动态力学网络的反卷积
Deconvolution of dynamic mechanical networks
摘要：
时间分辨的单分子生物物理实验产生的数据，除了从时间序列的直方图导出的平衡分布之外，还包含丰富的动态信息。在典型的力光谱设置中，分子通过连接器连接到读出设备，形成机械耦合的动态网络。平衡分布的反卷积，过滤掉链接器的影响，是一个简单而常见的做法。我们已经开发了一个类似的动态去卷积理论，用于提取任意复杂性和拓扑结构的网络中各个组件的动力学特性这一更具挑战性的任务。我们的方法确定了网络中给定分子的固有线性响应函数，描述了构象波动的功率谱。我们的方法的实用性证明了通过DNA手柄连接到两个光学捕获珠在恒定的拉伸力，我们通过布朗动力学模拟的蛋白质的特定情况下。蛋白质自由能景观中的每一个阱（对应于折叠、未折叠或可能的中间状态）都有其特有的平衡涨落。相关的线性响应函数是丰富的物理内容，因为它既取决于井的形状和它的扩散率-内摩擦的措施所产生的过程，如短暂的断裂和重组的蛋白质结构中的键。从自相关函数的平衡珠的波动在这个力钳设置测量，我们展示了如何实验可以准确地提取状态依赖的蛋白质扩散率使用一个简单的两步程序。
英文摘要：
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups the molecule is connected via linkers to a read-out device, forming a mechanically coupled dynamic network. Deconvolution of equilibrium distributions, filtering out the influence of the linkers, is a straightforward and common practice. We have developed an analogous dynamic deconvolution theory for the more challenging task of extracting kinetic properties of individual components in networks of arbitrary complexity and topology. Our method determines the intrinsic linear response functions of a given molecule in the network, describing the power spectrum of conformational fluctuations. The practicality of our approach is demonstrated for the particular case of a protein linked via DNA handles to two optically trapped beads at constant stretching force, which we mimic through Brownian dynamics simulations. Each well in the protein free energy landscape (corresponding to folded, unfolded, or possibly intermediate states) will have its own characteristic equilibrium fluctuations. The associated linear response function is rich in physical content, since it depends both on the shape of the well and its diffusivity---a measure of the internal friction arising from such processes like the transient breaking and reformation of bonds in the protein structure. Starting from the autocorrelation functions of the equilibrium bead fluctuations measured in this force clamp setup, we show how an experimentalist can accurately extract the state-dependent protein diffusivity using a straightforward two-step procedure.
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