Digitisation and Data Processing in Fourier Transform NMR

Lindon, John C.; Ferrige, Anthony G.

doi:10.1016/b978-0-08-026029-7.50004-7

Cited by 50 publications

(54 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3 (below), so that for NMR, A=0 in Eq. 3 [28,29]. Furthermore, the phase variation in FT-NMR is usually less than one cycle (G2π) across the spectrum [30,31], so phasing becomes relatively simple for NMR: choose a peak at one end of the spectrum, vary C until the absorption-mode spectrum is equal in height to the magnitude-mode spectrum, and then vary B using the same equation for a peak at the other end of the spectrum.…”

Section: Spectral Phase and Frequency-sweep Excitationmentioning

confidence: 99%

Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra Using MatLab

Thompson

Orden

et al. 2011

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

FT-ICR mass spectrometry has been limited to magnitude mode for almost 40 years due to the data processing methods used. However, it is well known that phase correction of the data can theoretically produce an absorption-mode spectrum with a mass-resolving power that is as much as twice as high as conventional magnitude mode, and that it also improves the quality of the peak shape. Temporally dispersed frequency sweep excitation followed by a time delay before detection results in a steep quadratic variation in the signal phase with frequency. Viewing this, it is possible to find the correct phase function by performing a quadratic least squares fit, modified by iterating through phase cycles until the correct quadratic function is found. Here, we present a robust manual method to rotate these signals mathematically and generate a "phased" absorption-mode spectrum. The method can, in principle, be automated. Baseline correction is also included to eliminate the accompanying baseline drift. The resulting experimental FT-ICR absorption-mode spectra exhibit a resolving power that is at least 50% higher than that of the magnitude mode.

show abstract

Section: Spectral Phase and Frequency-sweep Excitationmentioning

confidence: 99%

Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra Using MatLab

Thompson

Orden

et al. 2011

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…With broad lines and low signal to noise taken over a wide spectral width, the base line of an NMR spectrum is not flat (24,25). Correction routines (GEM routines IC, FB, and BF) were used to flatten the base line.…”

Section: Nmr Processingmentioning

confidence: 99%

Chemical Modification of the N-10 Ribityl Side Chain of Flavins EFFECTS ON PROPERTIES OF FLAVOPROTEIN DISULFIDE OXIDOREDUCTASES

Murthy¹,

Massey²

1995

Journal of Biological Chemistry

View full text Add to dashboard Cite

Three flavin derivatives modified at the 2-position of the flavin N-10 ribityl side chain were synthesized: arabinoflavin, 2-F-2-deoxyarabinoflavin, and 2-deoxyriboflavin. These were converted to the FAD level with FAD synthetase. Apoproteins of lipoamide dehydrogenase, glutathione reductase, and mercuric reductase, a family of flavoprotein oxidoreductases, were reconstituted with these flavins. Significant reduction of the catalytic activities was observed with the modified enzymes. During anaerobic reduction of the modified enzymes with substrate or dithiothreitol, decreased thermodynamic stability of the two-electron reduced enzyme forms (EH 2 ) and the accumulation of the fourelectron reduced forms (EH 4 ) noted. This effect was more pronounced in case of arabino-FAD-reconstituted enzymes than with the other two. It was found that NAD ؉ binding influences the interaction between the flavin and the reduced disulfide in the 2-F-arabino-FAD-lipoamide dehydrogenase, presumably by altering the relative oxidation-reduction potentials. Chemical modification of the isoalloxazine ring of flavins and incorporation of modified flavin derivatives into apoproteins has proven to be a powerful tool in understanding the relationship between protein structure and catalysis in flavoenzymes (1). The N-10 ribityl side chain of flavins has generally been considered as only a binding anchor with no positive role in catalysis. However, the x-ray crystal structures of various flavoproteins such as glutathione reductase (2, 3), acyl-CoA dehydrogenase (4, 5), lipoamide dehydrogenase (6), and old yellow enzyme (7) showed the involvement of ribityl hydroxyls in hydrogen bonds that could regulate catalytically important amino acid residues at the active sites. From the three-dimensional structure of medium chain acyl-CoA dehydrogenase, two hydrogen bridges pointing toward the thioester carbonyl were identified as activating the substrate (4, 5). One of them involves the flavin 2Ј-OH group and the other Glu-376. Recent studies of Ghisla et al. (8) with 2Ј-deoxy-FAD-reconstituted medium chain acyl-CoA dehydrogenase confirmed the crystal structure findings and for the first time demonstrated a role for the ribityl side chain in catalysis. Studies with 2Ј-F-arabino-FAD-reconstituted mercuric reductase (9, 39) showed that the two-electron reduced form in which the flavin remains oxidized and the active site disulfide reduced is destabilized by this modification and complete flavin reduction was observed. The crystal structures of glutathione reductase and lipoamide dehydrogenase (3, 6) have shown that the 2Ј-hydroxyl group is involved in an important hydrogen bond network in the oxidized forms of the proteins. The 2Ј-and 4Ј-hydroxyls and an adenine phosphate oxygen atom make two intramolecular hydrogen bonds that could play a significant role in determining the conformation of the bound prosthetic group (Fig. 1A). In the reduced form, the distance between 2Ј-OH and the active site Cys-63 decreases from 3.9 to 3.4 Å. Also Sol-601 now donates...

show abstract

“…In our discussion, we employ the commonly used complex representation , that can be obtained by letting and in [2] (2) where , and which are called the decay rates.…”

Section: Mathematical Model Of Nmr Signalsmentioning

confidence: 99%

“…The frequencies and damping factors of damped sinusoids are crucial to determining protein structures using NMR spectroscopy. The frequency resolution of the fast Fourier transform (FFT)-based algorithms [1], [2] is limited by the short acquisition time of the NMR data and measurement noise. Hence, to improve the resolution, many model-based methods [3]- [27] have been proposed for the parameter estimation of one-dimensional (1-D) and twodimensional (2-D) NMR data.…”

mentioning

confidence: 99%

A high-resolution technique for multidimensional NMR spectroscopy

Razavilar

Liu

1998

IEEE Trans. Biomed. Eng.

131

View full text Add to dashboard Cite

Abstract-In this paper, a scheme for estimating frequencies and damping factors of multidimensional nuclear magnetic resonance (NMR) data is presented. multidimensional NMR data can be modeled as the sum of several multidimensional damped sinusoids. The estimated frequencies and damping factors of multidimensional NMR data play important roles in determining protein structures. In this paper we present a high-resolution subspace method for estimating the parameters of NMR data. Unlike other methods, this algorithm makes full use of the rank-deficiency and Hankel properties of the prediction matrix composed of NMR data. Hence, it can estimate the signal parameters under low signal-to-noise ratio (SNR) by using a few data points. The effectiveness of the new algorithm is confirmed by computer simulations and it is tested by experimental data.

show abstract

Digitisation and Data Processing in Fourier Transform NMR

Cited by 50 publications

References 22 publications

Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra Using MatLab

Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra Using MatLab

Chemical Modification of the N-10 Ribityl Side Chain of Flavins EFFECTS ON PROPERTIES OF FLAVOPROTEIN DISULFIDE OXIDOREDUCTASES

A high-resolution technique for multidimensional NMR spectroscopy

Contact Info

Product

Resources

About