SIMULATING A BACTERIAL ORGANELLE: THE PHOTOSYNTHETIC CHROMATOPHORE

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 光合作用是地球上大部分生物圈从阳光中获取能量的生物能过程。这种高效的亚细胞过程依赖于光合作用单位(PSU)在多个尺度上的复杂组织，从亚纳米尺度的原子过程到作为PSU细胞器不可或缺的组成部分的宏观尺度的多蛋白质和脂类组装。在紫色细菌球形红假单胞菌中发现的一个这样的细胞器是色素体，它是内膜上一个70纳米宽的球状内陷，总共含有大约200种蛋白质、5000个叶绿素和1700个类胡萝卜素，允许有效的光合作用。这200个生色团蛋白由多个蛋白质复合体组成，包括20个光合作用反应中心(RC)[1，2]，20个捕光复合体1(LH1)[3，4]，150个捕光复合体2(LH2)[5，6]，5个Bc1复合体(Bc1)[7]和细胞色素C2s[8]，通常还有一个ATP合成酶[9]。涉及7000万个原子，继续开发粗粒化工具以及扩展VMD和NAMD能力将是必要的，以适应如此大的计算系统。作为最早的近细胞水平的模拟之一，色团系统还将努力测试VMD和NAMD的可扩展性，同时提供独特的机会来研究地球上生命所必需的最基本的过程之一，即将光转化为生物能源。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Photosynthesis is the bioenergetic process by which the majority of Earths biosphere derives energy from sunlight. This efficient sub-cellular process depends on the complex organization of the photosynthetic unit (PSU) at multiple scales spanning from sub-nanoscale atomic processes to macroscale multi-protein and lipid assemblies that are integral components of PSU organelles. One such organelle found in the purple bacterium Rhodobacter sphaeroides is the chromatophore, a 70 nm wide bulbous invagination of the inner membrane containing a total of approximately 200 proteins, 5,000 chlorophylls, and 1,700 carotenoids that permit efficient photosynthesis. These 200 chromatophore proteins consist of several multi-protein complexes, including 20 photosynthetic reaction centers (RC) [1, 2], 20 light harvesting complexes 1 (LH1) [3, 4], 150 light harvesting complexes 2 (LH2) [5, 6], five bc1 complexes (bc1) [7] and cytochrome c2s [8], and usually one ATP synthase [9]. Involving 70 million atoms, continued development of coarse-graining tools and the extension of VMD and NAMD capabilities will be necessary to accommodate such a large system computationally. Representing one of the first simulations at the near-cellular level, the chromatophore system will also strenuously test the scalability of VMD and NAMD while providing unique opportunities to investigate one of the most fundamental processes necessary for life on Earth, namely the conversion of light into bioenergy.