Cecilia Fruet, Mikel Martinez-Goikoetxea, Felipe Merino, Andrei N Lupas
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引用次数: 0
摘要
许多细菌都受到不同类型的多糖胶囊的保护,这种胶囊是由长的重复糖链形成的结构,有时是游离的,有时通过脂质尾部固定在外膜上。大肠杆菌中的 gfcABCDE-etp-etk 操作子的表达产生了一种被称为第 4 组胶囊的胶囊。在该操作子中编码的蛋白质中,GfcE 被认为为游离多糖链提供出口孔,但没有一个蛋白质与携带脂质锚的多糖链的出口有关。就这一功能而言,GfcD 作为操作子中编码的唯一外膜 β 管,一直是关注的焦点。AlphaFold 预测 GfcD 有两个 β 管结构域,一个是由 12 条链组成的 N 端结构域,另一个是由 13 条链组成的 C 端结构域。这立即表明疏水分子进入膜的侧向出口门,类似于为脂多糖出口孔 LptD 提出的出口门。在此,我们报告了一项对嵌入细菌外膜的 GfcD 的非转向分子动力学研究,在 C 端桶状结构的孔中插入了常见的多糖锚--脂质 A。我们的结果表明,横向孔道在模拟过程中不会塌陷,膜脂类不会穿透桶,但脂质 A 分子的脂质链很容易进入膜。
A computational model for lipid-anchored polysaccharide export by the outer membrane protein GfcD.
Many bacteria are protected by different types of polysaccharide capsules, structures formed of long repetitive glycan chains that are sometimes free and sometimes anchored to the outer membrane via lipid tails. One type, called group 4 capsule, results from the expression of the gfcABCDE-etp-etk operon in Escherichia coli. Of the proteins encoded in this operon, GfcE is thought to provide the export pore for free polysaccharide chains, but none of the proteins has been implicated in the export of chains carrying a lipid anchor. For this function, GfcD has been a focus of attention as the only outer membrane β-barrel encoded in the operon. AlphaFold predicts two β-barrel domains in GfcD, a canonical N-terminal one of 12 strands and an unusual C-terminal one of 13 strands, which features a large lateral aperture between strands β1 and β13. This immediately suggests a lateral exit gate for hydrophobic molecules into the membrane, analogous to the one proposed for the lipopolysaccharide export pore LptD. Here, we report an unsteered molecular dynamics study of GfcD embedded in the bacterial outer membrane, with the common polysaccharide anchor, lipid A, inserted in the pore of the C-terminal barrel. Our results show that the lateral aperture does not collapse during simulations and membrane lipids nevertheless do not penetrate the barrel but the lipid chains of the lipid A molecule readily exit into the membrane.
期刊介绍:
BJ publishes original articles, letters, and perspectives on important problems in modern biophysics. The papers should be written so as to be of interest to a broad community of biophysicists. BJ welcomes experimental studies that employ quantitative physical approaches for the study of biological systems, including or spanning scales from molecule to whole organism. Experimental studies of a purely descriptive or phenomenological nature, with no theoretical or mechanistic underpinning, are not appropriate for publication in BJ. Theoretical studies should offer new insights into the understanding ofexperimental results or suggest new experimentally testable hypotheses. Articles reporting significant methodological or technological advances, which have potential to open new areas of biophysical investigation, are also suitable for publication in BJ. Papers describing improvements in accuracy or speed of existing methods or extra detail within methods described previously are not suitable for BJ.