论文标题
通过粗粒分子动力学模拟解释的pyrene标记脂质的准分子形成
Excimer formation of pyrene labeled lipids interpreted by means of coarse-grained molecular dynamics simulations
论文作者
论文摘要
脂质双层中吡啶标记分子的准分子形成动力学取决于1-2 nm阶距离的分子运动。根据准分子光发射曲线的浓度依赖性，可以得出脂质自扩散系数的值。在过去的二十年中，该技术已被密集使用，与基于荧光探针跟踪的其他方法相比，自扩散的数值值相当大。在大多数情况下，对实验数据的解释取决于扩散限制的2D反应速率的模型，或与2D晶格随机步行进行比较。我们的方法使用逼真的分子动力学轨迹来重新解释这些实验。基于脂质MD仿真（Martini）的良好建立的粗粒粒模型，我们展示了如何将模拟结果与精液形成的实验数据相关联。我们的程序非常笼统，适用于所有扩散限制的动力学过程。我们方法的关键是与现实相比，确定脂质粗粒数值模型的加速度因子。我们发现扩散系数值的显着降低，特别是当考虑到Itterleaflet关联时。我们的工作并不指向扩散限制的机制偏离，而是表明跨双层传单的准分子形成可能会受到阻碍。
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.
