1
|
Tacconi L, Manvell AS, Briganti M, Czernia D, Weihe H, Konieczny P, Bendix J, Perfetti M. Exploiting High Order Magnetic Anisotropy for Advanced Magnetocaloric Refrigerants. Angew Chem Int Ed Engl 2025; 64:e202417582. [PMID: 39556465 PMCID: PMC11773312 DOI: 10.1002/anie.202417582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 10/28/2024] [Accepted: 11/18/2024] [Indexed: 11/20/2024]
Abstract
Three new 3 d-4 f complexes of general formula trans-[MF2(py)4][LnDOTA] (M=Cr3+ or Co3+, Ln=Dy3+ or Y3+, py=pyridine and DOTA=tetraazacyclododecane-N,N',N'',N'''-tetraacetate) have been synthetised. The fluoride-bridged systems were designed to achieve perfect tetragonal symmetry by combining four-fold symmetric lanthanide and transition metal building blocks. From single crystal measurements, an unprecedented switch of the tetragonal anisotropy of the Dy3+ complexes has been observed. A combination of spectroscopic observations, magnetometry measurements and ab initio calculations allowed us to pinpoint the origin of this phenomenon, which is related to the peculiar energy level structure of the complexes. Moreover, the fourfold anisotropy of the complex has been exploited to design a rotating magnetocaloric experiment showing that tetragonal anisotropy holds great potential to engineer a new class of more efficient magnetic refrigerants.
Collapse
Affiliation(s)
- Leonardo Tacconi
- Department of Chemistry “Ugo Schiff” & INSTM RUUniversità degli Studi di FirenzeVia della Lastruccia 350019Sesto F.no (FI)Italy
| | - Anna S. Manvell
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 5DK-2100CopenhagenDenmark
| | - Matteo Briganti
- Department of Chemistry “Ugo Schiff” & INSTM RUUniversità degli Studi di FirenzeVia della Lastruccia 350019Sesto F.no (FI)Italy
| | - Dominik Czernia
- Institute of Nuclear Physics PANRadzikowskiego 15231 342KrakówPoland
| | - Høgni Weihe
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 5DK-2100CopenhagenDenmark
| | - Piotr Konieczny
- Institute of Nuclear Physics PANRadzikowskiego 15231 342KrakówPoland
| | - Jesper Bendix
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 5DK-2100CopenhagenDenmark
| | - Mauro Perfetti
- Department of Chemistry “Ugo Schiff” & INSTM RUUniversità degli Studi di FirenzeVia della Lastruccia 350019Sesto F.no (FI)Italy
| |
Collapse
|
2
|
Atkin AM, Giansiracusa MJ, Calvello S, Rousset E, Gable RW, Phonsri W, Murray KS, Howard JK, Soncini A, Mole RA, Boskovic C. Inelastic Neutron Scattering Measurement of the Ground State Tunneling Gap in Tb and Ho Analogues of a Dy Field-Induced Single-Molecule Magnet. Inorg Chem 2023; 62:1141-1155. [PMID: 36630675 DOI: 10.1021/acs.inorgchem.2c03457] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recent advances in single-molecule magnet (SMM) research have placed great value on interpretation of inelastic neutron scattering (INS) data for rare earth (RE)-containing SMMs. Here, we present the synthesis of several rare earth complexes where combined magnetic and INS studies have been performed, supported by ab initio calculations. The reaction of rare earth nitrate salts with 2,2'-bipyridine (2,2'-bpy) and tetrahalocatecholate (X4Cat2-, X = Br, Cl) ligands in methanol (MeOH) afforded two new families of compounds [RE(2,2'-bpy)2(X4Cat)(X4CatH)(MeOH)] (X = Br and RE = Y, Eu, Gd, Tb, Dy, Ho, Yb for 1-RE; X = Cl and RE = Y, Tb, Dy, Ho, and Yb for 2-RE). Addition of triethylamine (Et3N) to the reaction mixture delivered Et3NH[RE(2,2'-bpy)2(Br4Cat)2] (3-RE, RE = Er and Yb). Interestingly, cerium behaves differently to the rest of the series, generating (2,2'-bpyH)2[Ce(Br4Cat)3(2,2'-bpy)] (4-Ce) with tetravalent Ce(IV) in contrast to the trivalent metal ions in 1-3. The static magnetic properties of 1-RE (RE = Gd, Tb, Dy and Ho) were investigated in conjunction with INS measurements on 1-Y, 1-Tb, and 1-Ho to probe their ground state properties and any crystal field excitations. To facilitate interpretation of the INS spectra and provide insight into the magnetic behavior, ab initio calculations were performed using the single-crystal X-ray diffraction structural data of 1-RE (RE = Tb, Dy and Ho). The ab initio calculations indicate ground doublets dominated by the maximal angular momentum projection states of Kramers type for 1-Dy and Ising type for 1-Tb and 1-Ho. Dynamic magnetic susceptibility measurements indicate that 1-Dy exhibits slow magnetic relaxation in the presence of a small applied magnetic field mainly through Raman pathways. Inelastic neutron scattering spectra exhibit distinct transitions corresponding to crystal field-induced tunneling gaps between the pseudo-doublet ground state components for 1-Tb and 1-Ho, which is one of the first direct experimental measurements with INS of such tunneling transitions in a molecular nanomagnet. The power of high-resolution INS is demonstrated with evidence of two distinct tunneling gaps measurable for the two crystallographically unique Tb coordination environments observed in the single crystal X-ray structure.
Collapse
Affiliation(s)
- Aiden M Atkin
- School of Chemistry, University of Melbourne, Parkville, Victoria3010, Australia
| | | | - Simone Calvello
- School of Chemistry, University of Melbourne, Parkville, Victoria3010, Australia.,Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC2232, Australia
| | - Elodie Rousset
- School of Chemistry, University of Melbourne, Parkville, Victoria3010, Australia
| | - Robert W Gable
- School of Chemistry, University of Melbourne, Parkville, Victoria3010, Australia
| | - Wasinee Phonsri
- School of Chemistry, Monash University, Clayton, Victoria3168, Australia
| | - Keith S Murray
- School of Chemistry, Monash University, Clayton, Victoria3168, Australia
| | - James K Howard
- Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC2232, Australia
| | - Alessandro Soncini
- School of Chemistry, University of Melbourne, Parkville, Victoria3010, Australia
| | - Richard A Mole
- Australian Nuclear Science and Technology Organisation, Locked Bag 2001, Kirrawee DC2232, Australia
| | - Colette Boskovic
- School of Chemistry, University of Melbourne, Parkville, Victoria3010, Australia
| |
Collapse
|
3
|
Islam MA, Autillo M, Guérin L, Tamain C, Moisy P, Bolvin H, Berthon C. Dipolar and Contact Paramagnetic NMR Chemical Shifts in An IV Complexes with Dipicolinic Acid Derivatives. Inorg Chem 2022; 61:10329-10341. [PMID: 35749686 DOI: 10.1021/acs.inorgchem.2c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Actinide +IV complexes (AnIV = ThIV, UIV, NpIV, and PuIV) with two dipicolinic acid derivatives (DPA and Et-DPA) have been studied by 1H and 13C NMR spectroscopies and first-principles calculations. The Fermi contact and dipolar contributions to the actinide-induced shifts (AIS) are evaluated from a temperature dependence analysis, combined with ab initio results. It allows an experimental estimation of the axial anisotropy of the magnetic susceptibility Δχax and of the hyperfine coupling constants of the NMR-active nuclei. Due to the compactness of the coordination sphere, the magnetic anisotropy of the paramagnetic center is small, and this makes the contact contribution to be the dominant one, even on the remote atoms. The sign of the hyperfine coupling constants and related spin densities is alternating on the nuclei of the ligand cycle, denoting a preponderant spin polarization mechanism. This is well reproduced by unrestricted density functional theory (DFT) calculations. Those values are furthermore slightly decreasing in the actinide series, which indicates a small decrease of the covalency from UIV to PuIV.
Collapse
Affiliation(s)
- Md Ashraful Islam
- Laboratoire de Chimie et Physique Quantiques, CNRS, Université Toulouse III, 118 Route de Narbonne, 31062 Toulouse, France
| | | | - Laetitia Guérin
- CEA, DES, ISEC, DMRC, Univ. Montpellier, Marcoule 30207, France
| | | | - Philippe Moisy
- CEA, DES, ISEC, DMRC, Univ. Montpellier, Marcoule 30207, France
| | - Hélène Bolvin
- Laboratoire de Chimie et Physique Quantiques, CNRS, Université Toulouse III, 118 Route de Narbonne, 31062 Toulouse, France
| | - Claude Berthon
- CEA, DES, ISEC, DMRC, Univ. Montpellier, Marcoule 30207, France
| |
Collapse
|
4
|
Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
Collapse
Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| |
Collapse
|
5
|
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: 26] [Impact Index Per Article: 8.7] [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.
Collapse
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
| |
Collapse
|
6
|
Woll KA, Van Petegem F. Calcium Release Channels: Structure and Function of IP3 Receptors and Ryanodine Receptors. Physiol Rev 2021; 102:209-268. [PMID: 34280054 DOI: 10.1152/physrev.00033.2020] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ca2+-release channels are giant membrane proteins that control the release of Ca2+ from the endoplasmic and sarcoplasmic reticulum. The two members, ryanodine receptors (RyRs) and inositol-1,4,5-trisphosphate Receptors (IP3Rs), are evolutionarily related and are both activated by cytosolic Ca2+. They share a common architecture, but RyRs have evolved additional modules in the cytosolic region. Their massive size allows for the regulation by tens of proteins and small molecules, which can affect the opening and closing of the channels. In addition to Ca2+, other major triggers include IP3 for the IP3Rs, and depolarization of the plasma membrane for a particular RyR subtype. Their size has made them popular targets for study via electron microscopic methods, with current structures culminating near 3Å. The available structures have provided many new mechanistic insights int the binding of auxiliary proteins and small molecules, how these can regulate channel opening, and the mechanisms of disease-associated mutations. They also help scrutinize previously proposed binding sites, as some of these are now incompatible with the structures. Many questions remain around the structural effects of post-translational modifications, additional binding partners, and the higher-order complexes these channels can make in situ. This review summarizes our current knowledge about the structures of Ca2+-release channels and how this informs on their function.
Collapse
Affiliation(s)
- Kellie A Woll
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
7
|
Leone L, Camorali S, Freire-García A, Platas-Iglesias C, Esteban Gomez D, Tei L. Scrutinising the role of intramolecular hydrogen bonding in water exchange dynamics of Gd(iii) complexes. Dalton Trans 2021; 50:5506-5518. [DOI: 10.1039/d1dt00204j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The water exchange rate in GdIII-complexes bearing substituted acetophenone moieties is modulated by the ability of peripherical substituents to establish hydrogen bonds with the coordinated and/or second sphere water molecules.
Collapse
Affiliation(s)
- Loredana Leone
- Dipartimento di Scienze e Innovazione Tecnologica (DiSIT). Università degli Studi del Piemonte Orientale “Amedeo Avogadro”
- I-15121 Alessandria
- Italy
| | - Sara Camorali
- Dipartimento di Scienze e Innovazione Tecnologica (DiSIT). Università degli Studi del Piemonte Orientale “Amedeo Avogadro”
- I-15121 Alessandria
- Italy
| | - Antía Freire-García
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química
- Facultade de Ciencias
- Universidade da Coruña
- 15071 A Coruña
- Spain
| | - Carlos Platas-Iglesias
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química
- Facultade de Ciencias
- Universidade da Coruña
- 15071 A Coruña
- Spain
| | - David Esteban Gomez
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química
- Facultade de Ciencias
- Universidade da Coruña
- 15071 A Coruña
- Spain
| | - Lorenzo Tei
- Dipartimento di Scienze e Innovazione Tecnologica (DiSIT). Università degli Studi del Piemonte Orientale “Amedeo Avogadro”
- I-15121 Alessandria
- Italy
| |
Collapse
|
8
|
Maiti BK, Govil N, Kundu T, Moura JJ. Designed Metal-ATCUN Derivatives: Redox- and Non-redox-Based Applications Relevant for Chemistry, Biology, and Medicine. iScience 2020; 23:101792. [PMID: 33294799 PMCID: PMC7701195 DOI: 10.1016/j.isci.2020.101792] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The designed "ATCUN" motif (amino-terminal copper and nickel binding site) is a replica of naturally occurring ATCUN site found in many proteins/peptides, and an attractive platform for multiple applications, which include nucleases, proteases, spectroscopic probes, imaging, and small molecule activation. ATCUN motifs are engineered at periphery by conjugation to recombinant proteins, peptides, fluorophores, or recognition domains through chemically or genetically, fulfilling the needs of various biological relevance and a wide range of practical usages. This chemistry has witnessed significant growth over the last few decades and several interesting ATCUN derivatives have been described. The redox role of the ATCUN moieties is also an important aspect to be considered. The redox potential of designed M-ATCUN derivatives is modulated by judicious choice of amino acid (including stereochemistry, charge, and position) that ultimately leads to the catalytic efficiency. In this context, a wide range of M-ATCUN derivatives have been designed purposefully for various redox- and non-redox-based applications, including spectroscopic probes, target-based catalytic metallodrugs, inhibition of amyloid-β toxicity, and telomere shortening, enzyme inactivation, biomolecules stitching or modification, next-generation antibiotic, and small molecule activation.
Collapse
Affiliation(s)
- Biplab K. Maiti
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Nidhi Govil
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Taraknath Kundu
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - José J.G. Moura
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
| |
Collapse
|
9
|
Softley CA, Bostock MJ, Popowicz GM, Sattler M. Paramagnetic NMR in drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:287-309. [PMID: 32524233 PMCID: PMC7311382 DOI: 10.1007/s10858-020-00322-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/26/2020] [Indexed: 05/05/2023]
Abstract
The presence of an unpaired electron in paramagnetic molecules generates significant effects in NMR spectra, which can be exploited to provide restraints complementary to those used in standard structure-calculation protocols. NMR already occupies a central position in drug discovery for its use in fragment screening, structural biology and validation of ligand-target interactions. Paramagnetic restraints provide unique opportunities, for example, for more sensitive screening to identify weaker-binding fragments. A key application of paramagnetic NMR in drug discovery, however, is to provide new structural restraints in cases where crystallography proves intractable. This is particularly important at early stages in drug-discovery programs where crystal structures of weakly-binding fragments are difficult to obtain and crystallization artefacts are probable, but structural information about ligand poses is crucial to guide medicinal chemistry. Numerous applications show the value of paramagnetic restraints to filter computational docking poses and to generate interaction models. Paramagnetic relaxation enhancements (PREs) generate a distance-dependent effect, while pseudo-contact shift (PCS) restraints provide both distance and angular information. Here, we review strategies for introducing paramagnetic centers and discuss examples that illustrate the utility of paramagnetic restraints in drug discovery. Combined with standard approaches, such as chemical shift perturbation and NOE-derived distance information, paramagnetic NMR promises a valuable source of information for many challenging drug-discovery programs.
Collapse
Affiliation(s)
- Charlotte A Softley
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mark J Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.
| |
Collapse
|
10
|
Joss D, Häussinger D. Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:284-312. [PMID: 31779884 DOI: 10.1016/j.pnmrs.2019.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 05/14/2023]
Abstract
In this review, lanthanide chelating tags and their applications to pseudocontact shift NMR spectroscopy as well as analysis of residual dipolar couplings are covered. A complete overview is presented of DOTA-derived and non-DOTA-derived lanthanide chelating tags, critical points in the design of lanthanide chelating tags as appropriate linker moieties, their stability under reductive conditions, e.g., for in-cell applications, the magnitude of the anisotropy transferred from the lanthanide chelating tag to the biomacromolecule under investigation and structural properties, as well as conformational bias of the lanthanide chelating tags are discussed. Furthermore, all DOTA-derived lanthanide chelating tags used for PCS NMR spectroscopy published to date are displayed in tabular form, including their anisotropy parameters, with all employed lanthanide ions, CB-Ln distances and tagging reaction conditions, i.e., the stoichiometry of lanthanide chelating tags, pH, buffer composition, temperature and reaction time. Additionally, applications of lanthanide chelating tags for pseudocontact shifts and residual dipolar couplings that have been reported for proteins, protein-protein and protein-ligand complexes, carbohydrates, carbohydrate-protein complexes, nucleic acids and nucleic acid-protein complexes are presented and critically reviewed. The vast and impressive range of applications of lanthanide chelating tags to structural investigations of biomacromolecules in solution clearly illustrates the significance of this particular field of research. The extension of the repertoire of lanthanide chelating tags from proteins to nucleic acids holds great promise for the determination of valuable structural parameters and further developments in characterizing intermolecular interactions.
Collapse
Affiliation(s)
- Daniel Joss
- University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
| | | |
Collapse
|
11
|
Srb P, Svoboda M, Benda L, Lepšík M, Tarábek J, Šícha V, Grüner B, Grantz-Šašková K, Brynda J, Řezáčová P, Konvalinka J, Veverka V. Capturing a dynamically interacting inhibitor by paramagnetic NMR spectroscopy. Phys Chem Chem Phys 2019; 21:5661-5673. [PMID: 30794275 DOI: 10.1039/c9cp00416e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transient and fuzzy intermolecular interactions are fundamental to many biological processes. Despite their importance, they are notoriously challenging to characterize. Effects induced by paramagnetic ligands in the NMR spectra of interacting biomolecules provide an opportunity to amplify subtle manifestations of weak intermolecular interactions observed for diamagnetic ligands. Here, we present an approach to characterizing dynamic interactions between a partially flexible dimeric protein, HIV-1 protease, and a metallacarborane-based ligand, a system for which data obtained by standard NMR approaches do not enable detailed structural interpretation. We show that for the case where the experimental data are significantly averaged to values close to zero the standard fitting of pseudocontact shifts cannot provide reliable structural information. We based our approach on generating a large ensemble of full atomic models, for which the experimental data can be predicted, ensemble averaged and finally compared to the experiment. We demonstrate that a combination of paramagnetic NMR experiments, quantum chemical calculations, and molecular dynamics simulations offers a route towards structural characterization of dynamic protein-ligand complexes.
Collapse
Affiliation(s)
- Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Ayotte Y, Marando VM, Vaillancourt L, Bouchard P, Heffron G, Coote PW, Larda ST, LaPlante SR. Exposing Small-Molecule Nanoentities by a Nuclear Magnetic Resonance Relaxation Assay. J Med Chem 2019; 62:7885-7896. [PMID: 31422659 DOI: 10.1021/acs.jmedchem.9b00653] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Small molecules can self-assemble in aqueous solution into a wide range of nanoentity types and sizes (dimers, n-mers, micelles, colloids, etc.), each having their own unique properties. This has important consequences in the context of drug discovery including issues related to nonspecific binding, off-target effects, and false positives and negatives. Here, we demonstrate the use of the spin-spin relaxation Carr-Purcell-Meiboom-Gill NMR experiment, which is sensitive to molecular tumbling rates and can expose larger aggregate species that have slower rotational correlations. The strategy easily distinguishes lone-tumbling molecules versus nanoentities of various sizes. The technique is highly sensitive to chemical exchange between single-molecule and aggregate states and can therefore be used as a reporter when direct measurement of aggregates is not possible by NMR. Interestingly, we found differences in solution behavior for compounds within structurally related series, demonstrating structure-nanoentity relationships. This practical experiment is a valuable tool to support drug discovery efforts.
Collapse
Affiliation(s)
- Yann Ayotte
- INRS-Centre Armand-Frappier Santé Biotechnologie , 531 Boulevard des Prairies , Laval , Québec H7V 1B7 , Canada
| | - Victoria M Marando
- NMX Research and Solutions, Inc. , 500 Boulevard Cartier Ouest , Laval , Québec , H7V 5B7 , Canada
| | - Louis Vaillancourt
- NMX Research and Solutions, Inc. , 500 Boulevard Cartier Ouest , Laval , Québec , H7V 5B7 , Canada
| | - Patricia Bouchard
- NMX Research and Solutions, Inc. , 500 Boulevard Cartier Ouest , Laval , Québec , H7V 5B7 , Canada
| | - Gregory Heffron
- Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| | - Paul W Coote
- NMX Research and Solutions, Inc. , 500 Boulevard Cartier Ouest , Laval , Québec , H7V 5B7 , Canada.,Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| | - Sacha T Larda
- NMX Research and Solutions, Inc. , 500 Boulevard Cartier Ouest , Laval , Québec , H7V 5B7 , Canada
| | - Steven R LaPlante
- INRS-Centre Armand-Frappier Santé Biotechnologie , 531 Boulevard des Prairies , Laval , Québec H7V 1B7 , Canada.,NMX Research and Solutions, Inc. , 500 Boulevard Cartier Ouest , Laval , Québec , H7V 5B7 , Canada.,Harvard Medical School , 240 Longwood Avenue , Boston , Massachusetts 02115 , United States
| |
Collapse
|
13
|
Valverde P, Quintana JI, Santos JI, Ardá A, Jiménez-Barbero J. Novel NMR Avenues to Explore the Conformation and Interactions of Glycans. ACS OMEGA 2019; 4:13618-13630. [PMID: 31497679 PMCID: PMC6714940 DOI: 10.1021/acsomega.9b01901] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/02/2019] [Indexed: 05/12/2023]
Abstract
This perspective article is focused on the presentation of the latest advances in NMR methods and applications that are behind the exciting achievements in the understanding of glycan receptors in molecular recognition events. Different NMR-based methodologies are discussed along with their applications to scrutinize the conformation and dynamics of glycans as well as their interactions with protein receptors.
Collapse
Affiliation(s)
- Pablo Valverde
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jon I. Quintana
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
| | - Jose I. Santos
- SGIker
UPV/EHU, Centro Joxe Mari Korta, Tolosa Hiribidea 72, 20018 Donostia, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- E-mail: (A.A.)
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technology
Park, Building 800, 48160 Derio, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
- Department
Organic Chemistry II, Faculty Science &
Technology, EHU-UPV, 48940 Leioa, Bizkaia, Spain
- E-mail: (J.J.-B.)
| |
Collapse
|
14
|
Maity S, Gundampati RK, Suresh Kumar TK. NMR Methods to Characterize Protein-Ligand Interactions. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Structural information pertaining to the interactions between biological macromolecules and ligands is of potential significance for understanding of molecular mechanisms in key biological processes. Recently, nuclear magnetic resonance (NMR) spectroscopic techniques has come of age and has widened its scope to characterize binding interactions of small molecules with biological macromolecules especially, proteins. NMR spectroscopy-based techniques are versatile due to their ability to examine weak binding interactions and for rapid screening the binding affinities of ligands with proteins at atomic resolution. In this review, we provide a broad overview of some of the important NMR approaches to investigate interactions of small organic molecules with proteins.
Collapse
Affiliation(s)
- Sanhita Maity
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Ravi Kumar Gundampati
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | | |
Collapse
|
15
|
Zimmermann K, Joss D, Müntener T, Nogueira ES, Schäfer M, Knörr L, Monnard FW, Häussinger D. Localization of ligands within human carbonic anhydrase II using 19F pseudocontact shift analysis. Chem Sci 2019; 10:5064-5072. [PMID: 31183057 PMCID: PMC6530540 DOI: 10.1039/c8sc05683h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/09/2019] [Indexed: 12/17/2022] Open
Abstract
Unraveling the native structure of protein-ligand complexes in solution enables rational drug design. We report here the use of 19F pseudocontact shift (PCS) NMR as a method to determine fluorine positions of high affinity ligands bound within the drug target human carbonic anhydrase II with high accuracy. Three different ligands were localized within the protein by analysis of the obtained PCS from simple one-dimensional 19F spectra with an accuracy of up to 0.8 Å. In order to validate the PCS, four to five independent magnetic susceptibility tensors induced by lanthanide chelating tags bound site-specifically to single cysteine mutants were refined. Least-squares minimization and a Monte-Carlo approach allowed the assessment of experimental errors on the intersection of the corresponding four to five PCS isosurfaces. By defining an angle score that reflects the relative isosurface orientation for different tensor combinations, it was established that the ligand can be localized accurately using only three tensors, if the isosurfaces are close to orthogonal. For two out of three ligands, the determined position closely matched the X-ray coordinates. Our results for the third ligand suggest, in accordance with previously reported ab initio calculations, a rotated position for the difluorophenyl substituent, enabling a favorable interaction with Phe-131. The lanthanide-fluorine distance varied between 22 and 38 Å and induced 19F PCS ranged from 0.078 to 0.409 ppm, averaging to 0.213 ppm. Accordingly, even longer metal-fluorine distances will lead to meaningful PCS, rendering the investigation of protein-ligand complexes significantly larger than 30 kDa feasible.
Collapse
Affiliation(s)
- Kaspar Zimmermann
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Daniel Joss
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Thomas Müntener
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Elisa S Nogueira
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Marc Schäfer
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Livia Knörr
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Fabien W Monnard
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| | - Daniel Häussinger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland .
| |
Collapse
|
16
|
Polshakov VI, Batuev EA, Mantsyzov AB. NMR screening and studies of target–ligand interactions. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
17
|
Pancaroglu R, Van Petegem F. Calcium Channelopathies: Structural Insights into Disorders of the Muscle Excitation–Contraction Complex. Annu Rev Genet 2018; 52:373-396. [DOI: 10.1146/annurev-genet-120417-031311] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ion channels are membrane proteins responsible for the passage of ions down their electrochemical gradients and across biological membranes. In this, they generate and shape action potentials and provide secondary messengers for various signaling pathways. They are often part of larger complexes containing auxiliary subunits and regulatory proteins. Channelopathies arise from mutations in the genes encoding ion channels or their associated proteins. Recent advances in cryo-electron microscopy have resulted in an explosion of ion channel structures in multiple states, generating a wealth of new information on channelopathies. Disease-associated mutations fall into different categories, interfering with ion permeation, protein folding, voltage sensing, ligand and protein binding, and allosteric modulation of channel gating. Prime examples of these are Ca2+-selective channels expressed in myocytes, for which multiple structures in distinct conformational states have recently been uncovered. We discuss the latest insights into these calcium channelopathies from a structural viewpoint.
Collapse
Affiliation(s)
- Raika Pancaroglu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
18
|
Pinto LF, Correa J, Zhao L, Riguera R, Fernandez-Megia E. Fast NMR Screening of Macromolecular Complexes by a Paramagnetic Spin Relaxation Filter. ACS OMEGA 2018; 3:2974-2983. [PMID: 31458565 PMCID: PMC6641404 DOI: 10.1021/acsomega.7b02074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/28/2018] [Indexed: 05/09/2023]
Abstract
The paramagnetic spin relaxation filter is described for the rapid NMR screening of intermolecular interactions between ligands and macromolecular anionic receptors with large transverse relaxation enhancements (R 2p). The addition of micromolar concentrations of Gd3+ to the mixture produces the immediate broadening/suppression of the NMR signals of interacting species while leaving unaffected those of noncompetitive binders (one-dimensional and two-dimensional experiments). The method is highly sensitive, unveiling interactions that are too weak to generate changes in chemical shifts or relaxation times. It is operationally very simple and hence, it is amenable to ready implementation by nonspecialists. Examples of application such as detecting the formation of interpolymer complexes, cyclodextrin host-guest interactions, and the screening of DNA ligands are included that demonstrate the reliability and broad applicability of the method.
Collapse
Affiliation(s)
| | | | - Libo Zhao
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Ricardo Riguera
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Eduardo Fernandez-Megia
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| |
Collapse
|
19
|
Paramagnetic NMR as a new tool in structural biology. Emerg Top Life Sci 2018; 2:19-28. [DOI: 10.1042/etls20170084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/25/2022]
Abstract
NMR (nuclear magnetic resonance) investigation through the exploitation of paramagnetic effects is passing from an approach limited to few specialists in the field to a generally applicable method that must be considered, especially for the characterization of systems hardly affordable with other techniques. This is mostly due to the fact that paramagnetic data are long range in nature, thus providing information for the structural and dynamic characterization of complex biomolecular architectures in their native environment. On the other hand, this information usually needs to be complemented by data from other sources. Integration of paramagnetic NMR with other techniques, and the development of protocols for a joint analysis of all available data, is fundamental for achieving a comprehensive characterization of complex biological systems. We describe here a few examples of the new possibilities offered by paramagnetic data used in integrated structural approaches.
Collapse
|
20
|
Nitsche C, Otting G. NMR studies of ligand binding. Curr Opin Struct Biol 2017; 48:16-22. [PMID: 29017071 DOI: 10.1016/j.sbi.2017.09.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/17/2022]
Abstract
NMR spectroscopy is an established tool in drug discovery, but its strength is commonly regarded to be largely confined to the early stages of hit discovery and fragment based drug design, where NMR offers unique capabilities of characterizing the binding modes of ligand molecules that bind sufficiently weakly to be in rapid exchange between bound and free state. Here we, first, provide a meta-review of recent reviews on NMR studies of ligand binding and, second, review recent progress towards NMR characterization of the ligand binding mode in stable protein-ligand complexes, with particular emphasis on the global positioning system (GPS) approach enabled by paramagnetic lanthanide tags.
Collapse
Affiliation(s)
- Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| |
Collapse
|
21
|
Vonci M, Mason K, Suturina EA, Frawley AT, Worswick SG, Kuprov I, Parker D, McInnes EJL, Chilton NF. Rationalization of Anomalous Pseudocontact Shifts and Their Solvent Dependence in a Series of C3-Symmetric Lanthanide Complexes. J Am Chem Soc 2017; 139:14166-14172. [DOI: 10.1021/jacs.7b07094] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele Vonci
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Kevin Mason
- Department
of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Elizaveta A. Suturina
- School
of Chemistry, The University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Andrew T. Frawley
- Department
of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Steven G. Worswick
- School
of Chemistry, The University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - Ilya Kuprov
- School
of Chemistry, The University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | - David Parker
- Department
of Chemistry, Durham University, South Road, Durham DH1 3LE, U.K
| | - Eric J. L. McInnes
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Nicholas F. Chilton
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| |
Collapse
|
22
|
Maiti BK, Almeida RM, Maia LB, Moura I, Moura JJG. Insights into the Molybdenum/Copper Heterometallic Cluster Assembly in the Orange Protein: Probing Intermolecular Interactions with an Artificial Metal-Binding ATCUN Tag. Inorg Chem 2017; 56:8900-8911. [PMID: 28742344 DOI: 10.1021/acs.inorgchem.7b00840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Orange protein (ORP) is a small bacterial protein, of unknown function, that contains a unique molybdenum/copper heterometallic cluster, [S2MoVIS2CuIS2MoVIS2]3- (Mo/Cu), non-covalently bound. The native cluster can be reconstituted in a protein-assisted mode by the addition of CuII plus tetrathiomolybdate to apo-ORP under controlled conditions. In the work described herein, we artificially inserted the ATCUN ("amino terminus Cu and Ni") motif in the Desulfovibrio gigas ORP (Ala1Ser2His3 followed by the native amino acid residues; modified protein abbreviated as ORP*) to increase our understanding of the Mo/Cu cluster assembly in ORP. The apo-ORP* binds CuII in a 1:1 ratio to yield CuII-ORP*, as clearly demonstrated by EPR (g||,⊥ = 2.183, 2.042 and ACu||,⊥ = 207 × 10-4 cm-1, 19 × 10-4 cm-1) and UV-visible spectroscopies (typical d-d transition bands at 520 nm, ε = 90 M-1 cm-1). The 1H NMR spectrum shows that His3 and His53 are significantly affected upon the addition of the CuII. The X-ray structure shows that these two residues are very far apart (Cα-Cα ≈ 27.9 Å), leading us to suggest that the metal-induced NMR perturbations are due to the interaction of two protein molecules with a single metal ion. Docking analysis supports the metal-mediated dimer formation. The subsequent tetrathiomolybdate binding, to yield the native Mo/Cu cluster, occurs only upon addition of dithiothreitol, as shown by UV-visible and NMR spectroscopies. Additionally, 1H NMR of AgI-ORP* (AgI used as a surrogate of CuI) showed that AgI strongly binds to a native methionine sulfur atom rather than to the ATCUN site, suggesting that CuII and CuI have two different binding sites in ORP*. A detailed mechanism for the formation of the Mo/Cu cluster is discussed, suggesting that CuII is reduced to CuI and transferred from the ATCUN motif to the methionine site; finally, CuI is transferred to the cluster-binding region, upon the interaction of two protein molecules. This result may suggest that copper trafficking is triggered by redox-dependent coordination properties of copper in a trafficking pathway.
Collapse
Affiliation(s)
- Biplab K Maiti
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Rui M Almeida
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Luisa B Maia
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - Isabel Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| | - José J G Moura
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal
| |
Collapse
|
23
|
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: 119] [Impact Index Per Article: 14.9] [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
| |
Collapse
|
24
|
Ma FH, Wang X, Chen JL, Wen X, Sun H, Su XC. Deciphering the Multisite Interactions of a Protein and Its Ligand at Atomic Resolution by Using Sensitive Paramagnetic Effects. Chemistry 2017; 23:926-934. [DOI: 10.1002/chem.201604393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Fei-He Ma
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xiao Wang
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Xin Wen
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| | - Han Sun
- Department of Structural Biology; Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Roessle-Str. 10 13125 Berlin Germany
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry and Collaborative, Innovation Center of Chemical Science and Engineering (Tianjin); Nankai University; Tianjin 300071 China
| |
Collapse
|
25
|
Blahut J, Hermann P, Tošner Z, Platas-Iglesias C. A combined NMR and DFT study of conformational dynamics in lanthanide complexes of macrocyclic DOTA-like ligands. Phys Chem Chem Phys 2017; 19:26662-26671. [DOI: 10.1039/c7cp05296k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A NMR study of the conformational dynamics of paramagnetic Eu3+ complexes provides parameters for isomer interconversion with unprecedented accuracy, while DFT reveals mechanistic details at the molecular level.
Collapse
Affiliation(s)
- Jan Blahut
- Department of Inorganic Chemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Petr Hermann
- Department of Inorganic Chemistry
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Zdeněk Tošner
- Faculty of Science
- Charles University
- Prague 2
- Czech Republic
| | - Carlos Platas-Iglesias
- Centro de Investigaciones Científicas Avanzadas (CICA) and Departamento de Química
- Facultade de Ciencias
- Universidade da Coruña
- 15071 A Coruña
- Spain
| |
Collapse
|
26
|
Marchetti R, Perez S, Arda A, Imberty A, Jimenez‐Barbero J, Silipo A, Molinaro A. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling. ChemistryOpen 2016; 5:274-96. [PMID: 27547635 PMCID: PMC4981046 DOI: 10.1002/open.201600024] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Indexed: 12/20/2022] Open
Abstract
Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.
Collapse
Affiliation(s)
- Roberta Marchetti
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Serge Perez
- Department Molecular Pharmacochemistry UMR 5063CNRS and University of GrenobleAlpes, BP 5338041 Grenoble cedex 9France
| | - Ana Arda
- Bizkaia Technological ParkCIC bioGUNEBuilding 801A-148160Derio-BizkaiaSpain
| | - Anne Imberty
- Centre de Recherche sur les CNRSand University of Grenoble Macromolécules Végétales, UPR 5301Alpes, BP 5338041Grenoble cedex 9France
| | | | - Alba Silipo
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| | - Antonio Molinaro
- Department of Chemical SciencestUniversity of Napoli Federico IIVia Cintia 480126NapoliItaly
| |
Collapse
|
27
|
Takano Y, Tashita R, Suzuki M, Nagase S, Imahori H, Akasaka T. Molecular Location Sensing Approach by Anisotropic Magnetism of an Endohedral Metallofullerene. J Am Chem Soc 2016; 138:8000-6. [PMID: 27314267 DOI: 10.1021/jacs.6b04037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Location recognition at the molecular scale provides valuable information about the nature of functional molecular materials. This study presents a novel location sensing approach based on an endohedral metallofullerene, Ce@C82, using its anisotropic magnetic properties, which lead to temperature-dependent paramagnetic shifts in (1)H NMR spectra. Five site-isomers of Ce@C82CH2-3,5-C6H3Me2 were synthesized to demonstrate the spatial sensing ability of Ce@C82. Single-crystal structures, absorption spectra, and density functional theory calculations were used to select the plausible addition positions in the radical coupling reaction, which preferentially happens on the carbon atoms with high electron density of the singly occupied molecular orbital (SOMO) and positive charge. Temperature-dependent NMR measurements demonstrated unique paramagnetic shifts of the (1)H peaks, which were derived from the anisotropic magnetism of the f-electron in the Ce atom of the isomers. It was found that the magnetic anisotropy axes can be easily predicted by theoretical calculations using the Gaussian 09 package. Further analysis revealed that the temperature-dependent trend in the shifts is clearly predictable from the distance and relative position of the proton from the Ce atom. Hence, the Ce-encapsulated metallofullerene Ce@C82 can provide spatial location information about nearby atoms through the temperature-dependent paramagnetic shifts of its NMR signals. It can act as a molecular probe for location sensing by utilizing the anisotropic magnetism of the encapsulated Ce atom. The potentially low toxicity and stability of the endohedral fullerene would make Ce@C82 suitable for applications in biology and material science.
Collapse
Affiliation(s)
- Yuta Takano
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Sakyo-ku, Kyoto 606-8501, Japan
| | - Ryo Tashita
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba , Tsukuba, Ibaraki 305-8577, Japan
| | - Mitsuaki Suzuki
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba , Tsukuba, Ibaraki 305-8577, Japan.,Department of Chemistry, Tokyo Gakugei University , Tokyo 184-8501, Japan
| | - Shigeru Nagase
- Fukui Institute for Fundamental Chemistry, Kyoto University , Sakyo-ku, Kyoto 606-8103, Japan
| | - Hiroshi Imahori
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University , Sakyo-ku, Kyoto 606-8501, Japan.,Department of Molecular Engineering, Graduate School of Engineering, Kyoto University , Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Akasaka
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba , Tsukuba, Ibaraki 305-8577, Japan.,Department of Chemistry, Tokyo Gakugei University , Tokyo 184-8501, Japan.,State Key Laboratory of Materials Processing and Die & Mold Technology, School of Materials Science and Technology, Huazhong University of Science and Technology , Wuhan 430074, China.,Foundation for Advancement of International Science , Tsukuba, Ibaraki 305-0821, Japan
| |
Collapse
|
28
|
Yuchi Z, Van Petegem F. Ryanodine receptors under the magnifying lens: Insights and limitations of cryo-electron microscopy and X-ray crystallography studies. Cell Calcium 2016; 59:209-27. [DOI: 10.1016/j.ceca.2016.04.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/08/2016] [Accepted: 04/09/2016] [Indexed: 10/21/2022]
|
29
|
Chen WN, Nitsche C, Pilla KB, Graham B, Huber T, Klein CD, Otting G. Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets. J Am Chem Soc 2016; 138:4539-46. [PMID: 26974502 DOI: 10.1021/jacs.6b00416] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure-guided drug design relies on detailed structural knowledge of protein-ligand complexes, but crystallization of cocomplexes is not always possible. Here we present a sensitive nuclear magnetic resonance (NMR) approach to determine the binding mode of tightly binding lead compounds in complex with difficult target proteins. In contrast to established NMR methods, it does not depend on rapid exchange between bound and free ligand or on stable isotope labeling, relying instead on a tert-butyl group as a chemical label. tert-Butyl groups are found in numerous protein ligands and deliver an exceptionally narrow and tall (1)H NMR signal. We show that a tert-butyl group also produces outstandingly intense intra- and intermolecular NOESY cross-peaks. These enable measurements of pseudocontact shifts generated by lanthanide tags attached to the protein, which in turn allows positioning of the ligand on the protein. Once the ligand has been located, assignments of intermolecular NOEs become possible even without prior resonance assignments of protein side chains. The approach is demonstrated with the dengue virus NS2B-NS3 protease in complex with a high-affinity ligand containing a tert-butyl group.
Collapse
Affiliation(s)
- Wan-Na Chen
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia.,Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Kala Bharath Pilla
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Bim Graham
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, VIC 3052, Australia
| | - Thomas Huber
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Gottfried Otting
- Australian National University , Research School of Chemistry, Canberra, ACT 2601, Australia
| |
Collapse
|