The stabilizing effects of O-glycosylation on the secondary structural integrity of the designed alpha-loop-alpha motif by molecular dynamics simulations.
In this study, various 400 ps molecular dynamics simulations were conducted to determine the stabilizing effect of O-glycosylation on the secondary structural integrity of the design alpha-loop-alpha motif, which has the optimal loop length of 7 Gly residues (denoted as N-A16G7A16-C). In general, O-glycosylation stabilizes the structural integrity of the model peptide regardless of the length and position of glycosylation sites because it decreases the opportunity for water molecules to compete for the intramolecular hydrogen bonds. The designed peptide exhibits the highest helicity when residues 11 and 31 are replaced with Ser residues followed by O-linked with 3 galactose residues, representing the "face-to-face" glycosylation near the loop. In this case, the loop exhibits an extended conformation and several new hydrogen bonds are observed between the main chain of the loop and the galactose residues, resulting in decreasing the fluctuation and increasing the stability of the entire peptide. When the glycosylation are made close to the loop, the secondary structural integrity of the alpha-loop-alpha motif increases with the number of galactose residues. In addition, "face-to-face" glycosylation increases the structural integrity of this motif to a greater extent than "back-to-back" glycosylation. However, when the glycosylation are created away from the loop and near the N- and C-termini, no general rule is found for the stabilizing effect.
Liu
Hsuan-Liang
HL
Department of Chemical Engineering, Graduate Institute of Biotechnology, National Taipei University of Technology, 1 Section 3 Chung-Hsiao East Road, Taipei, Taiwan 10608. f10894@ntut.edu.tw
Hwang
Chiao-Kai
CK
Lin
Jin-Chung
JC
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D015195:Drug Design; D006031:Glycosylation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D010455:Peptides