Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein
Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein
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分子模拟揭示了介导羧基体壳蛋白选择性渗透的分子原理
DOI：
10.1101/2020.06.14.151241
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发表时间：
2020
期刊：
影响因子：
--
通讯作者：
Faulkner M
中科院分区：
文献类型：
--
作者：
Faulkner M
细菌微区室（BMC）是纳米级蛋白质细胞器，使用类似于病毒衣壳的二十面体蛋白质外壳包裹细胞质中的酶。特别令人感兴趣的是羧化体（CB），其螯合CO2固定酶核酮糖-1，5-二磷酸羧化酶/加氧酶（Rubisco）以增强碳同化。羧基体壳作为代谢物进出羧基体的半渗透屏障，以增强CO2固定。蛋白质外壳如何以有效的方式引导分子的流入和流出仍然是难以捉摸的。在这里，我们使用分子动力学和伞形采样计算，以确定代谢底物，碳酸氢盐，CO2和核酮糖二磷酸和产品3-磷酸甘油酸与他们的过渡通过主要的羧基壳蛋白CcmK 2的自由能档案。我们阐明了基于静电荷的渗透性和关键氨基酸残基的CcmK 2功能介导的分子运输通过中央孔。形成中心孔的环的构象变化也可能是特定代谢物转运所必需的。通过对关键CcmK 2残基丝氨酸39进行定点诱变，实验验证了这些计算机模拟结果的重要性。这项研究提供了深入了解的机制，介导的分子运输通过壳的carboxysomes，适用于其他BMC。它还提供了一种预测方法来研究和操纵壳的渗透性，目的是为合成生物学中的新功能设计基于BMC的代谢模块。
Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO2fixation. How the protein shell directs influx and efflux of molecules in an effective manner has remained elusive. Here we use molecular dynamics and umbrella sampling calculations to determine the free-energy profiles of the metabolic substrates, bicarbonate, CO2and ribulose bisphosphate and the product 3-phosphoglycerate associated with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating molecular transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated experimentally by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates molecular transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intent of engineering BMC-based metabolic modules for new functions in synthetic biology.
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DOI：
10.1073/pnas.2007990117
发表时间：
2020-07-21
影响因子：
11.1
作者：
Huang, Fang;Kong, Wen-Wen;Liu, Lu-Ning
通讯作者：
Liu, Lu-Ning
DOI：
10.1139/b05-058
发表时间：
2005-07-01
期刊：
CANADIAN JOURNAL OF BOTANY-REVUE CANADIENNE DE BOTANIQUE
影响因子：
--
作者：
Long, BM;Price, GD;Badger, MR
通讯作者：
Badger, MR
使用原子力显微镜对细菌微区室进行纳米级可视化。
影响因子：
--
作者：
Jorge Rodriguez;M. Faulkner;Lu
通讯作者：
Lu
影响因子：
6.3
作者：
BERENDSEN, HJC;VANDERSPOEL, D;VANDRUNEN, R
通讯作者：
VANDRUNEN, R
影响因子：
6.8
作者：
Yeates TO;Thompson MC;Bobik TA
通讯作者：
Bobik TA