In silico mutagenesis and docking study of RSL Lectin
Sushil K. Mishra1,
1National Centre for Biomolecular Research, Faculty of Science, Masaryk University,
Kotlářská 2, 611 37 Brno, Czech Republic
2The Skaggs School of Pharmacy, 9500 Gilman Drive, La Jolla, CA 92093 University of California San Diego, CA, USA
Lectins are proteins showing highly specific and selective binding towards mono or oligosaccharides. This large family of the proteins encompasses many biological functions that involve the deciphering of the sugar code, like cell–cell signalization or host recognition in pathogen infection. Since host carbohydrates are responsible for specific attachment sites for pathogen proteins, it is of great interest to perform the computational study of the binding and nature of interactions in lectin-saccharides complexes.
The gram-negative bacterium Ralstonia solanacearum is a pathogen causing lethal wilt in many agricultural crops and it produces a potent L-fucose binding lectin (RSL). This lectin is a trimer of 90 amino acids long chain monomer units and attains six-bladed β-propeller structure after oligomerization. RSL lectin shows very strong affinity towards fucose and fucosylated oligosaccharides and in contrary to RS-IIL lectin from R. solanacearum, do not have ions in the binding sites but is still able to create stable enough complexes with carbohydrates.
This work will be focused on in silico mutagenesis, docking of fucose and fucosylated oligosaccharides in RSL lectin. Binding energy pattern of various saccharides was investigated by a series of docking simulations. Docking experiments were performed using the software AutoDock 3, AutoDock Vina, DOCK v.6.2 and ICM Dock [2-5]. Performance of various docking programs will be discussed with respect to binding energy of those saccharides measured from SPR experiment. In silico mutants of RSL lectin was prepared using in house developed program TRITON and docking of methyl-α-L-fucoside was done to identify the important residues around the binding site and define their contributions. Merits and disadvantages of the docking programs in modeling lectin-saccharide interactions will be discussed in detail. Energetically favorable mutations obtained from the study will be investigated further by computational methods like thermodynamic integration or free energy perturbation and eventually will be determined experimentally.
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This work has been supported by
Ministry of Education of the