芘标记脂类激基缔合物形成的粗粒度分子动力学模拟
Excimer formation of pyrene labeled lipids interpreted by means of coarse-grained molecular dynamics simulations
摘要：
芘标记的分子在脂质双层中的激基缔合物形成动力学取决于分子运动的距离为1-2 nm的顺序。从受激准分子光发射曲线的浓度依赖性，可以导出脂质自扩散系数的值。这种技术在过去的二十年中得到了广泛的应用，与基于荧光探针跟踪的其他方法相比，自扩散的数值相当大。在大多数情况下，实验数据的解释依赖于扩散限制的2d反应速率的模型，或与2d晶格无规行走的比较。我们的方法使用现实的分子动力学轨迹来重新解释这些实验。基于一个良好建立的粗粒度模型的脂质MD模拟（马提尼），我们展示了如何将模拟结果与实验数据的激基缔合物形成。我们的程序是相当普遍的，适用于所有的扩散限制动力学过程。我们的方法的关键是确定脂质粗粒度的数值模型与现实相比的加速因子。我们发现一个显着减少的扩散系数值，特别是当考虑到叶间协会。我们的工作并没有指出偏离扩散限制机制，但表明跨双层小叶的激基缔合物形成可能受到阻碍。
英文摘要：
The excimer formation dynamics of pyrene-labeled molecules in lipid bilayers depends on molecular motion over distances of the order of 1-2 nm. From the concentration dependence of the excimer photoemission curve, it is possible to derive a value for the lipid self-diffusion coefficient. This technique has been intensively used in the past twenty years, leading to rather large numerical values for self-diffusion compared with other approaches based on fluorescent probes tracking. In most cases, the interpretation of the experimental data rely on models for diffusion limited 2d reaction rates, or comparison with 2d lattice random walks. Our approach uses realistic molecular dynamics trajectories to reinterpret these experiments. Based on a well established coarse-grained model for lipid MD simulations (Martini), we show how to relate simulation results to experimental data on excimer formation. Our procedure is quite general and is applicable to all diffusion-limited kinetic processes. Key to our approach is the determination of the acceleration factor of lipid coarse-grained numerical models compared to reality. We find a significant reduction of the diffusion coefficient values, in particular when interleaflet association is taken into account. Our work does not point to deviation from a diffusion-limited mechanism but indicates that the excimer formation across bilayer leaflets could be hindered.
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