Biomedical subjects

G Bodenhausen

Publications and source records attributed to G Bodenhausen.

At least 19 recordsLinked to original sources

PubMed2001

Cross-correlated chemical shift modulation: a signature of slow internal motions in proteins.

A novel NMR experiment allows one to characterize slow motion in macromolecules. The method exploits the fact that motions, such as rotation about dihedral angles, induce correlated fluctuations of the isotropic chemical shifts of the nuclei in the vicinity. The relaxation of two-spin coherences involving C(alpha) and Cbeta nuclei in proteins provides information about correlated fluctuations of the isotropic chemical shifts of C(alpha) and Cbeta. The difference between the relaxation rates of double- and zero-quantum coherences and is shown to be affected by cross-correlated chemical shift modulation. In ubiquitin, evidence for slow motion is found in loops or near the ends of beta-strands and alpha-helices.

Algorithms↗

PubMed2001

Probing aerogels by multiple quantum filtered (131)Xe NMR spectroscopy.

At the interface between solid surfaces and cavities filled with gaseous or liquid xenon, the nuclear magnetization of (131)Xe (S = (3)/(2)) is subject to quadrupolar interactions which may lead to higher rank single-quantum coherences that can be described by tensor elements T(2,)(+/-)(1) and T(3,)(+/-)(1). This can be demonstrated by multiple-quantum filtered (MQF) NMR experiments. In gaseous xenon on Pyrex surfaces, the primary source of such coherences was shown to be coherent evolution induced by a nonvanishing average quadrupolar coupling. In this contribution, MQF NMR is applied to aerogels filled with liquid xenon to demonstrate the potential of this technique for material sciences. Xenon in the liquid phase provides a sufficient spin density to obtain reasonable signal-to-noise ratios. Coherent evolution and relaxation both contribute to the creation of higher rank coherences depending on the presence or absence of water molecules on the surface. These two processes can be distinguished experimentally and provide complementary information about the surface of the host material.

Journal Article↗

PubMed2000

Radiation damping compensation of selective pulses in water-protein exchange spectroscopy.

The observation of nuclear Overhauser effects (NOEs) between bound water and biological macromolecules such as proteins and nucleic acids can be improved by inverting the water resonance selectively while compensating for radiation damping effects. The efficiency of inversion, the offset profiles, and the appearance of 2D NOE-NOESY spectra can be improved in comparison with earlier methods.

Nuclear Magnetic Resonance, Biomolecular↗

PubMed1999

Offset profiles of selective pulses in isotopically labeled macromolecules.

The experimental verification of offset profiles and calibration of selective pulses in NMR is usually carried out with doped water samples but not under conditions typical of macromolecules with short T2, long T1, and possibly homo- and heteronuclear couplings. A new method for selective excitation in isotopically labeled macromolecules is shown to be particularly suited to this purpose. This is illustrated for a backbone amide resonance in a sample of 15N-labeled human ubiquitin.

Amides↗

PubMed1999

Mapping the B1 field distribution with nonideal gradients in a high-resolution NMR spectrometer.

To understand the behavior of many NMR experiments, it is important to determine the spatial distribution of the B1 field. In this paper, we show how this distribution can be mapped independently of spin density, coil responsiveness, and nonlinearities of the B0 field gradients. As a by-product we obtain a map of the (possibly nonlinear) spatial variation of the B0 field gradients used in the imaging procedure.

Deuterium Oxide↗

PubMed1999

Excitation of selected proton signals in NMR of isotopically labeled macromolecules

In isotopically labeled macromolecules, it is possible to excite the signal of a selected proton by shuttling magnetization back and forth between the chosen proton and a heteronucleus such as 13C or 15N, using two-way doubly selective heteronuclear cross-polarization. Selective excitation of a chosen proton can be followed by homonuclear coherence transfer to identify side-chain resonances of the corresponding amino acid in proteins. The resulting one-dimensional experiments yield information that can usually only be obtained from three-dimensional HSQC-TOCSY spectra. The method also provides efficient suppression of solvent signals without affecting resonances close to the solvent peak. Copyright 1999 Academic Press.

Journal Article↗

PubMed1999

Tilt angle dependence of cross-relaxation in off-resonance ROESY.

We present an efficient experimental method to evaluate whether the effective cross-relaxation rate between a pair of spins vanishes when applying an off-resonance spin-lock field. It is shown that the cross-relaxation rate can be made to vanish even when the two spins concerned resonate at different offsets and experience significantly different tilt angles of their respective spin-lock fields. This is verified experimentally using a sample of 15N-labeled human ubiquitin, through selective excitation of chosen amide protons. The results are relevant for the quantitative interpretation of off-resonance ROESY experiments.

Amides↗

PubMed1999

Identification of spin diffusion pathways in isotopically labeled biomolecules.

One-dimensional NOE experiments applicable to labeled macromolecules are presented which allow the manipulation of specific spin diffusion pathways and thus unambiguously identify clandestine spins through which the direct NOE is mediated. A treatment of spin diffusion using average Liouvillian theory is shown to describe adequately these phenomena. Experiments are carried out on an 15N-labeled sample of human ubiquitin.

Diffusion↗

PubMed1999

Measurement of relaxation rates of N(H) and H(alpha) backbone protons in proteins with tailored initial conditions.

Several methods are presented for the selective determination of spin-lattice and spin-spin relaxation rates of backbone protons in labeled proteins. The relaxation rates of amide protons in (15)N labeled proteins can be measured by using two-way selective cross-polarization (SCP). The measurement of H(alpha) relaxation rates can be achieved by combining this method with homonuclear Hartmann-Hahn transfer using doubly selective irradiation. Various schemes for selective or nonselective inversion of the longitudinal proton magnetization lead to different initial recovery rates. The methods have been applied to lysine K6 in (15)N-labeled human ubiquitin and to leucine L5 in (15)N- and (13)C-labeled octapeptide YG*G*F*LRRI (GFL) in which the marked residues are (15)N- and (13)C-labeled.

Carbon Isotopes↗

PubMed1999

Determination of coupling constants by deconvolution of multiplets in NMR

The structures of multiplets in one- and two-dimensional NMR spectra can be simplified by recursive deconvolution in the frequency domain. Deconvolution procedures are described for in-phase and antiphase doublets of delta functions. Recursive simplification is illustrated by applications to double-quantum-filtered correlation spectra (DQF-COSY) and selective correlation spectra (soft-COSY). Coupling constants can be measured reliably even if signals of opposite signs lead to partial cancellation. Copyright 1999 Academic Press.

Journal Article↗

PubMed1999

Attenuation of cross-peak intensities in QUIET-BIRD-NOESY experiments.

The buildup curves in QUIET-BIRD-NOESY experiments, which are designed to isolate two-spin subsystems within macromolecules, are attenuated by transverse relaxation and evolution under homonuclear couplings during the bilinear rotation decoupling (BIRD) pulse sandwich. If the signals of both source and target spins are attenuated equally (uniform damping), this is readily accounted for by normalizing the cross peaks with respect to the diagonal peaks. However, unequal attenuation of source and target spins (differential damping) affects the initial buildup slopes and hence leads to apparent cross-relaxation rates that are significantly distorted from their true values. A simple method for recognizing this situation and extracting accurate cross-relaxation rates is presented.

Linear Models↗

PubMed1999

Efficient determination of angles subtended by C(alpha)-H(alpha) and N-H(N) vectors in proteins via dipole-dipole cross-correlation.

The angle Theta(C(alpha)H(alpha)),NH(N) subtended by the internuclear vectors 13C(alpha)-H(alpha) and 15N-H(N) in doubly-labeled proteins can be determined by observing the effect of cross-correlation between the dipolar interactions on zero- and double-quantum coherences involving 13C(alpha) and 15N. Two complementary 2D experiments with the appearance of 15N-HN correlation spectra yield signal intensities that depend on the rate of interconversion through cross-correlated relaxation of in-phase and doubly antiphase zero- and double-quantum coherences. The ratio of the signal intensities in the two experiments bears a simple relationship to the cross-correlation rate, and hence to the angle Theta(C(alpha)H(alpha),NH(N)). Assuming planarity of the peptide bond, the dihedral angle psi (between C(alpha) and C) can be determined from the knowledge of Theta(C(alpha)H(alpha),NH(N)). The experiments are very time-effective and provide good sensitivity and excellent spectral resolution.

Carbon Isotopes↗

PubMed1997

The conformation of NAD+ bound to lactate dehydrogenase determined by nuclear magnetic resonance with suppression of spin diffusion.

We have reinvestigated the conformation of NAD+ bound to dogfish lactate dehydrogenase (LDH) by using an NMR experiment that allows one to exploit nuclear Overhauser effects to determine internuclear distances between pairs of protons, without perturbation of spin-diffusion effects from other protons belonging either to the cofactor or to the binding pocket of the enzyme. The analysis indicates that the structure of bound NAD+ is in accord with the conformation determined in the solid state by x-ray diffraction for the adenosine moiety, but deviates significantly from that of the nicotinamide. The NMR data indicate conformational averaging about the glycosidic bond of the nicotinamide nucleotide. In view of the strict stereospecificity of catalysis by LDH and the conformational averaging of bound NAD+ that we infer from solution-state NMR, we suggest that LDH binds the cofactor in both syn and anti conformations, but that binding interactions in the syn conformation are not catalytically productive.

Adenosine↗

PubMed1997

Lysine as helix C-capping residue in a synthetic peptide.

The structure of the synthetic peptide CH3CO(Leu-Ser-Leu-Leu-Leu-Ser-Leu)3Lys-NH2 in trifluoroethanol/water 60/40 (volume ratio) was characterized by two-dimensional nmr spectroscopy. The peptide, closely related to the amphiphilic helix models designed by W. F. De-Grado and co-workers to mimic protein ion channels [(1988) Science, Vol. 240, p. 1177-1181], folds into a regular helix spanning residues 1-20. Evidence for a helix C-terminal capping conformation, involving the terminal lysine residue, was observed from Overhauser effects and checked for consistency by restrained molecular dynamics simulations. The side-chain amino group of Lys22 forms a hydrogen bond with the carbonyl of Leu18, and the distorted helical geometry of the terminal dipeptide allows the inclusion of a water bridge between the backbone NH of the Lys22 residue and the carbonyls of Leu19 and Ser20.

Amino Acid Sequence↗

PubMed1996

Curious Consequences of Strong Coupling in NMR Experiments Involving Selective Pulses

This study is concerned with the effects of applying selective pulses to systems with strong second-order scalar couplings in isotropic phase, where different transitions (rs) are associated with different transition matrix elements F+(rs). Two unusual features can be distinguished: the nutation angle ("flip angle") depends on the matrix element of the irradiated transition (rs), and, in contrast to the behavior of an isolated spin-(1/2) system, the norm of the three single-transition operators [I(rs)x, I(rs)y, I(rs)z] associated with the fictitious spin-(1/2) space of the irradiated transition (rs) is generally not conserved. It is necessary to consider the single-transition operators [I(rp)x, I(rp)y, I(rp)z] and [I(sq)x, I(sq)y, I(sq)z] associated with all connected transitions (rp) and (sq) that share a common energy level r or s with the irradiated transition (rs). If the pulse applied to the (rs) transition is sufficiently selective, the transverse components I(rp)x, I(rp)y, I(sq)x, and I(sq)y, can be neglected, since their expectation values remain equal to zero after application of a selective pulse to the (rs) transition, but the longitudinal components I(rp)z and I(sq)z acquire nonvanishing expectation values. When the selective pulse affects several transitions simultaneously, the response varies from one transition to another, depending on the matrix elements and the connectivities. These effects manifest themselves in unusual amplitudes and phases of signals excited by selective pulses, in particular in selective two-dimensional correlation spectra.

Journal Article↗

PubMed1996

Quantitative Determination of Cross-Relaxation Rates in NMR Using Selective Pulses to Inhibit Spin Diffusion

Overhauser effects and hence internuclear distances can be measured accurately with selective experiments designed to suppress spin diffusion. It is essential to consider effects of both transverse and longitudinal relaxation during selective radiofrequency pulses. Fitting procedures allow one to refine selected cross-relaxation rate constants, and hence determine internuclear distances with improved accuracy. For the sake of illustration, selected cross-relaxation rates are determined that correspond to short- and long-range distances involving two diastereotopic sugar protons in a double-stranded B-DNA dodecamer. Such distances are difficult to distinguish by traditional Overhauser methods because of spin-diffusion effects.

Journal Article↗

PubMed1996

Suppression of spin diffusion in selected frequency bands of nuclear Overhauser spectra.

A variant of two-dimensional nuclear Overhauser effect spectroscopy (NOESY) is described that yields information about cross-relaxation rates between pairs of spins, while the migration of magnetization through several consecutive steps (spin diffusion via neighboring spins) is largely suppressed. This can be achieved by inserting a doubly-selective inversion pulse in a conventional NOESY sequence.

Base Sequence↗

PubMed1996

NMR of residual protons in partly deuterated anisotropic materials with phase-alternated decoupling of deuterium spins.

A new method is presented for decoupling spins with S = 1 like deuterium in anisotropic media while observing other spins such as residual protons in partly deuterated samples. The carrier frequency of a weak radiofrequency (RF) field is applied near the center of the doublet arising from the quadrupolar interaction of the S = 1 spins. The phase of the RF field is periodically reversed with intervals matching the reciprocal of the magnitude of the quadrupolar splitting. It is shown by theory and experiment that, even when the irradiating field is quite weak, the efficiency of this phase-alternated decoupling scheme is much better than for simple continuous-wave irradiation at the center of the doublet, an established technique which is usually referred to as double quantum decoupling. The phase-alternated experiment makes it possible to decouple large quadrupolar interactions with a weak RF field. A theoretical analysis and numerical simulations are presented to demonstrate the decoupling performance. Proton spectra of partly deuterated dibromobutane in a liquid crystalline solvent have been recorded to illustrate the efficiency of phase-alternated deuterium decoupling.

Chemical Phenomena↗