Conformational study on glycosylated asparagine-oligopeptides by NMR spectroscopy and molecular dynamics calculations.
The conformational properties of the homo oligomers of increasing chain length Boc-(Asn)(n)-NHMe (n = 2, 4, 5), (GlcNAc-beta-Asn)(n)-NHMe (n = 2, 4, 5, 8) and Boc-[GlcNAc(Ac)(3)-beta-Asn](n)-NHMe (n = 2, 4, 5) were studied by using NOE experiments and molecular dynamic calculations (MD). Sequential NOEs and medium range NOEs, including (i,i+2) interactions, were detected by ROESY experiments and quantified. The calculated inter-proton distances are longer than those characteristic of beta-turn secondary structures. Owing to the large conformational motions expected for linear peptides, MD simulations were performed without NMR constraints, with explicit water and by applying different treatments of the electrostatic interactions. In agreement with the NOE results, the simulations showed, for all peptides, the presence of both folded and unfolded structures. The existence of significant populations of beta-turn structures can be excluded for all the examined compounds, but two families of structures were more often recognized. The first one with sinusoidal or S-shaped forms, and another family of large turns together with some more extended conformations. Only the glycosylated pentapeptide shows in vacuo a large amount of structures with helical shaped form. The results achieved in water and in DMSO are compared and discussed, together with the effect of the glycosylation.
Mazzini
Stefania
S
Department of Molecular Sciences, University of Milano, Italy.
Scaglioni
Leonardo
L
Mondelli
Rosanna
R
Rocchi
Raniero
R
Biondi
Laura
L
Gobbo
Marina
M
D001216:Asparagine / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry; D004578:Electron Spin Resonance Spectroscopy; D006031:Glycosylation; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D013696:Temperature
D004151:Dipeptides; D009842:Oligopeptides; D001216:Asparagine