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 [NMR paper] Measurement of amide proton chemical shift anisotropy in perdeuterated proteins using CSA amplification |
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Sep 21, 2017 - 2:38 AM - by nmrlearner
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Measurement of amide proton chemical shift anisotropy in perdeuterated proteins using CSA amplification
Publication date: Available online 19 September 2017
Source:Journal of Magnetic Resonance
Author(s): Yuwei Ge, Ivan Hung, Xiaoli Liu, Maili Liu, Zhehong Gan, Conggang Li
Measuring 1H chemical shift anisotropy (CSA) is useful for probing proton environments and dynamics but remains a challenge due to strong homonuclear interaction and relatively small shift anisotropy, especially in proteins with multiple proton sites. Here the extended chemical shift anisotropy amplification (xCSA) method is applied for amide proton CSA measurement in uniformly 2H enriched proteins under fast magic angle spinning. The xCSA method is capable of distinguishing the sign of the CSA asymmetry parameter, complimenting other multiple-pulse recoupling methods. A three-dimensional xCSA experiment is demonstrated for measuring the proton CSA of amide sites in a GB1 protein sample and the possible correlation of amide proton CSA with protein secondary structure is discussed.
Graphical abstract
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0 Replies | 1 Views
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[NMR paper] A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium. |
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Sep 21, 2017 - 2:38 AM - by nmrlearner
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A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.
Related Articles A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.
J Phys Chem B. 2017 Sep 19;:
Authors: Sahu D, Iwahara J
Abstract
In the target DNA search process, sequence-specific DNA-binding proteins first nonspecifically bind to DNA and stochastically move from one site to another before reaching their targets. To rigorously assess how the translocation process influences NMR signals from proteins interacting with nonspecific DNA, we incorporated a discrete-state kinetic model for protein translocation on DNA into the McConnell equation. Using this equation, we simulated line shapes of NMR signals from proteins undergoing translocations on DNA through sliding, dissociation / reassociation, and intersegment transfer. Through this analysis, we validated an existing NMR approach for kinetic investigations of protein translocation on DNA, which utilizes NMR line shapes of two nonspecific DNA-protein complexes and their mixture. We found that, despite its use of simplistic two-state approximation neglecting the presence of many microscopic states, the previously proposed NMR approach provides accurate kinetic information on the intermolecular translocations of proteins between two DNA molecules. Interestingly, our results suggest that... [Read More]
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0 Replies | 1 Views
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Measuring Nano- to Microstructures from Relayed Dynamic Nuclear Polarization NMR #DNPNMR |
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Sep 21, 2017 - 2:38 AM - by nmrlearner
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From The DNP-NMR Blog:
Measuring Nano- to Microstructures from Relayed Dynamic Nuclear Polarization NMR #DNPNMR
p.p1 {margin: 0.0px 0.0px 0.0px 36.0px; text-indent: -36.0px; font: 12.0px Helvetica}
Pinon, A.C., et al., Measuring Nano- to Microstructures from Relayed Dynamic Nuclear Polarization NMR. The Journal of Physical Chemistry C, 2017. 121(29): p. 15993-16005.
http://dx.doi.org/10.1021/acs.jpcc.7b04438
We show how dynamic nuclear polarization (DNP) NMR can be used in combination with models for polarization dynamics to determine the domain sizes in complex materials. By selectively doping a source component with radicals and leaving the target undoped, we can measure experimental polarization buildup curves which can be compared with simulations based on heterogeneous distributions of polarization within the sample. The variation of the integrated DNP enhancement as a function of the polarization time is found to be characteristic of the geometry. We demonstrate the method experimentally on four different systems where we successfully determine domain sizes between 200 and 20 000 nm, specifically in powdered histidine hydrochloride monohydrate, pore lengths of mesoporous silica materials, and two domain sizes in two-component polymer film coatings. Additionally, we find that even in the apparently homogeneous frozen solutions used as polarization sources in most DNP experiments, polarization is relayed from protons near the radicals to the bulk of the solution by spin diffusion, which... [Read More]
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0 Replies | 1 Views
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[NMR paper] Structural insight into the XTACC3/XMAP215 interaction from CD and NMR studies on model peptides. |
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Sep 19, 2017 - 4:40 PM - by nmrlearner
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Structural insight into the XTACC3/XMAP215 interaction from CD and NMR studies on model peptides.
Related Articles Structural insight into the XTACC3/XMAP215 interaction from CD and NMR studies on model peptides.
Biopolymers. 2017 Sep 18;:
Authors: Partida-Hanon A, Treviño MA, Mompeán M, Jiménez MÁ, Bruix M
Abstract
TACC3 is a centrosomal adaptor protein that plays important roles during mitotic spindle assembly. It interacts with chTOG/XMAP215, which catalyzes the addition of tubulin dimers during microtubule growth. A 3D coiled-coil model for this interaction is available but the structural details are not well described. To characterize this interaction at atomic resolution, we have designed a simplified version of the system based on small peptides. Four different peptides have been studied by circular dichroism and nuclear magnetic resonance both singly and in all possible combinations; namely, five peptide pairs and two trios. In cosolvents, all single peptides tend to adopt helical conformations resembling those of the full-length protein. However, neither the single peptides nor pairs of peptides form coiled coils. We show that the simultaneous presence of all preformed helices is a prerequisite for binding. The simplest 3D model for the interaction, based on the NMR results, is proposed. Interestingly, the peptide's structure remains unaffected by mutations at essential positions... [Read More]
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0 Replies | 10 Views
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[NMR paper] Characterization of doubly ionic hydrogen bonds in protic ionic liquids by NMR deuteron quadrupole coupling constants - Differences to H-bonds in amides, peptides and proteins. |
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Sep 19, 2017 - 4:40 PM - by nmrlearner
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Characterization of doubly ionic hydrogen bonds in protic ionic liquids by NMR deuteron quadrupole coupling constants - Differences to H-bonds in amides, peptides and proteins.
Related Articles Characterization of doubly ionic hydrogen bonds in protic ionic liquids by NMR deuteron quadrupole coupling constants - Differences to H-bonds in amides, peptides and proteins.
Angew Chem Int Ed Engl. 2017 Sep 17;:
Authors: Ludwig R, Khudozhitkov AE, Stange P, Golub B, Paschek D, Stepanov AG, Kolokolov DI
Abstract
We present the first deuteron quadrupole coupling constants (DQCC) for selected protic ionic liquids (PILs) measured by solid-state NMR spectroscopy. The experimental data are supported by dispersion-corrected density functional theory (DFT-D3) calculations and molecular dynamics (MD) simulations. The DQCCs of the N-D bond in the triethylammonium cations are the lowest reported for deuterons in PILs indicating strong doubly ionic hydrogen bonds. The NMR coupling parameters are compared to those in amides, peptides, and proteins. The DQCCs show characteristic behaviour with increasing interaction strength of the counterion and variation of the H-bond motifs. We report the similar presence of the quadrupolar splitting pattern and the narrow liquid line... [Read More]
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0 Replies | 10 Views
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[NMR paper] Quantitative determination and validation of octreotide acetate using (1) H-NMR spectroscopy with internal standard method. |
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Sep 19, 2017 - 4:40 PM - by nmrlearner
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Quantitative determination and validation of octreotide acetate using (1) H-NMR spectroscopy with internal standard method.
Related Articles Quantitative determination and validation of octreotide acetate using (1) H-NMR spectroscopy with internal standard method.
Magn Reson Chem. 2017 Sep 15;:
Authors: Yu C, Zhang Q, Xu PY, Bai Y, Shen WB, Di B, Su MX
Abstract
Quantitative nuclear magnetic resonance (qNMR) is a well-established technique in quantitative analysis. We presented a validated (1) H quantitative nuclear magnetic resonance ((1) H-qNMR) method for assay of octreotide acetate (OCT-Ac), a kind of cyclic octopeptide. Deuterium oxide was used to remove the undesired exchangeable peaks, which was referred to as proton exchange, in order to make the quantitative signals isolated in the crowded spectrum of the peptide and ensure precise quantitative analysis. Gemcitabine hydrochloride was chosen as the suitable internal standard (IS). Experimental conditions, including relaxation delay time,the numbers of scans and pulse angle were optimized first. Then method validation was carried out in terms of selectivity, stability, linearity, precision and robustness. The assay result was compared with that by means of high performance liquid chromatography (HPLC), which is provided by Chinese Pharmacopoeia. The statistical F test, student t test and nonparametric test at 95% confidence level... [Read More]
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