Toward the understanding of the structure and dynamics of protein-carbohydrate interactions: molecular dynamics studies of the complexes between hevein and oligosaccharidic ligands

Herein we study, through all atom molecular dynamics simulations, the
complex between hevein and two N-acetylated chitin oligomers, namely
N,N'-diacetylchitobiose and N,N',N''-triacetylchitotriose. The results
of the simulations for two disaccharide complexes and one trisaccharide
complex show that a carbohydrate oligomer is able to move on the surface
of the relatively flat binding pocket of hevein, therefore occupying
different binding subpockets. Statistical analysis methods were also
applied in order to define the principal overall motions in the
complexes, showing how the different ligands in the simulations modulate
the protein motions. The oligosaccharide binding can be considered as
defined by a subtle balance between enthalpic (formation of
intermolecular interactions between the ligand and the receptor) and
entropic (due mainly to the possibility for the sugar to move on the
surface of the protein domain) effects, determining multiple binding
conformations. This structural and dynamical view could parallel the
results obtained by regularly used restrained MD simulations based on
NOE NMR data that provide a well defined structure for both the
disaccharide and trisaccharide complexes, and agrees with the
observations for longer oligosaccharide chains. (C) 2003 Elsevier Ltd.
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