Jeanine J. Prompers

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. Proteins 2002;46:177–189.

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 600xa0MHz and 800xa0MHz magnetic field strength at 30u2009°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.

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.