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Kozinenko VP, Kiryutin AS, Yurkovskaya AV. Exploring weak ligand-protein interactions by relaxometry of long-lived spin order. Phys Chem Chem Phys 2024; 26:15968-15977. [PMID: 38775038 DOI: 10.1039/d4cp00582a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Relaxation times of nuclear spins often serve as a valuable source of information on the dynamics of various biochemical processes. Measuring relaxation as a function of the external magnetic field turned out to be extremely useful for the studies of weak ligand-protein interactions. We demonstrate that observing the relaxation of the long-lived spin order instead of longitudinal magnetization extends the capability of this approach. We studied the field-dependent relaxation of the longitudinal magnetization and the singlet order (SO) of methylene protons in alanine-glycine dipeptide and citrate in the presence of human serum albumin (HSA). As a result, SO relaxation proved to be more sensitive to ligand-protein interaction, providing higher relaxation contrast for various HSA concentrations. To assess the parameters of the binding process in more details, we utilized a simple analytical relaxation model to fit the experimental field dependences for both SO and T1 relaxation. We also tested the validity of our approach in the experiments with trimethylsilylpropanoic acid (TSP) used as a competitor in ligand binding with HSA.
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2
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Masiewicz E, Ullah F, Mieloch A, Godlewski J, Kruk D. Dynamical properties of solid and hydrated collagen: Insight from nuclear magnetic resonance relaxometry. J Chem Phys 2024; 160:165101. [PMID: 38656443 DOI: 10.1063/5.0191409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/07/2024] [Indexed: 04/26/2024] Open
Abstract
1H spin-lattice Nuclear Magnetic Resonance relaxometry experiments have been performed for collagen and collagen-based artificial tissues in the frequency range of 10 kHz-20 MHz. The studies were performed for non-hydrated and hydrated materials. The relaxation data have been interpreted as including relaxation contributions originating from 1H-1H and 1H-14N dipole-dipole interactions, the latter leading to Quadrupole Relaxation Enhancement effects. The 1H-1H relaxation contributions have been decomposed into terms associated with dynamical processes on different time scales. A comparison of the parameters for the non-hydrated and hydrated systems has shown that hydration leads to a decrease in the dipolar relaxation constants without significantly affecting the dynamical processes. In the next step, the relaxation data for the hydrated systems were interpreted in terms of a model assuming two-dimensional translational diffusion of water molecules in the vicinity of the macromolecular surfaces and a sub-diffusive motion leading to a power law of the frequency dependencies of the relaxation rates. It was found that the water diffusion process is slowed down by at least two orders of magnitude compared to bulk water diffusion. The frequency dependencies of the relaxation rates in hydrated tissues and hydrated collagen are characterized by different power laws (ωH-β, where ωH denotes the 1H resonance frequency): the first of about 0.4 and the second close to unity.
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Affiliation(s)
- Elzbieta Masiewicz
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Farman Ullah
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Adrianna Mieloch
- Department of Human Histology and Embryology, University of Warmia and Mazury in Olsztyn, Warszawska 30, 10-082 Olsztyn, Poland
| | - Janusz Godlewski
- Department of Human Histology and Embryology, University of Warmia and Mazury in Olsztyn, Warszawska 30, 10-082 Olsztyn, Poland
| | - Danuta Kruk
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719 Olsztyn, Poland
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3
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Cerofolini L, Vasa K, Bianconi E, Salobehaj M, Cappelli G, Bonciani A, Licciardi G, Pérez-Ràfols A, Padilla-Cortés L, Antonacci S, Rizzo D, Ravera E, Viglianisi C, Calderone V, Parigi G, Luchinat C, Macchiarulo A, Menichetti S, Fragai M. Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates. Angew Chem Int Ed Engl 2023; 62:e202303202. [PMID: 37276329 DOI: 10.1002/anie.202303202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/07/2023]
Abstract
Several protein-drug conjugates are currently being used in cancer therapy. These conjugates rely on cytotoxic organic compounds that are covalently attached to the carrier proteins or that interact with them via non-covalent interactions. Human transthyretin (TTR), a physiological protein, has already been identified as a possible carrier protein for the delivery of cytotoxic drugs. Here we show the structure-guided development of a new stable cytotoxic molecule based on a known strong binder of TTR and a well-established anticancer drug. This example is used to demonstrate the importance of the integration of multiple biophysical and structural techniques, encompassing microscale thermophoresis, X-ray crystallography and NMR. In particular, we show that solid-state NMR has the ability to reveal effects caused by ligand binding which are more easily relatable to structural and dynamical alterations that impact the stability of macromolecular complexes.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Kristian Vasa
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti n.48, 06123, Perugia, Italy
| | - Maria Salobehaj
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Giulia Cappelli
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Alice Bonciani
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Giulia Licciardi
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Anna Pérez-Ràfols
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Giotto Biotech s.r.l, Sesto Fiorentino, Via della Madonna del Piano 6, 50019, Florence, Italy
| | - Luis Padilla-Cortés
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Sabrina Antonacci
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Domenico Rizzo
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Caterina Viglianisi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Vito Calderone
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
- Giotto Biotech s.r.l, Sesto Fiorentino, Via della Madonna del Piano 6, 50019, Florence, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti n.48, 06123, Perugia, Italy
| | - Stefano Menichetti
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Centre (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
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4
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Molecular Dynamics of Jelly Candies by Means of Nuclear Magnetic Resonance Relaxometry. Molecules 2023; 28:molecules28052230. [PMID: 36903475 PMCID: PMC10005792 DOI: 10.3390/molecules28052230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 03/04/2023] Open
Abstract
1H spin-lattice Nuclear Magnetic Resonance relaxation studies have been performed for different kinds of Haribo jelly and Vidal jelly in a very broad frequency range from about 10 kHz to 10 MHz to obtain insight into the dynamic and structural properties of jelly candies on the molecular level. This extensive data set has been thoroughly analyzed revealing three dynamic processes, referred to as slow, intermediate and fast dynamics occurring on the timescale of 10-6 s, 10-7 s and 10-8 s, respectively. The parameters have been compared for different kinds of jelly for the purpose of revealing their characteristic dynamic and structural properties as well as to enquire into how increasing temperature affects these properties. It has been shown that dynamic processes in different kinds of Haribo jelly are similar (this can be treated as a sign of their quality and authenticity) and that the fraction of confined water molecules is reduced with increasing temperature. Two groups of Vidal jelly have been identified. For the first one, the parameters (dipolar relaxation constants and correlation times) match those for Haribo jelly. For the second group including cherry jelly, considerable differences in the parameters characterizing their dynamic properties have been revealed.
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5
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Water Dynamics in Highly Concentrated Protein Systems-Insight from Nuclear Magnetic Resonance Relaxometry. Int J Mol Sci 2023; 24:ijms24044093. [PMID: 36835511 PMCID: PMC9963861 DOI: 10.3390/ijms24044093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
1H spin-lattice relaxation experiments have been performed for water-Bovine Serum Albumin (BSA) mixtures, including 20%wt and 40%wt of BSA. The experiments have been carried out in a frequency range encompassing three orders of magnitude, from 10 kHz to 10 MHz, versus temperature. The relaxation data have been thoroughly analyzed in terms of several relaxation models with the purpose of revealing the mechanisms of water motion. For this purpose, four relaxation models have been used: the data have been decomposed into relaxation contributions expressed in terms of Lorentzian spectral densities, then three-dimensional translation diffusion has been assumed, next two-dimensional surface diffusion has been considered, and eventually, a model of surface diffusion mediated by acts of adsorption to the surface has been employed. In this way, it has been demonstrated that the last concept is the most plausible. Parameters describing the dynamics in a quantitative manner have been determined and discussed.
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6
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Licciardi G, Rizzo D, Salobehaj M, Massai L, Geri A, Messori L, Ravera E, Fragai M, Parigi G. Large Protein Assemblies for High-Relaxivity Contrast Agents: The Case of Gadolinium-Labeled Asparaginase. Bioconjug Chem 2022; 33:2411-2419. [PMID: 36458591 PMCID: PMC9782335 DOI: 10.1021/acs.bioconjchem.2c00506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Biologics are emerging as the most important class of drugs and are used to treat a large variety of pathologies. Most of biologics are proteins administered in large amounts, either by intramuscular injection or by intravenous infusion. Asparaginase is a large tetrameric protein assembly, currently used against acute lymphoblastic leukemia. Here, a gadolinium(III)-DOTA derivative has been conjugated to asparaginase, and its relaxation properties have been investigated to assess its efficiency as a possible theranostic agent. The field-dependent 1H longitudinal relaxation measurements of water solutions of gadolinium(III)-labeled asparaginase indicate a very large increase in the relaxivity of this paramagnetic protein complex with respect to small gadolinium chelates, opening up the possibility of its use as an MRI contrast agent.
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Affiliation(s)
- Giulia Licciardi
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy,Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy,Consorzio
Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy
| | - Domenico Rizzo
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy,Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy,Consorzio
Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy
| | - Maria Salobehaj
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy,Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy,Consorzio
Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy
| | - Lara Massai
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy
| | - Andrea Geri
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy
| | - Luigi Messori
- Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy
| | - Enrico Ravera
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy,Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy,Consorzio
Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy
| | - Marco Fragai
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy,Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy,Consorzio
Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy
| | - Giacomo Parigi
- Magnetic
Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy,Department
of Chemistry “Ugo Schiff”, University of Florence, Via della Lastruccia 3, Sesto Fiorentino50019, Italy,Consorzio
Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino50019, Italy,
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7
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Kruk D, Masiewicz E, Budny J, Stankiewicz A, Lotarska S, Oztop M, Wieczorek Z. Diffusion in oils versus their viscosity – Insight from Nuclear Magnetic Resonance relaxometry. J FOOD ENG 2022. [DOI: 10.1016/j.jfoodeng.2021.110848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Kruk D, Masiewicz E, Budny J, Kolodziejski K, Zulewska J, Wieczorek Z. Relationship between macroscopic properties of honey and molecular dynamics – temperature effects. J FOOD ENG 2022. [DOI: 10.1016/j.jfoodeng.2021.110782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Wang Z, Pisano S, Ghini V, Kadeřávek P, Zachrdla M, Pelupessy P, Kazmierczak M, Marquardsen T, Tyburn JM, Bouvignies G, Parigi G, Luchinat C, Ferrage F. Detection of Metabolite-Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR. J Am Chem Soc 2021; 143:9393-9404. [PMID: 34133154 DOI: 10.1021/jacs.1c01388] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics, the systematic investigation of metabolites in biological fluids, cells, or tissues, reveals essential information about metabolism and diseases. Metabolites have functional roles in a myriad of biological processes, as substrates and products of enzymatic reactions but also as cofactors and regulators of large numbers of biochemical mechanisms. These functions involve interactions of metabolites with macromolecules. Yet, methods to systematically investigate these interactions are still scarce to date. In particular, there is a need for techniques suited to identify and characterize weak metabolite-macromolecule interactions directly in complex media such as biological fluids. Here, we introduce a method to investigate weak interactions between metabolites and macromolecules in biological fluids. Our approach is based on high-resolution NMR relaxometry and does not require any invasive procedure or separation step. We show that we can detect interactions between small and large molecules in human blood serum and quantify the size of the complex. Our work opens the way for investigations of metabolite (or other small molecules)-protein interactions in biological fluids for interactomics or pharmaceutical applications.
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Affiliation(s)
- Ziqing Wang
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Simone Pisano
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Veronica Ghini
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Morgan Kazmierczak
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l'Industrie BP 10002, 67166 Cedex Wissembourg, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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10
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Parigi G, Ravera E, Fragai M, Luchinat C. Unveiling protein dynamics in solution with field-cycling NMR relaxometry. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 124-125:85-98. [PMID: 34479712 DOI: 10.1016/j.pnmrs.2021.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Field-cycling NMR relaxometry is a well-established technique that can give information on molecular structure and dynamics of biological systems. It provides the nuclear relaxation rates as a function of the applied magnetic field, starting from fields as low as ~ 10-4 T up to about 1-3 T. The profiles so collected, called nuclear magnetic relaxation dispersion (NMRD) profiles, can be extended to include the relaxation rates at the largest fields achievable with high resolution NMR spectrometers. By exploiting this wide range of frequencies, the NMRD profiles can provide information on motions occurring on time scales from 10-6 to 10-9 s. 1H NMRD measurements have proved very useful also for the characterization of paramagnetic proteins, because they can help characterise a number of parameters including the number, distance and residence time of water molecules coordinated to the paramagnetic center, the reorientation correlation times and the electron spin relaxation time, and the electronic structure at the metal site.
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Affiliation(s)
- Giacomo Parigi
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) University of Florence, via Sacconi 6, Sesto Fiorentino, Italy; Department of Chemistry, "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy
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11
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Kruk D, Florek-Wojciechowska M, Oztop M, Ilhan E, Wieczorek Z. Water dynamics in eggs by means of Nuclear Magnetic Resonance relaxometry. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106976. [PMID: 33901897 DOI: 10.1016/j.jmr.2021.106976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
1H Nuclear Magnetic Resonance relaxometry has been applied to reveal dynamical properties of water molecules embedded into egg yolk and white of three species: turkey, chicken and quail. Two fractions of water molecules, referred to as confined-water and free-water fractions, have been revealed. It has been demonstrated that translation diffusion of the confined-water fraction is three-dimensional. The dynamics of the confined-water has been quantitatively described in terms of diffusion coefficients and rotational correlation times. The parameters have been compared for egg yolk and white for all the species. In addition to these quantities, the number of the confined-water molecules per unit volume has been provided for all cases. The obtained parameters provide insight into the dynamics of water in eggs of different origin and allow to identify similarities and differences between them in connection to the structure of the network formed by the macromolecular fraction of egg yolk and white.
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Affiliation(s)
- Danuta Kruk
- Department of Physics & Biophysics, Faculty of Food Sciences, University of Warmia & Mazury in Olsztyn, Michała Oczapowskiego 4, 10-719 Olsztyn, Poland.
| | - Małgorzata Florek-Wojciechowska
- Department of Physics & Biophysics, Faculty of Food Sciences, University of Warmia & Mazury in Olsztyn, Michała Oczapowskiego 4, 10-719 Olsztyn, Poland
| | - Mecit Oztop
- Department of Food Engineering, Middle East Technical University, Ankara, Turkey
| | - Esmanur Ilhan
- Department of Food Engineering, Middle East Technical University, Ankara, Turkey
| | - Zbigniew Wieczorek
- Department of Physics & Biophysics, Faculty of Food Sciences, University of Warmia & Mazury in Olsztyn, Michała Oczapowskiego 4, 10-719 Olsztyn, Poland
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12
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Kruk D, Florek – Wojciechowska M, Masiewicz E, Oztop M, Ploch-Jankowska A, Duda P, Wilczynski S. Water mobility in cheese by means of Nuclear Magnetic Resonance relaxometry. J FOOD ENG 2021. [DOI: 10.1016/j.jfoodeng.2021.110483] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Bellomo G, Ravera E, Calderone V, Botta M, Fragai M, Parigi G, Luchinat C. Revisiting paramagnetic relaxation enhancements in slowly rotating systems: how long is the long range? MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:25-31. [PMID: 37904766 PMCID: PMC10539754 DOI: 10.5194/mr-2-25-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/11/2021] [Indexed: 11/01/2023]
Abstract
Cross-relaxation terms in paramagnetic systems that reorient rigidly with slow tumbling times can increase the effective longitudinal relaxation rates of protons of more than 1 order of magnitude. This is evaluated by simulating the time evolution of the nuclear magnetization using a complete relaxation rate-matrix approach. The calculations show that the Solomon dependence of the paramagnetic relaxation rates on the metal-proton distance (as r - 6 ) can be incorrect for protons farther than 15 Å from the metal and thus can cause sizable errors in R 1 -derived distance restraints used, for instance, for protein structure determination. Furthermore, the chemical exchange of these protons with bulk water protons can enhance the relaxation rate of the solvent protons by far more than expected from the paramagnetic Solomon equation. Therefore, it may contribute significantly to the water proton relaxation rates measured at magnetic resonance imaging (MRI) magnetic fields in the presence of slow-rotating nanoparticles containing paramagnetic ions and a large number of exchangeable surface protons.
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Affiliation(s)
- Giovanni Bellomo
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
- present address: Laboratory of Clinical Neurochemistry, Neurology
Clinic, University of Perugia, Piazzale Lucio Severi 1/8, 06132 Perugia
(PG), Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Mauro Botta
- Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale “Amedeo Avogadro”, Viale T. Michel 11, 15121 Alessandria, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Department of Chemistry,
University of Florence, via Sacconi 6, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Sesto Fiorentino, Italy
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14
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Origin of the MRI Contrast in Natural and Hydrogel Formulation of Pineapple Juice. Bioinorg Chem Appl 2021; 2021:6666018. [PMID: 33488688 PMCID: PMC7803405 DOI: 10.1155/2021/6666018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
Magnetic resonance imaging (MRI) often requires contrast agents to improve the visualization in some tissues and organs, including the gastrointestinal tract. In this latter case, instead of intravascular administration, oral agents can be used. Natural oral contrast agents, such as fruit juice, have the advantages of better taste, tolerability, and lower price with respect to the artificial agents. We have characterized the relaxometry profiles of pineapple juice in order to understand the origin of the increase in relaxation rates (and thus of the MRI contrast) in reference to its content of manganese ions. Furthermore, we have characterized the relaxometry profiles of pineapple juice in the presence of alginate in different amounts; the interaction of the manganese ions with alginate slows down their reorientation time to some extent, with a subsequent increase in the relaxation rates. The relaxometry profiles were also compared with those of manganese(II) solutions in 50 mmol/dm3 sodium acetate solution (same pH of pineapple juice), which revealed sizable differences, mostly in the number of water molecules coordinated to the metal ion, their lifetimes, and in the constant of the Fermi-contact interaction. Finally, the fit of the transverse relaxivity shows that the increased viscosity in the hydrogel formulations can improve significantly the negative contrast of pineapple juice at the magnetic fields relevant for clinical MRI.
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15
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Kruk D, Rochowski P, Florek-Wojciechowska M, Sebastião PJ, Lurie DJ, Broche LM. 1H spin-lattice NMR relaxation in the presence of residual dipolar interactions - Dipolar relaxation enhancement. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 318:106783. [PMID: 32755749 DOI: 10.1016/j.jmr.2020.106783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/29/2020] [Accepted: 07/05/2020] [Indexed: 06/11/2023]
Abstract
A model of spin-lattice relaxation for spin-1/2 nuclei in the presence of a residual dipole-dipole coupling has been presented. For slow dynamics the model predicts a bi-exponential relaxation at low frequencies, when the residual dipole-dipole interaction dominates the Zeeman coupling. Moreover, according to the model a frequency-specific relaxation enhancement, referred to as Dipolar Relaxation Enhancement (DRE) in analogy to the Quadrupole Relaxation Enhancement (QRE) is expected. The frequency position of the relaxation maximum is determined by the amplitude of the residual dipole-dipole interaction. Experimental examples of relaxation properties that might be attributed to the DRE are presented. The DRE effect has the potential to be exploited, in analogy to QRE, as a unique source of information about molecular dynamics and structure.
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Affiliation(s)
- Danuta Kruk
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland.
| | - Pawel Rochowski
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland
| | | | - Pedro José Sebastião
- Department of Physics, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - David J Lurie
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - Lionel M Broche
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
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16
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Masiewicz E, Ashcroft GP, Boddie D, Dundas SR, Kruk D, Broche LM. Towards applying NMR relaxometry as a diagnostic tool for bone and soft tissue sarcomas: a pilot study. Sci Rep 2020; 10:14207. [PMID: 32848198 PMCID: PMC7449965 DOI: 10.1038/s41598-020-71067-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/22/2020] [Indexed: 01/26/2023] Open
Abstract
This work explores what Fast Field-Cycling Nuclear Magnetic Resonance (FFC-NMR) relaxometry brings for the study of sarcoma to guide future in vivo analyses of patients. We present the results of an ex vivo pilot study involving 10 cases of biopsy-proven sarcoma and we propose a quantitative method to analyse 1H NMR relaxation dispersion profiles based on a model-free approach describing the main dynamical processes in the tissues and assessing the amplitude of the Quadrupole Relaxation Enhancement effects due to 14N. This approach showed five distinct groups of dispersion profiles indicating five discrete categories of sarcoma, with differences attributable to microstructure and rigidity. Data from tissues surrounding sarcomas indicated very significant variations with the proximity to tumour, which may be attributed to varying water content but also to tissue remodelling processes due to the sarcoma. This pilot study illustrates the potential of FFC relaxometry for the detection and characterisation of sarcoma.
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Affiliation(s)
- Elzbieta Masiewicz
- Department of Physics and Biophysics, Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Słoneczna 54, 10-710, Olsztyn, Poland
- Faculty of Food Sciences, University of Warmia and Mazury in Olsztyn, Michała Oczapowskiego 4, 10-719, Olsztyn, Poland
| | - George P Ashcroft
- Department of Orthopaedics, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, Scotland, UK
| | - David Boddie
- Department of Orthopaedics, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, Scotland, UK
| | - Sinclair R Dundas
- Department of Pathology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, Scotland, UK
| | - Danuta Kruk
- Department of Physics and Biophysics, Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Słoneczna 54, 10-710, Olsztyn, Poland
| | - Lionel M Broche
- Bio-Medical Physics, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, Scotland, UK.
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17
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Kruk D, Masiewicz E, Wojciechowski M, Florek-Wojciechowska M, Broche LM, Lurie DJ. Slow dynamics of solid proteins - Nuclear magnetic resonance relaxometry versus dielectric spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2020; 314:106721. [PMID: 32276108 DOI: 10.1016/j.jmr.2020.106721] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
1H Nuclear Magnetic Resonance (NMR) relaxometry and Dielectric Spectroscopy (DS) have been exploited to investigate the dynamics of solid proteins. The experiments have been carried out in the frequency range of about 10 kHz-40 MHz for NMR relaxometry and 10-2Hz-20 MHz for DS. The data sets have been analyzed in terms of theoretical models allowing for a comparison of the correlation times revealed by NMR relaxometry and DS. The 1H spin-lattice relaxation profiles have been decomposed into relaxation contributions associated with 1H-1H and 1H-14N dipole - dipole interactions. The 1H-1H relaxation contribution has been interpreted in terms of three dynamical processes of time scales of 10-6s, 10-7s and 10-8s. It has turned out that the correlation times do not differ much among proteins and they are only weakly dependent on temperature. The analysis of DS relaxation spectra has also revealed three motional processes characterized by correlation times that considerably depend on temperature in contrast to those obtained from the 1H relaxation. This finding suggest that for solid proteins there is a contribution to the 1H spin-lattice relaxation associated with a kind of motion that is not probed in DS as it does not lead to a reorientation of the electric dipole moment.
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Affiliation(s)
- Danuta Kruk
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland.
| | - Elzbieta Masiewicz
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland
| | - Milosz Wojciechowski
- Faculty of Mathematics and Computer Science, University of Warmia & Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland
| | | | - Lionel M Broche
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - David J Lurie
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
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18
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Binding modes of Fe(III) with graphene oxide in aqueous solutions. Competition with Sr2+, Cs+, Na+ ions and Fe(III) chelators. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Kruk D, Masiewicz E, Borkowska AM, Rochowski P, Fries PH, Broche LM, Lurie DJ. Dynamics of Solid Proteins by Means of Nuclear Magnetic Resonance Relaxometry. Biomolecules 2019; 9:E652. [PMID: 31731514 PMCID: PMC6920843 DOI: 10.3390/biom9110652] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/16/2019] [Accepted: 10/19/2019] [Indexed: 01/21/2023] Open
Abstract
1H Nuclear magnetic resonance (NMR) relaxometry was exploited to investigate the dynamics of solid proteins. The relaxation experiments were performed at 37 °C over a broad frequency range, from approximately 10 kHz to 40 MHz. Two relaxation contributions to the overall 1H spin-lattice relaxation were revealed; they were associated with 1H-1H and 1H-14N magnetic dipole-dipole interactions, respectively. The 1H-1H relaxation contribution was interpreted in terms of three dynamical processes occurring on timescales of 10-6 s, 10-7 s, and 10-8 s, respectively. The 1H-14N relaxation contribution shows quadrupole relaxation enhancement effects. A thorough analysis of the data was performed revealing similarities in the protein dynamics, despite their different structures. Among several parameters characterizing the protein dynamics and structure (e.g., electric field gradient tensor at the position of 14N nuclei), the orientation of the 1H-14N dipole-dipole axis, with respect to the principal axis system of the electric field gradient, was determined, showing that, for lysozyme, it was considerably different than for the other proteins. Moreover, the validity range of a closed form expression describing the 1H-14N relaxation contribution was determined by a comparison with a general approach based on the stochastic Liouville equation.
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Affiliation(s)
- Danuta Kruk
- Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland; (E.M.); (A.M.B.); (P.R.)
| | - Elzbieta Masiewicz
- Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland; (E.M.); (A.M.B.); (P.R.)
| | - Anna M. Borkowska
- Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland; (E.M.); (A.M.B.); (P.R.)
| | - Pawel Rochowski
- Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Słoneczna 54, 10-710 Olsztyn, Poland; (E.M.); (A.M.B.); (P.R.)
| | - Pascal H. Fries
- Laboratoire de Reconnaissance Ionique et Chimie de Coordination, Service de Chimie Inorganique et Biologique (UMR E-3 CEA/UJF), CEA-Grenoble, INAC, 17 rue des Martyrs, CEDEX 09, 38054 Grenoble, France;
| | - Lionel M. Broche
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK; (L.M.B.); (D.J.L.)
| | - David J. Lurie
- Bio-Medical Physics, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, Scotland AB25 2ZD, UK; (L.M.B.); (D.J.L.)
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20
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Kadeřávek P, Bolik-Coulon N, Cousin SF, Marquardsen T, Tyburn JM, Dumez JN, Ferrage F. Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation. J Phys Chem Lett 2019; 10:5917-5922. [PMID: 31509419 DOI: 10.1021/acs.jpclett.9b02233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nuclear magnetic relaxation provides invaluable quantitative site-specific information on the dynamics of complex systems. Determining dynamics on nanosecond time scales requires relaxation measurements at low magnetic fields incompatible with high-resolution NMR. Here, we use a two-field NMR spectrometer to measure carbon-13 transverse and longitudinal relaxation rates at a field as low as 0.33 T (proton Larmor frequency 14 MHz) in specifically labeled side chains of the protein ubiquitin. The use of radiofrequency pulses enhances the accuracy of measurements as compared to high-resolution relaxometry approaches, where the sample is moved in the stray field of the superconducting magnet. Importantly, we demonstrate that accurate measurements at a single low magnetic field provide enough information to characterize complex motions on low nanosecond time scales, which opens a new window for the determination of site-specific nanosecond motions in complex systems such as proteins.
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Affiliation(s)
- Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Nicolas Bolik-Coulon
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | - Samuel F Cousin
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
| | | | - Jean-Max Tyburn
- Bruker BioSpin , 34 rue de l'Industrie BP 10002, 67166 Wissembourg Cedex, France
| | | | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie , École normale supérieure , PSL University, Sorbonne Université, CNRS, 75005 Paris , France
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21
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Fragai M, Ravera E, Tedoldi F, Luchinat C, Parigi G. Relaxivity of Gd-Based MRI Contrast Agents in Crosslinked Hyaluronic Acid as a Model for Tissues. Chemphyschem 2019; 20:2204-2209. [PMID: 31298452 DOI: 10.1002/cphc.201900587] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/11/2019] [Indexed: 12/12/2022]
Abstract
The efficiency of MRI contrast agents depends on the relaxation rate enhancement that they can induce at imaging fields. It is well known that, at these fields, large relaxation rates are obtained by binding of gadolinium(III) ions to large molecules. By the same token, the interaction of the gadolinium(III) complexes with macromolecules that are found in biological tissues can be responsible for an increase of the relaxation rate with respect to the value observed in liquids. We investigate here the relaxation enhancement of gadoteridol (Gd-HP-DO3A) in crosslinked hyaluronic acid, taken as model tissue, using fast field-cycling relaxometry. The analysis of the relaxation profiles as a function of the magnetic fields indicates that a sizable increase in the relaxation rates is due to a modest interaction of the contrast agent with the hydrogel and to the slower mobility of the water molecules outside the first-coordination sphere of the gadolinium(III) ion.
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Affiliation(s)
- Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Fabio Tedoldi
- Bracco Imaging Spa, Bracco Research Centre, Via Ribes 5, 10010, Colleretto Giacosa (TO), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
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22
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Cerofolini L, Giuntini S, Carlon A, Ravera E, Calderone V, Fragai M, Parigi G, Luchinat C. Characterization of PEGylated Asparaginase: New Opportunities from NMR Analysis of Large PEGylated Therapeutics. Chemistry 2019; 25:1984-1991. [DOI: 10.1002/chem.201804488] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/09/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Azzurra Carlon
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Vito Calderone
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM)University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di, Metallo Proteine (CIRMMP) Via L. Sacconi 6 50019 Sesto Fiorentino Italy
- Department of ChemistryUniversity of Florence Via della Lastruccia 3 50019 Sesto Fiorentino Italy
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23
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Wienen-Schmidt B, Jonker HRA, Wulsdorf T, Gerber HD, Saxena K, Kudlinzki D, Sreeramulu S, Parigi G, Luchinat C, Heine A, Schwalbe H, Klebe G. Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug–Kinase Binding. J Med Chem 2018; 61:5922-5933. [DOI: 10.1021/acs.jmedchem.8b00105] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Barbara Wienen-Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hendrik R. A. Jonker
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Tobias Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Krishna Saxena
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Denis Kudlinzki
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Sridhar Sreeramulu
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM/CIRMMP) and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Straße 7, N160-3.14, 60438 Frankfurt am Main, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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24
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Gineste S, Di Cola E, Amouroux B, Till U, Marty JD, Mingotaud AF, Mingotaud C, Violleau F, Berti D, Parigi G, Luchinat C, Balor S, Sztucki M, Lonetti B. Mechanistic Insights into Polyion Complex Associations. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stéphane Gineste
- Laboratoire
des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, Cedex 9 F-31062, Toulouse, France
| | - Emanuela Di Cola
- BioSoftMatter
Laboratorio Dip CBBM LITA, Universita di Milano, Via F lli Cervi
93 MI IT, 20090 Segrate, Italy
| | - Baptiste Amouroux
- Laboratoire
des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, Cedex 9 F-31062, Toulouse, France
| | - Ugo Till
- Laboratoire
des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, Cedex 9 F-31062, Toulouse, France
- Département
Sciences Agronomiques et Agroalimentaires, Université de Toulouse, Institut National Polytechnique de Toulouse - Ecole d’Ingénieurs de Purpan, 75 voie du TOEC, BP 57611, Cedex 03 F-31076 Toulouse, France
| | - Jean-Daniel Marty
- Laboratoire
des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, Cedex 9 F-31062, Toulouse, France
| | - Anne-Françoise Mingotaud
- Laboratoire
des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, Cedex 9 F-31062, Toulouse, France
| | - Christophe Mingotaud
- Laboratoire
des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, Cedex 9 F-31062, Toulouse, France
| | - Frédéric Violleau
- Laboratoire
de Chimie Agro-industrielle (LCA), Université de Toulouse, INRA, INPT, INP-EI PURPAN, Toulouse, France
| | - Debora Berti
- Department
of Chemistry “Ugo Schiff”, University of Florence and CSGI, Via della Lastruccia 3, 50019 Sesto Fiorentino Firenze, Italy
| | - Giacomo Parigi
- Department
of Chemistry Ugo Schiff and Magnetic Resonance Center (CERM), University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino Firenze, Italy
| | - Claudio Luchinat
- Department
of Chemistry Ugo Schiff and Magnetic Resonance Center (CERM), University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino Firenze, Italy
| | - Stéphanie Balor
- Plateforme
METi, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Michael Sztucki
- European Synchrotron
Radiation Facility-71, avenue des Martyrs,
CS 40220, Cedex 9 38043 Grenoble, France
| | - Barbara Lonetti
- Laboratoire
des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III - Paul Sabatier, 118 route de Narbonne, Cedex 9 F-31062, Toulouse, France
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25
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Neudert O, Mattea C, Stapf S. Molecular dynamics-based selectivity for Fast-Field-Cycling relaxometry by Overhauser and solid effect dynamic nuclear polarization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 276:113-121. [PMID: 28183023 DOI: 10.1016/j.jmr.2017.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
In the last decade nuclear spin hyperpolarization methods, especially Dynamic Nuclear Polarization (DNP), have provided unprecedented possibilities for various NMR techniques by increasing the sensitivity by several orders of magnitude. Recently, in-situ DNP-enhanced Fast Field Cycling (FFC) relaxometry was shown to provide appreciable NMR signal enhancements in liquids and viscous systems. In this work, a measurement protocol for DNP-enhanced NMR studies is introduced which enables the selective detection of nuclear spin hyperpolarized by either Overhauser effect or solid effect DNP. Based on field-cycled DNP and relaxation studies it is shown that these methods allow for the independent measurement of polymer and solvent nuclear spins in a concentrated solution of high molecular weight polybutadiene in benzene doped with α,γ-bisdiphenylene-β-phenylallyl radical. Appreciable NMR signal enhancements of about 10-fold were obtained for both constituents. Moreover, qualitative information about the dynamics of the radical and solvent was obtained. Selective DNP-enhanced FFC relaxometry is applied for the measurement of the 1H nuclear magnetic relaxation dispersion of both constituents with improved precision. The introduced method is expected to greatly facilitate NMR studies of complex systems with multiple overlapping signal contributions that cannot be distinguished by standard methods.
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Affiliation(s)
- Oliver Neudert
- Institute of Physics, Ilmenau University of Technology, D-98693 Ilmenau, Germany.
| | - Carlos Mattea
- Institute of Physics, Ilmenau University of Technology, D-98693 Ilmenau, Germany
| | - Siegfried Stapf
- Institute of Physics, Ilmenau University of Technology, D-98693 Ilmenau, Germany
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26
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Sarkar R, Mainz A, Busi B, Barbet-Massin E, Kranz M, Hofmann T, Reif B. Immobilization of soluble protein complexes in MAS solid-state NMR: Sedimentation versus viscosity. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 76-77:7-14. [PMID: 27017576 DOI: 10.1016/j.ssnmr.2016.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 05/12/2023]
Abstract
In recent years, MAS solid-state NMR has emerged as a technique for the investigation of soluble protein complexes. It was found that high molecular weight complexes do not need to be crystallized in order to obtain an immobilized sample for solid-state NMR investigations. Sedimentation induced by sample rotation impairs rotational diffusion of proteins and enables efficient dipolar coupling based cross polarization transfers. In addition, viscosity contributes to the immobilization of the molecules in the sample. Natural Deep Eutectic Solvents (NADES) have very high viscosities, and can replace water in living organisms. We observe a considerable amount of cross polarization transfers for NADES solvents, even though their molecular weight is too low to yield significant sedimentation. We discuss how viscosity and sedimentation both affect the quality of the obtained experimental spectra. The FROSTY/sedNMR approach holds the potential to study large protein complexes, which are otherwise not amenable for a structural characterization using NMR. We show that using this method, backbone assignments of the symmetric proteasome activator complex (1.1MDa), and high quality correlation spectra of non-symmetric protein complexes such as the prokaryotic ribosome 50S large subunit binding to trigger factor (1.4MDa) are obtained.
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Affiliation(s)
- Riddhiman Sarkar
- Munich Center for Integrated Protein Science (CIPSM) at Department of Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany; Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Andi Mainz
- Munich Center for Integrated Protein Science (CIPSM) at Department of Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany; Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany; Technische Universität Berlin, Fakultät II Mathematik und Naturwissenschaften, Institut für Chemie/OC/Biologische Chemie, Müller-Breslau-Straße 10, 10623 Berlin, Germany
| | - Baptiste Busi
- Munich Center for Integrated Protein Science (CIPSM) at Department of Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany; Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Emeline Barbet-Massin
- Munich Center for Integrated Protein Science (CIPSM) at Department of Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany; Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
| | - Maximilian Kranz
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universitat¨ Mu¨nchen, Lise-Meitner-Strasse 34, 85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technische Universitat¨ Mu¨nchen, Lise-Meitner-Strasse 34, 85354 Freising, Germany
| | - Bernd Reif
- Munich Center for Integrated Protein Science (CIPSM) at Department of Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, D-85747 Garching, Germany; Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (HMGU), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany.
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27
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NMR-detected brownian dynamics of αB-crystallin over a wide range of concentrations. Biophys J 2015; 108:98-106. [PMID: 25564856 DOI: 10.1016/j.bpj.2014.11.1858] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 02/05/2023] Open
Abstract
Knowledge about the global translational and rotational motion of proteins under crowded conditions is highly relevant for understanding the function of proteins in vivo. This holds in particular for human αB-crystallin, which is strongly crowded in vivo and inter alia responsible for preventing cataracts. Quantitative information on translational and rotational diffusion is not readily available, and we here demonstrate an approach that combines pulsed-field-gradient NMR for translational diffusion and proton T1ρ/T2 relaxation-time measurements for rotational diffusion, thus overcoming obstacles encountered in previous studies. The relaxation times measured at variable temperature provide a quantitative measure of the correlation function of protein tumbling, which cannot be approximated by a single exponential, because two components are needed for a minimal and adequate description of the data. We find that at high protein concentrations, rotational diffusion is decoupled from translational diffusion, the latter following the macroscopic viscosity change almost quantitatively, resembling the behavior of spherical colloids. Analysis of data reported in the literature shows that well-packed globular proteins follow a scaling relation between the hydrodynamic radius and the molar mass, Rh ∼ M(1/d), with a fractal dimension of d ∼ 2.5 rather than 3. Despite its oligomeric nature, Rh of αB-crystallin as derived from both NMR methods is found to be fully consistent with this relation.
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28
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Ravera E, Fragai M, Parigi G, Luchinat C. Differences in Dynamics between Crosslinked and Non-Crosslinked Hyaluronates Measured by using Fast Field-Cycling Relaxometry. Chemphyschem 2015; 16:2803-2809. [PMID: 26263906 DOI: 10.1002/cphc.201500446] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 11/11/2022]
Abstract
The dynamic properties of water molecules in gels containing linear and crosslinked hyaluronic acid polymers are investigated by using an integrated approach that includes relaxometry, solid-state NMR spectroscopy, and scanning electron microscopy. A model-free analysis of field-dependent nuclear relaxation is applied to obtain information on mobility and the population of different pools of water molecules in the gels. Differences between linear and crosslinked hyaluronic acid polymers are observed, indicating that crosslinking increases both the fraction and the correlation time of water molecules with slow dynamics.
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Affiliation(s)
- Enrico Ravera
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Marco Fragai
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Giacomo Parigi
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
| | - Claudio Luchinat
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino (Italy)
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29
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Ryabov Y. Coupling between overall rotational diffusion and domain motions in proteins and its effect on dielectric spectra. Proteins 2015; 83:1571-81. [PMID: 25900685 DOI: 10.1002/prot.24814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/23/2015] [Accepted: 04/05/2015] [Indexed: 11/08/2022]
Abstract
In this work, we formulate a closed-form solution of the model of a semirigid molecule for the case of fluctuating and reorienting molecular electric dipole moment. We illustrate with numeric calculations the impact of protein domain motions on dielectric spectra using the example of the 128 kDa protein dimer of Enzyme I. We demonstrate that the most drastic effect occurs for situations when the characteristic time of protein domain dynamics is comparable to the time of overall molecular rotational diffusion. We suggest that protein domain motions could be a possible explanation for the high-frequency contribution that accompanies the major relaxation dispersion peak in the dielectric spectra of protein aqueous solutions. We propose that the presented computational methodology could be used for the simultaneous analysis of dielectric spectroscopy and nuclear magnetic resonance data. Proteins 2015; 83:1571-1581. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Yaroslav Ryabov
- BC Portal Inc., 260 Congressional Ln. #204, Rockville, Maryland, 20852
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30
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Ravera E, Schubeis T, Martelli T, Fragai M, Parigi G, Luchinat C. NMR of sedimented, fibrillized, silica-entrapped and microcrystalline (metallo)proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:60-70. [PMID: 25797005 DOI: 10.1016/j.jmr.2014.12.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/06/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Resolution and sensitivity in solid state NMR (SSNMR) can rival the results achieved by solution NMR, and even outperform them in the case of large systems. However, several factors affect the spectral quality in SSNMR samples, and not all systems turn out to be equally amenable for this methodology. In this review we attempt at analyzing the causes of this variable behavior and at providing hints to increase the chances of experimental success.
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Affiliation(s)
- Enrico Ravera
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Tobias Schubeis
- Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Tommaso Martelli
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Giotto Biotech, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy.
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31
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Neudert O, Raich HP, Mattea C, Stapf S, Münnemann K. An Alderman-Grant resonator for S-Band Dynamic Nuclear Polarization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 242:79-85. [PMID: 24607825 DOI: 10.1016/j.jmr.2014.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/31/2014] [Accepted: 02/01/2014] [Indexed: 06/03/2023]
Abstract
An Alderman-Grant resonator with resonance at 2GHz (S-Band) was simulated, developed and constructed for Dynamic Nuclear Polarization (DNP) experiments at 73mT. The resonator fits into magnet bores with a minimum diameter of 20mm and is compatible with standard 3mm NMR tubes. The compact resonator design achieves good separation of electric and magnetic fields and therefore can be used with comparatively large sample volumes with only small sample heating effects comparable to those obtained with optimized X- and W-Band DNP setups. The saturation efficiency and sample heating effects were investigated for Overhauser DNP experiments of aqueous solutions of TEMPOL radical, showing relative saturation better than 0.9 and sample heating not exceeding a few Kelvin even at high microwave power and long irradiation time. An application is demonstrated, combining the DNP setup with a commercial fast field cycling NMR relaxometer. Using this resonator design at low microwave frequencies can provide DNP polarization for a class of low-field and time-domain NMR experiments and therefore may enable new applications that benefit from increased sensitivity.
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Affiliation(s)
- Oliver Neudert
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany.
| | - Hans-Peter Raich
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany.
| | - Carlos Mattea
- Institute of Physics, Ilmenau University of Technology, D-98693 Ilmenau, Germany.
| | - Siegfried Stapf
- Institute of Physics, Ilmenau University of Technology, D-98693 Ilmenau, Germany.
| | - Kerstin Münnemann
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany.
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32
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Linser R, Sarkar R, Krushelnitzky A, Mainz A, Reif B. Dynamics in the solid-state: perspectives for the investigation of amyloid aggregates, membrane proteins and soluble protein complexes. JOURNAL OF BIOMOLECULAR NMR 2014; 59:1-14. [PMID: 24595988 DOI: 10.1007/s10858-014-9822-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
Aggregates formed by amyloidogenic peptides and proteins and reconstituted membrane protein preparations differ significantly in terms of the spectral quality that they display in solid-state NMR experiments. Structural heterogeneity and dynamics can both in principle account for that observation. This perspectives article aims to point out challenges and limitations, but also potential opportunities in the investigation of these systems.
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Affiliation(s)
- Rasmus Linser
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA, 02115, USA
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33
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Luchinat C, Parigi G, Ravera E. Can metal ion complexes be used as polarizing agents for solution DNP? A theoretical discussion. JOURNAL OF BIOMOLECULAR NMR 2014; 58:239-249. [PMID: 23606273 DOI: 10.1007/s10858-013-9728-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/05/2013] [Indexed: 06/02/2023]
Abstract
Dynamic nuclear polarization (DNP) can be used to dramatically increase the NMR signal intensities in solutions and solids. DNP is usually performed using nitroxide radicals as polarizing agents, characterized by sharp EPR lines, fast rotation, fast diffusion, and favorable distribution of the unpaired electron. These features make the nitroxide radicals ideally suited for solution DNP. Here, we report some theoretical considerations on the different behavior of some inorganic compounds with respect to nitroxide radicals. The relaxation profiles of slow relaxing paramagnetic metal aqua ions [copper(II), manganese(II), gadolinium(III) and oxovanadium(IV)] and complexes have been re-analyzed according to the standard theory for dipolar and contact relaxation, in order to estimate the coupling factor responsible for the maximum DNP enhancement that can be achieved in solution and its dependence on field, temperature and relative importance of outer-sphere versus inner-sphere relaxation.
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Affiliation(s)
- Claudio Luchinat
- CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy,
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34
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Ferella L, Luchinat C, Ravera E, Rosato A. SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR. JOURNAL OF BIOMOLECULAR NMR 2013; 57:319-26. [PMID: 24243317 DOI: 10.1007/s10858-013-9795-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 11/11/2013] [Indexed: 05/09/2023]
Abstract
We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment.
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Affiliation(s)
- Lucio Ferella
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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35
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Fragai M, Luchinat C, Parigi G, Ravera E. Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 57:155-66. [PMID: 23990200 DOI: 10.1007/s10858-013-9776-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/23/2013] [Indexed: 05/09/2023]
Abstract
Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the literature and presenting new experimental data. A discussion on resolution and sensitivity in sedimented solutes is framed in this context.
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Affiliation(s)
- Marco Fragai
- Center for Magnetic Resonance (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, FI, Italy
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36
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Mainz A, Religa TL, Sprangers R, Linser R, Kay LE, Reif B. NMR-Spektroskopie an löslichen Proteinkomplexen mit Molekulargewicht im Mega-Dalton-Bereich. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Mainz A, Religa TL, Sprangers R, Linser R, Kay LE, Reif B. NMR spectroscopy of soluble protein complexes at one mega-dalton and beyond. Angew Chem Int Ed Engl 2013; 52:8746-51. [PMID: 23873792 DOI: 10.1002/anie.201301215] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/30/2013] [Indexed: 01/07/2023]
Affiliation(s)
- Andi Mainz
- Munich Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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38
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Luchinat C, Parigi G, Ravera E. Water and Protein Dynamics in Sedimented Systems: A Relaxometric Investigation. Chemphyschem 2013; 14:3156-61. [DOI: 10.1002/cphc.201300167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Indexed: 11/07/2022]
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