Retrieval of frequencies, amplitudes, damping factors, and phases from time-domain signals using a linear least-squares procedure

Barkhuijsen, H.; Beer, R. de; Bovée, W.M.M.J.; Ormondt, D. van

doi:10.1016/0022-2364(85)90187-8

Cited by 301 publications

(147 citation statements)

References 7 publications

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“…In the t 1 dimension of 1 H-15 N HSQC spectra, a 45 phase-shifted sine bell was applied prior to Fourier transformation, and a Lorentzian-toGaussian ®lter with NMRPipe parameters G1 10 Hz (inverse exponential width), G2 20 Hz (Gaussian width) and G3 0 (corresponding to a maximum at the ®rst point in the FID) was applied in the t 2 dimension. For the HNCACB, CBCA(CO)NH, HBHA(CBCACO)NH and (HB)CBCACO(CA)HA data sets, linear prediction (Barkhuijsen et al, 1985) was used to double the number of planes in the t 2 dimension. Where necessary, the residual water signal was reduced using a time-domain deconvolution approach (Marion et al, 1989).…”

Section: Nmr Data Processing and Analysismentioning

confidence: 99%

Equilibrium folding intermediates of a greek key β-barrel protein

Bagby

Inouye

et al. 1998

Journal of Molecular Biology

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Protein S is a calcium-binding protein comprising two Greek key b-barrel domains. We have used NMR and optical spectroscopies to show that, in the absence of calcium, the N-terminal domain of protein S forms two equilibrium folding intermediates that are in slow exchange. The intermediates arise from differential calcium-dependent folding of subdomains which are not contiguous along the polypeptide chain. The structures of these intermediates are incompatible with several previously proposed folding mechanisms for Greek key b-barrel domains. We propose a different mechanism that involves multiple nucleation sites for folding and sequential acquisition of native long-range interactions.

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Section: Nmr Data Processing and Analysismentioning

confidence: 99%

Equilibrium folding intermediates of a greek key β-barrel protein

Bagby

Inouye

et al. 1998

Journal of Molecular Biology

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“…Residual water in the I3C-resolved NOESY spectrum was further suppressed by means of a Karhunen-Loewe transformation as implemented in NMR3D (Mitschang et al, 1991). Prior to zero-filling and window multiplication, indirect dimensions were expanded by linear prediction (Barkhuisen et al, 1985). Usually, no more than half the number of acquired real points were added in this way.…”

Section: Nmr Experimentsmentioning

confidence: 99%

NMR assignments and relaxation studies of Thiobacillus versutus ferrocytochrome c‐550 indicate the presence of a highly mobile 13‐residues long C‐terminal tail

Ubbink¹,

Pfuhl

Oost

et al. 1996

Protein Science

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Cytochrome c-550 of Thiobacillus versutus functions as an electron transfer protein in a chain of redox proteins that enables I: versutus to grow on methylamine. It is a single-heme protein of 134 residues, related to mitochondrial cytochrome c. Cytochrome c-550, as well as several other bacterial c2-type cytochromes, contain a C-terminal extension of 13-16 amino acids of unknown function, compared to mitochondrial cytochrome c.NMR experiments were performed to obtain structural and dynamic information on the protein in solution. For this purpose, I: versutus cytochrome c-550 was labeled with '*N and I3C using I3C-methanol grown Paracoccus denitrificans as a host for heterologous expression. NMR assignments were obtained for the 'H, "N, and I3C nuclei in the backbone and the P-positions of the protein and the secondary structure was determined. "N-relaxation studies were performed to characterize the dynamic properties of the protein.The results indicate that the main part of I: versutus ferrocytochrome c-550 exists in solution as a rigid, well-ordered molecule with a secondary structure that is very similar to that of P. denitrificans cytochrome c-550, as observed in crystals. The C-terminal extension, however, is unstructured and highly mobile. The possible origin and function of the extension are discussed.

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“…For 1-D signals, we can cite the Kumaresan and Tufts method [13], state-space methods [14] and matrix pencil [15]. These methods and their variants have been applied successfully to NMR data, often using other acronyms such as LPSVD (Linear Prediction-Singular Value Decomposition), HSVD (Hankel-Singular Value Decomposition) and so on [16][17][18][19][20] (see also the review paper by Poullet et al [21] and the references therein for more details [26], MultiDimensional Embedding (MDE) [27] and 2-D ESPRIT [28].…”

Section: O S S I E Rmentioning

confidence: 99%

NMR Data Analysis: A Time-Domain Parametric Approach Using Adaptive Subband Decomposition

Djermoune

Tomczak

Brie

2013

Oil Gas Sci. Technol. – Rev. IFP Energies nouvelles

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and available online here Cet article fait partie du dossier thématique ci-dessous publié dans la revue OGST, Vol. 69, n°2, et téléchargeable ici Résumé -Analyse de données RMN : une approche paramétrique basée sur une décomposi-tion en sous-bandes adaptative -Dans ce papier, nous proposons une méthode rapide d'analyse de signaux de spectroscopie de Résonance Magnétique Nucléaire (RMN), dans le cas Lorentzien, fondée sur une décomposition adaptative en sous-bandes. Cette dernière est obtenue par une succession d'étages de filtrage/décimation aboutissant à un arbre de décomposition. À chaque noeud de l'arbre, les paramètres du signal correspondant à la sous-bande sont estimés par une méthode haute-résolution. Puis l'erreur d'estimation est utilisée dans un test d'arrêt qui permet de décider si la décomposition doit être poursuivie ou non dans cette branche. Ainsi, cette approche permet la sélection automatique du niveau de décimation ce qui conduit la décomposition à s'adapter au contenu fréquentiel du signal. De plus, la méthode entraîne une réduction du temps de calcul et facilite le choix des paramètres libres comparativement à une analyse globale du signal. Son efficacité est illustrée au travers d'exemples de signaux RMN 13 C 1-D et 2-D.

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Retrieval of frequencies, amplitudes, damping factors, and phases from time-domain signals using a linear least-squares procedure

Cited by 301 publications

References 7 publications

Equilibrium folding intermediates of a greek key β-barrel protein

Equilibrium folding intermediates of a greek key β-barrel protein

NMR assignments and relaxation studies of Thiobacillus versutus ferrocytochrome c‐550 indicate the presence of a highly mobile 13‐residues long C‐terminal tail

NMR Data Analysis: A Time-Domain Parametric Approach Using Adaptive Subband Decomposition

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