Biomedical subjects

Rafael Brüschweiler

Publications and source records attributed to Rafael Brüschweiler.

10 recordsLinked to original sources

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↗

PubMed2002

Contact model for the prediction of NMR N-H order parameters in globular proteins.

An analytical relationship is presented for the estimation of NMR S2 order parameters of N-HN vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the relationship to a number of proteins with high-resolution X-ray and NMR structures yields S2 values that are in good agreement with the ones determined from experimental relaxation data.

HIV Protease↗

PubMed2002

Model-free analysis of protein backbone motion from residual dipolar couplings.

On the basis of the measurement of NH residual dipolar couplings (RDCs) in 11 different alignment media, an RDC-based order parameter is derived for each residue in the protein ubiquitin. Dipolar couplings are motionally averaged in the picosecond to millisecond time range and, therefore, reflect motion slower than the inverse overall tumbling correlation time of the protein. It is found that there is considerable motion that is slower than the correlation time and could not be detected with previous NMR methodology. Amplitudes and anisotropies of the motion can be derived from the model-free analysis. The method can be applied provided that at least five sufficiently different alignment media can be found for the biomolecule under investigation.

Computer Simulation↗

PubMed2002

General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation.

A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin interactions responsible for spin relaxation. The covariance matrix, which is evaluated using a molecular dynamics (MD) simulation, is diagonalized yielding reorientational eigenmodes and amplitudes that reveal detailed information about correlated protein dynamics. The eigenvalue distribution allows one to quantitatively assess whether overall and internal motions are statistically separable. To each eigenmode belongs a correlation time that can be adjusted to optimally reproduce experimental relaxation parameters. A key feature of the method is that it does not require separability of overall tumbling and internal motions, which makes it applicable to a wide range of systems, such as folded, partially folded, and unfolded biomolecular systems and other macromolecules in solution. The approach was applied to NMR relaxation data of ubiquitin collected at multiple magnetic fields in the native form and in the partially folded A-state using MD trajectories with lengths of 6 and 70 ns. The relaxation data of native ubiquitin are well reproduced after adjustment of the correlation times of the 10 largest eigenmodes. For this state, a high degree of separability between internal and overall motions is present as is reflected in large amplitude and collectivity gaps between internal and overall reorientational modes. In contrast, no such separability exists for the A-state. Residual overall tumbling motion involving the N-terminal beta-sheet and the central helix is observed for two of the largest modes only. By adjusting the correlation times of the 10 largest modes, a high degree of consistency between the experimental relaxation data and the iRED model is reached for this highly flexible biomolecule.

Computer Simulation↗

PubMed2002

Dynamic and structural analysis of isotropically distributed molecular ensembles.

An efficient new method is presented for the characterization of motional correlations derived from a set of protein structures without requiring the separation of overall and internal motion. In this method, termed isotropically distributed ensemble (IDE) analysis, each structure is represented by an ensemble of isotropically distributed replicas corresponding to the situation found in an isotropic protein solution. This leads to a covariance matrix of the cartesian atomic positions with elements proportional to the ensemble average of scalar products of the position vectors with respect to the center of mass. Diagonalization of the covariance matrix yields eigenmodes and amplitudes that describe concerted motions of atoms, including overall rotational and intramolecular dynamics. It is demonstrated that this covariance matrix naturally distinguishes between "rigid" and "mobile" parts without necessitating a priori selection of a reference structure and an atom set for the orientational alignment process. The method was applied to the analysis of a 5-ns molecular dynamics trajectory of native ubiquitin and a 40-ns trajectory of a partially folded state of ubiquitin. The results were compared with essential dynamics analysis. By taking advantage of the spherical symmetry of the IDE covariance matrix, more than a 10-fold speed up is achieved for the computation of eigenmodes and mode amplitudes. IDE analysis is particularly suitable for studying the correlated dynamics of flexible and large molecules.

Computer Simulation↗

PubMed2002

Assignment strategy for proteins with known structure.

In protein NMR the assignment of nuclear spin resonances is a prerequisite for all subsequent applications, such as studies of ligand binding, protein-DNA interactions, and dynamics. Resonance assignment is a time consuming step even when the 3D x-ray structure of the protein is available. A new strategy is presented to solve the "inverse" assignment problem, which is the determination of the NMR resonance assignment from a known 3D protein structure. The protocol employs NMR data in the form of residual dipolar couplings and chemical shifts, while it does not require any sequential NMR connectivity information. The assignment problem is mathematically formulated in terms of a weighted matching problem that can be computationally efficiently solved by a combinatorial optimization algorithm. The protocol is applied to ubiquitin using two or three residual dipolar couplings per amino acid measured in Pfl phage medium together with chemical shift information. The algorithm yields for more than 90% of the protein backbone resonances the correct assignment.

Algorithms↗

PubMed2002

Principal component method for assessing structural heterogeneity across multiple alignment media.

The recent availability of residual dipolar coupling measurements in a variety of different alignment media raises the question to what extent biomolecular structure and dynamics are differentially affected by their presence. A computational method is presented that allows the sensitive assessment of such changes using dipolar couplings measured in six or more alignment media. The method is based on a principal component analysis of the covariance matrix of the dipolar couplings. It does not require a priori structural or dynamic information nor knowledge of the alignment tensors and their orientations. In the absence of experimental errors, the covariance matrix has at most five nonzero eigenvalues if the structure and dynamics of the biomolecule is the same in all media. In contrast, differential structural and dynamic changes lead to additional nonzero eigenvalues. Characteristic features of the eigenvalue distribution in the absence and presence of noise are discussed using dipolar coupling data calculated from conformational ensembles taken from a molecular dynamics trajectory of native ubiquitin.

Computational Biology↗