Improved Umbrella Visualization implemented in UnityMol gives valuable insight on sugar/protein interplay

Abstract

Among the various post-translational modifications, N-glycosylations are particularly important. They are linked to asparagine residues and their function as well as the one of the protein can be altered by modifications such as sialic acid hydrolysis. Since in vitro studies of N-glycans can be a challenging process (glycosylation chains have a great diversity and contain many reactive groups), in silico characterization using molecular dynamics simulation seems to be a good tool capable of overcoming experimental shortcomings thanks to exhaustive conformational samplings. In this paper, the Umbrella Visualization, a recent implementation into the molecular viewer UnityMol, is presented. This new and original visualization method is offering the possibility to follow and decipher the dynamics of very flexible sugar chains and enable the identification of the protein surface covered and potentially impacted by glycans. The latest module, described here and integrated within the Umbrella Visualization, complements the original statistical approach and allows for a meaningful description of glycan/protein interplay by combining, with shadow mapping, labelling, and hydrophobic properties of the surrounding aminoacids.