Retardation of the unfolding process by single N‐glycosylation of ribonuclease A based on molecular dynamics simulations

The conformational characteristics of glycosylated‐ and unglycosylated bovine pancreatic ribonuclease A (RNaseA) were traced with unfolding molecular dynamics simulations using CHARMM program at 470 K. The glycosylated RNase (Glc_RNase) possesses nearly identical protein structure with RNaseA, differing only by presence of a single acetylglucosamine residue N‐linked to Asn34 in the RNaseA. Attaching of monomeric N ‐acetylglucosamine residue to the Asn34 in RNaseA resulted in a change of denaturing process of Glc_RNase. Simulations showed that the unfolding of RNaseA involved significant weakening of nonlocal interactions whereas the glycosylation led Glc_RNase to preserve the nonlocal interactions even in its denatured form. Even in simulations over 8 ns at 470 K, Glc_RNase remained relatively stable as a less denatured conformation. However, conformation of RNaseA was changed to a fully unfolded state before 3 ns of the simulations at 470 K. This difference was due to fact that formation of hydrogen bond bridges and nonlocal contacts induced by the attached N ‐acetylglucosamine of Glc_RNase showing in the unfolding simulations. These high‐temperature unfolding MD simulations provided a theoretical basis for the previous experimental work in which Glc_RNase showed slower unfolding kinetics compared with unglycosylated RNaseA, suggesting that single N‐glycosylation induced retardation of unfolding process of the ribonuclease protein. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 114–123, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com