PubMed Health⌕ Search

Biomedical subjects

R Brüschweiler

Publications and source records attributed to R Brüschweiler.

16 recordsLinked to original sources
PubMed2001

Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for flexible parts in globular proteins.

An approach is presented for the interpretation of heteronuclear NMR spin relaxation data in mobile protein parts in terms of reorientational eigenmode dynamics. The method is based on the covariance matrix of the spatial functions of the nuclear spin interactions that cause relaxation expressed as spherical harmonics of rank 2. The approach was applied to characterize the dynamics of a loop region of ubiquitin. The covariance matrix was determined from a conformational ensemble generated by a 5 ns molecular dynamics simulation. It was found that the time correlation functions of the dominant eigenmodes decay in good approximation with a single correlation time. From the reorientational eigenmodes, their eigenvalues, and correlation times, NMR relaxation data were calculated in accordance with Bloch-Wangsness-Redfield relaxation theory and directly compared with experimental (15)N relaxation parameters. Using a fitting procedure, agreement between calculated and experimental data was improved significantly by adjusting eigenvalues and correlation times of the dominant modes. The presented procedure provides detailed information on correlated reorientational dynamics of flexible parts in globular proteins. The covariance matrix was linked to the covariance matrix of backbone dihedral angle fluctuations, allowing one to study the motional behavior of these degrees of freedom on nano- and subnanosecond time scales.

Models, Molecular↗
PubMed2001

Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins.

The effects of internal motions on residual dipolar NMR couplings of proteins partially aligned in a liquid-crystalline environment are analyzed using a 10 ns molecular dynamics (MD) computer simulation of ubiquitin. For a set of alignment tensors with different orientations and rhombicities, MD-averaged dipolar couplings are determined and subsequently interpreted for different scenarios in terms of effective alignment tensors, average orientations of dipolar vectors, and intramolecular reorientational vector distributions. Analytical relationships are derived that reflect similarities and differences between motional scaling of dipolar couplings and scaling of dipolar relaxation data (NMR order parameters). Application of the self-consistent procedure presented here to dipolar coupling measurements of biomolecules aligned in different liquid-crystalline media should allow one to extract in a "model-free" way average orientations of dipolar vectors and specific aspects of their motions.

Computer Simulation↗
PubMed2001

Characterization of NMR relaxation-active motions of a partially folded A-state analogue of ubiquitin.

The dominant dynamics of a partially folded A-state analogue of ubiquitin that give rise to NMR 15N spin relaxation have been investigated using molecular dynamics (MD) computer simulations and reorientational quasiharmonic analysis. Starting from the X-ray structure of native ubiquitin with a protonation state corresponding to a low pH, the A-state analogue was generated by a MD simulation of a total length of 33 ns in a 60%/40% methanol/water mixture using a variable temperature scheme to control and speed up the structural transformation. The N-terminal half of the A-state analogue consists of loosely coupled native-like secondary structural elements, while the C-terminal half is mostly irregular in structure. Analysis of dipolar N-H backbone correlation functions reveals reorientational amplitudes and time-scale distributions that are comparable to those observed experimentally. Thus, the trajectory provides a realistic picture of a partially folded protein that can be used for gaining a better understanding of the various types of reorientational motions that are manifested in spin-relaxation parameters of partially folded systems. For this purpose, a reorientational quasiharmonic reorientational analysis was performed on the final 5 ns of the trajectory of the A-state analogue, and for comparison on a 5 ns trajectory of native ubiquitin. The largest amplitude reorientational modes show a markedly distinct behavior for the two states. While for native ubiquitin, such motions have a more local character involving loops and the C-terminal end of the polypeptide chain, the A-state analogue shows highly collective motions in the nanosecond time-scale range corresponding to larger-scale movements between different segments. Changes in reorientational backbone entropy between the A-state analogue and the native state of ubiquitin, which were computed from the reorientational quasiharmonic analyses, are found to depend significantly on motional correlation effects.

Computer Simulation↗
PubMed2001

Collective reorientational motion and nuclear spin relaxation in proteins.

Significant progress in NMR methodology for measuring spin-relaxation data at many different 15N and 13C sites in proteins demands new and increasingly sophisticated ways of data interpretation. Recent work of our group concerning the use of anisotropic and reorientational collective motional models for spin-relaxation interpretation is briefly reviewed and a number of important aspects of collective reorientational motional models are discussed at the example of a 11 ns molecular dynamics computer simulation of the protein ubiquitin.

Anisotropy↗
PubMed2000

Characterization of collective and anisotropic reorientational protein dynamics.

Intramolecular reorientational dynamics of proteins are described in terms of reorientational quasiharmonic modes. These modes provide important insight into anisotropic and collective axial fluctuations of distinct molecular fragments, and they represent a highly compact description of intramolecular protein motions that are spectroscopically observable via nuclear spin relaxation. The method is applied to a molecular dynamics computer simulation of the protein ubiquitin.

Anisotropy↗
PubMed1998

Rotational Motion of a Solute Molecule in a Highly Viscous Liquid Studied by 13C NMR: 1,3-Dibromoadamantane in Polymeric Chlorotrifluoroethene

The viscosity-dependent retarding effect of a polymeric solvent on the rotation of small solute molecules is investigated by 13C NMR relaxation measurements. It is found that the relaxation data of 1,3-dibromoadamantane in highly viscous polymeric chlorotrifluoroethene can be explained neither by isotropic nor by realistic anisotropic tumbling in a single environment. The experimental data are rationalized in terms of fast exchange between at least two environments with correlation times differing by up to two orders of magnitude. The study shows that a uniform retardation of molecular tumbling by a polymeric solvent, desirable for shifting the NMR observation window in studies of intramolecular mobility, is not always feasible. Copyright 1998 Academic Press.

Journal Article↗
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↗
PubMed1995

Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling.

Structural characterization of biomolecules in solution by nuclear magnetic resonance (NMR) spectroscopy is based primarily on the use of interproton distances derived from homonuclear cross-relaxation experiments. Information about short time-scale dynamics, on the other hand, is obtained from relaxation rates of heteronuclear spin pairs such as 15N-1H. By combining the two types of data and utilizing the dependence of heteronuclear NMR relaxation rates on anisotropic diffusional rotational tumbling, it is possible to obtain structural information about long-range motional correlations between protein domains. This approach was applied to characterize the relative orientations and mobilities of the first three zinc-finger domains of the Xenopus transcription factor TFIIIA in aqueous solution. The data indicate that the motions of the individual zinc-finger domains are highly correlated on time scales shorter than 10 nanoseconds and that the average conformation of the three-finger polypeptide is elongated.

Anisotropy↗
PubMed1995

Hydration of the partially folded peptide RN-24 studied by multidimensional NMR.

Peptide-water interactions of a ribonuclease C-peptide analogue, RN-24 (Suc-AETAAAKFLRAHANH2), which exhibits significant helicity, have been studied in solution using homonuclear 2D and 3D NMR cross-relaxation experiments. Dipolar peptide proton-water proton interactions are indicated by a large number of NOESY-type cross peaks at the H2O resonance frequency, most of them with opposite sign relative to the diagonal. Some cross peaks arise from intrapeptide cross relaxation to labile protons of histidine, threonine, lysine and arginine side chains. The observed peptide-water interactions are rather uniformly distributed, involving peptide backbone and side chains equally. The data are consistent with rapid fluctuations of the conformational ensemble and the absence of peptide regions that are highly shielded from bulk solvent, even in a peptide that exhibits high propensities for formation of helical secondary structure.

Amino Acid Sequence↗
PubMed1993

NMR evidence for multiple conformations in a highly helical model peptide.

A monomeric model peptide, acetyl-WEAQAREALAKEAAARA-amide, has been structurally characterized using the complementary techniques of 1H 2D NMR and circular dichroism. Temperature-dependent CD measurements are consistent with a two-state helix/coil transition model and indicate a 65% contribution of helical conformers at 5 degrees C. Homonuclear 2D NMR experiments allowed the assignment of all proton resonances. The analysis of NOE-type cross-relaxation data established a large number of specific short- and medium-range NOE connectivities throughout the peptide, confirming the highly helical character of the peptide. However, the observation of long-range NOEs between the methyl protons of leucine-9 and backbone and side-chain protons of amino acids located at the N-terminus, as well as other unusual NOEs, unambiguously reflects the existence of significantly populated nonhelical structured conformers, indicating a multiconformational equilibrium. Implications of these observations with regard to secondary structure quantitation and current method limitations are discussed.

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↗
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↗