Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.
Steered molecular dynamics simulations of a type IV pilus probe initial stages of a force-induced conformational transition.
复制标题
DOI：
10.1371/journal.pcbi.1003032
复制
发表时间：
2013-04
影响因子：
4.3
通讯作者：
Tama F
中科院分区：
文献类型：
--
作者：
Baker JL;Biais N;Tama F
IV型皮利是由从各种感染性细菌表面突出的重复亚基构建的长的蛋白质细丝。它们涉及大量的功能，从细菌运动到小菌落形成到感染。研究最充分的IV型丝状体之一是来自淋病奈瑟菌的淋球菌IV型菌毛（GC-T4 P），淋病奈瑟菌是淋病的病原体。冷冻电子显微镜已被用来构建这种细丝的模型，提供深入了解IV型皮利的结构。此外，实验已经证明GC-T4 P可以承受非常大的张力，并转变为力诱导的构象。然而，力产生的细节，以及力诱导构象的原子级特征，是未知的。在这里，操纵分子动力学（SMD）模拟被用来在计算机上施加力的GC-T4 P的18个亚基段，以解决有关的相互作用，导致细菌皮利的非凡的力量的性质的问题。SMD模拟显示，掩埋的菌毛蛋白α1结构域在细丝的核心内保持彼此的疏水接触，导致GC-T4 P的结构稳定性。在丝状体表面，天然状态和拉伸状态下的菌毛蛋白球状头部结构域之间的间隙提供了外部环境和丝状体内部之间的水可进入路径，允许水进入菌毛蛋白α1结构域，如在氘交换实验中对VC-T4 P所报道的。实验观察到的力诱导的构象的结果进行了比较。特别是，暴露的氨基酸序列中的实验拉伸丝也被发现成为暴露在SMD模拟过程中，这表明力诱导的过渡的初始阶段被很好地捕获。此外，第二个序列被证明最初隐藏在天然丝中，并在拉伸时暴露出来。有大量的传染性细菌可能对人类有害。一些细菌感染是由称为IV型皮利的长的绳状细丝促进的，所述细丝从细菌细胞的表面延伸并附着到宿主细胞的表面。IV型菌毛可以长到许多微米长（细菌细胞本身平均只有几微米长，直径只有半微米），并且可以施加非常大的力（高达细菌体重的100，000倍）。因为它们从细胞表面延伸，IV型皮利是药物靶向的非常好的候选者。使用计算机模拟对这些细丝之一的一段施加力，以试图模拟感染期间菌毛在结合时所经历的张力的影响。确定了在牵拉状态下暴露于外部环境的细丝区域，试图鉴定可作为药物设计靶点的氨基酸序列。
Type IV pili are long, protein filaments built from a repeating subunit that protrudes from the surface of a wide variety of infectious bacteria. They are implicated in a vast array of functions, ranging from bacterial motility to microcolony formation to infection. One of the most well-studied type IV filaments is the gonococcal type IV pilus (GC-T4P) from Neisseria gonorrhoeae, the causative agent of gonorrhea. Cryo-electron microscopy has been used to construct a model of this filament, offering insights into the structure of type IV pili. In addition, experiments have demonstrated that GC-T4P can withstand very large tension forces, and transition to a force-induced conformation. However, the details of force-generation, and the atomic-level characteristics of the force-induced conformation, are unknown. Here, steered molecular dynamics (SMD) simulation was used to exert a force in silico on an 18 subunit segment of GC-T4P to address questions regarding the nature of the interactions that lead to the extraordinary strength of bacterial pili. SMD simulations revealed that the buried pilin α1 domains maintain hydrophobic contacts with one another within the core of the filament, leading to GC-T4P's structural stability. At the filament surface, gaps between pilin globular head domains in both the native and pulled states provide water accessible routes between the external environment and the interior of the filament, allowing water to access the pilin α1 domains as reported for VC-T4P in deuterium exchange experiments. Results were also compared to the experimentally observed force-induced conformation. In particular, an exposed amino acid sequence in the experimentally stretched filament was also found to become exposed during the SMD simulations, suggesting that initial stages of the force induced transition are well captured. Furthermore, a second sequence was shown to be initially hidden in the native filament and became exposed upon stretching. There are a large number of infectious bacteria that can be harmful to humans. Some bacterial infections are facilitated by long, tether-like filaments called type IV pili which extend from the surface of bacterial cells and attach to the surface of host cells. Type IV pilus filaments can grow to be many micrometers in length (bacterial cells themselves, on average, are only a couple of micrometers in length and half a micrometer in diameter), and can exert very large forces (up to 100,000 times the bodyweight of the bacteria). Because they extend from the surface of the cell, type IV pili are very good candidates for drug targeting. Computer simulation was used to exert forces on a segment of one of these filaments, in an effort to mimic the effects of tension that would be experienced by the pilus upon binding during infection. Regions of the filament that become exposed to the external environment in the pulled state were determined, in an attempt to identify amino acid sequences that could act as targets for drug design.
登录
查看更多内容
影响因子：
56.9
作者：
Chamot-Rooke, Julia;Mikaty, Guillain;Dumenil, Guillaume
通讯作者：
Dumenil, Guillaume
DOI：
10.1073/pnas.242523299
发表时间：
2002-12-10
影响因子：
11.1
作者：
Maier, B;Potter, L;Sheetz, MP
通讯作者：
Sheetz, MP
影响因子：
3.1
作者：
Forest, KT;Bernstein, SL;Tainer, JA
通讯作者：
Tainer, JA
影响因子：
16
作者：
Craig, L;Taylor, RK;Tainer, JA
通讯作者：
Tainer, JA
影响因子：
10.8
作者：
Audette, GF;van Schalk, EJ;Irvin, RT
通讯作者：
Irvin, RT