Stochastic Modeling of
Flexible Biomolecules Applied
to NMR Relaxation. 2. Interpretation of Complex Dynamics in Linear
Oligosaccharides
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Abstract
A computational stochastic approach is applied to the
description
of flexible molecules. By combining (i) molecular dynamics simulations,
(ii) hydrodynamics approaches, and (iii) a multidimensional diffusive
description for internal and global dynamics, it is possible to build
an efficient integrated approach to the interpretation of relaxation
processes in flexible systems. In particular, the model is applied
to the interpretation of nuclear magnetic relaxation measurements
of linear oligosaccharides, namely a mannose-containing trisaccharide
and the pentasaccharide LNF-1. Experimental data are reproduced with
sufficient accuracy without free model parameters
