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James H. Prestegard - One of the best experts on this subject based on the ideXlab platform.
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A device for the measurement of residual chemical shift anisotropy and residual Dipolar Coupling in soluble and membrane-associated proteins
Journal of Biomolecular NMR, 2010Co-Authors: James H. PrestegardAbstract:Residual Dipolar Coupling (RDC) and residual chemical shift anisotropy (RCSA) report on orientational properties of a Dipolar bond vector and a chemical shift anisotropy principal axis system, respectively. They can be highly complementary in the analysis of backbone structure and dynamics in proteins as RCSAs generally include a report on vectors out of a peptide plane while RDCs usually report on in-plane vectors. Both RDC and RCSA average to zero in isotropic solutions and require partial orientation in a magnetic field to become observable. While the alignment and measurement of RDC has become routine, that of RCSA is less common. This is partly due to difficulties in providing a suitable isotopic reference spectrum for the measurement of the small chemical shift offsets coming from RCSA. Here we introduce a device (modified NMR tube) specifically designed for accurate measurement of reference and aligned spectra for RCSA measurements, but with a capacity for RDC measurements as well. Applications to both soluble and membrane anchored proteins are illustrated.
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redcat a residual Dipolar Coupling analysis tool
Journal of Magnetic Resonance, 2004Co-Authors: Homayoun Valafar, James H. PrestegardAbstract:Abstract Recent advancements in the utilization of residual Dipolar Couplings (RDCs) as a means of structure validation and elucidation have demonstrated the need for, not only a more user friendly, but also a more powerful RDC analysis tool. In this paper, we introduce a software package named REsidual Dipolar Coupling Analysis Tool (REDCAT) designed to address the above issues. REDCAT is a user-friendly program with its graphical-user-interface developed in Tcl/Tk, which is highly portable. Furthermore, the computational engine behind this GUI is written in C/C++ and its computational performance is therefore excellent. The modular implementation of REDCAT’s algorithms, with separation of the computational engine from the graphical engine allows for flexible and easy command line interaction. This feature can be utilized for the design of automated data analysis sessions. Furthermore, this software package is portable to Linux clusters for high throughput applications. In addition to basic utilities to solve for order tensors and back calculate Couplings from a given order tensor and proposed structure, a number of improved algorithms have been incorporated. These include the proper sampling of the Null-space (when the system of linear equations is under-determined), more sophisticated filters for invalid order-tensor identification, error analysis for the identification of the problematic measurements and simulation of the effects of dynamic averaging processes.
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Structural and Dynamic Analysis of Residual Dipolar Coupling Data for Proteins
Journal of the American Chemical Society, 2001Co-Authors: Joel R. Tolman, Hashim M. Al-hashimi, Lewis E. Kay, James H. PrestegardAbstract:The measurement of residual Dipolar Couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from residual Dipolar Coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on residual Dipolar Coupling measurements. We also illustrate this new methodology using an extensive set of residual Dipolar Coupling measurements made on 15N,13C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the 1UBQ X-ray structure (Vijay-Kumar, e...
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measurement of cross correlation between Dipolar Coupling and chemical shift anisotropy in the spin relaxation of13c 15n labeled proteins
Journal of Magnetic Resonance, 1998Co-Authors: Ranajeet Ghose, Kai Huang, James H. PrestegardAbstract:Abstract We present a simple method for extracting interference effects between chemical shift anisotropy (CSA) and Dipolar Coupling from spin relaxation measurements in macromolecules, and we apply this method to extracting cross-correlation rates involving interference of amide 15 N CSA and 15 N– 1 H Dipolar Coupling and interference of carbonyl 13 C′ CSA and 15 N– 13 C′ Dipolar Coupling, in a small protein. A theoretical basis for the interpretation of these rates is presented. While it proves difficult to quantitatively separate the structural and dynamic contributions to these cross-correlation rates in the presence of anisotropic overall tumbling and a nonaxially symmetric chemical shift tensor, some useful qualitative correlations of data with protein structure can be seen when simplifying assumptions are made.
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improved estimation of csa Dipolar Coupling cross correlation rates from laboratory frame relaxation experiments
Journal of Magnetic Resonance, 1998Co-Authors: Ranajeet Ghose, James H. PrestegardAbstract:Abstract We have investigated the underlying assumptions in estimating cross-correlation rates between chemical shift anisotropy (CSA) and Dipolar Coupling mechanisms in a scalar-coupled two-spin IS system, from laboratory frame relaxation experiments. It has been shown that for an arbitrary relaxation delay, the difference in relaxation rates of the individual components of an in-phase (or antiphase) doublet is not related to the CSA–Dipolar Coupling cross-correlation rate in a simple way. This is especially true in the case where the difference in the decay rates of the in-phase and antiphase terms of the density matrix becomes comparable to the magnitude of the scalar Coupling between the two spins. Improved means of extracting cross-correlation rates in these cases are presented.
Joel R. Tolman - One of the best experts on this subject based on the ideXlab platform.
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NMR Studies of Biomolecular Dynamics and Structural Plasticity Using Residual Dipolar Couplings
Annual Reports on NMR Spectroscopy, 2003Co-Authors: Joel R. Tolman, Hashim M. Al-hashimiAbstract:Abstract Due to their exquisite sensitivity to bond vector orientations and distances, residual Dipolar Couplings are emerging as a powerful NMR methodology for probing the conformational dynamics of biomolecules. The global organization of multi-domain proteins and complexes can now be accurately established in solution, providing insights into distinguishing structural features under different solution environments or with respect to the solid state. Collective motions of domains or secondary structural elements occurring over sub-millisecond timescales, which have resisted characterization using traditional techniques, can now be directly probed using suitable residual Dipolar Coupling-based techniques. Advances in methods for achieving molecular alignment and data interpretation are enabling characterization of motions with increasingly high resolution. There are now approaches for determining residual Dipolar Coupling-based generalized order parameters, which can complement their spin relaxation counterparts due to their broader timescale sensitivity. The existence of multiple conformations can now more easily be detected and the residual Dipolar Coupling data used to confirm or refute models for the conformational fluctuations. It can be expected that future biomolecular NMR studies will increasingly benefit from residual Dipolar Coupling applications which can recognize and account for molecular flexibility.
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Structural and Dynamic Analysis of Residual Dipolar Coupling Data for Proteins
Journal of the American Chemical Society, 2001Co-Authors: Joel R. Tolman, Hashim M. Al-hashimi, Lewis E. Kay, James H. PrestegardAbstract:The measurement of residual Dipolar Couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from residual Dipolar Coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on residual Dipolar Coupling measurements. We also illustrate this new methodology using an extensive set of residual Dipolar Coupling measurements made on 15N,13C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the 1UBQ X-ray structure (Vijay-Kumar, e...
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Dipolar Couplings as a probe of molecular dynamics and structure in solution
Current opinion in structural biology, 2001Co-Authors: Joel R. TolmanAbstract:The introduction of residual Dipolar Coupling methodology has increased the scope of structural biological problems that can be addressed by NMR spectroscopy. Conformational changes, the relative orientation of domains, and intermolecular complexes can now be characterized accurately and rapidly using NMR. The development of residual Dipolar Coupling methodology for the rapid recognition of homologous protein folds and for studies of submillisecond timescale dynamics has also seen considerable progress.
Ayyalusamy Ramamoorthy - One of the best experts on this subject based on the ideXlab platform.
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nitrogen 15 chemical shift anisotropy and 1h 15n Dipolar Coupling tensors associated with the phenylalanine residue in the solid state
Chemical Physics Letters, 1999Co-Authors: Jose S Santos, Ayyalusamy RamamoorthyAbstract:Abstract Nitrogen-15 chemical shift anisotropy (CSA) and 1 H – 15 N Dipolar Coupling tensors associated with the Phe-16 residue of the magainin2 peptide are reported in this Letter. The experimental results predict that the magnitudes of the 15 N CSA tensor are σ11N=55±2, σ22N=80±2 and σ33N=220±2 ppm. The results also suggest that the least shielded element, σ33N, is in the peptide plane making an angle of 22±3° with the N–H bond vector whereas σ11N and σ22N are 45±15° away from the peptide plane and the normal to the peptide plane, respectively. The magnitudes of the principal elements of the 15 N CSA tensors associated with 15 N -Phe-16 and 15 N -Gly-18 sites of the magainin2 peptide are significantly different while the orientation of the tensors in the molecular frame is the same.
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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...
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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...
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two dimensional chemical shift heteronuclear Dipolar Coupling spectra obtained with polarization inversion spin exchange at the magic angle and magic angle sample spinning pisemamas
Solid State Nuclear Magnetic Resonance, 1995Co-Authors: Ayyalusamy Ramamoorthy, Stanley J OpellaAbstract:High-resolution two-dimensional 15N chemical shift/1H-15N Dipolar Coupling polarization inversion spin exchange at the magic angle (PISEMA) spectra of a polycrystalline sample of 15N-acetylvaline were obtained with and without magic-angle sample spinning. These spectra demonstrate the advantages of the PISEMA experiment over conventional approaches to separated local-field spectroscopy, especially the high resolution in the Dipolar dimension where the spinning sidebands have uniformly narrow linewidths.
Francois Montaigne - One of the best experts on this subject based on the ideXlab platform.
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measurement of the dynamical Dipolar Coupling in a pair of magnetic nanodisks using a ferromagnetic resonance force microscope
Physical Review Letters, 2012Co-Authors: Benjamin Pigeau, Christian Hahn, G De Loubens, V V Naletov, O Klein, K Mitsuzuka, D Lacour, M Hehn, S Andrieu, Francois MontaigneAbstract:We perform a spectroscopic study of the collective spin-wave dynamics occurring in a pair of magnetic nanodisks coupled by the magnetoDipolar interaction. We take advantage of the stray field gradient produced by the magnetic tip of a ferromagnetic resonance force microscope to continuously tune and detune the relative resonance frequencies between two adjacent nano-objects. This reveals the anticrossing and hybridization of the spin-wave modes in the pair. At the exact tuning, the measured frequency splitting between the binding and antibinding modes corresponds to the strength of the dynamical Dipolar Coupling $\ensuremath{\Omega}$. This accurate ferromagnetic resonance force microscope determination of $\ensuremath{\Omega}$ is measured versus the separation between the nanodisks. It agrees quantitatively with calculations of the expected dynamical magnetoDipolar interaction in our sample.
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Measurement of the dynamical Dipolar Coupling in a pair of magnetic nano-disks using a Ferromagnetic Resonance Force Microscope
Physical Review Letters, 2012Co-Authors: Benjamin Pigeau, Christian Hahn, G De Loubens, V V Naletov, O Klein, K Mitsuzuka, D Lacour, M Hehn, S Andrieu, Francois MontaigneAbstract:We perform an extensive experimental spectroscopic study of the collective spin-wave dynamics occurring in a pair of magnetic nano-disks coupled by the magneto-Dipolar interaction. For this, we take advantage of the stray field gradient produced by the magnetic tip of a ferromagnetic resonance force microscope (f-MRFM) to continuously tune and detune the relative resonance frequencies between two adjacent nano-objects. This reveals the anti-crossing and hybridization of the spin-wave modes in the pair of disks. At the exact tuning, the measured frequency splitting between the binding and anti-binding modes precisely corresponds to the strength of the dynamical Dipolar Coupling $\Omega$. This accurate f-MRFM determination of $\Omega$ is measured as a function of the separation between the nano-disks. It agrees quantitatively with calculations of the expected dynamical magneto-Dipolar interaction in our sample.
Dusan Uhrin - One of the best experts on this subject based on the ideXlab platform.
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determination of sugar structures in solution from residual Dipolar Coupling constants methodology and application to methyl β d xylopyranoside
Journal of the American Chemical Society, 2004Co-Authors: Tran N Pham, Sarah L Hinchley, David W H Rankin, Tibor Liptaj, Dusan UhrinAbstract:We have developed methodology for the determination of solution structures of small molecules from residual Dipolar Coupling constants measured in dilute liquid crystals. The power of the new technique is demonstrated by the determination of the structure of methyl β-d-xylopyranoside (I) in solution. An oriented sample of I was prepared using a mixture of C12E5 and hexanol in D2O. Thirty residual Dipolar Coupling constants, ranging from −6.44 to 4.99 Hz, were measured using intensity-based J-modulated NMR techniques. These include 15 DHH, 4 1DCH, and 11 nDCH Coupling constants. The accuracy of the Dipolar Coupling constants is estimated to be <±0.02 Hz. New constant-time HMBC NMR experiments were developed for the measurement of nDCH Coupling constants, the use of which was crucial for the successful structure determination of I, as they allowed us to increase the number of fitted parameters. The structure of I was refined using a model in which the directly bonded interatom distances were fixed at their ...
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measurement of small one bond proton carbon residual Dipolar Coupling constants in partially oriented 13 c natural abundance oligosaccharide samples analysis of heteronuclear 1 j ch modulated spectra with the bird inversion pulse
Journal of Magnetic Resonance, 2002Co-Authors: Tran N Pham, Tibor Liptaj, Krystyna Bromek, Dusan UhrinAbstract:Two 2D J-modulated HSQC-based experiments were designed for precise determination of small residual Dipolar one-bond carbon-proton Coupling constants in (13)C natural abundance carbohydrates. Crucial to the precision of a few hundredths of Hz achieved by these methods was the use of long modulation intervals and BIRD pulses, which acted as semiselective inversion pulses. The BIRD pulses eliminated effective evolution of all but (1)J(CH) Couplings, resulting in signal modulation that can be described by simple modulation functions. A thorough analysis of such modulation functions for a typical four-spin carbohydrate spin system was performed for both experiments. The results showed that the evolution of the (1)H-(1)H and long-range (1)H-(13)C Couplings during the BIRD pulses did not necessitate the introduction of more complicated modulation functions. The effects of pulse imperfections were also inspected. While weakly coupled spin systems can be analyzed by simple fitting of cross peak intensities, in strongly coupled spin systems the evolution of the density matrix needs to be considered in order to analyse data accurately. However, if strong Coupling effects are modest the errors in Coupling constants determined by the "weak Coupling" analysis are of similar magnitudes in oriented and isotropic samples and are partially cancelled during Dipolar Coupling calculation. Simple criteria have been established as to when the strong Coupling treatment needs to be invoked.