins at atomic resolution.
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36
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Keller K, Mertens V, Qi M, Nalepa AI, Godt A, Savitsky A, Jeschke G, Yulikov M. Computing distance distributions from dipolar evolution data with overtones: RIDME spectroscopy with Gd(iii)-based spin labels. Phys Chem Chem Phys 2017; 19:17856-17876. [DOI: 10.1039/c7cp01524k] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extraction of distance distributions between high-spin paramagnetic centers from relaxation induced dipolar modulation enhancement (RIDME) data is affected by the presence of overtones of dipolar frequencies.
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Affiliation(s)
- Katharina Keller
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Valerie Mertens
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Anna I. Nalepa
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)
- Bielefeld University
- 33615 Bielefeld
- Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion
- D-45470 Mülheim an der Ruhr
- Germany
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Maxim Yulikov
- Laboratory of Physical Chemistry
- Department of Chemistry and Applied Biosciences
- ETH Zurich
- 8093 Zurich
- Switzerland
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37
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Denis-Quanquin S, Riobé F, Delsuc MA, Maury O, Giraud N. Paramagnetic DOSY: An Accurate Tool for the Analysis of the Supramolecular Interactions between Lanthanide Complexes and Proteins. Chemistry 2016; 22:18123-18131. [DOI: 10.1002/chem.201603460] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Sandrine Denis-Quanquin
- Laboratoire de Chimie; UMR 5182, CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon; 46 allée d'Italie 69007 Lyon France
| | - François Riobé
- Laboratoire de Chimie; UMR 5182, CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon; 46 allée d'Italie 69007 Lyon France
| | - Marc-André Delsuc
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC); UMR 7104; 1 rue Laurent Fries, BP 10142 67404 Illkirch cedex France
| | - Olivier Maury
- Laboratoire de Chimie; UMR 5182, CNRS, Ecole Normale Supérieure de Lyon, Université de Lyon; 46 allée d'Italie 69007 Lyon France
| | - Nicolas Giraud
- Equipe RMN en milieu orienté, ICMMO, UMR CNRS 8182, Univ Paris Sud; Université Paris-Saclay; 91405 Orsay cedex France
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38
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Sala D, Giachetti A, Luchinat C, Rosato A. A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple lanthanide ions. JOURNAL OF BIOMOLECULAR NMR 2016; 66:175-185. [PMID: 27771862 DOI: 10.1007/s10858-016-0065-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
The binding of paramagnetic metal ions to proteins produces a number of different effects on the NMR spectra of the system. In particular, when the magnetic susceptibility of the metal ion is anisotropic, pseudocontact shifts (PCSs) arise and can be easily measured. They constitute very useful restraints for the solution structure determination of metal-binding proteins. In this context, there has been great interest in the use of lanthanide(III) ions to induce PCSs in diamagnetic proteins, e.g. through the replacement native calcium(II) ions. By preparing multiple samples in each of which a different ion of the lanthanide series is introduced, it is possible to obtain multiple independent PCS datasets that can be used synergistically to generate protein structure ensembles (typically called bundles). For typical NMR-based determination of protein structure, it is necessary to perform an energetic refinement of such initial bundles to obtain final structures whose geometric quality is suitable for deposition in the PDB. This can be conveniently done by using restrained molecular dynamics simulations (rMD) in explicit solvent. However, there are no available protocols for rMD using multiple PCS datasets as part of the restraints. In this work, we extended the PCS module of the AMBER MD package to handle multiple datasets and tuned a previously developed protocol for NMR structure refinement to achieve consistent convergence with PCS restraints. Test calculations with real experimental data show that this new implementation delivers the expected improvement of protein geometry, resulting in final structures that are of suitable quality for deposition. Furthermore, we observe that also initial structures generated only with traditional restraints can be successfully refined using traditional and PCS restraints simultaneously.
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Affiliation(s)
- Davide Sala
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Andrea Giachetti
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
| | - Antonio Rosato
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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39
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Benda L, Mareš J, Ravera E, Parigi G, Luchinat C, Kaupp M, Vaara J. Pseudo-Contact NMR Shifts over the Paramagnetic Metalloprotein CoMMP-12 from First Principles. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608829] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ladislav Benda
- Institut für Chemie, Theoretische Chemie; Technische Universität Berlin; Sekr. C7, Straße des 17. Juni 135 10623 Berlin Germany
- Institut des Sciences Analytiques; UMR 5280 CNRS/ ENS Lyon/ UCB Lyon 1; 5 rue de la Doua 69100 Villeurbanne France
| | - Jiří Mareš
- NMR Research Unit; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Enrico Ravera
- Magnetic Resonance Center; University of Florence and; Interuniversity Consortium for Magnetic Resonance of Metalloproteins; Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center; University of Florence and; Interuniversity Consortium for Magnetic Resonance of Metalloproteins; Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center; University of Florence and; Interuniversity Consortium for Magnetic Resonance of Metalloproteins; Sesto Fiorentino Italy
- Department of Chemistry; University of Florence; Sesto Fiorentino Italy
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie; Technische Universität Berlin; Sekr. C7, Straße des 17. Juni 135 10623 Berlin Germany
| | - Juha Vaara
- NMR Research Unit; University of Oulu; P.O. Box 3000 90014 Oulu Finland
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40
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Benda L, Mareš J, Ravera E, Parigi G, Luchinat C, Kaupp M, Vaara J. Pseudo-Contact NMR Shifts over the Paramagnetic Metalloprotein CoMMP-12 from First Principles. Angew Chem Int Ed Engl 2016; 55:14713-14717. [PMID: 27781358 DOI: 10.1002/anie.201608829] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/08/2022]
Abstract
Long-range pseudo-contact NMR shifts (PCSs) provide important restraints for the structure refinement of proteins when a paramagnetic metal center is present, either naturally or introduced artificially. Here we show that ab initio quantum-chemical methods and a modern version of the Kurland-McGarvey approach for paramagnetic NMR (pNMR) shifts in the presence of zero-field splitting (ZFS) together provide accurate predictions of all PCSs in a metalloprotein (high-spin cobalt-substituted MMP-12 as a test case). Computations of 314 13 C PCSs using g- and ZFS tensors based on multi-reference methods provide a reliable bridge between EPR-parameter- and susceptibility-based pNMR formalisms. Due to the high sensitivity of PCSs to even small structural differences, local structures based either on X-ray diffraction or on various DFT optimizations could be evaluated critically by comparing computed and experimental PCSs. Many DFT functionals provide insufficiently accurate structures. We also found the available 1RMZ PDB X-ray structure to exhibit deficiencies related to binding of a hydroxamate inhibitor. This has led to a newly refined PDB structure for MMP-12 (5LAB) that provides a more accurate coordination arrangement and PCSs.
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Affiliation(s)
- Ladislav Benda
- Institut für Chemie, Theoretische Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin, Germany.,Institut des Sciences Analytiques, UMR 5280 CNRS/ ENS Lyon/ UCB Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Jiří Mareš
- NMR Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
| | - Enrico Ravera
- Magnetic Resonance Center, University of Florence and, Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center, University of Florence and, Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center, University of Florence and, Interuniversity Consortium for Magnetic Resonance of Metalloproteins, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Juha Vaara
- NMR Research Unit, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland
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Damjanović M, Morita T, Horii Y, Katoh K, Yamashita M, Enders M. How Ions Arrange in Solution: Detailed Insight from NMR Spectroscopy of Paramagnetic Ion Pairs. Chemphyschem 2016; 17:3423-3429. [DOI: 10.1002/cphc.201600804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Marko Damjanović
- Institute of Inorganic Chemistry Heidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany), Tel: +49-6221-54-6247, Fax: +49-6221-54-161-6247
| | - Takaumi Morita
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Yoji Horii
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Keiichi Katoh
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Masahiro Yamashita
- Department of Chemistry Graduate School of Science Tohoku University 6-3 Aramaki-Aza-Aoba Sendai 980-8578 Japan
| | - Markus Enders
- Institute of Inorganic Chemistry Heidelberg University Im Neuenheimer Feld 270 69120 Heidelberg Germany), Tel: +49-6221-54-6247, Fax: +49-6221-54-161-6247
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42
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Dubey A, Mondal S, Chandra K, Atreya HS. Rapid identification of amino acid types in proteins using phase modulated 2D HN(CACB) and 2D HN(COCACB). JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 267:22-29. [PMID: 27078090 DOI: 10.1016/j.jmr.2016.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/16/2016] [Accepted: 04/06/2016] [Indexed: 06/05/2023]
Abstract
We present a simple approach to rapidly identify amino acid types in proteins from a 2D spectrum. The method is based on the fact that (13)C(β) chemical shifts of different amino acid types fall in distinct spectral regions. By evolving the (13)C chemical shifts in the conventional HNCACB or HN(CO)CACB type experiment for a single specified delay period, the phase of the cross peaks of different amino acid residues are modulated depending on their (13)C(β) shift values. Following this specified evolution period, the 2D HN projections of these experiments are acquired. The (13)C evolution period can be chosen such that all residues belonging to a given set of amino acid types have the same phase pattern (positive or negative) facilitating their identification. This approach does not require the preparation of any additional samples, involves the analysis of 2D [(15)N-(1)H] HSQC-type spectra obtained from the routinely used triple resonance experiments with minor modifications, and is applicable to deuterated proteins. The method will be useful for quick assignment of signals that shift during ligand binding or in combination with selective labeling/unlabeling approaches for identification of amino acid types to aid the sequential assignment process.
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Affiliation(s)
- Abhinav Dubey
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India; NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Somnath Mondal
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India; Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kousik Chandra
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India
| | - Hanudatta S Atreya
- NMR Research Centre, Indian Institute of Science, Bangalore 560012, India.
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43
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Tang M, Mao K, Li S, Zhuang J, Diallo K. Paramagnetic effects on the NMR spectra of isotropic bicelles with headgroup modified chelator lipids and metal ions. Phys Chem Chem Phys 2016; 18:15524-7. [PMID: 27240538 DOI: 10.1039/c6cp01443g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We characterized the paramagnetic effects of nine metal ions on NMR signals of isotropic bicelles with headgroup-modified lipids. We found that Mn(2+), Gd(3+) and Dy(3+) show evidence for influencing NMR signals on the surface more than inside and on the disc edge, providing distance information in the bilayers.
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Affiliation(s)
- Ming Tang
- Department of Chemistry, College of Staten Island - PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA.
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44
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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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45
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Swarbrick JD, Ung P, Dennis ML, Lee MD, Chhabra S, Graham B. Installation of a Rigid EDTA-Like Motif into a Protein α-Helix for Paramagnetic NMR Spectroscopy with Cobalt(II) Ions. Chemistry 2015; 22:1228-32. [DOI: 10.1002/chem.201503139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 12/02/2015] [Indexed: 11/06/2022]
Affiliation(s)
- James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville 3052 Victoria Australia
| | - Phuc Ung
- Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville 3052 Victoria Australia
| | - Matthew L. Dennis
- Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville 3052 Victoria Australia
| | - Michael D. Lee
- Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville 3052 Victoria Australia
| | - Sandeep Chhabra
- Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville 3052 Victoria Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences; Monash University; 381 Royal Parade Parkville 3052 Victoria Australia
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46
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Takeuchi K, Arthanari H, Shimada I, Wagner G. Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR. JOURNAL OF BIOMOLECULAR NMR 2015; 63:323-331. [PMID: 26497830 PMCID: PMC4749451 DOI: 10.1007/s10858-015-9991-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 10/01/2015] [Indexed: 05/18/2023]
Abstract
Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality spectra in high field magnets (>600 MHz) by taking advantage of the slow (15)N transverse relaxation and compensating for the inherently low (15)N sensitivity. The (15)N TROSY transverse relaxation rates increase modestly with molecular weight but the TROSY gain in peak heights depends strongly on the magnetic field strength. Theoretical simulations predict that the narrowest line width for the TROSY (15)NH component can be obtained at 900 MHz, but sensitivity reaches its maximum around 1.2 GHz. Based on these considerations, a (15)N-detected 2D (1)H-(15)N TROSY-HSQC ((15)N-detected TROSY-HSQC) experiment was developed and high-quality 2D spectra were recorded at 800 MHz in 2 h for 1 mM maltose-binding protein at 278 K (τc ~ 40 ns). Unlike for (1)H detected TROSY, deuteration is not mandatory to benefit (15)N detected TROSY due to reduced dipolar broadening, which facilitates studies of proteins that cannot be deuterated, especially in cases where production requires eukaryotic expression systems. The option of recording (15)N TROSY of proteins expressed in H2O media also alleviates the problem of incomplete amide proton back exchange, which often hampers the detection of amide groups in the core of large molecular weight proteins that are expressed in D2O culture media and cannot be refolded for amide back exchange. These results illustrate the potential of (15)NH-detected TROSY experiments as a means to exploit the high resolution offered by high field magnets near and above 1 GHz.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan
- PRESTO, JST, Tokyo, 135-0063, Japan
| | - Haribabu Arthanari
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Ichio Shimada
- Molecular Profiling Research Center for Drug Discovery, National Institute for Advanced Industrial Science and Technology, Tokyo, 135-0063, Japan.
- Graduate Schools of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Gerhard Wagner
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA.
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47
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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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48
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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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49
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Pilla KB, Leman JK, Otting G, Huber T. Capturing conformational States in proteins using sparse paramagnetic NMR data. PLoS One 2015; 10:e0127053. [PMID: 25992808 PMCID: PMC4436263 DOI: 10.1371/journal.pone.0127053] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 04/10/2015] [Indexed: 12/20/2022] Open
Abstract
Capturing conformational changes in proteins or protein-protein complexes is a challenge for both experimentalists and computational biologists. Solution nuclear magnetic resonance (NMR) is unique in that it permits structural studies of proteins under greatly varying conditions, and thus allows us to monitor induced structural changes. Paramagnetic effects are increasingly used to study protein structures as they give ready access to rich structural information of orientation and long-range distance restraints from the NMR signals of backbone amides, and reliable methods have become available to tag proteins with paramagnetic metal ions site-specifically and at multiple sites. In this study, we show how sparse pseudocontact shift (PCS) data can be used to computationally model conformational states in a protein system, by first identifying core structural elements that are not affected by the environmental change, and then computationally completing the remaining structure based on experimental restraints from PCS. The approach is demonstrated on a 27 kDa two-domain NS2B-NS3 protease system of the dengue virus serotype 2, for which distinct closed and open conformational states have been observed in crystal structures. By changing the input PCS data, the observed conformational states in the dengue virus protease are reproduced without modifying the computational procedure. This data driven Rosetta protocol enables identification of conformational states of a protein system, which are otherwise difficult to obtain either experimentally or computationally.
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Affiliation(s)
- Kala Bharath Pilla
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Julia Koehler Leman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States of America
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- * E-mail:
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50
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Crick DJ, Wang JX, Graham B, Swarbrick JD, Mott HR, Nietlispach D. Integral membrane protein structure determination using pseudocontact shifts. JOURNAL OF BIOMOLECULAR NMR 2015; 61:197-207. [PMID: 25604936 PMCID: PMC4412549 DOI: 10.1007/s10858-015-9899-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/13/2015] [Indexed: 05/16/2023]
Abstract
Obtaining enough experimental restraints can be a limiting factor in the NMR structure determination of larger proteins. This is particularly the case for large assemblies such as membrane proteins that have been solubilized in a membrane-mimicking environment. Whilst in such cases extensive deuteration strategies are regularly utilised with the aim to improve the spectral quality, these schemes often limit the number of NOEs obtainable, making complementary strategies highly beneficial for successful structure elucidation. Recently, lanthanide-induced pseudocontact shifts (PCSs) have been established as a structural tool for globular proteins. Here, we demonstrate that a PCS-based approach can be successfully applied for the structure determination of integral membrane proteins. Using the 7TM α-helical microbial receptor pSRII, we show that PCS-derived restraints from lanthanide binding tags attached to four different positions of the protein facilitate the backbone structure determination when combined with a limited set of NOEs. In contrast, the same set of NOEs fails to determine the correct 3D fold. The latter situation is frequently encountered in polytopical α-helical membrane proteins and a PCS approach is thus suitable even for this particularly challenging class of membrane proteins. The ease of measuring PCSs makes this an attractive route for structure determination of large membrane proteins in general.
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Affiliation(s)
- Duncan J. Crick
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jue X. Wang
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - James D. Swarbrick
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Helen R. Mott
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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