BioChip Research Center, Hoseo University, Asan 336-795, Republic of Korea.
J Mol Graph Model. 2010 Feb 26;28(6):487-94. doi: 10.1016/j.jmgm.2009.11.003. Epub 2009 Dec 3.
Unfolding behavior of glycosylated- and unglycosylated proteinase inhibitor Pars intercerebralis major peptide C (PMPC) at 350 K were traced with molecular dynamics simulations using the CHARMM program. The fucosylated PMPC (FPMPC) possesses a nearly identical protein structure with PMPC, differing only by the presence of a single fucose residue linked to Thr9 in the PMPC. Attachment of a monomeric fucose residue to the Thr9 in PMPC resulted in a change of the denaturing process of FPMPC. Simulations showed that the unfolding of PMPC involved significant weakening of non-local interactions whereas fucosylation led FPMPC to preserve the non-local interactions, even in its denatured form. Even in simulations over 16 ns at 350 K, FPMPC remained relatively stable in a less denatured conformation. However, the conformation of PMPC transformed to a fully unfolded state within 5 ns in the simulation at 350 K. This difference was due to the formation of fucose-mediated hydrogen bonds and non-local contacts by the attached fucose residue of FPMPC. In the case of FPMPC, fucosyl residue was involved in maintaining a rigid beta-sheet cluster through interaction with the hydrogen bond network. These high-temperature unfolding MD simulations provide a theoretical basis for a previous experimental work in which FPMPC showed stable unfolding thermodynamics compared to unfucosylated PMPC, suggesting that single fucosylation induces conformational stabilization of PMPC by tertiary contacts.
在 350 K 下，使用 CHARMM 程序通过分子动力学模拟追踪了糖基化和未糖基化蛋白酶抑制剂 Pars intercerebralis major peptide C（PMPC）的展开行为。与 PMPC 仅有的区别是在 PMPC 的 Thr9 上存在一个连接的单糖基化的岩藻糖残基，使得糖基化的 PMPC（FPMPC）具有几乎相同的蛋白质结构。PMPC 上 Thr9 上连接一个单体岩藻糖残基导致 FPMPC 的变性过程发生变化。模拟表明，PMPC 的展开涉及非局部相互作用的显著减弱，而糖基化导致 FPMPC 即使在变性形式下也能保留非局部相互作用。即使在 350 K 下进行超过 16 ns 的模拟，FPMPC 在较少变性构象下仍保持相对稳定。然而，在 350 K 下的模拟中，PMPC 的构象在 5 ns 内转变为完全展开状态。这种差异归因于 FPMPC 中连接的岩藻糖残基形成的岩藻糖介导的氢键和非局部接触。在 FPMPC 的情况下，岩藻糖残基通过与氢键网络相互作用参与维持刚性β-折叠簇。这些高温展开 MD 模拟为之前的实验工作提供了理论基础，其中 FPMPC 显示出与未糖基化的 PMPC 相比稳定的展开热力学，表明单糖基化通过三级接触诱导 PMPC 的构象稳定。
