SIMULATING A BACTERIAL ORGANELLE: THE PHOTOSYNTHETIC CHROMATOPHORE

这个子项目是许多利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 光合作用是一种生物能量过程，地球的生物圈从阳光中获取能量。这种有效的亚细胞过程取决于光合单元（PSU）在多个尺度上的复杂组织，从亚纳米级原子过程到宏观尺度的多蛋白质和脂质组装体，这些组装体是PSU细胞器的组成部分。 在紫色细菌类球红细菌中发现的一种这样的细胞器是色素细胞，其是内膜的70 nm宽的球状内陷，含有总共约200种蛋白质、5，000种叶绿素和1，700种类胡萝卜素，其允许有效的光合作用。 这200种色素细胞蛋白由几种多蛋白复合物组成，包括20种光合反应中心（RC）[1，2]，20种捕光复合物1（LH 1）[3，4]，150种捕光复合物2（LH 2）[5，6]，5种bc 1复合物（bc 1）[7]和细胞色素c2 s [8]，通常还有一种ATP合酶[9]。 涉及7000万个原子，继续开发粗粒化工具和扩展VMD和NAMD能力将是必要的，以适应这样一个大型系统的计算。 作为近细胞水平的首批模拟之一，色素细胞系统还将努力测试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，即光转化为生物能。

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.