title: The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis.
abstract: Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure.
authors.affiliation: Department of Chemistry, Faculty of sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
authors.forename: Z
authors.initials: Z
authors.lastname: Ghanbari
authors.affiliation: Department of Chemistry, Faculty of sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
authors.forename: M R
authors.initials: MR
authors.lastname: Housaindokht
authors.affiliation: Department of Chemistry, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
authors.forename: M R
authors.initials: MR
authors.lastname: Bozorgmehr
authors.affiliation: Department of Chemistry, Faculty of sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
authors.forename: M
authors.initials: M
authors.lastname: Izadyar
mesh_terms: D001665:Binding Sites; D002254:Carbonates / Q000378:metabolism; D006031:Glycosylation; D006801:Humans; D007501:Iron / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011134:Polysaccharides / Q000378:metabolism; D000072417:Protein Domains; D012997:Solvents; D014168:Transferrin / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D002254:Carbonates; D011134:Polysaccharides; D012997:Solvents; D014168:Transferrin; D007501:Iron
keywords: Carbonate binding site; Glycosylation; Lobe–lobe interaction; Separated lobe transferrin