NMR relaxation in multipolar AX systems under spin locking conditions

13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Side Chain Dynamics Predictions by Current AMBER and CHARMM Force Fields

Molecular simulations with seven current AMBER- and CHARMM-based force fields yield markedly differing internal bond vector autocorrelation function predictions for many of the 223 methine and methylene H-C bonds of the 56-residue protein GB3. To enable quantification of accuracy, ¹³C R₁, R₂, and heteronuclear NOE relaxation rates have been determined for the methine and stereochemically assigned methylene C^α and C^β positions. With only three experimental relaxation values for each bond vector, central to this analysis is the accuracy with which MD-derived autocorrelation curves can be represented by a 3-parameter equation which, in turn, maps onto the NMR relaxation values. In contrast to the more widely used extended Lipari-Szabo order parameter representation, 95% of these MD-derived internal autocorrelation curves for GB3 can be fitted to within 1.0% rmsd over the time frame from 30 ps to 4 ns by a biexponential Larmor frequency-selective representation (LF-S²). Applying the LF-S² representation to the experimental relaxation rates and uncertainties serves to determine the boundary range for the autocorrelation function of each bond vector consistent with the experimental data. Not surprisingly, all seven force fields predict the autocorrelation functions for the more motionally restricted ¹H^α-¹³C^α and ¹H^β-¹³C^β bond vectors with reasonable accuracy. However, for the ¹H^β-¹³C^β bond vectors exhibiting aggregate order parameter S² values less than 0.85, only 1% of the MD-derived predictions lie with 1 σ of the experimentally determined autocorrelation functions and only 7% within 2 σ. On the other hand, substantial residue type-specific improvements in predictive performance were observed among the recent AMBER force fields. This analysis indicates considerable potential for the use of ¹³C relaxation measurements in guiding the optimization of the side chain dynamics characteristics of protein molecular simulations.

NMR relaxation in multipolar AMX systems under spin-locking conditions

A relaxation network has been calculated for multipolar AMX systems under application of a spin-locking RF field. Systems of this type are of interest in the study of proteins with fractional (2)H enrichment. All possible auto- and cross-correlation terms involving dipolar, quadrupolar, and CSA interactions have been taken into account. The results show the presence of spectral densities at zero frequency for interactions associated with the locked nuclei, which are nonvanishing in the absence of fast motions. In addition, the application of a spin-locking field blocks certain cross-correlation interactions, thereby considerably simplifying the relaxation network. Copyright 2000 Academic Press.