Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics.
Molecular dynamics and NMR spectroscopy studies of E. coli lipopolysaccharide structure and dynamics.
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DOI：
10.1016/j.bpj.2013.08.002
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发表时间：
2013-09
影响因子：
3.4
通讯作者：
E. Wu;O. Engström;Sunhwan Jo;Danielle Stuhlsatz;M. S. Yeom;Jeffery B. Klauda;G. Widmalm;W. Im
中科院分区：
文献类型：
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作者：
E. Wu;O. Engström;Sunhwan Jo;Danielle Stuhlsatz;M. S. Yeom;Jeffery B. Klauda;G. Widmalm;W. Im
脂多糖（LPS）是革兰氏阴性菌外膜的一种组分，由三个区域组成：脂质A、核心寡糖和O-抗原多糖。利用CHARMM 36脂质和碳水化合物力场，我们构建了一个大肠杆菌R1（核心）O 6（抗原）LPS分子的模型。构建了几个全原子双层，并仅用脂质A（利帕）和不同长度的0（LPS 0）、5（LPS 5）和10（LPS 10）O 6抗原重复单元进行模拟;单个O 6抗原单元含有5个糖残基。从1H，1H-NOESY实验中，从O-抗原多糖样品获得交叉弛豫速率。虽然一些实验偏差是由于自旋扩散，剩余的有效质子-质子距离显示一般非常好的协议之间的NMR实验和分子动力学模拟。模拟结果表明，增加LPS分子长度对LPS结构和动力学以及LPS双层性质有影响。LPS双分子层中的末端残基更灵活，并且沿着膜法线延伸。随着核心和O-抗原的加入，全脂质面积增加，脂质双层顺序降低。此外，来自混合LPS 0/5和LPS 0/10双层模拟的结果表明，在较高浓度的LPS 5和LPS 10下，LPS O-抗原构象与膜更正交并且柔性更低。混合LPS双层的O-抗原浓度对脂质面积和疏水厚度没有显著影响。离子和水渗透的分析表明，水分子可以渗透到内核区域内，水合作用是保持双层结构完整性的关键。
Lipopolysaccharide (LPS), a component of Gram-negative bacterial outer membranes, comprises three regions: lipid A, core oligosaccharide, and O-antigen polysaccharide. Using the CHARMM36 lipid and carbohydrate force fields, we have constructed a model of anEscherichia coliR1 (core) O6 (antigen) LPS molecule. Several all-atom bilayers are built and simulated with lipid A only (LIPA) and varying lengths of 0 (LPS0), 5 (LPS5), and 10 (LPS10) O6 antigen repeating units; a single unit of O6 antigen contains five sugar residues. From1H,1H-NOESY experiments, cross-relaxation rates are obtained from an O-antigen polysaccharide sample. Although some experimental deviations are due to spin-diffusion, the remaining effective proton-proton distances show generally very good agreement between NMR experiments and molecular dynamics simulations. The simulation results show that increasing the LPS molecular length has an impact on LPS structure and dynamics and also on LPS bilayer properties. Terminal residues in a LPS bilayer are more flexible and extended along the membrane normal. As the core and O-antigen are added, per-lipid area increases and lipid bilayer order decreases. In addition, results from mixed LPS0/5 and LPS0/10 bilayer simulations show that the LPS O-antigen conformations at a higher concentration of LPS5 and LPS10 are more orthogonal to the membrane and less flexible. The O-antigen concentration of mixed LPS bilayers does not have a significant effect on per-lipid area and hydrophobic thickness. Analysis of ion and water penetration shows that water molecules can penetrate inside the inner core region, and hydration is critical to maintain the integrity of the bilayer structure.