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.
Colombo
Giorgio
G
Istituto di Chimica del Riconoscimento Molecolare, CNR via Mario Bianco, 9, I-20131 Milan, Italy. g.colombo@icrm.cnr.it
Meli
Massimiliano
M
Cañada
Javier
J
Asensio
Juan Luis
JL
Jiménez-Barbero
Jesús
J
D023181:Antimicrobial Cationic Peptides; D003198:Computer Simulation; D008024:Ligands; D008958:Models, Molecular; D009844:Oligosaccharides / Q000737:chemistry* / Q000378:metabolism; D037121:Plant Lectins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D014312:Trisaccharides / Q000737:chemistry / Q000378:metabolism
D023181:Antimicrobial Cationic Peptides; D008024:Ligands; D009844:Oligosaccharides; D037121:Plant Lectins; D014312:Trisaccharides; C045875:hevein; C019117:N,N',N''-triacetylchitotriose