Abstract
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, and , 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.
Highlights
We focused on the most convenient choices from the computational point of view; the method was implemented in the form of an integrated package, the Stochastic Augmented Liouville Equation Method (SALEM), which operates from scratch reading the single reference structure, evaluating all the internal parameters based on some assumed
We tested our method on a collection of oligosaccharides, for which previous analyses based on specific stochastic models were presented
The results reported in the previous section showed that the semi-flexible Brownian (SFB) model reproduced the observed relaxation times and the NOEs of the set of oligosaccharides reported here, with an average accuracy of 5–10%, proving the ability of capturing the long-range dynamics of these systems
Summary
Monitoring and describing molecular dynamics are an important area of investigation in modern physical chemistry. Internal and global motions in solution affect directly or indirectly most spectroscopic methods aimed at the characterization of non-rigid molecules such as Nuclear Magnetic Resonance (NMR) relaxation [1,2,3], fluorescence anisotropy decay [4], timeresolved X-ray [5] and in single-molecule experiments such as site-directed spin-labelled electron spin resonance [6,7], Förster fluorescence resonance energy transfer [8] and atomic force microscopy [9]. Nuclear Magnetic Resonance (NMR) spectroscopy is known to be an important and powerful experimental technique for the observation of the dynamic properties of macromolecules. Some of the macroscopic physical observables are the relaxation times
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