Using molecular dynamics trajectories to predict nuclear spin relaxation behaviour in large spin systems

Kuprov, Ilya; Morris, Laura C.; Glushka, John; Prestegard, James H.

doi:10.1016/j.jmr.2020.106891

Cited by 7 publications

(1 citation statement)

References 46 publications

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“…Still, the present general purpose SFB model showed a good performance if compared with straightforward results obtained via molecular dynamics simulations, especially considering that O(

s) trajectories were required in the latter case [ 28 , 39 ]. As mentioned before, the only free parameter here was

, which was adapted case by case, but as a rule of thumb, a starting value of 2 Å usually provided good agreement with the experiment.…”

Section: Discussionmentioning

confidence: 95%

Stochastic Modelling of 13C NMR Spin Relaxation Experiments in Oligosaccharides

2021

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A framework for the stochastic description of relaxation processes in flexible macromolecules including dissipative effects has been recently introduced, starting from an atomistic view, describing the joint relaxation of internal coordinates and global degrees of freedom, and depending on parameters recoverable from classic force fields (energetics) and medium modelling at the continuum level (friction tensors). The new approach provides a rational context for the interpretation of magnetic resonance relaxation experiments. In its simplest formulation, the semi-flexible Brownian (SFB) model has been until now shown to reproduce correctly correlation functions and spectral densities related to orientational properties obtained by direct molecular dynamics simulations of peptides. Here, for the first time, we applied directly the SFB approach to the practical evaluation of high-quality 13C nuclear magnetic resonance relaxation parameters, T1 and T2, and the heteronuclear NOE of several oligosaccharides, which were previously interpreted on the basis of refined ad hoc modelling. The calculated NMR relaxation parameters were in agreement with the experimental data, showing that this general approach can be applied to diverse classes of molecular systems, with the minimal usage of adjustable parameters.

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“…Still, the present general purpose SFB model showed a good performance if compared with straightforward results obtained via molecular dynamics simulations, especially considering that O(

s) trajectories were required in the latter case [ 28 , 39 ]. As mentioned before, the only free parameter here was

, which was adapted case by case, but as a rule of thumb, a starting value of 2 Å usually provided good agreement with the experiment.…”

Section: Discussionmentioning

confidence: 95%