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首页> 美国卫生研究院文献>Biophysical Journal >Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex.
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Computational simulation of the docking of Prochlorothrix hollandica plastocyanin to potosystem I: modeling the electron transfer complex.

机译：荷兰原绿藻（Prochlorothrix hollandica）质体蓝蛋白对接potosystem的计算模拟：模拟电子传递复合物。

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We have used several docking algorithms (GRAMM, FTDOCK, DOT, AUTODOCK) to examine protein-protein interactions between plastocyanin (Pc)/photosystem I (PSI) in the electron transfer reaction. Because of the large size and complexity of this system, it is faster and easier to use computer simulations than conduct x-ray crystallography or nuclear magnetic resonance experiments. The main criterion for complex selection was the distance between the copper ion of Pc and the P700 chlorophyll special pair. Additionally, the unique tyrosine residue (Tyr(12)) of the hydrophobic docking surface of Prochlorothrix hollandica Pc yields a specific interaction with the lumenal surface of PSI, thus providing the second constraint for the complex. The structure that corresponded best to our criteria was obtained by the GRAMM algorithm. In this structure, the solvent-exposed histidine that coordinates copper in Pc is at the van der Waals distance from the pair of stacked tryptophans that separate the chlorophylls from the solvent, yielding the shortest possible metal-to-metal distance. The unique tyrosine on the surface of the Prochlorothrix Pc hydrophobic patch also participates in a hydrogen bond with the conserved Asn(633) of the PSI PsaB polypeptide (numbering from the Synechococcus elongatus crystal structure). Free energy calculations for complex formation with wild-type Pc, as well as the hydrophobic patch Tyr(12)Gly and Pro(14)Leu Pc mutants, were carried out using a molecular mechanics Poisson-Boltzman, surface area approach (MM/PBSA). The results are in reasonable agreement with our experimental studies, suggesting that the obtained structure can serve as an adequate model for P. hollandica Pc-PSI complex that can be extended for the study of other cyanobacterial Pc/PSI reaction pairs.
机译：我们已经使用了几种对接算法（GRAMM，FTDOCK，DOT，AUTODOCK）来检查电子转移反应中质体蓝蛋白（Pc）/光系统I（PSI）之间的蛋白质-蛋白质相互作用。由于该系统的大型和复杂性，使用计算机模拟比进行X射线晶体学或核磁共振实验更快，更容易。复杂选择的主要标准是Pc的铜离子与P700叶绿素特殊对之间的距离。此外，Prochlorothrix hollandica Pc的疏水对接表面的独特酪氨酸残基（Tyr（12））与PSI的管腔表面产生特定的相互作用，从而为复合物提供了第二个约束条件。通过GRAMM算法获得了最符合我们标准的结构。在这种结构中，与Pc中的铜配位的溶剂暴露的组氨酸与将叶绿素与溶剂分开的一对成对色氨酸的范德华距离为范德华斯距离，从而使金属间距离最短。 Prochlorothrix Pc疏水膜片表面上独特的酪氨酸还与PSI PsaB多肽的保守Asn（633）形成氢键（编号为Synechococcus elongatus晶体结构）。使用分子力学Poisson-Boltzman表面积法（MM / PBSA）对与野生型Pc以及疏水性Tyr（12）Gly和Pro（14）Leu Pc突变体形成复合物的自由能进行了计算）。结果与我们的实验研究合理吻合，表明所获得的结构可以作为荷兰假单胞菌Pc-PSI复合物的适当模型，该模型可以扩展用于研究其他蓝细菌Pc / PSI反应对。

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