Bibliographies thématiques / Paramagnetic restraints

Littérature scientifique sur le sujet « Paramagnetic restraints »

Auteur : Grafiati
Publié le 10 mars 2023

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Articles de revues sur le sujet "Paramagnetic restraints"

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Querci, Leonardo, Inês B. Trindade, Michele Invernici, José Malanho Silva, Francesca Cantini, Ricardo O. Louro et Mario Piccioli. « NMR of Paramagnetic Proteins : 13C Derived Paramagnetic Relaxation Enhancements Are an Additional Source of Structural Information in Solution ». Magnetochemistry 9, no 3 (26 février 2023) : 66. http://dx.doi.org/10.3390/magnetochemistry9030066.

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In paramagnetic metalloproteins, longitudinal relaxation rates of 13C′ and 13Cα nuclei can be measured using 13C detected experiments and converted into electron spin-nuclear spin distance restraints, also known as Paramagnetic Relaxation Enhancement (PRE) restraints. 13C are less sensitive to paramagnetism than 1H nuclei, therefore, 13C based PREs constitute an additional, non-redundant, structural information. We will discuss the complementarity of 13C PRE restraints with 1H PRE restraints in the case of the High Potential Iron Sulfur Protein (HiPIP) PioC, for which the NMR structure of PioC has been already solved by a combination of classical and paramagnetism-based restraints. We will show here that 13C R1 values can be measured also at very short distances from the paramagnetic center and that the obtained set of 13C based restraints can be added to 1H PREs and to other classical and paramagnetism based NMR restraints to improve quality and quantity of the NMR information.
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Arnesano, Fabio, Lucia Banci et Mario Piccioli. « NMR structures of paramagnetic metalloproteins ». Quarterly Reviews of Biophysics 38, no 2 (mai 2005) : 167–219. http://dx.doi.org/10.1017/s0033583506004161.

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1. Introduction 1681.1 Genomic annotation of metalloproteins 1681.2 Why NMR structures? 1681.3 Why paramagnetic metalloproteins? 1692. General theory 1702.1 Nuclear and electron spins 1702.2 Hyperfine coupling 1712.3 The effect of the hyperfine coupling on the NMR shift: the hyperfine shift 1732.4 The effect of the hyperfine coupling on nuclear relaxation 1742.5 Interplay between electron spin properties and features of the NMR spectra 1783. Paramagnetism-based structural restraints 1803.1 Contact shifts and relaxation rates as restraints 1813.2 Locating the metal ion within the protein frame: pseudocontact shifts 1843.3 Cross-correlation rates 1863.4 Residual dipolar couplings 1883.5 Interplay between different restraints 1904. NMR without1H detection 1914.1 The protocol for 13C-detected protonless assignment of backbone and side-chains 1944.2 Protonless heteronuclear NMR experiments tailored to paramagnetic systems 1965. The use of lanthanides as paramagnetic probes 1986. The case of Cu(II) proteins 2027. Perspectives 2088. Acknowledgments 2099. References 209Metalloproteins represent a large share of the proteome and many of them contain paramagnetic metal ions. The knowledge, at atomic resolution, of their structure in solution is important to understand processes in which they are involved, such as electron transfer mechanisms, enzymatic reactions, metal homeostasis and metal trafficking, as well as interactions with their partners. Formerly considered as unfeasible, the first structure in solution by nuclear magnetic resonance (NMR) of a paramagnetic protein was obtained in 1994. Methodological and instrumental advancements pursued over the last decade are such that NMR structure of paramagnetic proteins may be now routinely obtained. We focus here on approaches and problems related to the structure determination of paramagnetic proteins in solution through NMR spectroscopy. After a survey of the background theory, we show how the effects produced by the presence of a paramagnetic metal ion on the NMR parameters, which are in many cases deleterious for the detection of NMR spectra, can be overcome and turned into an additional source of structural restraints. We also briefly address features and perspectives given by the use of 13C-detected protonless NMR spectroscopy for proteins in solution. The structural information obtained through the exploitation of a paramagnetic center are discussed for some Cu2+-binding proteins and for Ca2+-binding proteins, where the replacement of a diamagnetic metal ion with suitable paramagnetic metal ions suggests novel approaches to the structural characterization of proteins containing diamagnetic and NMR-silent metal ions.
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Gong, Zhou, Shuai Yang, Qing-Fen Yang, Yue-Ling Zhu, Jing Jiang et Chun Tang. « Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR ». Biophysics Reports 5, no 5-6 (15 novembre 2019) : 244–53. http://dx.doi.org/10.1007/s41048-019-00099-2.

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AbstractNMR structure calculation is inherently integrative, and can incorporate new experimental data as restraints. As RNAs have lower proton densities and are more conformational heterogenous than proteins, the refinement of RNA structures can benefit from additional types of restraints. Paramagnetic relaxation enhancement (PRE) provides distance information between a paramagnetic probe and protein or RNA nuclei. However, covalent conjugation of a paramagnetic probe is difficult for RNAs, thus limiting the use of PRE NMR for RNA structure characterization. Here, we show that the solvent PRE can be accurately measured for RNA labile imino protons, simply with the addition of an inert paramagnetic cosolute. Demonstrated on three RNAs that have increasingly complex topologies, we show that the incorporation of the solvent PRE restraints can significantly improve the precision and accuracy of RNA structures. Importantly, the solvent PRE data can be collected for RNAs without isotope enrichment. Thus, the solvent PRE method can work integratively with other biophysical techniques for better characterization of RNA structures.
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Luchinat, Claudio, Giacomo Parigi, Enrico Ravera et Mauro Rinaldelli. « Solid-State NMR Crystallography through Paramagnetic Restraints ». Journal of the American Chemical Society 134, no 11 (8 mars 2012) : 5006–9. http://dx.doi.org/10.1021/ja210079n.

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Jeschke, Gunnar. « Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches ». Biomolecules 12, no 10 (25 septembre 2022) : 1369. http://dx.doi.org/10.3390/biom12101369.

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Labelling techniques such as electron paramagnetic resonance spectroscopy and single-molecule fluorescence resonance energy transfer, allow access to distances in the range of tens of angstroms, corresponding to the size of proteins and small to medium-sized protein complexes. Such measurements do not require long-range ordering and are therefore applicable to systems with partial disorder. Data from spin-label-based measurements can be processed into distance distributions that provide information about the extent of such disorder. Using such information in modelling presents several challenges, including a small number of restraints, the influence of the label itself on the measured distance and distribution width, and balancing the fitting quality of the long-range restraints with the fitting quality of other restraint subsets. Starting with general considerations about integrative and hybrid structural modelling, this review provides an overview of recent approaches to these problems and identifies where further progress is needed.
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Yang, Feng, Xiao Wang, Bin-Bin Pan et Xun-Cheng Su. « Single-armed phenylsulfonated pyridine derivative of DOTA is rigid and stable paramagnetic tag in protein analysis ». Chemical Communications 52, no 77 (2016) : 11535–38. http://dx.doi.org/10.1039/c6cc06114a.

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Single-armed DOTA-like phenylsulfonated pyridine derivatives are rigid and stable paramagnetic tags for site-specific labelling of proteins. The respective protein conjugates yield valuable long-range structural restraints for proteins.
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Kuenze, Georg, Richard Bonneau, Julia Koehler Leman et Jens Meiler. « Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints ». Structure 27, no 11 (novembre 2019) : 1721–34. http://dx.doi.org/10.1016/j.str.2019.08.012.

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Lee, Michael D., Matthew L. Dennis, James D. Swarbrick et Bim Graham. « Enantiomeric two-armed lanthanide-binding tags for complementary effects in paramagnetic NMR spectroscopy ». Chemical Communications 52, no 51 (2016) : 7954–57. http://dx.doi.org/10.1039/c6cc02325h.

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Bellomo, Giovanni, Enrico Ravera, Vito Calderone, Mauro Botta, Marco Fragai, Giacomo Parigi et Claudio Luchinat. « Revisiting paramagnetic relaxation enhancements in slowly rotating systems : how long is the long range ? » Magnetic Resonance 2, no 1 (29 janvier 2021) : 25–31. http://dx.doi.org/10.5194/mr-2-25-2021.

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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 R1-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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Joss, Daniel, Florine Winter et Daniel Häussinger. « A novel, rationally designed lanthanoid chelating tag delivers large paramagnetic structural restraints for biomolecular NMR ». Chemical Communications 56, no 84 (2020) : 12861–64. http://dx.doi.org/10.1039/d0cc04337k.

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Thèses sur le sujet "Paramagnetic restraints"

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ANDRALOJC, WITOLD JACEK. « Conformational heterogeneity in multidomain biological systems studied through averaged NMR restraints ». Doctoral thesis, 2016. http://hdl.handle.net/2158/1072773.

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Jack, Fernando Edmond. « ATCUN-derived paramagnetic distance restraints in the study of an SH3 domain ». 2004. http://link.library.utoronto.ca/eir/EIRdetail.cfm?Resources__ID=80942&T=F.

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Camacho, Zarco Aldo Roman. « Paramagnetic tools for the structural analysis of high molecular weight proteins ». Doctoral thesis, 2015. http://hdl.handle.net/11858/00-1735-0000-0028-866B-E.

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Livres sur le sujet "Paramagnetic restraints"

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Jack, Fernando Edmond. ATCUN-derived paramagnetic distance restraints in the study of an SH3 domain. 2004.

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Chapitres de livres sur le sujet "Paramagnetic restraints"

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Bertini, Ivano, Claudio Luchinat, Giacomo Parigi et Enrico Ravera. « Paramagnetic restraints for structure and dynamics of biomolecules ». Dans Solution NMR of Paramagnetic Molecules, 277–312. Elsevier, 2017. http://dx.doi.org/10.1016/b978-0-444-63436-8.00007-7.

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