Biomedical subjects

Rafael Brüschweiler

Publications and source records attributed to Rafael Brüschweiler.

At least 19 recordsLinked to original sources

PubMed2006

Enhanced covariance spectroscopy from minimal datasets.

A novel approach is described for the determination of reliable high-resolution homonuclear NMR covariance spectra from minimal datasets. It uses a sparse sampling scheme along the indirect dimension together with a comprehensive analysis of finite sampling effects that eliminates spurious correlations. The scheme, which is demonstrated for TOCSY and COSY, offers a substantial speed up over current methods, rendering it suitable for high-throughput screening applications.

Image Enhancement↗

PubMed2006

Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings.

Determination of protein structure classically results in a single average configuration that takes no account of conformational fluctuation. Dynamics are, however, inherently linked to structure and crucial to our understanding of biological function. In this study we have used analytical descriptions of dynamic averaging of residual dipolar couplings (RDCs) to simultaneously determine the backbone structure and dynamics of protein GB3. RDCs alone are used to determine an ultrahigh-resolution structure that compares very closely with a refined X-ray structure (rmsd of 0.34 A overall backbone residues). Dynamic amplitudes reporting on motions up to the millisecond time scale reproduce the main characteristics of dynamics previously determined in conjunction with the crystal structure. The use of RDCs alone allows a bias-free comparison with a purely static approach to structure determination. Extensive cross validation clearly demonstrates that the dynamic description is superior to the static approximation. The demonstration that this level of structural resolution and dynamic detail can be extracted from RDCs supports previous indications that these parameters contain extremely precise information about biomolecular conformational sampling.

Models, Molecular↗

PubMed2006

The sequence-dependent unfolding pathway plays a critical role in the amyloidogenicity of transthyretin.

Human transthyretin (TTR) is an amyloidogenic protein whose aggregation is associated with several types of amyloid diseases. The following mechanism of TTR amyloid formation has been proposed. TTR tetramer at first dissociates into native monomers, which is the rate-limiting step in fibril formation. The monomeric species then partially unfold to form amyloidogenic intermediates that subsequently undergo a downhill self-assembly process. The amyloid deposit can be facilitated by disease-associated point mutations. However, only subtle structural differences were observed between the crystal structures of the wild type and the disease-associated variants. To investigate how single-point mutations influence the effective energy landscapes of TTR monomers, molecular dynamics (MD) simulations were performed on wild-type TTR and two pathogenic variants. Principal coordinate analysis on MD-generated ensembles has revealed multiple unfolding pathways for each protein. Amyloidogenic intermediates with the dislocated C strand-loop-D strand motif were observed only on the unfolding pathways of V30M and L55P variants and not for wild-type TTR. Our study suggests that the sequence-dependent unfolding pathway plays a crucial role in the amyloidogenicity of TTR. Analyses of side chain concerted motions indicate that pathogenic mutations on "edge strands" disrupt the delicate side chain correlated motions, which in turn may alter the sequence of unfolding events.

Amyloid↗

PubMed2006

Reorientational contact-weighted elastic network model for the prediction of protein dynamics: comparison with NMR relaxation.

A new model for the prediction of protein backbone motions is presented. The model, termed reorientational contact-weighted elastic network model, is based on a multidimensional reorientational harmonic potential of the backbone amide bond vector orientations and it is applied to the interpretation of dynamics parameters obtained from NMR relaxation data. The individual energy terms are weighted as a function of the intervector distances and by the contact strengths of each bond vector with respect to its local environment. Correlated reorientational motional properties of the bond vectors are obtained by means of normal mode analysis. Application to a set of proteins with known three-dimensional structures yields good to excellent agreement between predicted and experimental NMR order parameters presenting an improvement over the local contact model. The reorientational eigenmodes of the reorientational contact-weighted elastic network model method provide direct information on the collective nature of protein backbone motions. The dominant eigenmodes have a notably low collectivity, which is consistent with the behavior found for reorientational eigenmodes from molecular dynamics simulations.

Binding Sites↗

PubMed2005

Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings.

Despite their importance for biological activity, slower molecular motions beyond the nanosecond range remain poorly understood. We have assembled an unprecedented set of experimental NMR data, comprising up to 27 residual dipolar couplings per amino acid, to define the nature and amplitude of backbone motion in protein G using the Gaussian axial fluctuation model in three dimensions. Slower motions occur in the loops, and in the beta-sheet, and are absent in other regions of the molecule, including the alpha-helix. In the beta-sheet an alternating pattern of dynamics along the peptide sequence is found to form a long-range network of slow motion in the form of a standing wave extending across the beta-sheet, resulting in maximal conformational sampling at the interaction site. The alternating nodes along the sequence match the alternation of strongly hydrophobic side chains buried in the protein core. Confirmation of the motion is provided through extensive cross-validation and by independent hydrogen-bond scalar coupling analysis that shows this motion to be correlated. These observations strongly suggest that dynamical information can be transmitted across hydrogen bonds and have important implications for understanding collective motions and long-range information transfer in proteins.

Amino Acids↗

PubMed2005

Double-quantum biased covariance spectroscopy: application to the 2D INADEQUATE experiment.

A novel processing scheme is presented that converts a two-dimensional double-quantum NMR spectrum into a single-quantum correlation spectrum. The covariance-like spectrum is computed from the 2D Fourier transform spectrum by emphasizing contributions that fulfill the double-quantum condition resulting in a symmetric spectrum that is easier to analyze. The method is demonstrated for the 2D INADEQUATE experiment.

Carbon Isotopes↗

PubMed2004

Indirect covariance NMR spectroscopy.

A novel NMR scheme is presented that establishes homonuclear spin correlations without requiring direct detection of the spin species. This covariance NMR method is experimentally demonstrated for a mixture of amino acids and for the uniformly 13C-labeled cyclic decapeptide antamanide using a 13C-edited TOCSY experiment. The method opens up new avenues for the experimental analysis of molecules containing insensitive spins encountered in biomolecular NMR and analytical chemistry including metabolomics.

Fourier Analysis↗

PubMed2004

Theory of covariance nuclear magnetic resonance spectroscopy.

Covariance nuclear magnetic resonance (NMR) spectroscopy provides an effective way for establishing nuclear spin connectivities in molecular systems. The method, which identifies correlated spin dynamics in terms of covariances between 1D spectra, benefits from a high spectral resolution along the indirect dimension without requiring apodization and Fourier transformation along this dimension. The theoretical treatment of covariance NMR spectroscopy is given for NOESY and TOCSY experiments. It is shown that for a large class of 2D NMR experiments the covariance spectrum and the 2D Fourier transform spectrum can be related to each other by means of Parseval's theorem. A general procedure is presented for the construction of a symmetric spectrum with improved resolution along the indirect frequency domain as compared to the 2D FT spectrum.

Computer Simulation↗

PubMed2004

Spectral deconvolution of chemical mixtures by covariance NMR.

A method is presented for the deconvolution of the NMR spectrum of a chemical mixture without requiring physical separation of its components. The method, which is termed "Demix", is based on a principal component analysis of a series of one-dimensional (1D) spectra that are statistically modulated during preparation and TOCSY mixing periods. The largest principal components correspond to the 1D NMR spectra of the scalar J-coupled spin networks of the individual components of the mixture. The method is demonstrated for aqueous mixtures of the amino acids Glu, Leu, Lys, and Val.

Amino Acids↗

PubMed2004

Covariance nuclear magnetic resonance spectroscopy.

Covariance nuclear magnetic resonance (NMR) spectroscopy is introduced, which is a new scheme for establishing nuclear spin correlations from NMR experiments. In this method correlated spin dynamics is directly displayed in terms of a covariance matrix of a series of one-dimensional (1D) spectra. In contrast to two-dimensional (2D) Fourier transform NMR, in a covariance spectrum the spectral resolution along the indirect dimension is determined by the favorable spectral resolution obtainable along the detection dimension, thereby reducing the time-consuming sampling requirement along the indirect dimension. The covariance method neither involves a second Fourier transformation nor does it require separate phase correction or apodization along the indirect dimension. The new scheme is demonstrated for cross-relaxation (NOESY) and J-coupling based magnetization transfer (TOCSY) experiments.

Fourier Analysis↗

PubMed2004

Estimates of methyl 13C and 1H CSA values (Deltasigma) in proteins from cross-correlated spin relaxation.

Simple pulse schemes are presented for the measurement of methyl (13)C and (1)H CSA values from (1)H-(13)C dipole/(13)C CSA and (1)H-(13)C dipole/(1)H CSA cross-correlated relaxation. The methodology is applied to protein L and malate synthase G. Average (13)C CSA values are considerably smaller for Ile than Leu/Val (17 vs 25 ppm) and are in good agreement with previous solid state NMR studies of powders of amino acids and dipeptides and in reasonable agreement with quantum-chemical DFT calculations of methyl carbon CSA values in peptide fragments. Small averaged (1)H CSA values on the order of 1 ppm are measured, consistent with a solid state NMR determination of the methyl group (1)H CSA in dimethylmalonic acid.

Bacterial Proteins↗

PubMed2004

Covariance NMR spectroscopy by singular value decomposition.

Covariance NMR is demonstrated for homonuclear 2D NMR data collected using the hypercomplex and TPPI methods. Absorption mode 2D spectra are obtained by application of the square-root operation to the covariance matrices. The resulting spectra closely resemble the 2D Fourier transformation spectra, except that they are fully symmetric with the spectral resolution along both dimensions determined by the favorable resolution achievable along omega2. An efficient method is introduced for the calculation of the square root of the covariance spectrum by applying a singular value decomposition (SVD) directly to the mixed time-frequency domain data matrix. Applications are shown for 2D NOESY and 2QF-COSY data sets and computational benchmarks are given for data matrix dimensions typically encountered in practice. The SVD implementation makes covariance NMR amenable to routine applications.

Magnetic Resonance Spectroscopy↗

PubMed2004

Prediction of methyl-side chain dynamics in proteins.

A simple analytical model is presented for the prediction of methyl-side chain dynamics in comparison with S(2) order parameters obtained by NMR relaxation spectroscopy. The model, which is an extension of the local contact model for backbone order parameter prediction, uses a static 3D protein structure as input. It expresses the methyl-group S(2) order parameters as a function of local contacts of the methyl carbon with respect to the neighboring atoms in combination with the number of consecutive mobile dihedral angles between the methyl group and the protein backbone. For six out of seven proteins the prediction results are good when compared with experimentally determined methyl-group S(2) values with an average correlation coefficient r = 0.65+/-0.14. For the unusually rigid cytochrome c(2) no significant correlation between prediction and experiment is found. The presented model provides independent support for the reliability of current side-chain relaxation methods along with their interpretation by the model-free formalism.

Carbon↗

PubMed2004

Projection angle restraints for studying structure and dynamics of biomolecules.

This chapter presents a methodology that allows for the structural and dynamic characterization of biomolecules by means of projection restraints obtained from residual magnetic dipolar couplings. Dipolar couplings reflect the projection of individual internuclear vectors onto the alignment tensor. This technique allows determination of the dynamics of the protein backbone on time-scales, namely, between the rotational tumbling correlation time and approx 50 micros. This range of time-scales has been previously inaccessible by other nuclear magnetic resonance (NMR) techniques. In addition, information about the anisotropy of the motion is obtained.

Models, Chemical↗

PubMed2003

Self-consistency analysis of dipolar couplings in multiple alignments of ubiquitin.

A self-consistency analysis of backbone N-H residual dipolar couplings of ubiquitin collected in 10 different media is described to assess the degree of structural and dynamic heterogeneous behavior across the media. The SECONDA method, which works with and without any structural or dynamic information about the molecular system, is based on a principal component analysis and is very sensitive to the presence of heterogeneities or experimental errors. It is found that the regular secondary structural elements behave highly homogeneously, while small heterogeneities are manifested in the loop region 51-63. Many residues that exhibit increased dynamics in NMR relaxation experiments are inert with respect to changes in the alignment.

Models, Molecular↗

PubMed2003

Efficient RMSD measures for the comparison of two molecular ensembles. Root-mean-square deviation.

Quantitative measures are presented for comparing the conformations of two molecular ensembles. The measures are based on Kabsch's formula for the root-mean-square deviation (RMSD) and the covariance matrix of atomic positions of isotropically distributed ensembles (IDE). By using a Taylor series expansion, it is shown that the RMSD can be expressed solely in terms of the IDE matrices. A fast approximate method is introduced for the pairwise RMSD determination whose computational cost scales linearly with the number of structures. A similarity measure for two structural ensembles that is based on the trace metric of the differences of powers of the IDE matrices is presented. The measures are illustrated for conformational ensembles generated by a molecular dynamics computer simulation of a partially folded A-state analog of ubiquitin.

Computational Biology↗

PubMed2003

New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins.

NMR relaxation experiments of isotopically labeled proteins provide a wealth of information on reorientational global and local dynamics on nanosecond and subnanosecond timescales for folded and nonfolded proteins in solution. Recent methodological advances in the interpretation of relaxation data have led to a better understanding of the overall tumbling behavior, the separability of internal and overall motions, and the presence of correlated dynamics between different nuclear sites, as well as to new insights into the relationship between reorientational dynamics and primary and tertiary protein structure. Some of the new methods are particularly useful when dealing with nonfolded protein states.

Algorithms↗

PubMed2003

Cross-correlation suppressed T1 and NOE experiments for protein side-chain 13CH2 groups.

Relaxation measurements of side-chain 13CH2-groups of uniformly 13C labeled human ubiquitin were performed at 600 MHz and 800 MHz magnetic field strength at 30 degrees C. Dipole-dipole cross-correlated relaxation effects in T1 experiments were suppressed by the combination of radio-frequency pulses and pulsed field gradients during the relaxation delay leading to monoexponential relaxation decays that allow a more accurate extraction of the 13C T1 relaxation times. Heteronuclear [1H]-13C NOEs obtained by using different proton saturation schemes indicate that the influence of cross-correlation is small. The experimental T1 and NOE data were interpreted in a model-free way in terms of a generalized order parameter and an internal correlation time.

Amino Acids↗