Relevant bibliographies by topics / Chemical Shift Perturbations

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Chemical Shift Perturbations'

Author: Grafiati
Published: 4 June 2021
Last updated: 2 February 2022

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Journal articles on the topic "Chemical Shift Perturbations"

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Stark, Jaime, and Robert Powers. "Rapid Protein−Ligand Costructures Using Chemical Shift Perturbations." Journal of the American Chemical Society 130, no. 2 (January 2008): 535–45. http://dx.doi.org/10.1021/ja0737974.

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Kukic, Predrag, Damien Farrell, Lawrence P. McIntosh, Bertrand García-Moreno E., Kristine Steen Jensen, Zigmantas Toleikis, Kaare Teilum, and Jens Erik Nielsen. "Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations." Journal of the American Chemical Society 135, no. 45 (October 31, 2013): 16968–76. http://dx.doi.org/10.1021/ja406995j.

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Artikis, Efrosini, and Charles L. Brooks. "Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides." Biophysical Journal 117, no. 2 (July 2019): 258–68. http://dx.doi.org/10.1016/j.bpj.2019.06.003.

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ten Brink, Tim, Clémentine Aguirre, Thomas E. Exner, and Isabelle Krimm. "Performance of Protein–Ligand Docking with Simulated Chemical Shift Perturbations." Journal of Chemical Information and Modeling 55, no. 2 (October 30, 2014): 275–83. http://dx.doi.org/10.1021/ci500446s.

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González-Ruiz, Domingo, and Holger Gohlke. "Steering Protein−Ligand Docking with Quantitative NMR Chemical Shift Perturbations." Journal of Chemical Information and Modeling 49, no. 10 (October 2, 2009): 2260–71. http://dx.doi.org/10.1021/ci900188r.

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Xu, Yunyao, Dongyu Zhang, Rivkah Rogawski, Crina M. Nimigean, and Ann E. McDermott. "Identifying coupled clusters of allostery participants through chemical shift perturbations." Proceedings of the National Academy of Sciences 116, no. 6 (January 24, 2019): 2078–85. http://dx.doi.org/10.1073/pnas.1811168116.

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Allosteric couplings underlie many cellular signaling processes and provide an exciting avenue for development of new diagnostics and therapeutics. A general method for identifying important residues in allosteric mechanisms would be very useful, but remains elusive due to the complexity of long-range phenomena. Here, we introduce an NMR method to identify residues involved in allosteric coupling between two ligand-binding sites in a protein, which we call chemical shift detection of allostery participants (CAP). Networks of functional groups responding to each ligand are defined through correlated NMR perturbations. In this process, we also identify allostery participants, groups that respond to both binding events and likely play a role in the coupling between the binding sites. Such residues exhibit multiple functional states with distinct NMR chemical shifts, depending on binding status at both binding sites. Such a strategy was applied to the prototypical ion channel KcsA. We had previously shown that the potassium affinity at the extracellular selectivity filter is strongly dependent on proton binding at the intracellular pH sensor. Here, we analyzed proton and potassium binding networks and identified groups that depend on both proton and potassium binding (allostery participants). These groups are viewed as candidates for transmitting information between functional units. The vital role of one such identified amino acid was validated through site-specific mutagenesis, electrophysiology functional studies, and NMR-detected thermodynamic analysis of allosteric coupling. This strategy for identifying allostery participants is likely to have applications for many other systems.
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Yu, Zhuoqin, Pengfei Li, and Kenneth M. Merz. "Using Ligand-Induced Protein Chemical Shift Perturbations To Determine Protein–Ligand Structures." Biochemistry 56, no. 18 (April 27, 2017): 2349–62. http://dx.doi.org/10.1021/acs.biochem.7b00170.

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Aguirre, Clémentine, Tim ten Brink, Olivier Cala, Jean-François Guichou, and Isabelle Krimm. "Protein–ligand structure guided by backbone and side-chain proton chemical shift perturbations." Journal of Biomolecular NMR 60, no. 2-3 (September 26, 2014): 147–56. http://dx.doi.org/10.1007/s10858-014-9864-9.

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Ju, Dapeng, Wei Zhang, Jiawei Yan, Haijiao Zhao, Wei Li, Jiawen Wang, Meimei Liao, et al. "Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals." Science Translational Medicine 12, no. 542 (May 6, 2020): eaba0769. http://dx.doi.org/10.1126/scitranslmed.aba0769.

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Transcriptional regulation lies at the core of the circadian clockwork, but how the clock-related transcription machinery controls the circadian phase is not understood. Here, we show both in human cells and in mice that RuvB-like ATPase 2 (RUVBL2) interacts with other known clock proteins on chromatin to regulate the circadian phase. Pharmacological perturbation of RUVBL2 with the adenosine analog compound cordycepin resulted in a rapid-onset 12-hour clock phase-shift phenotype at human cell, mouse tissue, and whole-animal live imaging levels. Using simple peripheral injection treatment, we found that cordycepin penetrated the blood-brain barrier and caused rapid entrainment of the circadian phase, facilitating reduced duration of recovery in a mouse jet-lag model. We solved a crystal structure for human RUVBL2 in complex with a physiological metabolite of cordycepin, and biochemical assays showed that cordycepin treatment caused disassembly of an interaction between RUVBL2 and the core clock component BMAL1. Moreover, we showed with spike-in ChIP-seq analysis and binding assays that cordycepin treatment caused disassembly of the circadian super-complex, which normally resides at E-box chromatin loci such as PER1, PER2, DBP, and NR1D1. Mathematical modeling supported that the observed type 0 phase shifts resulted from derepression of E-box clock gene transcription.
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Kharche, Shalmali, Manali Joshi, Amitabha Chattopadhyay, and Durba Sengupta. "Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1." PLOS Computational Biology 17, no. 5 (May 20, 2021): e1008593. http://dx.doi.org/10.1371/journal.pcbi.1008593.

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The dynamic interactions between G protein-coupled receptors (GPCRs) and their cognate protein partners are central to several cell signaling pathways. For example, the association of CXC chemokine receptor 1 (CXCR1) with its cognate chemokine, interleukin-8 (IL8 or CXCL8) initiates pathways leading to neutrophil-mediated immune responses. The N-terminal domain of chemokine receptors confers ligand selectivity, but unfortunately the conformational dynamics of this intrinsically disordered region remains unresolved. In this work, we have explored the interaction of CXCR1 with IL8 by microsecond time scale coarse-grain simulations, complemented by atomistic models and NMR chemical shift predictions. We show that the conformational plasticity of the apo-receptor N-terminal domain is restricted upon ligand binding, driving it to an open C-shaped conformation. Importantly, we corroborated the dynamic complex sampled in our simulations against chemical shift perturbations reported by previous NMR studies and show that the trends are similar. Our results indicate that chemical shift perturbation is often not a reporter of residue contacts in such dynamic associations. We believe our results represent a step forward in devising a strategy to understand intrinsically disordered regions in GPCRs and how they acquire functionally important conformational ensembles in dynamic protein-protein interfaces.
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Dissertations / Theses on the topic "Chemical Shift Perturbations"

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Aguirre, Clémentine. "Analyse quantitative des perturbations de déplacement chimique pour la détermination de structures tridimensionnelles de complexes protéine-ligand." Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10217/document.

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Les interactions intermoléculaires entre une protéine et ses différents partenaires représentent des cibles de plus en plus prisées pour l'élaboration de composés thérapeutiques capables d'intervenir dans des processus biologiques. La méthode FBDD (Fragment-Based Drug Design) permet de concevoir des molécules bioactives tels que des inhibiteurs, à partir de la structure tridimensionnelle du complexe formé entre la protéine et une molécule fragment. Dans le cadre de ce projet de thèse nous proposons d'utiliser le déplacement chimique pour l'étude des structures 3D de ces complexes protéine-ligand. Nous nous focaliserons sur la mesure des perturbations de déplacement chimique CSP (Chemical Shift Perturbations) des atomes d'une protéine cible, induites par la liaison d'un fragment. Nous démontrerons la puissance de cet outil RMN à travers la simulation des CSP induits par l'interaction d'un fragment sur une protéine cible et leur comparaison aux CSP expérimentaux. L'analyse sera réalisée sur deux protéines cibles et la comparaison des données expérimentales et simulées permettra dans un premier temps de mettre en évidence un réarrangement structural de la protéine Bcl-xL lors de son interaction avec un fragment. Puis, dans un second temps, nous montrerons que cette analyse quantitative des CSP peut permettre de déterminer l'orientation des fragments dans le site d'interaction de la protéine PRDX5. Nous comparerons alors les performances de la méthode pour différents types de protons proposant ainsi de nouvelles pistes pour la compréhension du comportement des CSP vis-à-vis de leurs contributions électroniques
Intermolecular interactions between protein and its partners represent highly attractive targets for the elaboration of therapeutic compounds abble to interfere in biological processes. A novel approach in drug design called Fragment-Based Drug Design (FBDD) consists of designing bioactive molecules like inhibitors, from the 3D structure of the complex formed between a protein and a fragment molecule (MW < 300g/mol). Here we suggest using the chemical shift, to study these protein-ligand structures. We will particularly focus on the measurement of Chemical Shift Perturbations (CSP) induced by the fragment-binding on protein’s nuclei. We will evidence the potency of this NMR tool through simulation of CSP induced by fragment interaction on protein target and the comparison with experimental CSP. Two protein targets will be used and the comparison between experimental and simulated data will evidence on one hand, the structural rearrangement of the protein Bcl-xL upon fragment-binding. On the other hand, we will demonstrate that this quantitative use of CSP is unable to determinate fragment orientations inside the protein PRDX5 binding site. We will compare the performances of the method for different kinds of protein and proposing answers to better understand the behaviour of CSP toward their different electronic contributions
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McManus, Jamie. "Residual broadening in high-resolution NMR of quadrupolar nuclei in solids." Thesis, University of Exeter, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367404.

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Guerriero, Andrew. "Variable pressure NMR analyses to assess compressive motion in PETNR and catalytically germane PETNR:Ligand complexes." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/variable-pressure-nmr-analyses-to-assess-compressive-motion-in-petnr-and-catalytically-germane-petnrligand-complexes(f9d8a882-b05b-47ac-86c4-3987c78e5494).html.

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The involvement of dynamical fluctuations in driving enzymatic processes is widely accepted. With respect to NQM tunnelling enzymes, the role of promoting motions in facilitating hydrogenic transfers is well studied. Few studies have however, specifically attributed, dedicated dynamical fluctuations characterised by their timescales and magnitudes, as a function of a reaction coordinate, to specific groups in a protein system. An effectively full suite of backbone resonance assignments were obtained for PETNR and on relevant ligand complexes. This provided an essential platform on which residue specific, backbone amide fluctuations were assessed. This thesis documents the application of pressure up to 1500 bar, in tandem with high resolution TROSY based NMR analysis, as a means of studying residue specific, conformer exchange perturbations. Residue specific amide compression profiles of the PETNR:FMN free enzyme system, and complexes with progesterone and tetrahydropyridine dinucleotides have been obtained. The binding of progesterone appears to induce conformational tightening of residues within the active site vicinity. The complexation of PETNR:FMN with tetrahydropyridine dinucleotides, appears to stimulate conformational shifts towards intermediate, and in some cases, slow exchange regimes in multiple residues about the active site vicinity. This is evidenced by extensive intensity attenuation of 1H-15N TROSY resonances, on the binding of tetrahydropyridine dinucleotides at 1 bar pressure, and on going from 1 bar to 1500 bar pressure. Multiple regions of sequence, spatially clustering about the active site vicinity within a 10 Å sphere of the FMN binding pocket, display appreciable sensitivity to ligand binding. Differential responses of residues to the application of high pressure between complexes was noted within segments of these regions. A region of sequence, named the β-hairpin flap displays significant differential compression profiles between the PETNR:FMN free enzyme system, and associated progesterone and tetrahydropyridine dinucleotide complexes. A role in mediating ligand engagement is proposed for R130 and R142 in the β-hairpin flap. A central hydrogen bonding network, perhaps constituting a putative proton wire in the active site of the PETNR:FMN:Progesterone complex, has been identified that could enable the shuttling of protons following catalytic protonation of oxidative substrate. The resonance response behaviour of G185 acts as a sensitive reporter on the formation of these interactions, revealed by an interrogation of the differences in chemical shift changes on progesterone binding, and in response to high pressure. The recruitment of high resolution crystallographic data sets readily supported a structural and dynamical interpretation of the observed chemical shift responses to ligand binding at 1 bar pressure, and on the application high pressure. A definitive atomistic identification of fast motion contribution to activation barrier compression was not obtained. Nevertheless, detailed, residue specific amide compression profiles, and shifts in backbone amide conformational exchange regimes in response to ground state ligand binding, and at high pressure, have been catalogued in the PETNR:FMN free enzyme system. These dynamical profiles in the free enzyme are contrasted against comparative, residue specific observations in analogue complexes of the oxidative and reductive half reactions of PETNR.
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González, Ruiz Domingo [Verfasser]. "QCSPScore : a new scoring function for driving protein-ligand docking with quantitative chemical shifts perturbations / von Domingo González Ruiz." 2009. http://d-nb.info/1002457734/34.

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Zienau, Jan [Verfasser]. "Niedrig-skalierende Møller-Plesset-Störungstheorie zweiter Ordnung unter Verwendung von Auxiliarbasen und quantenchemische Berechnung von NMR-Verschiebungen supramolekularer Systeme = Low-order scaling second-order Møller-Plesset perturbation theory using auxiliary basis sets and quantum-chemical calculation of NMR chemical shifts for supramolecular systems / vorgelegt von Jan Zienau." 2009. http://d-nb.info/997154772/34.

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Book chapters on the topic "Chemical Shift Perturbations"

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Williamson, Mike P. "Chemical Shift Perturbation." In Modern Magnetic Resonance, 1–19. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-28275-6_76-1.

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Williamson, Mike P. "Chemical Shift Perturbation." In Modern Magnetic Resonance, 995–1012. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-28388-3_76.

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Ohsawa, Kosuke. "Total Synthesis of Thielocin B1 and NMR Chemical Shift Perturbation Experiments with PAC3 Homodimer." In Springer Theses, 25–62. Tokyo: Springer Japan, 2015. http://dx.doi.org/10.1007/978-4-431-55447-9_2.

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Chekmenev, Eduard A., Joana Paulino, Riqiang Fu, and Timothy A. Cross. "Anisotropic and Isotropic Chemical Shifts Perturbations from Solid State NMR Spectroscopy for Structural and Functional Biology." In Modern Magnetic Resonance, 1–15. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-28275-6_87-1.

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Chekmenev, Eduard A., Joana Paulino, Riqiang Fu, and Timothy A. Cross. "Anisotropic and Isotropic Chemical Shifts Perturbations from Solid State NMR Spectroscopy for Structural and Functional Biology." In Modern Magnetic Resonance, 505–19. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-28388-3_87.

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Conference papers on the topic "Chemical Shift Perturbations"

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Narain, Niven R., Vivek K. Vishnudas, Viatscheslav R. Akmaev, and Rangaprasad Sarangarajan. "Abstract A34: Novel chemical systems biology approach with the Berg Interrogative Biology® platform provides a window into hallmark shift in cancer metabolism." In Proceedings: AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations--Jun 27-30, 2012; Boston, MA. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.csb12-a34.

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Saji, Genn. "Radiation-Induced Electrolytic Corrosion of LWRS: (Part 2) — Verification of In- and Out-Core Redox Potential Differences." In 2016 24th International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/icone24-60895.

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The author recently identified that there should exist a “differential radiation cell” mechanism in the reactor water, prompting “radiation-induced electrolytic (RIE)” phenomena. This mechanism was identified while trying to theoretically reconstruct the potential differences observed in two in-pile test loops; NRI-Rez in Czech Republic and INCA Loop in Sweden. Part 2 of this series focuses on the theoretical reconstruction of the observed potential differences. Assuming a state of equilibrium, the author tried to develop a formalism by extending the Nernst equation to reproduce the observed redox potential differences. The radiological potential shift term is separated from the Nernst equation where the latter deals only with stable molecular and ionic species. The radiological effect is described as a perturbation term to the Nernst equation representing a potential shift due to radiation-chemical reactions which should diminish to zero without radiation. The theory generally reproduced the experimental results after fitting the theoretical curve at a single point of the potential for both PWR and BWR-NWC water chemistry environments. This discrepancy is likely due to the “conductive-dielectric property” of the reactor water.
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