The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Robert G Griffin - One of the best experts on this subject based on the ideXlab platform.
-
Chemical Shift anisotropy selective inversion
Journal of Magnetic Resonance, 2009Co-Authors: Marc A Caporini, Anthony Bielecki, Christopher J. Turner, Robert G GriffinAbstract:Abstract Magic angle spinning (MAS) is used in solid-state NMR to remove the broadening effects of the Chemical Shift anisotropy (CSA). In this work we investigate a technique that can reintroduce the CSA in order to selectively invert transverse magnetization. The technique involves an amplitude sweep of the radio frequency field through a multiple of the spinning frequency. The selectivity of this inversion mechanism is determined by the size of the CSA. We develop a theoretical framework to describe this process and demonstrate the CSA selective inversion with numerical simulations and experimental data. We combine this approach with cross-polarization (CP) for potential applications in multi-dimensional MAS NMR.
-
15n Chemical Shift anisotropy of the schiff base in bacteriorhodopsin intermediates
Biophysical Journal, 2009Co-Authors: Melody L Makjurkauskas, Robert G Griffin, Alexander B Barnes, Yoh Matsuki, Marina Belenky, Judith HerzfeldAbstract:Bacteriorhodopsin is a prototypical ion pump with a retinylidine chromophore. Ion translocation involves photo-isomerization and distortion of the chromophore, coupled with deprotonation and reprotonation of the Schiff base (SB) on opposite sides of the transport channel. Thus the SB changes its connectivity between the early and late M states, while the SB is deprotonated. Previous solid-state NMR experiments have shown that in the early M state, the SB is more strongly hydrogen-bonded than in the late M state, as indicated by the isotropic 15N Chemical Shifts. However, the three principle values of the Chemical Shift tensor are more sensitive to the environment than the isotropic average, and should yield further insight into differences between the two M states. At sufficiently low spinning frequencies, redistribution of the signal intensity from the center band to the sidebands allows calculation of the Chemical Shift anisotropy.View Large Image | View Hi-Res Image | Download PowerPoint SlideThe intensity of the weakest detected sideband corresponds to one site in a molecular weight of ∼500 kDa. With the signal enhancement provided by dynamic nuclear polarization, we have recorded high signal-to-noise spectra of M (see Figure) and reliably obtained the principal values of the Shift tensor.
-
determination of the peptide torsion angle φ by15n Chemical Shift and13cα 1hαdipolar tensor correlation in solid state mas nmr
Journal of Magnetic Resonance, 1998Co-Authors: Mei Hong, John D Gross, Robert G GriffinAbstract:Abstract We demonstrate a dipolar-Chemical Shift correlation technique for sign-sensitive determination of the torsion angle φ in solid peptides and proteins under magic-angle spinning. The indirect dimension of the experiment is obtained by separate but synchronous evolution of the magnetization under the 15 N Chemical Shift and the C-H dipolar coupling. The resulting sum and difference spectrum of the two frequencies, with more than ten independent sidebands, depends strongly on the relative orientation of the 15 N Chemical Shift tensor and the C α -H α bond. This relative orientation reflects the C(O) i−1 -N-C α -C(O) i torsion angle. The technique can distinguish φ angles over the full range of 360° when the amide 15 N Chemical Shift tensor does not possess reflection symmetry with respect to the peptide plane. Thus it complements our previous HNCH experiment, in which two mirror-symmetric conformers of the H N -N bond relative to the C α -H α bond around the N-C α axis cannot be distinguished.
Peter Bornert - One of the best experts on this subject based on the ideXlab platform.
-
Chemical Shift encoding based water fat separation methods
Journal of Magnetic Resonance Imaging, 2014Co-Authors: Holger Eggers, Peter BornertAbstract:The suppression of signal from fat constitutes a basic requirement in many applications of magnetic resonance imaging. To date, this is predominantly achieved during data acquisition, using fat saturation, inversion recovery, or water excitation methods. Postponing the separation of signal from water and fat until image reconstruction holds the promise of resolving some of the problems associated with these methods, such as failure in the presence of field inhomogeneities or contrast agents. In this article, methods are reviewed that rely on the difference in Chemical Shift between the hydrogen atoms in water and fat to perform such a retrospective separation. The basic principle underlying these so-called Dixon methods is introduced, and some fundamental implementations of the required Chemical Shift encoding in the acquisition and the subsequent water–fat separation in the reconstruction are described. Practical issues, such as the selection of key parameters and the appearance of typical artifacts, are illustrated, and a broad range of applications is demonstrated, including abdominal, cardiovascular, and musculoskeletal imaging. Finally, advantages and disadvantages of these Dixon methods are summarized, and emerging opportunities arising from the availability of information on the amount and distribution of fat are discussed. J. Magn. Reson. Imaging 2014;40:251–268. © 2014 Wiley Periodicals, Inc.
-
compressed sensing for Chemical Shift based water fat separation
Magnetic Resonance in Medicine, 2010Co-Authors: Mariya Doneva, Peter Bornert, Holger Eggers, Alfred Mertins, John M Pauly, Michael LustigAbstract:Multi echo Chemical Shift-based water-fat separation methods allow for uniform fat suppression in the presence of main field inhomogeneities. However, these methods require additional scan time for Chemical Shift encoding. This work presents a method for water-fat separation from undersampled data (CS-WF), which combines compressed sensing and Chemical Shift-based water-fat separation. Undersampling was applied in the k-space and in the Chemical Shift encoding dimension to reduce the total scanning time. The method can reconstruct high quality water and fat images in 2D and 3D applications from undersampled data. As an extension, multipeak fat spectral models were incorporated into the CS-WF reconstruction to improve the water-fat separation quality. In 3D MRI, reduction factors of above three can be achieved, thus fully compensating the additional time needed in three-echo water-fat imaging. The method is demonstrated on knee and abdominal in vivo data.
David S Wishart - One of the best experts on this subject based on the ideXlab platform.
-
ShiftX2: significantly improved protein Chemical Shift prediction
Journal of Biomolecular NMR, 2011Co-Authors: Beomsoo Han, Yifeng Liu, Simon W. Ginzinger, David S WishartAbstract:A new computer program, called ShiftX2, is described which is capable of rapidly and accurately calculating diamagnetic ^1H, ^13C and ^15N Chemical Shifts from protein coordinate data. Compared to its predecessor (ShiftX) and to other existing protein Chemical Shift prediction programs, ShiftX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain Chemical Shifts (up to 6×) than many other Shift predictors. In particular, ShiftX2 is able to attain correlation coefficients between experimentally observed and predicted backbone Chemical Shifts of 0.9800 (^15N), 0.9959 (^13Cα), 0.9992 (^13Cβ), 0.9676 (^13C′), 0.9714 (^1HN), 0.9744 (^1Hα) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. The correlation between ShiftX2’s predicted and observed side chain Chemical Shifts is 0.9787 (^13C) and 0.9482 (^1H) with RMS errors of 0.9754 and 0.1723 ppm, respectively. ShiftX2 is able to achieve such a high level of accuracy by using a large, high quality database of training proteins (>190), by utilizing advanced machine learning techniques, by incorporating many more features (χ_2 and χ_3 angles, solvent accessibility, H-bond geometry, pH, temperature), and by combining sequence-based with structure-based Chemical Shift prediction techniques. With this substantial improvement in accuracy we believe that ShiftX2 will open the door to many long-anticipated applications of Chemical Shift prediction to protein structure determination, refinement and validation. ShiftX2 is available both as a standalone program and as a web server ( http://www.Shiftx2.ca ).
-
a simple method to adjust inconsistently referenced 13c and 15n Chemical Shift assignments of proteins
Journal of Biomolecular NMR, 2005Co-Authors: Yunjun Wang, David S WishartAbstract:Inconsistent 13C and 15N Chemical Shift referencing is a continuing problem associated with protein Chemical Shift assignments deposited in BioMagResBank (BMRB). Here we describe a simple and robust approach that can quantitatively determine the 13C and 15N referencing offsets solely from Chemical Shift assignment data and independently of 3D coordinate data. This novel structure-independent approach permitted the assessment and determination of 13C and 15N reference offsets for all protein entries deposited in the BMRB. Tests on 452 proteins with known 3D structures show that this structure-independent approach yields 13C and 15N referencing offsets that exhibit excellent agreement with those calculated on the basis of 3D structures. Furthermore, this protocol appears to improve the accuracy of Chemical Shift-derived secondary structural identification, and has been formally incorporated into a computer program called PSSI (http//www.pronmr.com).
-
protein Chemical Shift analysis a practical guide
Biochemistry and Cell Biology, 1998Co-Authors: David S Wishart, Alex M NipAbstract:Proper protein Chemical Shift analysis requires careful experimental measurements and the implementation of standardized referencing procedures. In this article we outline the steps necessary to en...
-
1h 13c and 15n Chemical Shift referencing in biomolecular nmr
Journal of Biomolecular NMR, 1995Co-Authors: David S Wishart, Colin G Bigam, Jian Yao, Frits Abildgaard, H J Dyson, Eric Oldfield, John L Markley, Brian D SykesAbstract:A considerable degree of variability exists in the way that 1H, 13C and 15N Chemical Shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future Chemical Shift referencing and for conversion from many common 1H, 13C and 15N Chemical Shift standards, now used in biomolecular NMR, to those proposed here.
-
the 13c Chemical Shift index a simple method for the identification of protein secondary structure using 13c Chemical Shift data
Journal of Biomolecular NMR, 1994Co-Authors: David S Wishart, Brian D SykesAbstract:A simple technique for identifying protein secondary structures through the analysis of backbone 13C Chemical Shifts is described. It is based on the Chemical-Shift Index [Wishart et al. (1992) Biochemistry, 31, 1647–1651] which was originally developed for the analysis of 1Hα Chemical Shifts. By extending the Chemical-Shift Index to include 13Cα, 13Cβ and carbonyl 13C Chemical Shifts, it is now possible to use four independent Chemical-Shift measurements to identify and locate protein secondary structures. It is shown that by combining both 1H and 13C Chemical-Shift indices to produce a ‘consensus’ estimate of secondary structure, it is possible to achieve a predictive accuracy in excess of 92%. This suggests that the secondary structure of peptides and proteins can be accurately obtained from 1H and 13C Chemical Shifts, without recourse to NOE measurements.
Mei Hong - One of the best experts on this subject based on the ideXlab platform.
-
cα Chemical Shift tensors in helical peptides by dipolar modulated Chemical Shift recoupling nmr
Journal of Biomolecular NMR, 2002Co-Authors: Xiaolan Yao, Satoru Yamaguchi, Mei HongAbstract:The Cα Chemical Shift tensors of proteins contain information on the backbone conformation. We have determined the magnitude and orientation of the Cα Chemical Shift tensors of two peptides with α-helical torsion angles: the Ala residue in G*AL (φ=−65.7°, ψ=−40°), and the Val residue in GG*V (φ=−81.5°, ψ=−50.7°). The magnitude of the tensors was determined from quasi-static powder patterns recoupled under magic-angle spinning, while the orientation of the tensors was extracted from Cα–Hα and Cα–N dipolar modulated powder patterns. The helical Ala Cα Chemical Shift tensor has a span of 36 ppm and an asymmetry parameter of 0.89. Its σ11 axis is 116° ± 5° from the Cα–Hα bond while the σ22 axis is 40° ± 5° from the Cα–N bond. The Val tensor has an anisotropic span of 25 ppm and an asymmetry parameter of 0.33, both much smaller than the values for β-sheet Val found recently (Yao and Hong, 2002). The Val σ33 axis is tilted by 115° ± 5° from the Cα–Hα bond and 98° ± 5° from the Cα–N bond. These represent the first completely experimentally determined Cα Chemical Shift tensors of helical peptides. Using an icosahedral representation, we compared the experimental Chemical Shift tensors with quantum Chemical calculations and found overall good agreement. These solid-state Chemical Shift tensors confirm the observation from cross-correlated relaxation experiments that the projection of the Cα Chemical Shift tensor onto the Cα–Hα bond is much smaller in α-helices than in β-sheets.
-
determination of calpha Chemical Shift tensor orientation in peptides by dipolar modulated Chemical Shift recoupling nmr spectroscopy
Journal of the American Chemical Society, 2002Co-Authors: Xiaolan Yao, Mei HongAbstract:We present a new method for determining the orientation of Chemical Shift tensors in polycrystalline solids with site resolution and demonstrate its application to the determination of the Calpha Chemical Shift tensor orientation in a model peptide with beta-sheet torsion angles. The tensor orientation is obtained under magic angle spinning by modulating a recoupled Chemical Shift anisotropy (CSA) pattern with various dipolar couplings. These dipolar-modulated Chemical Shift patterns constitute the indirect dimension of a 2D spectrum and are resolved according to the isotropic Chemical Shifts of different sites in the direct dimension. These dipolar-modulated CSA spectra are equivalent to the projection of a 2D static separated-local-field spectrum onto its Chemical Shift dimension, except that its dipolar dimension is multiplied with a modulation function. Both (13)C-(1)H and (13)C-(15)N dipolar couplings can modulate the CSA spectra of the Calpha site in an amino acid and yield the relative orientations of the Chemical Shift principal axes to the C-H and C-N bonds. We demonstrate the C-H and C-N modulated CSA experiments on methylmalonic acid and N-tBoc-glycine, respectively. The MAS results agree well with the results of the 2D separated-local-field spectra, thus confirming the validity of this MAS dipolar-modulation approach. Using this technique, we measured the Val Calpha tensor orientation in N-acetylvaline, which has beta-sheet torsion angles. The sigma(11) axis is oriented at 158 degrees (or 22 degrees) from the C-H bond, while the sigma(22) axis is tilted by 144 degrees (or 36 degrees) from the C-N bond. Both the orientations and the magnitude of this Chemical Shift tensor are in excellent agreement with quantum Chemical calculations.
-
determination of the peptide torsion angle φ by15n Chemical Shift and13cα 1hαdipolar tensor correlation in solid state mas nmr
Journal of Magnetic Resonance, 1998Co-Authors: Mei Hong, John D Gross, Robert G GriffinAbstract:Abstract We demonstrate a dipolar-Chemical Shift correlation technique for sign-sensitive determination of the torsion angle φ in solid peptides and proteins under magic-angle spinning. The indirect dimension of the experiment is obtained by separate but synchronous evolution of the magnetization under the 15 N Chemical Shift and the C-H dipolar coupling. The resulting sum and difference spectrum of the two frequencies, with more than ten independent sidebands, depends strongly on the relative orientation of the 15 N Chemical Shift tensor and the C α -H α bond. This relative orientation reflects the C(O) i−1 -N-C α -C(O) i torsion angle. The technique can distinguish φ angles over the full range of 360° when the amide 15 N Chemical Shift tensor does not possess reflection symmetry with respect to the peptide plane. Thus it complements our previous HNCH experiment, in which two mirror-symmetric conformers of the H N -N bond relative to the C α -H α bond around the N-C α axis cannot be distinguished.
Ayyalusamy Ramamoorthy - One of the best experts on this subject based on the ideXlab platform.
-
Chemical Shift tensor the heart of nmr insights into biological aspects of proteins
Progress in Nuclear Magnetic Resonance Spectroscopy, 2010Co-Authors: Hazime Saito, Isao Ando, Ayyalusamy RamamoorthyAbstract:1.1 A brief account of the Chemical Shift The Chemical Shift of a nucleus, i, in a molecule arises from the nuclear shielding effect of an applied magnetic field, caused by an induced magnetic field resulting from circulation of surrounding electrons [1–6]. The magnitude of such an induced magnetic field is proportional to the strength of the applied external magnetic field B0, so that the effective field Beff at the nucleus is given as Beff=B0(1−σi) (1) where σi is the second-rank nuclear shielding tensor and 1 is the unit matrix. In normal NMR experiments B0 is a uniform field along the z-axis; therefore, σi= σizz. The resonance NMR frequency, νi, of a given nucleus in a molecule is thus related to its gyromagnetic ratio, γi, as given by
-
solid state 13c nmr Chemical Shift anisotropy tensors of polypeptides
Journal of the American Chemical Society, 2001Co-Authors: Ayyalusamy RamamoorthyAbstract:Carbon-13 Chemical Shift anisotropy (CSA) tensors for various carbon sites of polypeptides, and for carbon sites in α-helical and β-sheet conformations of poly-l-alanine, and polyglycine, are presented. The carbonyl 13C CSA tensors were determined from one-dimensional CPMAS spectra obtained at a slow spinning speed, whereas the CSA tensors of Cα and other carbons in side chains of peptides were determined using 2D PASS experiments on powder samples. The results suggest that the spans of 13Carbonyl CSA tensors of alanine and glycine residues in various peptides are similar, even though the magnitude of individual components of the CSA tensor and the isotropic Chemical Shift are different. In addition, the δ22 element is the only component of the 13Carbonyl CSA tensor that significantly depends on the CO···HN hydrogen-bond length. Solid-state NMR experimental results also suggest that 13Carbonyl and 13Cα CSA tensors are similar for α-helical and β-sheet conformations of poly-l-alanine, which is in agreement...
-
characterization of 15n Chemical Shift and 1h 15n dipolar coupling interactions in a peptide bond of uniaxially oriented and polycrystalline samples by one dimensional dipolar Chemical Shift solid state nmr spectroscopy
Journal of the American Chemical Society, 1998Co-Authors: D K Lee, Richard J Wittebort, Ayyalusamy RamamoorthyAbstract:The magnitudes and orientations of the principal elements of the 15N Chemical Shift and 1H−15N dipolar coupling interaction tensors pertaining to the glycine residue in 15N-acetyl glycine (NAG) and [15N-Gly]collagen were determined by the analysis of one-dimensional dipolar Chemical Shift powder patterns. A one-dimensional 1H−15N dipolar 15N Chemical Shift spectrum was obtained on a [15N-Gly]collagen fiber sample with the fiber axis oriented parallel to the external magnetic field. The dipolar Chemical Shift spectrum enabled the orientation of the peptide plane to be determined relative to the direction of the applied magnetic field or the triple-helix axis of the collagen fiber. The magnitudes of the principal elements of the tensors and their orientations in the molecular frame for these two sites are quite different. The magnitudes of the Chemical Shift tensors are 42.3, 67, and 223.4 ppm for [15N-Gly]collagen and 37, 82.8, and 220.4 ppm for NAG. The angle (βN) between the least shielded 15N Chemical s...
-
magnitudes and orientations of the principal elements of the 1h Chemical Shift 1h 15n dipolar coupling and 15n Chemical Shift interaction tensors in 15ne1 tryptophan and 15nπ histidine side chains determined by three dimensional solid state nmr spect
Journal of the American Chemical Society, 1997Co-Authors: Ayyalusamy Ramamoorthy, C H Wu, Stanley J OpellaAbstract:The magnitudes and orientations of the principal elements of the 1H Chemical Shift, 1H−15N dipolar coupling, and 15N Chemical Shift interaction tensors in 15Ne1-tryptophan and 15Nπ-histidine nitrogen sites were determined by the analysis of three-dimensional powder patterns obtained from 15N-labeled powder samples of the amino acids. Although the magnitudes of the principal elements of the 1H and 15N Chemical Shift tensors for these two sites are quite different, their molecular orientations in the molecular frame are very similar. The least shielded 15N Chemical Shift tensor element, σ33N, and the most shielded 1H Chemical Shift tensor element, σ11H, are approximately colinear with the N−H bond in both cases. The principal elements, σ22H and σ22N, are in the plane of the indole ring for tryptophan and in the plane of the imidazole ring for histidine but oppose each other. σ11N and σ33H are perpendicular to the planes of these heterocyclic rings. The Chemical Shift tensors of the 1H and 15N nuclei in thes...