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Статті в журналах з теми "Paramagnetic restraints"

Автор: Grafiati

Опубліковано: 10 березня 2023

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1

Querci, Leonardo, Inês B. Trindade, Michele Invernici, José Malanho Silva, Francesca Cantini, Ricardo O. Louro, and Mario Piccioli. "NMR of Paramagnetic Proteins: 13C Derived Paramagnetic Relaxation Enhancements Are an Additional Source of Structural Information in Solution." Magnetochemistry 9, no. 3 (February 26, 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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2

Arnesano, Fabio, Lucia Banci, and Mario Piccioli. "NMR structures of paramagnetic metalloproteins." Quarterly Reviews of Biophysics 38, no. 2 (May 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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3

Gong, Zhou, Shuai Yang, Qing-Fen Yang, Yue-Ling Zhu, Jing Jiang, and Chun Tang. "Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR." Biophysics Reports 5, no. 5-6 (November 15, 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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4

Luchinat, Claudio, Giacomo Parigi, Enrico Ravera, and Mauro Rinaldelli. "Solid-State NMR Crystallography through Paramagnetic Restraints." Journal of the American Chemical Society 134, no. 11 (March 8, 2012): 5006–9. http://dx.doi.org/10.1021/ja210079n.

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5

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

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Анотація:

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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6

Yang, Feng, Xiao Wang, Bin-Bin Pan, and 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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7

Kuenze, Georg, Richard Bonneau, Julia Koehler Leman, and Jens Meiler. "Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints." Structure 27, no. 11 (November 2019): 1721–34. http://dx.doi.org/10.1016/j.str.2019.08.012.

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8

Lee, Michael D., Matthew L. Dennis, James D. Swarbrick, and 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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9

Bellomo, Giovanni, Enrico Ravera, Vito Calderone, Mauro Botta, Marco Fragai, Giacomo Parigi, and Claudio Luchinat. "Revisiting paramagnetic relaxation enhancements in slowly rotating systems: how long is the long range?" Magnetic Resonance 2, no. 1 (January 29, 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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10

Joss, Daniel, Florine Winter, and 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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11

Balayssac, Stéphane, Ivano Bertini, Moreno Lelli, Claudio Luchinat, and Massimiliano Maletta. "Paramagnetic Ions Provide Structural Restraints in Solid-State NMR of Proteins." Journal of the American Chemical Society 129, no. 8 (February 2007): 2218–19. http://dx.doi.org/10.1021/ja068105a.

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12

Hou, Xue-Ni, and Hidehito Tochio. "Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints." Biophysical Reviews 14, no. 1 (January 11, 2022): 55–66. http://dx.doi.org/10.1007/s12551-021-00916-4.

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13

Babini, Elena, Ivano Bertini, Francesco Capozzi, Isabella C. Felli, Moreno Lelli, and Claudio Luchinat. "Direct Carbon Detection in Paramagnetic Metalloproteins To Further Exploit Pseudocontact Shift Restraints." Journal of the American Chemical Society 126, no. 34 (September 2004): 10496–97. http://dx.doi.org/10.1021/ja047573m.

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14

Perez, Alberto, Kari Gaalswyk, Christopher P. Jaroniec, and Justin L. MacCallum. "High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid‐State NMR Restraints." Angewandte Chemie 131, no. 20 (April 17, 2019): 6636–40. http://dx.doi.org/10.1002/ange.201811895.

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15

Perez, Alberto, Kari Gaalswyk, Christopher P. Jaroniec, and Justin L. MacCallum. "High Accuracy Protein Structures from Minimal Sparse Paramagnetic Solid‐State NMR Restraints." Angewandte Chemie International Edition 58, no. 20 (May 13, 2019): 6564–68. http://dx.doi.org/10.1002/anie.201811895.

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16

Koehler, Julia, and Jens Meiler. "Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects." Progress in Nuclear Magnetic Resonance Spectroscopy 59, no. 4 (November 2011): 360–89. http://dx.doi.org/10.1016/j.pnmrs.2011.05.001.

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17

Hass, Mathias AS, and Marcellus Ubbink. "Structure determination of protein–protein complexes with long-range anisotropic paramagnetic NMR restraints." Current Opinion in Structural Biology 24 (February 2014): 45–53. http://dx.doi.org/10.1016/j.sbi.2013.11.010.

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18

Jeschke, Gunnar. "The contribution of modern EPR to structural biology." Emerging Topics in Life Sciences 2, no. 1 (February 6, 2018): 9–18. http://dx.doi.org/10.1042/etls20170143.

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Electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labelling is applicable to biomolecules and their complexes irrespective of system size and in a broad range of environments. Neither short-range nor long-range order is required to obtain structural restraints on accessibility of sites to water or oxygen, on secondary structure, and on distances between sites. Many of the experiments characterize a static ensemble obtained by shock-freezing. Compared with characterizing the dynamic ensemble at ambient temperature, analysis is simplified and information loss due to overlapping timescales of measurement and system dynamics is avoided. The necessity for labelling leads to sparse restraint sets that require integration with data from other methodologies for building models. The double electron–electron resonance experiment provides distance distributions in the nanometre range that carry information not only on the mean conformation but also on the width of the native ensemble. The distribution widths are often inconsistent with Anfinsen's concept that a sequence encodes a single native conformation defined at atomic resolution under physiological conditions.

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19

Shi, Lei, Nathaniel J. Traaseth, Raffaello Verardi, Martin Gustavsson, Jiali Gao, and Gianluigi Veglia. "Paramagnetic-Based NMR Restraints Lift Residual Dipolar Coupling Degeneracy in Multidomain Detergent-Solubilized Membrane Proteins." Journal of the American Chemical Society 133, no. 7 (February 23, 2011): 2232–41. http://dx.doi.org/10.1021/ja109080t.

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20

He, Lichun, Benjamin Bardiaux, Mumdooh Ahmed, Johannes Spehr, Renate König, Heinrich Lünsdorf, Ulfert Rand, Thorsten Lührs, and Christiane Ritter. "Structure determination of helical filaments by solid-state NMR spectroscopy." Proceedings of the National Academy of Sciences 113, no. 3 (January 5, 2016): E272—E281. http://dx.doi.org/10.1073/pnas.1513119113.

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The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers.

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21

Cetiner, E. C., H. R. A. Jonker, C. Helmling, D. B. Gophane, C. Grünewald, S. Th Sigurdsson, and H. Schwalbe. "Paramagnetic-iterative relaxation matrix approach: extracting PRE-restraints from NOESY spectra for 3D structure elucidation of biomolecules." Journal of Biomolecular NMR 73, no. 12 (October 12, 2019): 699–712. http://dx.doi.org/10.1007/s10858-019-00282-0.

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22

Rinaldelli, Mauro, Enrico Ravera, Vito Calderone, Giacomo Parigi, Garib N. Murshudov, and Claudio Luchinat. "Simultaneous use of solution NMR and X-ray data inREFMAC5 for joint refinement/detection of structural differences." Acta Crystallographica Section D Biological Crystallography 70, no. 4 (March 19, 2014): 958–67. http://dx.doi.org/10.1107/s1399004713034160.

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The programREFMAC5 fromCCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints inREFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably `ideal' geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

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23

Nadaud, Philippe S., Jonathan J. Helmus, Stefanie L. Kall, and Christopher P. Jaroniec. "Paramagnetic Ions Enable Tuning of Nuclear Relaxation Rates and Provide Long-Range Structural Restraints in Solid-State NMR of Proteins." Journal of the American Chemical Society 131, no. 23 (June 17, 2009): 8108–20. http://dx.doi.org/10.1021/ja900224z.

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24

Furuita, Kyoko, Saori Kataoka, Toshihiko Sugiki, Yoshikazu Hattori, Naohiro Kobayashi, Takahisa Ikegami, Kazuhiro Shiozaki, Toshimichi Fujiwara, and Chojiro Kojima. "Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints." Journal of Biomolecular NMR 61, no. 1 (November 27, 2014): 55–64. http://dx.doi.org/10.1007/s10858-014-9882-7.

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25

Tamaki, Hajime, Ayako Egawa, Kouki Kido, Tomoshi Kameda, Masakatsu Kamiya, Takashi Kikukawa, Tomoyasu Aizawa, Toshimichi Fujiwara, and Makoto Demura. "Structure determination of uniformly 13C, 15N labeled protein using qualitative distance restraints from MAS solid-state 13C-NMR observed paramagnetic relaxation enhancement." Journal of Biomolecular NMR 64, no. 1 (January 2016): 87–101. http://dx.doi.org/10.1007/s10858-015-0010-0.

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26

Scherer, Andreas, Berk Yildirim, and Malte Drescher. "The effect of the zero-field splitting in light-induced pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy." Magnetic Resonance 4, no. 1 (February 8, 2023): 27–46. http://dx.doi.org/10.5194/mr-4-27-2023.

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Abstract. Laser-induced magnetic dipole (LaserIMD) spectroscopy and light-induced double electron–electron resonance (LiDEER) spectroscopy are important techniques in the emerging field of light-induced pulsed dipolar electron paramagnetic resonance (EPR) spectroscopy (light-induced PDS). These techniques use the photoexcitation of a chromophore to the triplet state and measure its dipolar coupling to a neighboring electron spin, which allows the determination of distance restraints. To date, LaserIMD and LiDEER have been analyzed with software tools that were developed for a pair of two S=1/2 spins and that neglected the zero-field splitting (ZFS) of the excited triplet. Here, we explore the limits of this assumption and show that the ZFS can have a significant effect on the shape of the dipolar trace. For a detailed understanding of the effect of the ZFS, a theoretical description for LaserIMD and LiDEER is derived, taking into account the non-secular terms of the ZFS. Simulations based on this model show that the effect of the ZFS is not that pronounced in LiDEER for experimentally relevant conditions. However, the ZFS leads to an additional decay in the dipolar trace in LaserIMD. This decay is not that pronounced in Q-band but can be quite noticeable for lower magnetic field strengths in X-band. Experimentally recorded LiDEER and LaserIMD data confirm these findings. It is shown that ignoring the ZFS in the data analysis of LaserIMD traces can lead to errors in the obtained modulation depths and background decays. In X-band, it is additionally possible that the obtained distance distribution is plagued by long distance artifacts.

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27

Gillespie, Joel R., and David Shortle. "Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. distance restraints from paramagnetic relaxation and calculation of an ensemble of structures." Journal of Molecular Biology 268, no. 1 (April 1997): 170–84. http://dx.doi.org/10.1006/jmbi.1997.0953.

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28

Banci, Lucia, Ivano Bertini, Gabriele Cavallaro, Andrea Giachetti, Claudio Luchinat, and Giacomo Parigi. "Paramagnetism-Based Restraints for Xplor-NIH." Journal of Biomolecular NMR 28, no. 3 (March 2004): 249–61. http://dx.doi.org/10.1023/b:jnmr.0000013703.30623.f7.

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29

Banci, Lucia, Ivano Bertini, Gabriele Cavallaro, Andrea Giachetti, Claudio Luchinat, and Giacomo Parigi. "Erratum: Paramagnetism-based restraints for Xplor-NIH." Journal of Biomolecular NMR 29, no. 2 (June 2004): 221. http://dx.doi.org/10.1023/b:jnmr.0000019276.57093.f3.

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30

Banci, Lucia, Ivano Bertini, Isabella C. Felli, and Josephine Sarrou. "Backbone-only restraints for fast determination of the protein fold: The role of paramagnetism-based restraints. Cytochrome b562 as an example." Journal of Magnetic Resonance 172, no. 2 (February 2005): 191–200. http://dx.doi.org/10.1016/j.jmr.2004.07.024.

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31

Bertini, Ivano, Yogesh K. Gupta, Claudio Luchinat, Giacomo Parigi, Massimiliano Peana, Luca Sgheri, and Jing Yuan. "Paramagnetism-Based NMR Restraints Provide Maximum Allowed Probabilities for the Different Conformations of Partially Independent Protein Domains." Journal of the American Chemical Society 129, no. 42 (October 2007): 12786–94. http://dx.doi.org/10.1021/ja0726613.

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32

Cao, Jialei, Juan Lu, Xiufeng Zhou, Zuoshan Wang, and Xiaobin Li. "Functional control of ZnO nanoparticles by F, C-codoping." Functional Materials Letters 07, no. 01 (February 2014): 1350071. http://dx.doi.org/10.1142/s1793604713500719.

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F , C -codoped ZnO nanoparticles were synthesized by the precipitation method. X-ray photoelectron spectroscopy spectra (XPS) measurements confirmed the existence of F – Zn , C – F , – CF 2– and O – C – O bonds in the lattices of ZnO nanoparticles. The band gap of ZnO was narrowed due to F and C dopants, which should be beneficial for the improvement of the photocatalytic activity. However, our experiments demonstrated that F , C -codoping restrained the photocatalytic activity of ZnO nanoparticles. To detect the possible microstructural defects, the analysis of electron paramagnetic resonance (EPR) was performed. It was suggested that the positive-charged [Formula: see text] defects were formed by the substitution of F ions for O lattice sites. [Formula: see text] defects are deep donors and act as recombination centers for photo-generated electrons and holes, which could result in the decrease of the photocatalytic activity. Although the photocatalytic activity of F , C -codoped ZnO is depressed, the antibacterial activity still keeps a comparable level in comparison with that of pure ZnO . Therefore, this material has a potential application in textiles.

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33

Godfrey, C., P. M. A. Gadsby, A. J. Thomson, C. Greenwood, and A. Coddington. "Electron-paramagnetic-resonance and magnetic-circular-dichroism studies on the formate dehydrogenase-nitrate reductase particle from Pseudomonas aeruginosa." Biochemical Journal 243, no. 1 (April 1, 1987): 241–48. http://dx.doi.org/10.1042/bj2430241.

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The membrane-bound respiratory particle complex of Pseudomonas aeruginosa, which reduces nitrate to nitrite using formate as the electron donor, was prepared and characterized by e.p.r. and low-temperature magnetic c.d. (m.c.d.) spectroscopy. The particle complex has two enzymic components, namely nitrate reductase (NiR) and formate dehydrogenase (FDH), which are multi-centred proteins containing molybdenum, iron-sulphur clusters and cytochrome. By using results from work on the purified extracted enzymes NiR and FDH to aid in the assignment, it has been possible to observe spectroscopically all the components of the electron-transfer chain in the intact particle. This led to a proposal for the organization of the metal components of the FDH-NiR chain. Molybdenum ions are at opposite ends of the chain and interact with, respectively, the formate-CO2 couple and the nitrate-nitrite couple. The molybdenum ion at the low-potential end of the chain passes electrons to cytochrome b of FDH, a bishistidine-co-ordinated haem with unusual steric restraint at the iron. The next component is a [4Fe-4S] cluster. This comprises all the components of FDH. Electrons are passed to the molybdenum of NiR via a number, probably two, of [4Fe-4S] clusters. No evidence has been found in this work for the presence of a quinone to mediate electron transfer between FDH and NiR. Cytochrome c appears to be able to feed electrons into the chain at the level of one of the [4Fe-4S] centres of NiR.

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34

Ubbink, Marcellus, Mikael Ejdebäck, B. Göran Karlsson, and Derek S. Bendall. "The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics." Structure 6, no. 3 (March 1998): 323–35. http://dx.doi.org/10.1016/s0969-2126(98)00035-5.

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35

Cortes, D. Marien, Luis G. Cuello, and Eduardo Perozo. "Molecular Architecture of Full-Length KcsA." Journal of General Physiology 117, no. 2 (January 29, 2001): 165–80. http://dx.doi.org/10.1085/jgp.117.2.165.

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The molecular architecture of the NH2 and COOH termini of the prokaryotic potassium channel KcsA has been determined using site-directed spin-labeling methods and paramagnetic resonance EPR spectroscopy. Cysteine mutants were generated (residues 5–24 and 121–160) and spin labeled, and the X-band CW EPR spectra were obtained from liposome-reconstituted channels at room temperature. Data on probe mobility (ΔHo−1), accessibility parameters (ΠO2 and ΠNiEdda), and inter-subunit spin-spin interaction (Ω) were used as structural constraints to build a three-dimensional folding model of these cytoplasmic domains from a set of simulated annealing and restrained molecular dynamics runs. 32 backbone structures were generated and averaged using fourfold symmetry, and a final mean structure was obtained from the eight lowest energy runs. Based on the present data, together with information from the KcsA crystal structure, a model for the three-dimensional fold of full-length KcsA was constructed. In this model, the NH2 terminus of KcsA forms an α-helix anchored at the membrane–water interface, while the COOH terminus forms a right-handed four-helix bundle that extend some 40–50 Å towards the cytoplasm. Functional analysis of COOH-terminal deletion constructs suggest that, while the COOH terminus does not play a substantial role in determining ion permeation properties, it exerts a modulatory role in the pH-dependent gating mechanism.

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36

Zhang, Ke, Zinan Wang, Huaitao Shi, Xiaotian Bai, and Zhan Wang. "Research on Vibration Characteristics of a Ceramic Spindle Based on the Reverse Magnetic Effect." Shock and Vibration 2019 (May 2, 2019): 1–15. http://dx.doi.org/10.1155/2019/6934087.

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The electromagnetic radial force about a ceramic spindle affects the spindle dynamic, which determines the quality of processing. Using a Timoshenko beam unit to build the dynamic model for the ceramic spindle, the dynamic characteristic of an angular contact ball bearing is analyzed using a nonlinear bearing model. The electromagnetic magnetization model was established based on Maxwell’s theory to calculate electromagnetic magnetic density and radial force. The influence about the reverse magnetic field characteristic of the ceramic rotating shaft and dynamic stiffness of the contact ball bearing on the dynamic phenomena of the spindle is analyzed, which is verified by experiments. The results show that the magnetic effect produced by the reverse magnetic of ceramic rotation shaft has a great influence on the electromagnetic radial force. Compared with the paramagnetic effect of the metal shaft, the dynamic characteristics of the spindle can be significantly improved. Considering the coupling relationship between the radial force of the magnetic field and the bearing contact force, dynamic stiffness, and other factors, the accuracy of the model simulation is highly consistent with the test results. In particular, the ceramic spindle model has been successful in predicting with high accuracy and is suitable for multiple extreme working conditions. The parameters, such as initial eccentricity of the rotor, bearing preload, and rotating speed, can be adjusted to restrain the vibration of spindle. The ceramic spindle model provides a theoretical basis for the dynamics development of a high-speed spindle.

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37

Ritsch, Irina, Laura Esteban-Hofer, Elisabeth Lehmann, Leonidas Emmanouilidis, Maxim Yulikov, Frédéric H. T. Allain, and Gunnar Jeschke. "Characterization of Weak Protein Domain Structure by Spin-Label Distance Distributions." Frontiers in Molecular Biosciences 8 (April 12, 2021). http://dx.doi.org/10.3389/fmolb.2021.636599.

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Function of intrinsically disordered proteins may depend on deviation of their conformational ensemble from that of a random coil. Such deviation may be hard to characterize and quantify, if it is weak. We explored the potential of distance distributions between spin labels, as they can be measured by electron paramagnetic resonance techniques, for aiding such characterization. On the example of the intrinsically disordered N-terminal domain 1–267 of fused in sarcoma (FUS) we examined what such distance distributions can and cannot reveal on the random-coil reference state. On the example of the glycine-rich domain 188–320 of heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) we studied whether deviation from a random-coil ensemble can be robustly detected with 19 distance distribution restraints. We discuss limitations imposed by ill-posedness of the conversion of primary data to distance distributions and propose overlap of distance distributions as a fit criterion that can tackle this problem. For testing consistency and size sufficiency of the restraint set, we propose jack-knife resampling. At current desktop computers, our approach is expected to be viable for domains up to 150 residues and for between 10 and 50 distance distribution restraints.

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38

Gaalswyk, Kari, Zhihong Liu, Hans J. Vogel, and Justin L. MacCallum. "An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling." Frontiers in Molecular Biosciences 8 (August 12, 2021). http://dx.doi.org/10.3389/fmolb.2021.676268.

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Paramagnetic nuclear magnetic resonance (NMR) methods have emerged as powerful tools for structure determination of large, sparsely protonated proteins. However traditional applications face several challenges, including a need for large datasets to offset the sparsity of restraints, the difficulty in accounting for the conformational heterogeneity of the spin-label, and noisy experimental data. Here we propose an integrative approach to structure determination combining sparse paramagnetic NMR with physical modelling to infer approximate protein structural ensembles. We use calmodulin in complex with the smooth muscle myosin light chain kinase peptide as a model system. Despite acquiring data from samples labeled only at the backbone amide positions, we are able to produce an ensemble with an average RMSD of ∼2.8 Å from a reference X-ray crystal structure. Our approach requires only backbone chemical shifts and measurements of the paramagnetic relaxation enhancement and residual dipolar couplings that can be obtained from sparsely labeled samples.

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39

Bondarenko, Vasyl, Marta M. Wells, Qiang Chen, Kevin C. Singewald, Sunil Saxena, Yan Xu, and Pei Tang. "19F Paramagnetic Relaxation-Based NMR for Quaternary Structural Restraints of Ion Channels." ACS Chemical Biology, September 18, 2019. http://dx.doi.org/10.1021/acschembio.9b00692.

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40

Mühlberg, Lars, Tuncay Alarcin, Thorben Maass, Robert Creutznacher, Richard Küchler, and Alvaro Mallagaray. "Ligand-induced structural transitions combined with paramagnetic ions facilitate unambiguous NMR assignments of methyl groups in large proteins." Journal of Biomolecular NMR, April 10, 2022. http://dx.doi.org/10.1007/s10858-022-00394-0.

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AbstractNMR spectroscopy allows the study of biomolecules in close-to-native conditions. Structural information can be inferred from the NMR spectra when an assignment is available. Protein assignment is usually a time-consuming task, being specially challenging in the case of large, supramolecular systems. Here, we present an extension of existing state-of-the-art strategies for methyl group assignment that partially overcomes signal overlapping and other difficulties associated to isolated methyl groups. Our approach exploits the ability of proteins to populate two or more conformational states, allowing for unique NOE restraints in each protein conformer. The method is compatible with automated assignment algorithms, granting assignments beyond the limits of a single protein state. The approach also benefits from long-range structural restraints obtained from metal-induced pseudocontact shifts (PCS) and paramagnetic relaxation enhancements (PREs). We illustrate the method with the complete assignment of the 199 methyl groups of a MILproSVproSAT methyl-labeled sample of the UDP-glucose pyrophosphorylase enzyme from Leishmania major (LmUGP). Protozoan parasites of the genus Leishmania causes Leishmaniasis, a neglected disease affecting over 12 million people worldwide. LmUGP is responsible for the de novo biosynthesis of uridine diphosphate-glucose, a precursor in the biosynthesis of the dense surface glycocalyx involved in parasite survival and infectivity. NMR experiments with LmUGP and related enzymes have the potential to unravel new insights in the host resistance mechanisms used by Leishmania major. Our efforts will help in the development of selective and efficient drugs against Leishmania.

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41

Sjodt, Megan, and Robert Clubb. "Nitroxide Labeling of Proteins and the Determination of Paramagnetic Relaxation Derived Distance Restraints for NMR Studies." BIO-PROTOCOL 7, no. 7 (2017). http://dx.doi.org/10.21769/bioprotoc.2207.

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42

Alphonse, Sébastien, Imane Djemil, Andrea Piserchio, and Ranajeet Ghose. "Structural basis for the recognition of the bacterial tyrosine kinase Wzc by its cognate tyrosine phosphatase Wzb." Proceedings of the National Academy of Sciences 119, no. 26 (June 23, 2022). http://dx.doi.org/10.1073/pnas.2201800119.

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Bacterial tyrosine kinases (BY-kinases) comprise a family of protein tyrosine kinases that are structurally distinct from their functional counterparts in eukaryotes and are highly conserved across the bacterial kingdom. BY-kinases act in concert with their counteracting phosphatases to regulate a variety of cellular processes, most notably the synthesis and export of polysaccharides involved in biofilm and capsule biogenesis. Biochemical data suggest that BY-kinase function involves the cyclic assembly and disassembly of oligomeric states coupled to the overall phosphorylation levels of a C-terminal tyrosine cluster. This process is driven by the opposing effects of intermolecular autophosphorylation, and dephosphorylation catalyzed by tyrosine phosphatases. In the absence of structural insight into the interactions between a BY-kinase and its phosphatase partner in atomic detail, the precise mechanism of this regulatory process has remained poorly defined. To address this gap in knowledge, we have determined the structure of the transiently assembled complex between the catalytic core of the Escherichia coli (K-12) BY-kinase Wzc and its counteracting low–molecular weight protein tyrosine phosphatase (LMW-PTP) Wzb using solution NMR techniques. Unambiguous distance restraints from paramagnetic relaxation effects were supplemented with ambiguous interaction restraints from static spectral perturbations and transient chemical shift changes inferred from relaxation dispersion measurements and used in a computational docking protocol for structure determination. This structurepresents an atomic picture of the mode of interaction between an LMW-PTP and its BY-kinase substrate, and provides mechanistic insight into the phosphorylation-coupled assembly/disassembly process proposed to drive BY-kinase function.

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43

Li, Jianping, Yang Shen, Yanke Chen, Zhengfeng Zhang, Shaojie Ma, Qianfen Wan, Qiong Tong, Clemens Glaubitz, Maili Liu, and Jun Yang. "Structure of membrane diacylglycerol kinase in lipid bilayers." Communications Biology 4, no. 1 (March 5, 2021). http://dx.doi.org/10.1038/s42003-021-01802-1.

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AbstractDiacylglycerol kinase (DgkA) is a small integral membrane protein, responsible for the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. Its structures reported in previous studies, determined in detergent micelles by solution NMR and in monoolein cubic phase by X-ray crystallography, differ significantly. These differences point to the need to validate these detergent-based structures in phospholipid bilayers. Here, we present a well-defined homo-trimeric structure of DgkA in phospholipid bilayers determined by magic angle spinning solid-state NMR (ssNMR) spectroscopy, using an approach combining intra-, inter-molecular paramagnetic relaxation enhancement (PRE)-derived distance restraints and CS-Rosetta calculations. The DgkA structure determined in lipid bilayers is different from the solution NMR structure. In addition, although ssNMR structure of DgkA shows a global folding similar to that determined by X-ray, these two structures differ in monomeric symmetry and dynamics. A comparative analysis of DgkA structures determined in three different detergent/lipid environments provides a meaningful demonstration of the influence of membrane mimetic environments on the structure and dynamics of membrane proteins.

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