13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Sidechain Dynamics Predictions by Current AMBER and CHARMM Force Fields.
Related Articles 13C NMR Relaxation Analysis of Protein GB3 for the Assessment of Sidechain Dynamics Predictions by Current AMBER and CHARMM Force Fields.
J Chem
Theory Comput. 2020 Apr 08;:
Authors: Anderson
JS, Hernandez G, LeMaster DM
Abstract
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? and C? 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 timeframe 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?-13C? and 1H?-13C? bond vectors with reasonable accuracy. However, for the 1H?-13C? bond vectors exhibiting aggregate order parameter S2 values less than 0.85, only 1% of the MD-derived predictions lie with 1 ? of the experimentally determined autocorrelation functions and only 7% within 2 ?. 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 sidechain dynamics characteristics of protein molecular simulations.
PMID: 32268062 [PubMed - as supplied by publisher]
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