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Melchiorre G, Giustiniano F, Rathore S, Pileio G. Singlet-assisted diffusion-NMR (SAD-NMR): extending the scope of diffusion tensor imaging via singlet NMR. Front Chem 2023; 11:1224336. [PMID: 37601902 PMCID: PMC10436527 DOI: 10.3389/fchem.2023.1224336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
In this study, long-lived nuclear singlet order methods are combined with diffusion tensor imaging with the purpose of characterizing the full diffusion tensor of molecules diffusing freely in large pores of up to a millimeter in size. Such sizes are out of reach in conventional diffusion tensor imaging because of the limitations imposed by the relaxation decay constant of the longitudinal magnetization. A singlet-assisted diffusion tensor imaging methodology able to circumvent such limitations is discussed, and the new possibilities that it offers are demonstrated through simulation and experiments on plastic phantoms containing cylindrical channels of 1 mm in diameter.
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Affiliation(s)
| | | | | | - Giuseppe Pileio
- School of Chemistry, University of Southampton, Southampton, United Kingdom
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2
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Di Stasi R, Diana D, De Rosa L, Fattorusso R, D'Andrea LD. Biochemical and Conformational Characterization of Recombinant VEGFR2 Domain 7. Mol Biotechnol 2020; 61:860-872. [PMID: 31531759 DOI: 10.1007/s12033-019-00211-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Angiogenesis is a biological process finely tuned by a plethora of pro- and anti-angiogenic molecules, among which vascular endothelial growth factors (VEGFs). Their biological activity is expressed through the interaction with three cognate receptor tyrosine kinases, VEGFR1, 2, and 3. VEGFR2 is the primary regulator of angiogenesis. Ligand-induced VEGFR2 dimerization and activation depend on direct ligand binding to extracellular domains 2 and 3 of receptor and in the establishment of interactions between proximal membrane domains. VEGFR2 domain 7 has been shown to play a crucial role in receptor dimerization and regulation, therefore, representing a convenient target for the allosteric modulation of VEGFR2 activity. The ability to prepare a functional VEGFR2D7 domain represents the starting point to the development of novel VEGFR2 binders acting as allosteric inhibitors of receptor activity. Here, we describe a robust and efficient procedure for the preparation in E. coli of the VEGFR2 domain 7. The protein was obtained with a good yield and was properly folded. It was investigated in a biochemical and structural study, providing information on its conformational arrangement and in solution properties.
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Affiliation(s)
- Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Naples, Italy.
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università della Campania "L. Vanvitelli", Via Vivaldi, 43 - 81100, Caserta, Italy
| | - Luca D D'Andrea
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Naples, Italy.
- Istituto di Biostrutture e Bioimmagini, CNR, Via Nizza 52, 10126, Turin, Italy.
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Mahrous EA, Farag MA. Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review. J Adv Res 2014; 6:3-15. [PMID: 25685540 PMCID: PMC4293671 DOI: 10.1016/j.jare.2014.10.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 01/06/2023] Open
Abstract
Today, most investigations of the plant metabolome tend to be based on either nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS), with or without hyphenation with chromatography. Although less sensitive than MS, NMR provides a powerful complementary technique for the identification and quantification of metabolites in plant extracts. NMR spectroscopy, well appreciated by phytochemists as a particularly information-rich method, showed recent paradigm shift for the improving of metabolome(s) structural and functional characterization and for advancing the understanding of many biological processes. Furthermore, two dimensional NMR (2D NMR) experiments and the use of chemometric data analysis of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the development of NMR in the field of metabolomics with special focus on 2D NMR spectroscopic techniques and their applications in phytomedicines quality control analysis and drug discovery from natural sources, raising more attention at its potential to reduce the gap between the pace of natural products research and modern drug discovery demand.
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Affiliation(s)
- Engy A Mahrous
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo, Kasr el Aini st. P.B. 11562, Egypt
| | - Mohamed A Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Cairo, Kasr el Aini st. P.B. 11562, Egypt
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Heisel KA, Goto JJ, Krishnan VV. NMR Chromatography: Molecular Diffusion in the Presence of Pulsed Field Gradients in Analytical Chemistry Applications. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ajac.2012.36053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Mamedov I, Parac-Vogt TN, Logothetis NK, Angelovski G. Synthesis and characterization of dinuclear heterometallic lanthanide complexes exhibiting MRI and luminescence response. Dalton Trans 2010; 39:5721-7. [DOI: 10.1039/b925556g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Amsden B, Misra G, Marshall M, Turner N. Synthesis and Characterization of Biodegradable Networks Providing Saturated-Solution Prolonged Delivery. J Pharm Sci 2008; 97:860-74. [PMID: 17701973 DOI: 10.1002/jps.21023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Numerous peptide drugs require continuous and local delivery to obtain optimum therapeutic effect. Herein, we describe the incorporation of a model peptide drug, vitamin B12, as well as goserelin acetate, in biodegradable elastomer cylinders through photo-cross-linking. The elastomer was prepared from acrylated star-poly(epsilon-caprolactone-co-D,L-lactide). Release was manipulated through the incorporation of poly(ethylene glycol) diacrylate (PEGD) into the network at concentrations up to 30% (w/w). The PEGD in the network caused rapid swelling that remained constant throughout the release period. The degree of swelling was low, ranging from 10 to 45% (w/w), and increasing as the PEGD content increased. Release proceeded with a minimal initial burst, and extended periods of nearly constant release, ranging from approximately 5 to 70% mass fraction released, were obtained. The release rate was independent of particle size and increased as the cylinder diameter decreased, as the amount of PEGD increased, as the molecular weight of PEGD increased, and as the agent loading increased. Moreover, goserelin acetate, which has a comparable diffusivity but greater aqueous solubility, was released at a greater rate than vitamin B12. This release behavior is explained as a balance between agent dissolution in the swollen polymer matrix and diffusion through the polymer matrix bulk.
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Affiliation(s)
- Brian Amsden
- Department of Chemical Engineering, Queen's University, Kingston, Ontario, Canada K7L 3N6.
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7
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Alcaraz LA, del Alamo M, Barrera FN, Mateu MG, Neira JL. Flexibility in HIV-1 assembly subunits: solution structure of the monomeric C-terminal domain of the capsid protein. Biophys J 2007; 93:1264-76. [PMID: 17526561 PMCID: PMC1929042 DOI: 10.1529/biophysj.106.101089] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The protein CA forms the mature capsid of human immunodeficiency virus. Hexamerization of the N-terminal domain and dimerization of the C-terminal domain, CAC, occur during capsid assembly, and both domains constitute potential targets for anti-HIV inhibitors. CAC homodimerization occurs mainly through its second helix, and is abolished when its sole tryptophan is mutated to alanine. Previous thermodynamic data obtained with the dimeric and monomeric forms of CAC indicate that the structure of the mutant resembles that of a monomeric intermediate found in the folding and association reactions of CAC. We have solved the three-dimensional structure in aqueous solution of the monomeric mutant. The structure is similar to that of the subunits in the dimeric, nonmutated CAC, except the segment corresponding to the second helix, which is highly dynamic. At the end of this region, the polypeptide chain is bent to bury several hydrophobic residues and, as a consequence, the last two helices are rotated 90 degrees when compared to their position in dimeric CAC. The previously obtained thermodynamic data are consistent with the determined structure of the monomeric mutant. This extraordinary ability of CAC to change its structure may contribute to the different modes of association of CA during HIV assembly, and should be taken into account in the design of new drugs against this virus.
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Affiliation(s)
- Luis A Alcaraz
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche (Alicante), Spain
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Zhang Y, Amsden BG. Application of an Obstruction-Scaling Model To Diffusion of Vitamin B12 and Proteins in Semidilute Alginate Solutions. Macromolecules 2005. [DOI: 10.1021/ma0522357] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Zhang
- Department of Chemical Engineering, Queen's University, Kingston ON, Canada K7L 3N6
| | - Brian G. Amsden
- Department of Chemical Engineering, Queen's University, Kingston ON, Canada K7L 3N6
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Price WS, Tsuchiya F, Arata Y. Lysozyme Aggregation and Solution Properties Studied Using PGSE NMR Diffusion Measurements. J Am Chem Soc 1999. [DOI: 10.1021/ja992265n] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William S. Price
- Contribution from the Water Research Institute, Sengen 2-1-6, Tsukuba, Ibaraki 305-0047, Japan
| | - Fumihiko Tsuchiya
- Contribution from the Water Research Institute, Sengen 2-1-6, Tsukuba, Ibaraki 305-0047, Japan
| | - Yoji Arata
- Contribution from the Water Research Institute, Sengen 2-1-6, Tsukuba, Ibaraki 305-0047, Japan
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Larive CK, Lunte SM, Zhong M, Perkins MD, Wilson GS, Gokulrangan G, Williams T, Afroz F, Schöneich C, Derrick TS, Middaugh CR, Bogdanowich-Knipp S. Separation and analysis of peptides and proteins. Anal Chem 1999; 71:389R-423R. [PMID: 10409086 DOI: 10.1021/a1990013o] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C K Larive
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045
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Krishnan V, Thornton KH, Cosman M. An improved experimental scheme to measure self-diffusion coefficients of biomolecules with an advantageous use of radiation damping. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(99)00143-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Price WS, Barzykin AV, Hayamizu K, Tachiya M. A model for diffusive transport through a spherical interface probed by pulsed-field gradient NMR. Biophys J 1998; 74:2259-71. [PMID: 9591653 PMCID: PMC1299569 DOI: 10.1016/s0006-3495(98)77935-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In biological systems, because of higher intracellular viscosity and/or the restriction of the diffusion space inside cells, the (apparent) diffusion coefficient of an intracellular species (e.g., water) is generally smaller than when it is in the extracellular medium. This difference affects the spin-echo signal attenuation in the pulsed field gradient NMR experiment and thus affords a means of separating the intracellular from the extracellular species, thereby providing a basis for studying transmembrane transport. Such experiments have commonly been analyzed using the macroscopic model of Kärger (see Adv. Magn. Reson. 21:1-89 (1988)). In our previous study, we considered a microscopic model of diffusive transport through a spherical interface using the short gradient pulse approximation (J. Magn. Reson. A114:39-46 (1995)). The spins in the external medium were modeled with the "partially absorbing wall" condition or as having a small but finite lifetime. In the present paper, we extend our treatment to the case in which there is no limitation upon the lifetime in either medium. We also consider a simple modification of Kärger's model that more properly accounts for the restricted intracellular diffusion. Importantly, it was found that the exact solution within the short gradient pulse approximation developed here and the modified Kärger model are in close agreement in the (experimentally relevant) long-time limit. The results of this study show that when there is no limitation upon the lifetime of the transported species in either phase, the spin-echo attenuation curve is very sensitive to transport.
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Affiliation(s)
- W S Price
- Water Research Institute, Tsukuba, Ibaraki, Japan.
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