Unraveling the problems of protein - saccharide interactions via computational chemistry
Z. Kříž1, J. Adam1, O. Šulák1, M. Wimmerová1,2 , J. Koča1,3
1National Centre for Biomolecular Research, Faculty of Science, Masaryk University,
Kamenice 5, 625 00 Brno.
2Institute of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno.
3Institute of Chemistry, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno.
zdenek@chemi.muni.cz
Keywords: Lectin, monosaccharides, Molecular Docking, Scoring function.
Detailed knowledge of interactions between proteins and small molecules
is important for understanding of
significant processes in organisms. Saccharides and various
glycoconjugates play a significant role in many host-pathogen interactions.
Lectins are sugar-binding proteins of non-immunoglobulin nature that
agglutinate cells or precipitate glycoconjugates. Their specificity is usually
defined by the monosaccharides or oligosaccharides that are best at inhibiting
the agglutination or precipitation the lectin causes. Lectins are of interest
because of their wide variety of properties and potential applications
(pharmacology, immunology, cancer therapy, agriculture ...).
Since host carbohydrates have been known for many years to constitute
specific attachment sites for pathogen protein receptors, there is a
great interest in structure-function studies of bacterial proteins
enabling the pathogen attachment to host glycans. However, only a
limited number of their complexes with receptors have been
characterized by crystallography [1]. The molecular modeling methods can help
in the study of the complexes.
The study will be focused on docking of a set
of monosaccharides into two different lectins originally from bacteria Pseudomonas aeruginosa (PA-IIL) [2] and Ralstonia solanacearum (RS-20L) using the Dock v. 6.0 program [3]. The best docked structures (using standard
scoring function) were scored again using AMBER scoring function with solvation
energy based on implicit solvent model. The same structures were also solvated
using TIP3P water model and MD simulations have been run. The binding energies
were afterwards calculated from the trajectories. There will be shown the
differences in calculated binding energies by using different scoring functions
and also the effect of solvation energy on the binding energy.
1.
Mitchell, E.P.,
Houles. C., Sudakevitz, D., Wimmerova, M., Gautier, C., Perez, S., Wu, A.M.,
Gilboa-Garber, N., Imberty, A. Nat.
Struct Biol., 9 (2002), 918.
2. Mitchell, E.P., Sabin, Ch., Šnajdrová L., Pokorná M.,
Perret, S., Gautier, C., Hofr, C., Gilboa-Garber, N., Koča, J., Wimmerová, M.
Imberty, A. Proteins, 58, (2005), 735.
3. Lang, T. P., Moustakas, D., Brozell, S., Carrascal, N., Mukherjee, S., Pegg, S., Raha, K., Shivakumar, D., Rizzo, R., Case, D., Shoichet, B., Kuntz, I.: Dock 6.0, University of California, San Francisco, 2006.
Acknowledgements.
This work has been financially supported by Ministry of Education (MSM0021622413 and LC06030) and Grant Agency of Czech Republic (GD204/03/016 and GA303/06/0570).