Molecular dynamics study of protein-oligosaccharide interaction mechanisms in chitinases

Protein-carbohydrate interactions, essential in many biomolecular recognition events, are investigated by extended molecular dynamic (MD) simulations with explicit water. The aim is to obtain atomic level information on the binding and to gain a deeper understanding of the factors determining the interactions between an oligosaccharide and a protein. The study concentrates on 42kDa chitinase from Trichoderma harzianum containing an extended binding site providing a number of strong and specific interactions with up to 6-7 sugar units. Since these interactions come from a limited number of loops, the substrate binding specificity can be altered by locally directed saturation mutagenesis. While experimentally determined three-dimensional structures were not available for the enzyme of interest, structural models were constructed based on the known structures of homologues. Experimentally determined sugar-protein complex structures of related chitinases were used in the initial simulations to evaluate the suitability of the force field parameters and simulation procedures. Classical MD (Gromacs) with a conventional force field and with a soft-core potential [1] is used to explore the conformational space of the chitinase loops and to study the functional behavior of the N-acetylglucosamine oligosaccharides and their derivates. Trajectories obtained from the simulations are used in analyzing the binding, especially the hydrogen bonding and hydrophobic interactions occurring via N/O-acetyl or O-methyl groups. When available, results from nuclear magnetic resonance spectroscopy are used to support and direct the computational studies and mutagenesis work. [1] Tappura et al.. J. Comput. Chem. 21 (2000) 388 and Proteins 44 (2001) 167.