Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Abstract

Nuclear Magnetic Resonance (NMR) became during the two last decades an important method for biomolecular structure determination. NMR permits to study biomolecules in solution and gives access to the molecular flexibility at atomic level on a complete structure: in that respect, it is occupying a unique place i n structural biology. During the first years of its development, NMR was trying to meet the requirements previously defined in X-ray crystallography. But, NMR then started to determine its own criteria for the definition of a structure. Indeed, the atomic coordinates of an NMR structure are calculated using restraints on geometrical parameters (angles and distances) of the structure, which are only indirectly related to atom positions: in that respect, NMR and X-ray crystallography are very different. The indirect relation between the NMR measurements and the molecular structure and dynamics makes critical the precision and the interpretation of the NMR parameters and the development of quantitative analysis methods. The methods published since 1997 for liquid-NMR of proteins are reviewed here. First, methods for structure determination are presented, as well as methods for spectral assignment and for structure quality assessment. Second, the quantitative analysis of structure mobility i s reviewed.

Using Molecular Dynamics Simulations To Provide New Insights into Protein Structure on the Nanosecond Timescale: Comparison with Experimental Data and Biological Inferences for the Hyaluronan-Binding Link Module of TSG-6

“…Prediction of NOESY Cross-Peak Intensities and Comparison with Experimental Data. Several NMR experiments, described and performed previously, 26 were used to obtain NOE distance constraints: a 2D 1 H-NOESY (unlabeled protein) in D 2 O, a 3D 13 C-NOESY-HSQC ( 13 C, 15 Nlabeled protein) in H 2 O, a 3D 15 N-NOESY-HSQC, and a 3D 15 N-HSQC-NOESY-HSQC ( 15 N-labeled protein) both in H 2 O. In order to make a comparison between the simulation and this experimental data, the raw intensities of assigned peaks were measured in each spectrum.…”

“…10 A more detailed analysis of protein dynamics in solution can be performed using experimental techniques such as fluorescence anisotropy, 11 measurements of NMR relaxation parameters, and residual dipolar couplings. [12][13][14] While NMR relaxation is in principle capable of investigating ns-time scale protein dynamics at residue-specific positions, a serious problem is encountered because both internal motion and overall tumbling contribute to dipolar relaxation. Since overall tumbling in proteins occurs on the nanosecond time scale, separation of the two processes cannot be achieved effectively even in the ideal case of isotropic motion.…”

Protein structure prediction: Combining de novo modeling with sparse experimental data

“…The first kind of these additional experimental data is based on the NMR measurements of three bond coupling constants, which are widely used in the determination of different dihedral angles (for example 3 J NHH ). 12,13 The second method is based on the long-range distances between C atoms and between side chains, which can be obtained in the experiments based on the nuclear overhauser effect (NOE). Both of these methods are commonly used in the protein structure determination but, on the other hand, they are much more difficult in processing and analyzing than the data obtained from chemical shifts measurements.…”