Caracterização in silico das estruturas e funcionamento de proteínas quanto a sua glicosilação

Abstract

The increased scientifical and comercial interest in recombinant proteins caused an increase on demand for its production. However, due to the posttranslational modifications of certain proteins, some protein expression systems are incapable of producing some proteins correctly. Protein glycosylation is a post-translational modification that occurs in over 50% of eukaryote proteins, and the correct glycosylation is necessary for the biological activity of some proteins. However, some expression systems, like Escherichia coli, does not have the machinery necessary for glycosylation, causing some of these glycoproteins, when produced heterologously, to not function properly. This present work performs an in silico analysis of glycoprotein structure and activity in the presence and absence of its glycan, through molecular dynamics and docking. Four proteins, all part of the lectin type, were selected for this analysis; A 10 nanosecond molecular dynamics run was performed for each protein with and without its glycan, using the GROMACS software. These structures were then clustered and docked with their respective ligands. The structural analysis was performed using the GROMACS, Bio3D and PyMol softwares. Docking was performed using the Autodock Vina, CLC Drug Discovery and Swiss-Dock softwares. The PLIP web-server was used to analyze the hydrogen bonds of the docked complex. The results showed that three of the four proteins had a greater structural stability in their glycosylated form. The docking results also showed that the same three proteins had a greater docking affinity in their glycosylated form. These results show that it’s possible to combine molecular dynamics and docking as an protein glycosylated structure analysis pipeline. However, further studies are needed to verify if these results can be reproduced in longer simulations.