Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction

Rovnyak, David; Frueh, Dominique P.; Sastry, Mallika; Sun, Zhen Yu J.; Stern, Alan; Hoch, Jeffrey C.; Wagner, Gerhard

doi:10.1016/j.jmr.2004.05.016

Cited by 223 publications

(215 citation statements)

References 29 publications

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“…With very low α, or for many cases of radial sampling, the apparent noise would be larger due to the presence of artifacts. For general CRS, the signal and noise levels for ring j (σ j and η j , respectively) would be: [22] where σ 0 and η 0 are the signal level and the standard deviation of the noise distribution, respectively, for a single sampling point. The signal level σ of the spectrum is not dependent on the sampling pattern, due to the normalization by 1/N j :…”

Section: Sensitivity Considerationsmentioning

confidence: 99%

“…With the recent push to discover faster methods for measuring multidimensional NMR spectra, significant attention has been focused on alternatives to the conventional Cartesian sampling of the time domain, such as the "radial" approaches, which measure points along radial spokes [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17], or the methods that measure a randomly-selected subset of the points from a Cartesian grid, often weighted according to the signal envelope [18][19][20][21][22]. These efforts have been motivated by the discovery that it is possible, in many cases, to use one of the new patterns coupled to a suitable processing method to obtain very high resolution spectral information, with very limited sampling of the time domain.…”

Section: Introductionmentioning

confidence: 99%

“…These efforts have been motivated by the discovery that it is possible, in many cases, to use one of the new patterns coupled to a suitable processing method to obtain very high resolution spectral information, with very limited sampling of the time domain. Until very recently, most groups exploring these techniques have employed alternative methods for processing the data to produce spectral information, rather than the conventional multidimensional Fourier transform (FT), such as reconstruction from projections [8][9][10]13,16,17,23], analysis of projected peak positions [1][2][3][4][5][6][7]14,15,24,25], maximum entropy reconstruction [18][19][20]22,26] or multidimensional decomposition [21,27].…”

Section: Introductionmentioning

confidence: 99%

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Sampling of the NMR time domain along concentric rings

Coggins

Zhou

2007

Journal of Magnetic Resonance

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We present a novel approach to sampling the NMR time domain, whereby the sampling points are aligned on concentric rings, which we term concentric ring sampling (CRS). Radial sampling constitutes a special case of CRS where each ring has the same number of points and the same relative orientation. We derive theoretically that the most efficient CRS approach is to place progressively more points on rings of larger radius, with the number of points growing linearly with the radius, a method that we call linearly increasing CRS (LCRS). For cases of significant undersampling to reduce measurement time, a randomized LCRS (RLCRS) is also described. A theoretical treatment of these approaches is provided, including an assessment of artifacts and sensitivity. The analytical treatment of sensitivity also addresses the sensitivity of radially sampled data processed by Fourier transform. Optimized CRS approaches are found to produce artifact-free spectra of the same resolution as Cartesian sampling, for the same measurement time. Additionally, optimized approaches consistently yield fewer and smaller artifacts than radial sampling, and have a sensitivity equal to Cartesian and better than radial sampling. We demonstrate the method using numerical simulations, as well as a 3-D HNCO experiment on protein G B1 domain.

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Section: Sensitivity Considerationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Sampling of the NMR time domain along concentric rings

Coggins

Zhou

2007

Journal of Magnetic Resonance

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“…Specifically, modifications to the pulse sequence for non-linear acquisition were made according to Vladislav Orekhov (Swedish NMR Centre, see Biopack manual). For the non-TOCSY experiments, 415 complex fids were acquired using a sampling scheme generated using the COAST software (Rovnyak et al 2004), corresponding to a maximum of 60 and 32 points in the 13 C and 15 N dimensions respectively, and a reduction in acquisition time of ~ 4.5 fold. For the C(CO)NH-TOCSY experiment 1000 complex fids were collected, using a sampling schedule generated from the non-uniform sampling scheduler from Mark Maciejewski (http://sbtools.uchc.edu/nmr/sample%5Fscheduler/) corresponding to a maximum of 100 points in 13 C and 32 points in 15 N, leading to a reduction in acquisition time of ~ 2-fold.…”

mentioning

confidence: 99%

NMR assignment of the arenaviral protein Z from Lassa fever virus

2008

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The arenavirus protein Z from Lassa fever virus was recently found to inhibit mRNA translation through direct interaction with eIF4E. Here, we report the NMR assignment of this RING-containing protein that was determined by triple resonance NMR techniques. Keywords LFV-Z; RING domain; Heteronuclear NMR; translational repressor Biological contextMany arenaviruses cause fatal human hemorrhagic fevers. Infection by Lassa fever virus (LFV) or lymphocytic choriomeningitis virus (LCMV), two members of this arenavirus family, was studied in NIH3T3 cells by indirect immunofluorescence (Borden et al. 1998). The 11kDa arenavirus protein Z was found to directly bind the promyelocytic leukemia (PML) protein, an important regulator of mammalian cell growth. Upon infection, Z causes the relocation of PML nuclear bodies to the cytoplasm. This is likely a means to evade host cell apoptosis, given that PML promotes apoptosis. Also, the purified Z protein inhibits mRNA translation in reticulocyte lysates through direct interaction with the translation initiation factor 4E (eIF4E) (Kentsis et al. 2001). In eukaryotes, eIF4E recognizes the 5'-terminal cap structure of the mRNA, and recruits the large scaffold factor eIF4G to the mRNA. This mRNA-protein complex then binds the 40S preinitiation complex. In contrast to eIF4G and the 4E binding proteins (4E-BPs) that increase eIF4E affinity for the cap, Z was shown to decrease this affinity. Interestingly, all of these regulatory proteins bind the dorsal surface of eIF4E. Also, eIF4G and the 4E-BPs interact with eIF4E through a conserved α-helical recognition motif (YXXXXLϕ, where X is variable and ϕ is a hydrophobic residue), while Z does not contain this motif. Instead, the Z protein contains a RING domain. The RING is a ~60-residue zinc-binding motif that usually uses conserved cysteines and a histidine to bind two zinc atoms. As a first step in providing the structural basis of translation repression by Z, we have undertaken NMR studies and report here the NMR assignments of LFV-Z. Understanding the structure of Z and its interactions with host cell proteins such as PML and eIF4E, may lead to novel therapeutic strategies for Lassa fever infection.Further, Z is used as a model RING protein to study the self-assembly properties of these small domains. For instance, Z assembles into structures visible by electron microscopy (Kentsis et al. 2002a). Such super-molecular assembly of RING domains enhances their biochemical activities e.g. BRCA1/BARD1 and Mdm2 become more efficient E3 ligases when assembled while the Z bodies better inhibit the cap binding activity of eIF4E than Z monomers (Kentsis Correspondence to: Laurent Volpon, laurent.volpon@umontreal.ca. et al. 2002b; Poyunoskvy et al. 2007). Thus, NMR studies could yield molecular insights into these assembly processes. NIH Public Access Methods and experimentsThe full-length cDNA coding for LFV-Z was cloned into pGEX6p-1 (gift from Dr de la Torre and Althea A. Capul, Scripps Research Institute, La Jolla, California) and w...

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“…Backbone resonance assignments were obtained at 45°C using the following three-dimensional experiments, employing conventional or nonuniform sampling in the 15 N and 13 C dimensions: HN(CA)CO, HNCO, HN(CO)CA, HNCA, CBCA-(CO)NH, and HNCACB (15). Nonuniform sampling datasets were processed using the multidimensional decomposition algorithm (16).…”

Section: Methodsmentioning

confidence: 99%

Intracellular Trafficking of the KV1.3 Potassium Channel Is Regulated by the Prodomain of a Matrix Metalloprotease

Nguyen¹,

Galea

Schmunk³

et al. 2013

Journal of Biological Chemistry

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Background: Noncanonical functions of matrix metalloproteases are poorly characterized. Results: The prodomain of MMP23 co-localizes with and traps K V 1.3 channels intracellularly, thereby suppressing K V 1.3 currents. Conclusion: A novel metalloprotease-independent channel-modulating function of the MMP23 prodomain has been identified. Significance: The topological similarity of the prodomain of MMP23 and KCNE proteins suggests a shared mechanism of channel modulation.

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Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction

Cited by 223 publications

References 29 publications

Sampling of the NMR time domain along concentric rings

Sampling of the NMR time domain along concentric rings

NMR assignment of the arenaviral protein Z from Lassa fever virus

Intracellular Trafficking of the KV1.3 Potassium Channel Is Regulated by the Prodomain of a Matrix Metalloprotease

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