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Biomedical subjects

R R Ernst

Publications and source records attributed to R R Ernst.

At least 19 recordsLinked to original sources
PubMed1999

Detection of intermolecular chemical exchange through decorrelation of two-spin order.

An initial correlation between two spins is lost when they are separated by intermolecular chemical exchange. This effect, termed "decorrelation by chemical exchange," manifests itself in a decay of the corresponding two-spin modes. It can be used for monitoring intermolecular chemical exchange, as is demonstrated for l-tryptophan where the decay of 1H15N two-spin order provides information on the exchange of indole protons with solvent water.

Amides↗
PubMed1998

Quantitative investigation of dipole-CSA cross-correlated relaxation by ZQ/DQ spectroscopy.

A zero-quantum/double-quantum HNCO(H) constant time experiment is presented for the quantitative evaluation of dipole-CSA cross-correlated relaxation involving the 1HN, 15N, and 13C' nuclei of the peptide plane. A simple procedure that allows the extraction of cross-correlated relaxation rate constants from intensity ratios of well-resolved doublet components along omega1 is described. The experiment is demonstrated on fully 13C, 15N-labeled ubiquitin.

Anisotropy↗
PubMed1998

Experiments and strategies for the assignment of fully 13C/15N-labelled polypeptides by solid state NMR.

High-resolution heteronuclear NMR correlation experiments and strategies are proposed for the assignment of fully 13C/15N-labelled polypeptides in the solid state. By the combination of intra-residue and inter-residue 13C-15N correlation experiments with 13C-13C spin-diffusion studies, it becomes feasible to partially assign backbone and side-chain resonance in solid proteins. The performance of sequences using 15N instead of 13C detection is evaluated regarding sensitivity and resolution for a labelled dipeptide (L-Val-L-Phe). The techniques are used for a partial assignment of the 15N and 13C resonances in human ubiquitin.

Amino Acid Sequence↗
PubMed1997

Backbone dynamics and structural characterization of the partially folded A state of ubiquitin by 1H, 13C, and 15N nuclear magnetic resonance spectroscopy.

Structure and dynamics of the partially folded A state of ubiquitin in a 60%/40% methanol/water mixture at pH 2 was studied by two- and three-dimensional nuclear magnetic resonance spectroscopy (NMR) using fully 13C,15N-labeled ubiquitin. Complete backbone 13CO, 13Calpha, 15N, and 1HN assignment was achieved. 13CO and 13Calpha chemical shifts and 1H-1H nuclear Overhauser enhancement (NOE) connectivities indicate different behavior for the N-terminal and the C-terminal halves of the protein. In the N-terminal half of the A state, comprising the antiparallel beta-sheet and the central alpha-helix, the native secondary structural elements are largely conserved. The C-terminal half, which is in the native form rich in beta-strand character, undergoes a methanol-induced transition to a dynamic state with a uniformly high propensity for helical structure. This behavior is also reflected in backbone 15N relaxation data, indicating the presence of three loosely coupled secondary structural segments with enhanced internal mobility as compared to the native state.

Binding Sites↗
PubMed1997

Determination of orientational anisotropy in glassy solids by 2D dipolar spectra with sample flipping.

A method is proposed for the quantitative measurement of orientational anisotropy in glassy solids based on 2D dipolar NMR spectra with sample flipping (dipolar DECODER experiment). Purely dipolar spectra are obtained by chemical shift refocusing by a multiple pulse sequence. The experiment is applied to an investigation of a doubly 13C-labeled sample of bisphenol-A polycarbonate deformed in a channel-die apparatus. The orientational distribution function is determined by an expansion of the distribution in terms of spherical harmonics up to degree four.

Anisotropy↗
PubMed1997

Frequency- and phase-modulated heteronuclear decoupling in rotating solids.

The mechanism of heteronuclear dipolar decoupling by the TPPM sequences, proposed by Bennett et al. (J. Chem. Phys. 103 (1995) 6951) is investigated by comparison with a modified pulse sequence, called TPFM, that uses frequency instead of phase modulation. By combining frequency and phase modulations, circularly modulated sequences are designed. The fact that only the left-handed modulation sequence FMPML leads to improved proton decoupling, while the right-handed modulation sequence FMPMR is ineffective, proves that the efficient decoupling is caused by a secondary resonance effect.

Chemical Phenomena↗
PubMed1995

Determination of heteronuclear three-bond J-coupling constants in peptides by a simple heteronuclear relayed E.COSY experiment.

A simple heteronuclear relayed E.COSY pulse sequence with a minimum number of pulses is proposed for the quantitative determination of heteronuclear three-bond J-coupling constants in uniformly 13C-enriched polypeptide samples. Numerous heteronuclear three-bond coupling constants, including 3JHNC, 3JHNC beta, 3JH beta C, and 3JH alpha C gamma, can be determined for each residue from a single heteronuclear relayed E.COSY spectrum. Couplings relevant for stereospecific assignments as well as for the determination of dihedral angles in the amino acid backbone and in side chains are obtained. The method is demonstrated on the uniformly 13C-enriched decapeptide antamanide (-Val1-Pro2-Pro3-Ala4-Phe5-Phe6-Pro7-Pro8-Phe9-Phe1 0-).

Amino Acid Sequence↗
PubMed1993

Conformational backbone dynamics of the cyclic decapeptide antamanide. Application of a new multiconformational search algorithm based on NMR data.

A general procedure for the analysis of biomolecular structures by NMR in the presence of rapid conformational dynamics has been applied to the study of the cyclic decapeptide antamanide. Two-dimensional experiments, relaxation measurements in the rotating frame, and homo- and heteronuclear coupling constant determinations have been used to characterize the dynamic properties of the molecule, in combination with a novel search algorithm for investigating multiconformational equilibria. Direct evidence for the presence of a conformational exchange process with an activation energy of approximately 20 kJ mol-1 and an exchange lifetime of approximately 25 microseconds at 320 K has been obtained from rotating frame relaxation measurements. This evidence is combined with the information derived from the multiconformational search algorithm MEDUSA to propose sets of structures that coexist in a dynamic exchange equilibrium.

Algorithms↗
PubMed1993

Local monitoring of proton spin diffusion in static and rotating samples via spy detection.

A method is described for investigating local proton "spin diffusion" by means of a 13C spin probe. The procedure does not require spectral resolution of proton resonance lines and can be applied in the laboratory frame of reference as well as in the rotating frame. Experimental results are presented for a static single crystal of ferrocene and for a powder sample under magic-angle spinning. The spin-diffusion rate constant is found to be proportional to the spinning speed in the range from 1 to 8 kHz.

Carbon↗
PubMed1991

Multi-conformational peptide dynamics derived from NMR data: a new search algorithm and its application to antamanide.

A search algorithm, called MEDUSA, is presented which allows the determination of multiple conformations of biomolecules in solution with exchange rate constants typically between 10(3) and 10(7) s-1 on the basis of experimental high-resolution NMR data. Multiples of structures are generated which are consistent as ensembles with NMR cross-relaxation rates (NOESY, ROESY), scalar J-coupling constants, and T1 rho measurements. The algorithm is applied to the cyclic decapeptide antamanide dissolved in chloroform. The characteristic radio-frequency field dependence of the T1 rho relaxation rates found for the NH protons of Val1 and Phe6 can be explained by a dynamical exchange between two structures.

Algorithms↗
PubMed1990

The structure of gramicidin A in dimethylsulfoxide/acetone.

It has been demonstrated by two-dimensional NMR cross-relaxation spectroscopy that gramicidin A exists in dimethylsulfoxide/acetone solution in random coil form. This contradicts earlier conclusions by Hawkes et al. [Hawkes, G. E., Lian, L. Y., Randall, E. W., Sales, K. D. & Curzon, E. H. (1987) Eur. J. Biochem. 166, 437-445] that were based on the interpretation of vicinal proton coupling constants.

Acetone↗
PubMed1988

Three-dimensional NMR spectroscopy of a protein in solution.

The geometric information used to solve three-dimensional (3D) structures of proteins by NMR spectroscopy resides in short (less than 5 A) interproton-distance data. To obtain these distances, the 1H-NMR spectrum must first be assigned using correlation and nuclear Overhauser effect (NOE) experiments to demonstrate through-bond (scalar) and through-space connectivities, respectively. Because the NOE is proportional to r-6, distance information can then be derived. The increased resolution afforded by extending NMR experiments into a second dimension enables one to detect and interpret effects that would not be possible in one dimension owing to extensive spectral overlap and much reduced information. A number of small protein structures have previously been solved in this way. Extending this methodology to larger proteins, however, requires yet an additional improvement in resolution as overlap of cross-peaks in the two-dimensional (2D) NMR spectra present a major barrier to their unambiguous identification. One way of increasing the resolution is to extend the 2D-NMR experiments into a third dimension. We report here the applicability of three-dimensional NMR to macromolecules using the 46-residue protein alpha 1-purothionin as an example.

Antimicrobial Cationic Peptides↗
PubMed1983

Improved spectral resolution in cosy 1H NMR spectra of proteins via double quantum filtering.

A double quantum filter is inserted into a two-dimensional correlated (COSY) 1H NMR experiment to obtain phase-sensitive spectra in which both cross peak and diagonal peak multiplets have anti-phase fine structure, and in which the cross peaks and the major contribution to the diagonal peaks have absorption lineshapes in both dimensions. The elimination of the dispersive character of the diagonal peaks in phase-sensitive, double quantum-filtered COSY spectra allows identification of cross peaks lying immediately adjacent to the diagonal, which represents a significant improvement over the conventional COSY experiment.

Magnetic Resonance Spectroscopy↗