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Journal of Biomolecular NMR

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https://www.readbyqxmd.com/read/28534082/conformational-dynamics-and-alignment-properties-of-loop-lanthanide-binding-tags-lbts-studied-in-interleukin-1%C3%AE
#1
Dominic Barthelmes, Katja Barthelmes, Kai Schnorr, Hendrik R A Jonker, Bianca Bodmer, Karen N Allen, Barbara Imperiali, Harald Schwalbe
Encodable lanthanide binding tags (LBTs) have become an attractive tool in modern structural biology as they can be expressed as fusion proteins of targets of choice. Previously, we have demonstrated the feasibility of inserting encodable LBTs into loop positions of interleukin-1β (Barthelmes et al. in J Am Chem Soc 133:808-819, 2011). Here, we investigate the differences in fast dynamics of selected loop-LBT interleukin-1β constructs by measuring (15)N nuclear spin relaxation experiments. We show that the loop-LBT does not significantly alter the dynamic motions of the host protein in the sub-τc-timescale and that the loop-LBT adopts a rigid conformation with significantly reduced dynamics compared to the terminally attached encodable LBT leading to increased paramagnetic alignment strength...
May 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28508110/joint-non-uniform-sampling-of-all-incremented-time-delays-for-quicker-acquisition-in-protein-relaxation-studies
#2
Mateusz Urbańczyk, Michał Nowakowski, Wiktor Koźmiński, Krzysztof Kazimierczuk
NMR relaxometry plays crucial role in studies of protein dynamics. The measurement of longitudinal and transverse relaxation rates of [Formula: see text]N is the main source of information on backbone motions. However, even the most basic approach exploiting a series of [Formula: see text]N HSQC spectra can require several hours of measurement time. Standard non-uniform sampling (NUS), i.e. random under-sampling of indirect time domain, typically cannot reduce this by more than 2-4[Formula: see text] due to relatively low "compressibility" of these spectra...
May 15, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28508109/solvent-accessibility-of-discrete-residue-positions-in-the-polypeptide-hormone-glucagon-by-19-f-nmr-observation-of-4-fluorophenylalanine
#3
Yaguang Hou, Wanhui Hu, Xiaona Li, John J Skinner, Dongsheng Liu, Kurt Wüthrich
The amino acid 4-fluoro-L-phenylalanine (4F-Phe) was introduced at the positions of Phe6 and Phe22 in the 29-residue polypeptide hormone glucagon by expressing glucagon in E. coli in the presence of an excess of 4F-Phe. Glucagon regulates blood glucose homeostasis by interaction with the glucagon receptor (GCGR), a class B GPCR. By referencing to the 4F-Phe chemical shifts at varying D2O concentrations, the solvent exposure of the two Phe sites along the glucagon sequence was determined, showing that 4F-Phe6 was fully solvent exposed and 4F-Phe22 was only partially exposed...
May 15, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28500543/impact-of-spin-label-rigidity-on-extent-and-accuracy-of-distance-information-from-pre-data
#4
K A Schnorr, D B Gophane, C Helmling, E Cetiner, K Pasemann, B Fürtig, A Wacker, N S Qureshi, M Gränz, D Barthelmes, H R A Jonker, E Stirnal, S Th Sigurdsson, H Schwalbe
Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, (Ureido)U-TEMPO was incorporated into the 3' terminal end of helix P1 while, the recently developed rigid spin-label Çm was incorporated in the 5' terminal end of helix P1...
May 12, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28477231/comparison-of-the-free-and-ligand-bound-imino-hydrogen-exchange-rates-for-the-cocaine-binding-aptamer
#5
Zachary R Churcher, Miguel A D Neves, Howard N Hunter, Philip E Johnson
Using NMR magnetization transfer experiments, the hydrogen exchange rate constants (k ex ) of the DNA imino protons in the cocaine-binding aptamer have been determined for the free, cocaine-bound, and quinine-bound states. The secondary structure of the cocaine-binding aptamer is composed of three stems built around a three-way junction. In the free aptamer the slowest exchanging imino protons are located in the middle of the stems. The highest k ex values were found for a nucleotide in the GAA loop of stem 3 and for nucleotides at the end of the stems that form the three-way junction structure and in the tandem GA mismatch...
May 5, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28474302/f-1-f-2-selective-nmr-spectroscopy
#6
Erik Walinda, Daichi Morimoto, Masahiro Shirakawa, Kenji Sugase
Fourier transform NMR spectroscopy has provided unprecedented insight into the structure, interaction and dynamic motion of proteins and nucleic acids. Conventional biomolecular NMR relies on the acquisition of three-dimensional and four-dimensional (4D) data matrices to establish correlations between chemical shifts in the frequency domains F 1, F 2, F 3 and F 1, F 2, F 3, F 4 respectively. While rich in information, these datasets require a substantial amount of acquisition time, are visually highly unintuitive, require expert knowledge to process, and sample dark and bright regions of the frequency domains equally...
May 4, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28434103/structure-restraints-from-heteronuclear-pseudocontact-shifts-generated-by-lanthanide-tags-at-two-different-sites
#7
Benjamin J G Pearce, Shereen Jabar, Choy-Theng Loh, Monika Szabo, Bim Graham, Gottfried Otting
Pseudocontact shifts (PCS) encode long-range information on 3D structures of protein backbones and side-chains. The level of structural detail that can be obtained increases with the number of different sites tagged with a paramagnetic metal ion to generate PCSs. Here we show that PCSs from two different sites can suffice to determine the structure of polypeptide chains and their location and orientation relative to the magnetic susceptibility tensor χ, provided that PCSs are available for (1)H as well as heteronuclear spins...
April 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28421403/erratum-to-ccpnmr-analysisassign-a-flexible-platform-for-integrated-nmr-analysis
#8
Simon P Skinner, Rasmus H Fogh, Wayne Boucher, Timothy J Ragan, Luca G Mureddu, Geerten W Vuister
No abstract text is available yet for this article.
April 18, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28393280/nmr-line-shape-analysis-of-a-multi-state-ligand-binding-mechanism-in-chitosanase
#9
Shoko Shinya, Mariana G Ghinet, Ryszard Brzezinski, Kyoko Furuita, Chojiro Kojima, Sneha Shah, Evgenii L Kovrigin, Tamo Fukamizo
Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomerization of the bound-state into the final conformation. Mapping of the chemical shift perturbations in two sequential steps of the mechanism highlighted involvement of the substrate-binding subsites and the hinge region in the binding reaction...
April 9, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28393279/non-equilibrium-hydrogen-exchange-for-determination-of-h-bond-strength-and-water-accessibility-in-solid-proteins
#10
Kristof Grohe, Kumar Tekwani Movellan, Suresh Kumar Vasa, Karin Giller, Stefan Becker, Rasmus Linser
We demonstrate measurement of non-equilibrium backbone amide hydrogen-deuterium exchange rates (HDX) for solid proteins. The target of this study are the slowly exchanging residues in solid samples, which are associated with stable secondary-structural elements of proteins. These hydrogen exchange processes escape methods measuring equilibrium exchange rates of faster processes. The method was applied to a micro-crystalline preparation of the SH3 domain of chicken α-spectrin. Therefore, from a 100% back-exchanged micro-crystalline protein preparation, the supernatant buffer was exchanged by a partially deuterated buffer to reach a final protonation level of approximately 20% before packing the sample in a 1...
April 9, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28365903/lanthanoid-tagging-via-an-unnatural-amino-acid-for-protein-structure-characterization
#11
Wen-Xue Jiang, Xin-Hua Gu, Xu Dong, Chun Tang
Lanthanoid pseudo-contact shift (PCS) provides long-range structural information between a paramagnetic tag and protein nuclei. However, for proteins with native cysteines, site-specific attachment may only utilize functional groups orthogonal to sulfhydryl chemistry. Here we report two lanthanoid probes, DTTA-C3-yne and DTTA-C4-yne, which can be conjugated to an unnatural amino acid pAzF in the target protein via azide-alkyne cycloaddition. Demonstrated with ubiquitin and cysteine-containing enzyme EIIB, we show that large PCSs of distinct profiles can be generated for each tag/lanthanoid combination...
April 1, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28357518/longitudinal-relaxation-optimized-amide-1-h-cest-experiments-for-studying-slow-chemical-exchange-processes-in-fully-protonated-proteins
#12
Tairan Yuwen, Lewis E Kay
Chemical Exchange Saturation Transfer (CEST) experiments are increasingly used to study slow timescale exchange processes in biomolecules. Although (15)N- and (13)C-CEST have been the approaches of choice, the development of spin state selective (1)H-CEST pulse sequences that separate the effects of chemical and dipolar exchange [T. Yuwen, A. Sekhar and L. E. Kay, Angew Chem Int Ed Engl 2016 doi: 10.1002/anie.201610759 (Yuwen et al. 2017)] significantly increases the utility of (1)H-based experiments. Pulse schemes have been described previously for studies of highly deuterated proteins...
March 29, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28332026/interpolating-and-extrapolating-with-hmsist-%C3%A2-seeking-a-tmax-for-optimal-sensitivity-resolution-and-frequency-accuracy
#13
Sven G Hyberts, Scott A Robson, Gerhard Wagner
Non-Uniform Sampling has the potential to exploit the optimal resolution of high-field NMR instruments. This is not possible in 3D and 4D NMR experiments when using traditional uniform sampling due to the long overall measurement time. Nominally, uniformly sampled time domain data acquired to a maximum evolution time tmax can be extended to high resolution via a virtual maximum evolution time t*max while extrapolating with linear prediction or iterative soft thresholding (IST). At the high resolution obtainable with extrapolation of US data, however, the accuracy of peak positions is compromised as observed when comparing inter- and intra-residue peaks in a 3D HNCA experiment...
March 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28317074/probing-conformational-dynamics-in-biomolecules-via-chemical-exchange-saturation-transfer-a-primer
#14
Pramodh Vallurupalli, Ashok Sekhar, Tairan Yuwen, Lewis E Kay
Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes...
March 19, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28286915/cross-correlated-relaxation-rates-between-protein-backbone-h-x-dipolar-interactions
#15
Beat Vögeli
The relaxation interference between dipole-dipole interactions of two separate spin pairs carries structural and dynamics information. In particular, when compared to individual dynamic behavior of those spin pairs, such cross-correlated relaxation (CCR) rates report on the correlation between the spin pairs. We have recently mapped out correlated motion along the backbone of the protein GB3, using CCR rates among and between consecutive H(N)-N and H(α)-C(α) dipole-dipole interactions. Here, we provide a detailed account of the measurement of the four types of CCR rates...
March 12, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28271365/noesy-watercontrol-a-new-noesy-sequence-for-the-observation-of-under-water-protein-resonances
#16
Allan M Torres, Gang Zheng, William S Price
Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω2). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω2...
March 7, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28243768/reconstruction-of-non-uniformly-sampled-five-dimensional-nmr-spectra-by-signal-separation-algorithm
#17
Krzysztof Kosiński, Jan Stanek, Michał J Górka, Szymon Żerko, Wiktor Koźmiński
A method for five-dimensional spectral reconstruction of non-uniformly sampled NMR data sets is proposed. It is derived from the previously published signal separation algorithm, with major alterations to avoid unfeasible processing of an entire five-dimensional spectrum. The proposed method allows credible reconstruction of spectra from as little as a few hundred data points and enables sensitive resonance detection in experiments with a high dynamic range of peak intensities. The efficiency of the method is demonstrated on two high-resolution spectra for rapid sequential assignment of intrinsically disordered proteins, namely 5D HN(CA)CONH and 5D (HACA)CON(CO)CONH...
February 28, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28243767/practical-considerations-for-investigation-of-protein-conformational-dynamics-by-15-n-r-1%C3%AF-relaxation-dispersion
#18
Erik Walinda, Daichi Morimoto, Masahiro Shirakawa, Kenji Sugase
It is becoming increasingly apparent that proteins are not static entities and that their function often critically depends on accurate sampling of multiple conformational states in aqueous solution. Accordingly, the development of methods to study conformational states in proteins beyond their ground-state structure ("excited states") has crucial biophysical importance. Here we investigate experimental schemes for optimally probing chemical exchange processes in proteins on the micro- to millisecond timescale by (15)N R 1ρ relaxation dispersion...
February 28, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28289927/nmr-assignments-of-sparsely-labeled-proteins-using-a-genetic-algorithm
#19
Qi Gao, Gordon R Chalmers, Kelley W Moremen, James H Prestegard
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid ((15)N or (13)C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging...
April 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28247186/site-selective-13-c-labeling-of-proteins-using-erythrose
#20
Ulrich Weininger
NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with (13)C and/or (1)H, which is achieved in the most general way by using site-selectively (13)C-enriched glucose (1- and 2-(13)C) as the carbon source in bacterial expression systems...
March 2017: Journal of Biomolecular NMR
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