Conformational dynamics of Peb4 exhibit “mother’s arms” chain model: a molecular dynamics study

Peb4 from <i>Campylobacter jejuni</i> is an intertwined dimeric, periplasmic holdase, which also exhibits peptidyl prolyl cis/trans isomerase (PPIase) activity. Peb4 gene deletion alters the outer membrane protein profile and impairs cellular adhesion and biofilm formation for <i>C. jejuni</i>. Earlier crystallographic study has proposed that the PPIase domains are flexible and might form a cradle for holding the substrate and these aspects of Peb4 were explored using sub-microsecond molecular dynamics simulations in solution environment. Our simulations have revealed that PPIase domains are highly flexible and undergo a large structural change where they move apart from each other by 8 nm starting at .5 nm. Further, this large conformational change renders Peb4 as a compact protein with crossed-over conformation, forms a central cavity, which can “cradle” the target substrate. As reported for other chaperone proteins, flexibility of linker region connecting the chaperone and PPIase domains is key to forming the “crossed-over” conformation. The conformational transition of the Peb4 protein from the X-ray structure to the crossed-over conformation follows the “mother’s arms” chain model proposed for the FkpA chaperone protein. Our results offer insights into how Peb4 and similar chaperones can use the conformational heterogeneity at their disposal to perform its much-revered biological function.

空肠弯曲菌（Campylobacter jejuni）来源的Peb4是一种缠绕型二聚体周质持留分子伴侣（holdase），同时兼具肽基脯氨酰顺反异构酶（peptidyl prolyl cis/trans isomerase，PPIase）活性。Peb4基因敲除会改变空肠弯曲菌的外膜蛋白质谱，并削弱其细胞黏附与生物膜形成能力。早期晶体学研究提出，PPIase结构域具有高度柔性，可形成承托底物的凹槽；本研究通过溶液环境下的亚微秒分子动力学模拟，对Peb4的这些特性展开了探究。模拟结果显示，PPIase结构域柔性极强，会发生大幅构象变化：两个结构域从初始的0.5 nm间距开始，彼此分离可达8 nm。进一步分析表明，该大型构象转变使Peb4成为具有交叉构象的紧凑蛋白质，形成可"cradle"目标底物的中央空腔。正如其他分子伴侣蛋白的相关研究所示，连接分子伴侣结构域与PPIase结构域的接头区域的柔性，是形成"crossed-over"构象的关键。Peb4蛋白从晶体结构到交叉构象的构象转变，遵循了针对FkpA分子伴侣蛋白提出的"mother’s arms"链模型。本研究结果揭示了Peb4及其同类分子伴侣如何利用自身可及的构象异质性，来行使其广受认可的生物学功能。