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Geoffrey Bodenhausen

Publications and source records attributed to Geoffrey Bodenhausen.

At least 19 recordsLinked to original sources
PubMed2007

Singlet-state exchange NMR spectroscopy for the study of very slow dynamic processes.

Singlet states with lifetimes that are longer than spin-lattice relaxation times TS > T1 offer unique opportunities for studying very slow dynamic processes in solution-state NMR. A set of novel experiments can achieve broadband excitation of singlet states in pairs of coupled spins. The most elaborate of these experiments, two-dimensional singlet-state exchange spectroscopy (SS-EXSY), is independent of the offsets of the two spins, their relative chemical shifts, and their scalar couplings. The new methods open the way to study very slow chemical exchange or translational diffusion using mixing times taum = Ts >> T1. The lifetimes TS of singlet states of pairs of protons in a partially deuterated saccharide are shown to be longer than the longitudinal proton relaxation times T1 in the same compound by a factor of ca. 37.

Furans↗
PubMed2006

Slow backbone dynamics of the C-terminal fragment of human centrin 2 in complex with a target peptide probed by cross-correlated relaxation in multiple-quantum NMR spectroscopy.

The C-terminal domain of human centrin 2 (C-HsCen2) strongly binds to P1-XPC, a peptide comprising 17 amino acids with a NWKLLAKGLLIRERLKR sequence. This peptide corresponds to residues N847-R863 of XPC, a protein involved in the recognition of damaged DNA during the initial step of the nucleotide excision repair pathway. The slow internal dynamics of the protein backbone in the C-HsCen-P1-XPC complex was studied by measuring the relaxation rates of zero- and double-quantum coherences involving neighboring pairs of carbonyl 13C and amide 15N nuclei. These relaxation rates, which reflect dynamics on time scales in the range of micro- to milliseconds, vary significantly along the protein backbone. Analysis of the relaxation rates at different CaCl2 concentrations and ionic strengths shows that these slow motions are mainly affected by the binding of a Ca2+ ion to the lower-affinity EF-hand III. Moreover, we discuss the possible functional role of residues that undergo differential exchange in the formation of HsCen homodimers.

Calcium-Binding Proteins↗
PubMed2006

Measuring fast hydrogen exchange rates by NMR spectroscopy.

We introduce a method to measure hydrogen exchange rates based on the observation of the coherence of a neighboring spin S such as (15)N that has a scalar coupling J(IS) to the exchanging proton I. The decay of S(x) coherence under a Carr-Purcell-Meiboom-Gill (CPMG) multiple echo train is recorded in the presence and absence of proton decoupling. This method allows one to extract proton exchange rates up to 10(5)s(-1). We could extend the pH range for the study of the indole proton in tryptophan, allowing the determination of the exchange constants of the cationic, zwitterionic, and anionic forms of tryptophan.

Algorithms↗
PubMed2006

Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts.

We propose a strategy based on the combination of experimental NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlated relaxation rates and chemical shift analysis for the determination of Psi torsion angles in proteins. The method allows the determination of a dihedral angle that is not easily accessible by nuclear magnetic resonance (NMR). The measurement of dihedral angle restraints can be used for structure calculation, which is known to improve the quality of NMR structures. The method is of particular interest in the case of large proteins, for which spectral assignment of the nuclear Overhauser effect spectra, and therefore straightforward structural determination, is out of reach. One advantage of the method is that it is reasonably simple to implement, and could be used in association with other methods aiming at obtaining structural information on complex systems, such as residual dipolar coupling measurements. An illustrative example is analyzed in the case of the 30-kDa protein 6-phosphogluconolactonase.

Animals↗
PubMed2006

Protein backbone dynamics through 13C'-13Calpha cross-relaxation in NMR spectroscopy.

Internal dynamics of proteins are usually characterized by the analysis of (15)N relaxation rates that reflect the motions of NH(N) vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C'C(alpha) vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2N(z)() and 2N(z)(). This amounts to "anchoring" the and operators to the N(z)() term from the amide of the next residue. In combination with symmetrical reconversion, this method greatly reduces various artifacts. The experiment is carried out on human ubiquitin at 284.1 K, where the correlation time is 7.1 ns. The motions of the C'C(alpha) vector appear more restricted than those of the NH(N) vector.

Nuclear Magnetic Resonance, Biomolecular↗
PubMed2006

Lifetimes of the singlet-states under coherent off-resonance irradiation in NMR spectroscopy.

Singlet-states |S=(|alphabeta> - |betaalpha>)/sq.rt.2 can be excited in pairs of coupled spins I and S, first by preparing either a non-vanishing zero-quantum coherence I(+)S(-) or a state of longitudinal two-spin order I(z)S(z) and then by applying a coherent radio-frequency (RF) irradiation with a carrier frequency omega(rf) = (Omega(I) + Omega(S))/2 that lies half-way between the chemical shifts of the two spins involved. The life-times T(S) can be much longer than the spin-lattice relaxation time T(1) of longitudinal magnetization, but singlet-states are ultimately relaxed, not only by dipolar interactions between the active spins or with the external spins, but also as a result of a non-vanishing offset Deltaomega = omega(rf) - (Omega(I) + Omega(S))/2 or an insufficient amplitude of the RF irradiation that fails to fulfill the condition omega(1) >> DeltaOmega = (Omega(I) - Omega(S)). In this work, the effect of off-resonance irradiation is explored and an approximate formula for the effective relaxation rate of the singlet population is provided on the basis of perturbation theory. The qualitative features of the dependence of the relaxation rate of the singlet population on the offset Deltaomega and on the difference DeltaOmega of the chemical shifts of the two spins are illustrated by comparison with numerical simulations.

Journal Article↗
PubMed2006

Indirect detection of nitrogen-14 in solids via protons by nuclear magnetic resonance spectroscopy.

This Communication describes the indirect detection of 14N nuclei (spin I=1) in solids by nuclear magnetic resonance (NMR) spectroscopy. The two-dimensional correlation method used here is closely related to the heteronuclear multiple quantum correlation (HMQC) experiment introduced in 1979 to study molecules in liquids, which has recently been used to study solids spinning at the magic angle. The difference is that the coherence transfer from neighboring 1H nuclei to 14N is achieved via a combination of J couplings and residual dipolar splittings (RDS). Projections of the two-dimensional correlation spectra onto the 14N dimension yield powder patterns which reflect the 14N quadrupolar interaction. In contrast to the indirect detection of 14N via 13C nuclei that was recently demonstrated [Gan, J. Am. Chem. Soc. 128 (2006) 6040; Cavadini et. al., J. Am. Chem. Soc., 128 (2006) 7706], this approach may benefit from enhanced sensitivity, and does not require isotopic enrichment in 13C, although the 1H line-widths may have to be reduced upon selective deuteration.

Glycine↗
PubMed2006

Nitrogen-14 NMR spectroscopy using residual dipolar splittings in solids.

It is shown that nuclear magnetic resonance (NMR) spectra of nitrogen-14 (spin I = 1) can be obtained by indirect detection in powders spinning at the magic angle (MAS). The method relies on the transfer of coherence from a neighboring nucleus with S = 1/2, such as carbon-13, to single- or double-quantum transitions of nitrogen-14 nuclei. The transfer of coherence occurs through second-order quadrupole-dipole cross terms, also known as residual dipolar splittings. The two-dimensional NMR spectra reveal powder patterns determined by the second-order quadrupolar interactions of nitrogen-14. Analysis of the spectra yields the quadrupolar coupling constant, CQ, and asymmetry parameter, etaQ, of nitrogen-14. These parameters can be related to the structure of nitrogen-containing solids.

Carbon Isotopes↗
PubMed2006

Kinetics of RNA refolding in dynamic equilibrium by 1H-detected 15N exchange NMR spectroscopy.

By implementing new NMR methods that were designed to map very slow exchange processes we have investigated and characterized the refolding kinetics of a thermodynamically stable 34mer RNA sequence in dynamic equilibrium. The RNA sequence was designed to undergo a topologically favored conformational exchange between different hairpin folds, serving as a model to estimate the minimal time required for more complex RNA folding processes. Chemically prepared RNA sequences with sequence-selective (15)N labels provided the required signal separation and allowed a straightforward signal assignment of the imino protons by HNN correlation experiments. The 2D version of the new (1)H-detected (15)N exchange spectroscopy (EXSY) pulse sequence provided cross-peaks for resonances belonging to different folds that interchange on the time scale of longitudinal relaxation of (15)N nuclei bound to imino protons. The 34mer RNA sequence exhibits two folds which exchange on the observable time scale (tau(obs) approximately T(1){(15)Nu} < 5 s) and a third fold which is static on this time scale. A 1D version of the (15)N exchange experiment allowed the measurement of the exchange rates between the two exchanging folds as a function of temperature and the determination of the corresponding activation energies E(a) and frequency factors A. We found that the refolding rates are strongly affected by an entropically favorable preorientation of the replacing strand. The activation energies are comparable to values obtained for the slow refolding of RNA sequences of similar thermodynamic stability but less favorable topology.

Base Sequence↗
PubMed2006

Cross polarization from spins I=12 to spins S=1 in nuclear magnetic resonance with magic angle sample spinning.

Spin locking of the nuclear magnetization of a spin with S=1 such as deuterium in the presence of a radio-frequency field under magic angle spinning (MAS) is described in terms of adiabatic modulations of the energy levels. In a brief initial period, part of the initial density operator nutates about the Hamiltonian and is dephased. The remaining spin-locked state undergoes persistent oscillatory transfer processes between various coherences with a periodicity given by the rotation of the sample. While all crystallites in the powder undergo such periodic transfer processes, the phases of the oscillations depend on the angle gamma of the crystallites. The angle gamma is the azimuthal angle defining the orientation of the unique axis of the quadrupolar interaction tensor in a rotor-fixed frame. The theory is extended to describe cross-polarization between spins S=1 and I=12 under MAS. There are four distinct Hartmann-Hahn matching conditions that correspond to four zero-quantum matching conditions, all of which are shifted and broadened compared to their spin S=12 counterparts. These matching conditions are further split into a family of sideband conditions separated by the spinning frequency. The theory allows the calculation of both shifts and broadening factors of the matching conditions, as verified by simulations and experiments.

Journal Article↗
PubMed2006

Quenching echo modulations in NMR spectroscopy.

In NMR spectroscopy, homonuclear scalar couplings normally lead to modulations of spin echoes that tend to interfere with the accurate determination of transverse relaxation rates by Carr-Purcell-Meiboom-Gill (CPMG) multiple refocusing experiments. Surprisingly, the echo modulations are largely cancelled when the refocusing pulses applied to the coupling partner deviate slightly from ideal pi rotations due to tilted effective radio-frequency (RF) fields, even at offsets that are much smaller than the radio-frequency amplitude. Experiments and simulations illustrate these effects for two-spin IS systems containing donor and acceptor (15)N nuclei I=N (D) and S=N(A) in RNA Watson-Crick base pairs with homonuclear scalar couplings J(IS)=(2h)J(N(D), N(A)) across the hydrogen bonds.

Magnetic Resonance Spectroscopy↗
PubMed2006

Quadrupolar transfer pathways.

A set of graphical conventions called quadrupolar transfer pathways is proposed to describe a wide range of experiments designed for the study of quadrupolar nuclei with spin quantum numbers I=1, 3/2, 2, 5/2, etc. These pathways, which inter alea allow one to appreciate the distinction between quadrupolar and Zeeman echoes, represent a generalization of the well-known coherence transfer pathways. Quadrupolar transfer pathways not merely distinguish coherences with different orders -2I < or = p< or = +2I, but allow one to follow the fate of coherences associated with single transitions that have the same coherence order p=m(I)(r)-m(I)(s) but can be distinguished by a satellite order q=(m(I)(r))(2)-(m(I)(s))(2).

Journal Article↗
PubMed2005

Predicting internal protein dynamics from structures using coupled networks of hindered rotators.

Internal motions in proteins, such as oscillations of internuclear vectors u(N(i)H(i) (N)) of amide bonds about their equilibrium position, can be characterized by a local order parameter. This dynamic parameter can be determined experimentally by measuring the longitudinal and transverse relaxation rates of (15)N(i) nuclei by suitable NMR methods. In this paper, it is shown that local variations of order parameters S(ii) (2) can be predicted from the knowledge of the structure. To this effect, the diffusive motion of the internuclear vector u(N(i)H(i) (N)) is described in a potential that takes into account the deviations of the angles theta(ij) between u(N(i)H(i) (N)) and neighboring vectors u(N(j)H(j) (N)) from their average value and similarly of deviations of the angles subtended between u(N(i)H(i) (N)) and u(X(j)Y(j)), where X(j) and Y(j) are heavy atoms in the vicinity of the u(N(i)H(i) (N)) vector under investigation. It is shown how the concept of vicinity can be defined by a simple cutoff threshold, i.e., by neglecting vectors u(X(j)Y(j)) with distances d(N(i),X(j))>7.5 A. The local order parameters S(ii) (2) can be predicted from the structure using a limited set of coordinates of heavy atoms. The inclusion of a larger number of heavy atoms does not improve the predictions. Applications to calmodulin, calbindin, and interleukin 4 illustrate the success and limitations of the predictions.

Algorithms↗
PubMed2005

Slow diffusion by singlet state NMR spectroscopy.

Small diffusion coefficients can be measured by using populations of singlet states that have a relaxation time constant, T(s), which can be much longer than the longitudinal relaxation time, T1. Spatial information can be encoded with pulsed field gradients in the manner of stimulated echo sequences. Singlet states can be excited via double-quantum coherences to enhance the efficiency of phase encoding and decoding.

Journal Article↗
PubMed2005

Chemical shift anisotropy tensors of carbonyl, nitrogen, and amide proton nuclei in proteins through cross-correlated relaxation in NMR spectroscopy.

The principal components and orientations of the chemical shift anisotropy (CSA) tensors of the carbonyl (C'), nitrogen (N), and amide proton (H(N)) nuclei of 64 distinct amide bonds in human ubiquitin have been determined in isotropic solution by a set of 14 complementary auto- and cross-correlated relaxation rates involving the CSA interactions of the nuclei of interest and several dipole-dipole (DD) interactions. The CSA parameters thus obtained depend to some degree on the models used for local motions. Three cases have been considered: restricted isotropic diffusion, three-dimensional Gaussian axial fluctuations (3D-GAF), and independent out-of-plane motions of the NH(N) vectors with respect to the peptide planes.

Amides↗
PubMed2005

Anisotropic local motions and location of amide protons in proteins.

A new method has been developed to obtain dynamic and structural information about peptide planes in proteins by a combination of measurements of weak short-range cross-correlation rates R(H(N)N/NC') that are due to concerted fluctuations of the H(N)-N and N-C' dipole-dipole interactions and stronger long-range cross-correlation rates R(C'H(N)/H(N)N) and R(NH(N)/H(N)C(alpha)). The rates were interpreted using the axially symmetric Gaussian axial fluctuation model (GAF). The oscillation amplitudes as well as the positions of H(N) atoms with respect to peptide planes in ubiquitin were determined. Most N-H(N) bonds were found not to lie exactly along the bisector of the N-C' and N-C(alpha) bonds but to be slightly tilted toward the carbon-terminal side of the peptide.

Amides↗