Carbohydrates are involved in a lot of intra and extracellular signalling pathways.
Interaction between carbohydrates and proteins belongs to the most important biological interactions and these interactions are widespread in all living systems. Our research is mainly focused to lectin molecules.
Lectins are carbohydrate-binding proteins that are highly specific for sugar moieties. Lectin-saccharide interactions relate to the virulence of several bacteria that are capable of acting as opportunistic human pathogens or fytopathogens. We investigate lectins from several opportunistic human pathogens Pseudomonas aeruginosa , Chromobacterium violaceum , phytopathogens Ralstonia solanacearum and fungi Aleuria Aurantia.
We use various methods of computational chemistry to understand interaction between proteins and carbohydrates. Methods of molecular dynamics using AMBER software package are used to simulate physiological conditions more precisely to further optimize the results of docking and to evaluate the energetic properties [ Mishra ]. The Linear Interaction Energy LIE method is also used to calculate binding affinities [ Mishra b ] a well as Hamiltonian replica-exchange simulations [ Mishra ].
Computational studies of lectin-carbohydrate interactions | CEITEC - výzkumné centrum
Virtual screening and docking are used for identification of compounds that might inhibit interaction of sacharide with PA-IIL lectin from human opportunistic pathogen - bacteria Pseudomonas aeruginosa and be potentially used as a new generation of antibiotics. A specific goal is finding the best ligand drug molecule that competitively binds with the carbohydrate binding domain of the lectin, that can inhibit the attachment of P. Within the method, databases of ligands e. ZINC database are screened for best binding ligands using molecular docking using e.
AutoDock software. Some lectin molecules display distinct differences in sugar preference despite only small differences in structure of binding site.
We construct in silico mutants in order to analyze the principles driving the sugar preference. Comparison of computed values with experimental one enables to asses reliability of the in silico method to correctly model the interaction and the preference changes in regard to mutations in the binding site [ Wimmerova , Mishra a ].
Physical Chemistry Chemical Physics , 13 31 , Download PDF Flyer. DOI: The interactions between carbohydrates and proteins have been extensively explored in a wide range of physiological and pathological processes over several decades.
The recent emergence of glycomics has strengthened this interest and notably contributed to spectacular progress in understanding how carbohydrates mediate and regulate complex biological events. Synthesis and Biological Applications of Glycoconjugates gives a summary of contemporary findings in glycoconjugate research.
Readers will be updated on major achievements in chemical methods and biological applications employed in modern glycomics.
The Ebook should be of interest to a broad community of students and professional researchers in both academia and industry.