Lili-Mip trajectories and results.zip

The unique viviparous Pacific Beetle cockroaches provide nutrition to their embryo by secreting milk proteins Lili-Mip, which is a lipid-binding glycoprotein that crystallizes in-vivo. The resolved in-vivo crystal structure of variably glycosylated Lili-Mip shows a classical Lipocalin fold with an eight-stranded antiparallel beta-barrel enclosing a fatty acid. The availability of physiologically unaltered glycoprotein structure makes Lili-Mip a very attractive model system to investigate the role of glycans on protein structure, dynamics, and function. Towards that end, we have employed all-atom molecular dynamics simulations on various glycosylated stages of a bound and free Lili-Mip protein and characterized the impact of glycans and the bound lipid on the dynamics of this glycoconjugate. Our work provides important molecular-level mechanistic insights into the role of glycans in the nutrient storage function of the Lili-Mip protein. Our analyses show that the glycans stabilize spatially proximal residues and regulate the low amplitude opening motions of the residues at the entrance of the binding pocket. Glycans also preserve the native orientation and conformational flexibility of ligand. However, we find that extreme glycosylation with highly complex glycans or deglycosylation affects the conformation and dynamics noticeably. A simple but effective distance- and correlation-based network analyses of the protein also reveal the key residues regulating the architecture and ligand binding characteristics of the barrel in response to glycosylation.

独特的胎生太平洋甲虫蟑螂（Pacific Beetle Cockroach）通过分泌乳蛋白Lili-Mip为胚胎提供营养，该蛋白是一种脂结合糖蛋白（lipid-binding glycoprotein），可在体内结晶。已解析的可变糖基化Lili-Mip的体内晶体结构，呈现出经典的脂质运载蛋白（Lipocalin）折叠模式，其包含一个包裹脂肪酸的八链反平行β桶状结构。这种生理状态未发生改变的糖蛋白结构的解析，使得Lili-Mip成为研究糖基（glycans）对蛋白质结构、动力学与功能调控作用的极具吸引力的模型系统。基于此研究目标，我们针对结合态与游离态Lili-Mip蛋白的不同糖基化阶段开展了全原子分子动力学（all-atom molecular dynamics）模拟，并解析了糖基与结合态脂质对该糖结合物（glycoconjugate）动力学特性的影响。本研究为阐明糖基在Lili-Mip蛋白营养储存功能中的作用机制提供了重要的分子水平见解。分析结果表明，糖基可稳定空间上邻近的氨基酸残基，并调控结合口袋入口处残基的小幅度开放运动。糖基还可维持配体的天然构象取向与构象灵活性。但研究发现，过度糖基化（携带高度复杂糖基）或去糖基化，均会显著影响该蛋白的构象与动力学特性。针对该蛋白开展的简便高效的基于距离与相关性的网络分析，也揭示了响应糖基化修饰、调控β桶结构与配体结合特性的关键氨基酸残基。