Protein dynamics scalar couplings

In liquid-state NMR, spin relaxation due to cross-correlation of two anisotropic spin interactions can provide useful information about molecular structure and dynamics. These effects are manifest as differential line widths or line intensities in the NMR spectra. Recently, new experiments were developed for the accurate measurement of numerous cross-correlated relaxation rates in scalar coupled multi-spin systems. The recently introduced concept of transverse relaxation optimized spectroscopy (TROSY) is also based on cross-correlated relaxation. Brutscher outlined the basic concepts and experimental techniques necessary for understanding and exploiting cross-correlated relaxation effects in macromolecules. In addition, he presented some examples showing the potential of cross-correlated relaxation for high-resolution NMR studies of proteins and nucleic acids. 

Recently, Lindorff-Larsen el al.uo included the order parameter (S 2) in the target function, and refined an ubiquitin X-ray structure by restrained molecular dynamics (Section 6.4) to obtain an NMR structure ensemble (Section 6.5) from the trajectories. They simulated the values of RDCs (Section 9.1) and side chain scalar coupling from the calculated ensemble to confirm that the method can determine the protein three-dimensional structure and dynamic structure simultaneously. The simulated values were in good agreement with the corresponding measurement data. The simulation accuracy was improved from the preliminary calculated structure without the order parameters. The approach is typically important, because they tried to link the ensemble with a dynamic structure directly. 

Backbone scalar couplings are widely used in NMR studies of structure and dynamics of biomolecules [93]. Additionally, there is a substantial interest in precise determination of residual dipolar couplings for structural studies of weakly oriented biomolecules. Most of the relevant coupling constants in proteins are rather small - of the magnitude from a few to a hundred hertz. Therefore, in order to achieve the sufficient resolution in indirectly measured dimensions, the majority of traditional methods devoted to coupling constants determination in biomolecules are limited to two-dimensional techniques, which frequently suffer from peak overlap. However, the random sampling of evolution time domain allows one to obtain spectra of resolution limited only by transverse relaxation... 

K. Lindorff-Larsen, R.B. Best, M. Vendruscolo, Interpreting dynamically-averaged scalar couplings in proteins, J. Biomol. NMR 32 (2005) 273-280. 

Widmalm in a short review based mostly on the results of his laboratory has presented a perspective on structures of carbohydrates. He has underlined the central position of the solution state NMR spectroscopy in these studies starting with analysis of the primary structure of glycans (components and sequence), followed by conformational and dynamics analysis to the study of interaction with proteins. He has also anticipated that among other NMR parameters DFT calculated vicinal proton-proton, proton-carbon and carbon-carbon scalar couplings will aid these investigations. 

As an attempt to connect the first discussion, which was concerned with diffusion-reaction coupling, with Dr. Williams presentation of enzymes as dynamic systems, I wanted to direct attention to a number of specific systems. These are the energy-transducing proteins that couple scalar chemical reactions to vectorial flow processes. For example, I am thinking of active transport (Na-K ATPase), muscular contraction (actomyosin ATPase), and the light-driven proton pump of the well-known purple... 

Lindorflf-Larsen et have presented the DER protocol (dynamic-ens-amble refinement) for determining protein structures. The structures are validated with back-calculated backbone RCDs and side-chain scalar Vcc and JcN couplings. 

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