1
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Poulin-Ponnelle C, Duvail M, Dumas T, Berthon C. Contribution of Molecular Dynamics in pNMR for the Structural Determination of An V and An VI Complexes in Solution. Inorg Chem 2022; 61:15895-15909. [PMID: 36166623 DOI: 10.1021/acs.inorgchem.2c02040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we propose to use classical molecular dynamics (MD) coupled with 1H NMR spectroscopy to study the conformations of different actinyl AnVI (An = U, Np, and Pu) and AnV (An = Np) complexes with tetra-ethyl dyglicolamide (TEDGA) ligands in order to have a better representation of such complexes in solution. Molecular dynamics simulations showed its effectiveness in interpreting the experiments by the calculation of geometric factors needed for the determination of magnetic properties of these complexes. We demonstrated that different conformations of the AnV and AnVI complexes with TEDGA exist in solution with different coordination modes, which is experimentally confirmed by 1H NMR and EXAFS spectroscopies. Furthermore, MD simulations provide additional insights into the structures of complexes in solution since conformations with fast exchanges, which are not accessible from NMR experiments, have been observed by MD simulations.
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Affiliation(s)
| | - Magali Duvail
- ICSM, Univ. Montpellier, CEA, CNRS, ENSCM, Bagnols sur Cèze 30207, France
| | - Thomas Dumas
- LILA, Univ. Montpellier, CEA, Bagnols sur Cèze 30207, France
| | - Claude Berthon
- LILA, Univ. Montpellier, CEA, Bagnols sur Cèze 30207, France
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2
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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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3
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Ravera E, Parigi G, Luchinat C. What are the methodological and theoretical prospects for paramagnetic NMR in structural biology? A glimpse into the crystal ball. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:173-179. [PMID: 31331762 DOI: 10.1016/j.jmr.2019.07.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/16/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
NMR spectroscopy is very sensitive to the presence of unpaired electrons, which perturb the NMR chemical shifts, J splittings and nuclear relaxation rates. These paramagnetic effects have attracted increasing attention over the last decades, and their use is expected to increase further in the future because they can provide structural information not easily achievable with other techniques. In fact, paramagnetic data provide long range structural restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements with the X-ray data. They are also precious for obtaining information on the conformational variability of biomolecular systems, possibly in conjunction with SAXS and/or DEER data. We foresee that new tools will be developed in the next years for the simultaneous analysis of the paramagnetic data with data obtained from different techniques, in order to take advantage synergistically of the information content of all of them. Of course, the use of the paramagnetic data for structural purposes requires the knowledge of the relationship between these data and the molecular coordinates. Recently, the equations commonly used, dating back to half a century ago, have been questioned by first principle quantum chemistry calculations. Our prediction is that further theoretical/computational improvements will essentially confirm the validity of the old semi-empirical equations for the analysis of the experimental paramagnetic data.
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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
| | - 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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4
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Cerofolini L, Silva JM, Ravera E, Romanelli M, Geraldes CFGC, Macedo AL, Fragai M, Parigi G, Luchinat C. How Do Nuclei Couple to the Magnetic Moment of a Paramagnetic Center? A New Theory at the Gauntlet of the Experiments. J Phys Chem Lett 2019; 10:3610-3614. [PMID: 31181162 DOI: 10.1021/acs.jpclett.9b01128] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The recent derivation, based on pure quantum chemistry (QC) first-principles, of the pseudocontact shifts (PCSs) caused by a paramagnetic metal center on far away nuclei has cast doubts on the validity of the semiempirical (SE) theory, predicting PCSs to arise from the metal magnetic susceptibility anisotropy. The SE theory has been used and applied countless times, especially in the last 2 decades, to obtain structural information on proteins containing paramagnetic metal ions. We show here that the QC and SE predictions can be directly tested against experiments, provided a suitable macromolecular system is used. The SE approach yields a good prediction of the experimental PCSs while the QC one does not. It appears that the classic theory is able to grasp satisfactorily the underlying physics.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Life Sciences and Coimbra Chemistry Center , University of Coimbra , Coimbra 3004-531 , Portugal
- UCIBIO-Requimte, Faculty of Sciences and Technology , Universidade NOVA de Lisboa , Caparica 2829-516 , Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Maurizio Romanelli
- Department of Earth Sciences , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences and Coimbra Chemistry Center , University of Coimbra , Coimbra 3004-531 , Portugal
| | - Anjos L Macedo
- UCIBIO-Requimte, Faculty of Sciences and Technology , Universidade NOVA de Lisboa , Caparica 2829-516 , Portugal
| | - Marco Fragai
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
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5
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Carlon A, Ravera E, Parigi G, Murshudov GN, Luchinat C. Joint X-ray/NMR structure refinement of multidomain/multisubunit systems. JOURNAL OF BIOMOLECULAR NMR 2019; 73:265-278. [PMID: 30311122 PMCID: PMC6692505 DOI: 10.1007/s10858-018-0212-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/06/2018] [Indexed: 06/08/2023]
Abstract
Data integration in structural biology has become a paradigm for the characterization of biomolecular systems, and it is now accepted that combining different techniques can fill the gaps in each other's blind spots. In this frame, one of the combinations, which we have implemented in REFMAC-NMR, is residual dipolar couplings from NMR together with experimental data from X-ray diffraction. The first are exquisitely sensitive to the local details but does not give any information about overall shape, whereas the latter encodes more the information about the overall shape but at the same time tends to miss the local details even at the highest resolutions. Once crystals are obtained, it is often rather easy to obtain a complete X-ray dataset, however it is time-consuming to obtain an exhaustive NMR dataset. Here, we discuss the effect of including a-priori knowledge on the properties of the system to reduce the number of experimental data needed to obtain a more complete picture. We thus introduce a set of new features of REFMAC-NMR that allow for improved handling of RDC data for multidomain proteins and multisubunit biomolecular complexes, and encompasses the use of pseudo-contact shifts as an additional source of NMR-based information. The new feature may either help in improving the refinement, or assist in spotting differences between the crystal and the solution data. We show three different examples where NMR and X-ray data can be reconciled to a unique structural model without invoking mobility.
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Affiliation(s)
- Azzurra Carlon
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - 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
| | - 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
| | - Garib N. Murshudov
- MRC Laboratory for Molecular Biology, Francis Crick Ave, CB2 0QH Cambridge, UK
| | - 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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6
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Bertini I, Felli IC, Luchinat C, Parigi G, Pierattelli R. Towards a protocol for solution structure determination of copper(II) proteins: the case of Cu(II)Zn(II) superoxide dismutase. Chembiochem 2016; 8:1422-9. [PMID: 17583552 DOI: 10.1002/cbic.200700006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have developed an optimized protocol to solve the solution structure of copper(II) proteins. After assignment, proton-proton NOEs are used for the shell where 1H spectra are conveniently observed. In a shell closer to the metal ion, 13C NMR spectra with band-selective homonuclear decoupling provide the assignment of all nuclei except for those of the metal ligands. A convenient method for the measurement of 13C longitudinal-relaxation rates (R1) of carbonyls and carboxylate moieties is proposed. 1H NOEs and 1H and 13C R1 data are sufficient to produce a good/reasonable solution structure, as demonstrated for a monomeric species of superoxide dismutase, a 153-residue protein.
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Affiliation(s)
- Ivano Bertini
- CERM and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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7
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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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8
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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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9
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Rinaldelli M, Carlon A, Ravera E, Parigi G, Luchinat C. FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data. JOURNAL OF BIOMOLECULAR NMR 2015; 61:21-34. [PMID: 25416616 DOI: 10.1007/s10858-014-9877-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 11/15/2014] [Indexed: 05/17/2023]
Abstract
Pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) arising from the presence of paramagnetic metal ions in proteins as well as RDCs due to partial orientation induced by external orienting media are nowadays routinely measured as a part of the NMR characterization of biologically relevant systems. PCSs and RDCs are becoming more and more popular as restraints (1) to determine and/or refine protein structures in solution, (2) to monitor the extent of conformational heterogeneity in systems composed of rigid domains which can reorient with respect to one another, and (3) to obtain structural information in protein-protein complexes. The use of both PCSs and RDCs proceeds through the determination of the anisotropy tensors which are at the origin of these NMR observables. A new user-friendly web tool, called FANTEN (Finding ANisotropy TENsors), has been developed for the determination of the anisotropy tensors related to PCSs and RDCs and has been made freely available through the WeNMR ( http://fanten-enmr.cerm.unifi.it:8080 ) gateway. The program has many new features not available in other existing programs, among which the possibility of a joint analysis of several sets of PCS and RDC data and the possibility to perform rigid body minimizations.
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Affiliation(s)
- Mauro Rinaldelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, via Sacconi 6, Sesto Fiorentino, Florence, Italy
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10
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Rinaldelli M, Ravera E, Calderone V, Parigi G, Murshudov GN, Luchinat C. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:958-67. [PMID: 24699641 PMCID: PMC4306559 DOI: 10.1107/s1399004713034160] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/18/2013] [Indexed: 11/12/2022]
Abstract
The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.
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Affiliation(s)
- Mauro Rinaldelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Vito Calderone
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Garib N. Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
- Department of Chemistry ‘Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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11
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Morales KA, Yang Y, Long Z, Li P, Taylor AB, Hart PJ, Igumenova TI. Cd2+ as a Ca2+ surrogate in protein-membrane interactions: isostructural but not isofunctional. J Am Chem Soc 2013; 135:12980-3. [PMID: 23937054 PMCID: PMC4749353 DOI: 10.1021/ja406958k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to its favorable spectroscopic properties, Cd(2+) is frequently used as a probe of Ca(2+) sites in proteins. We investigate the ability of Cd(2+) to act as a structural and functional surrogate of Ca(2+) in protein-membrane interactions. C2 domain from protein kinase Cα (C2α) was chosen as a paradigm for the Ca(2+)-dependent phosphatidylserine-binding peripheral membrane domains. We identified the Cd(2+)-binding sites of C2α using NMR spectroscopy, determined the 1.6 Å crystal structure of Cd(2+)-bound C2α, and characterized metal-ion-dependent interactions between C2α and phospholipid membranes using fluorescence spectroscopy and ultracentrifugation experiments. We show that Cd(2+) forms a tight complex with the membrane-binding loops of C2α but is unable to support its membrane-binding function. This is in sharp contrast with Pb(2+), which is almost as effective as Ca(2+) in driving the C2α-membrane association process. Our results provide the first direct evidence for the specific role of divalent metal ions in mediating protein-membrane interactions, have important implications for metal substitution studies in proteins, and illustrate the potential diversity of functional responses caused by toxic metal ions.
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Affiliation(s)
- Krystal A. Morales
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Yuan Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Zheng Long
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Alexander B. Taylor
- Department of Biochemistry and the X-ray Crystallography Core Laboratory, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - P. John Hart
- Department of Biochemistry and the X-ray Crystallography Core Laboratory, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Tatyana I. Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
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12
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Tan E, Rao F, Pasunooti S, Pham TH, Soehano I, Turner MS, Liew CW, Lescar J, Pervushin K, Liang ZX. Solution structure of the PAS domain of a thermophilic YybT protein homolog reveals a potential ligand-binding site. J Biol Chem 2013; 288:11949-59. [PMID: 23504327 DOI: 10.1074/jbc.m112.437764] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Bacillus subtilis protein YybT (or GdpP) and its homologs were recently established as stress signaling proteins that exert their biological effect by degrading the bacterial messenger cyclic di-AMP. YybT homologs contain a small Per-ARNT-Sim (PAS) domain (~80 amino acids) that can bind b-type heme with 1:1 stoichiometry despite the small size of the domain and the lack of a conserved heme iron-coordinating residue. We determined the solution structure of the PAS domain of GtYybT from Geobacillus thermodenitrificans by NMR spectroscopy to further probe its function. The solution structure confirms that PASGtYybT adopts the characteristic PAS fold composed of a five-stranded antiparallel β sheet and a few short α-helices. One α-helix and three central β-strands of PASGtYybT are noticeably shorter than those of the typical PAS domains. Despite the small size of the protein domain, a hydrophobic pocket is formed by the side chains of nonpolar residues stemming from the β-strands and α-helices. A set of residues in the vicinity of the pocket and in the C-terminal region at the dimeric interface exhibits perturbed NMR parameters in the presence of heme or zinc protoporphyrin. Together, the results unveil a compact PAS domain with a potential ligand-binding pocket and reinforce the view that the PASYybT domains function as regulatory domains in the modulation of cellular cyclic di-AMP concentration.
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Affiliation(s)
- Edward Tan
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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Knight MJ, Felli IC, Pierattelli R, Bertini I, Emsley L, Herrmann T, Pintacuda G. Rapid Measurement of Pseudocontact Shifts in Metalloproteins by Proton-Detected Solid-State NMR Spectroscopy. J Am Chem Soc 2012; 134:14730-3. [DOI: 10.1021/ja306813j] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael J. Knight
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Isabella C. Felli
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Ivano Bertini
- Department of Chemistry “Ugo
Schiff“ and Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, 50019
Sesto Fiorentino, Italy
| | - Lyndon Emsley
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Torsten Herrmann
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Guido Pintacuda
- Centre de RMN à Très
Hauts Champs, UMR 5280 CNRS/ENS Lyon/UCB Lyon 1, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France
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Amero CD, Boomershine WP, Xu Y, Foster M. Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner. Biochemistry 2008; 47:11704-10. [PMID: 18922021 PMCID: PMC2650222 DOI: 10.1021/bi8015982] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNase P is the ubiquitous ribonucleoprotein metalloenzyme responsible for cleaving the 5'-leader sequence of precursor tRNAs during their maturation. While the RNA subunit is catalytically active on its own at high monovalent and divalent ion concentrations, four protein subunits are associated with archaeal RNase P activity in vivo: RPP21, RPP29, RPP30, and POP5. These proteins have been shown to function in pairs: RPP21-RPP29 and POP5-RPP30. We have determined the solution structure of RPP21 from the hyperthermophilic archaeon Pyrococcus furiosus ( Pfu) using conventional and paramagnetic NMR techniques. Pfu RPP21 in solution consists of an unstructured N-terminus, two alpha-helices, a zinc binding motif, and an unstructured C-terminus. Moreover, we have used chemical shift perturbations to characterize the interaction of RPP21 with RPP29. The data show that the primary contact with RPP29 is localized to the two helices of RPP21. This information represents a fundamental step toward understanding structure-function relationships of the archaeal RNase P holoenzyme.
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Affiliation(s)
- Carlos D Amero
- Biophysics Program, Ohio State University, Columbus OH 43210
| | | | - Yiren Xu
- Department of Biochemistry, Ohio State University, Columbus OH 43210
| | - Mark Foster
- Biophysics Program, Ohio State University, Columbus OH 43210
- Department of Biochemistry, Ohio State University, Columbus OH 43210
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Schmitz C, Stanton-Cook MJ, Su XC, Otting G, Huber T. Numbat: an interactive software tool for fitting Deltachi-tensors to molecular coordinates using pseudocontact shifts. JOURNAL OF BIOMOLECULAR NMR 2008; 41:179-89. [PMID: 18574699 DOI: 10.1007/s10858-008-9249-z] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Accepted: 05/26/2008] [Indexed: 05/14/2023]
Abstract
Pseudocontact shift (PCS) effects induced by a paramagnetic lanthanide bound to a protein have become increasingly popular in NMR spectroscopy as they yield a complementary set of orientational and long-range structural restraints. PCS are a manifestation of the chi-tensor anisotropy, the Deltachi-tensor, which in turn can be determined from the PCS. Once the Deltachi-tensor has been determined, PCS become powerful long-range restraints for the study of protein structure and protein-ligand complexes. Here we present the newly developed package Numbat (New User-friendly Method Built for Automatic Deltachi-Tensor determination). With a Graphical User Interface (GUI) that allows a high degree of interactivity, Numbat is specifically designed for the computation of the complete set of Deltachi-tensor parameters (including shape, location and orientation with respect to the protein) from a set of experimentally measured PCS and the protein structure coordinates. Use of the program for Linux and Windows operating systems is illustrated by building a model of the complex between the E. coli DNA polymerase III subunits epsilon186 and theta using PCS.
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Affiliation(s)
- Christophe Schmitz
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, QLD 4072, Australia
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16
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Zhuang T, Lee HS, Imperiali B, Prestegard JH. Structure determination of a Galectin-3-carbohydrate complex using paramagnetism-based NMR constraints. Protein Sci 2008; 17:1220-31. [PMID: 18413860 DOI: 10.1110/ps.034561.108] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The determination of the location and conformation of a natural ligand bound to a protein receptor is often a first step in the rational design of molecules that can modulate receptor function. NMR observables, including NOEs, often provide the basis for these determinations. However, when ligands are carbohydrates, interactions mediated by extensive hydrogen-bonding networks often reduce or eliminate NOEs between ligand and protein protons. In these cases, it is useful to look to other distance- and orientation-dependent observables that can constrain the geometry of ligand-protein complexes. Here we illustrate the use of paramagnetism-based NMR constraints, including pseudo-contact shifts (PCS) and field-induced residual dipolar couplings (RDCs). When a paramagnetic center can be attached to the protein, field-induced RDCs and PCS reflect only bound-state properties of the ligand, even when averages over small fractions of bound states and large fractions of free states are observed. The effects can also be observed over a long range, making it possible to attach a paramagnetic center to a remote part of the protein. The system studied here is a Galectin-3-lactose complex. A lanthanide-binding peptide showing minimal flexibility with respect to the protein was integrated into the C terminus of an expression construct for the Galectin-3-carbohydrate-binding domain. Dysprosium ion, which has a large magnetic susceptibility anisotropy, was complexed to the peptide, making it possible to observe both PCSs and field-induced RDCs for the protein and the ligand. The structure determined from these constraints shows agreement with a crystal structure of a Galectin-3-N-acetyllactosamine complex.
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Affiliation(s)
- Tiandi Zhuang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
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17
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Casabianca LB, de Dios AC. Ab initiocalculations of NMR chemical shifts. J Chem Phys 2008; 128:052201. [DOI: 10.1063/1.2816784] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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18
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Hass MAS, Ringkjøbing Jensen M, Led JJ. Probing electric fields in proteins in solution by NMR spectroscopy. Proteins 2008; 72:333-43. [DOI: 10.1002/prot.21929] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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