Molecular dynamics simulation of the unfolding of individual bacteriorhodopsin helices in sodium dodecyl sulfate micelles.
Molecular dynamics simulation of the unfolding of individual bacteriorhodopsin helices in sodium dodecyl sulfate micelles.
复制标题
十二烷基硫酸钠胶束中单个细菌视紫红质螺旋展开的分子动力学模拟。
DOI：
10.1021/bi201770y
复制
发表时间：
2012
期刊：
影响因子：
2.9
通讯作者：
Lanyi,JanosK
中科院分区：
文献类型：
--
作者：
Krishnamani,Venkatramanan;Lanyi,JanosK
我们报告的分子动力学模拟的趋势在二级结构的变化的七个单独的螺旋细菌视紫红质插入十二烷基硫酸钠（SDS）胶束时，其依赖于氨基酸序列。结果表明，胶束中螺旋的分配及其稳定性取决于跨膜段的疏水性。螺旋A、B和E是稳定的，并在整个100 ns模拟时间内保持其初始二级结构。相反，螺旋C、D、F和G在前10 ns内显示结构扰动。不稳定性位于跨膜段内的带电残基附近。螺旋的整体结构不稳定性与其分配到胶束表面及其与那里的极性基团的相互作用有关。进行计算机模拟实验以补充前一篇文章（DOI 10.1021/bi 201769 z）中所述的检查SDS中细菌视紫红质部分变性的体外实验。模拟结果与实验结果所揭示的趋势一致，但严重低估了螺旋向延伸螺旋转化的程度。原因可能是采样时间不够长，或者更有趣的是，螺旋间残基相互作用在螺旋的展开中起作用。
We report molecular dynamics simulations of the trends in the changes in secondary structure of the seven individual helices of bacteriorhodopsin when inserted into sodium dodecyl sulfate (SDS) micelles, and their dependence on the amino acid sequence. The results indicate that the partitioning of the helices in the micelles and their stability are dependent on the hydrophobicity of the transmembrane segments. Helices A, B, and E are stable and retain their initial secondary structure throughout the 100 ns simulation time. In contrast, helices C, D, F, and G show structural perturbations within the first 10 ns. The instabilities are localized near charged residues within the transmembrane segments. The overall structural instability of the helix is correlated with its partitioning to the surface of the micelle and its interaction with polar groups there. The in silico experiments were performed to complement the in vitro experiments that examined the partial denaturation of bacteriorhodopsin in SDS described in the preceding article (DOI 10.1021/bi201769z). The simulations are consistent with the trends revealed by the experimental results but strongly underestimate the extent of helix to extended coil transformation. The reason may be either that the sampling time was not sufficiently long or, more interestingly, that interhelix residue interactions play a role in the unfolding of the helices.