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贝叶斯推断方案从受限单分子轨迹中提取扩散率和势场。

A Bayesian inference scheme to extract diffusivity and potential fields from confined single-molecule trajectories.

机构信息

Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale U696, Palaiseau, France.

出版信息

Biophys J. 2012 May 16;102(10):2288-98. doi: 10.1016/j.bpj.2012.01.063. Epub 2012 May 15.

Abstract

Currently used techniques for the analysis of single-molecule trajectories only exploit a small part of the available information stored in the data. Here, we apply a Bayesian inference scheme to trajectories of confined receptors that are targeted by pore-forming toxins to extract the two-dimensional confining potential that restricts the motion of the receptor. The receptor motion is modeled by the overdamped Langevin equation of motion. The method uses most of the information stored in the trajectory and converges quickly onto inferred values, while providing the uncertainty on the determined values. The inference is performed on the polynomial development of the potential and on the diffusivities that have been discretized on a mesh. Numerical simulations are used to test the scheme and quantify the convergence toward the input values for forces, potential, and diffusivity. Furthermore, we show that the technique outperforms the classical mean-square-displacement technique when forces act on confined molecules because the typical mean-square-displacement analysis does not account for them. We also show that the inferred potential better represents input potentials than the potential extracted from the position distribution based on Boltzmann statistics that assumes statistical equilibrium.

摘要

目前用于分析单分子轨迹的技术仅利用了数据中存储的可用信息的一小部分。在这里,我们将贝叶斯推理方案应用于受孔形成毒素靶向的受限受体的轨迹,以提取限制受体运动的二维约束势。受体运动由过阻尼朗之万运动方程建模。该方法使用轨迹中存储的大部分信息,并快速收敛到推断值,同时提供确定值的不确定性。推理是在势的多项式展开和已在网格上离散的扩散系数上进行的。数值模拟用于测试方案并量化对力、势和扩散系数的输入值的收敛性。此外,我们表明,当力作用于受限分子时,该技术优于经典的均方根位移技术,因为典型的均方根位移分析不考虑它们。我们还表明,与基于玻尔兹曼统计假设统计平衡的基于位置分布提取的势相比,推断出的势更好地表示输入势。

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本文引用的文献

2
Mean square displacement analysis of single-particle trajectories with localization error: Brownian motion in an isotropic medium.
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Oct;82(4 Pt 1):041914. doi: 10.1103/PhysRevE.82.041914. Epub 2010 Oct 20.
3
Single-molecule spectroscopy and imaging of biomolecules in living cells.
Anal Chem. 2010 Mar 15;82(6):2192-203. doi: 10.1021/ac9024889.
4
Quantifying biomolecule diffusivity using an optimal Bayesian method.
Biophys J. 2010 Feb 17;98(4):596-605. doi: 10.1016/j.bpj.2009.10.051.
5
Lipid rafts as a membrane-organizing principle.
Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621.
7
Inferring maps of forces inside cell membrane microdomains.
Phys Rev Lett. 2009 Jan 30;102(4):048103. doi: 10.1103/PhysRevLett.102.048103. Epub 2009 Jan 29.
8
Crowding effects on diffusion in solutions and cells.
Annu Rev Biophys. 2008;37:247-63. doi: 10.1146/annurev.biophys.37.032807.125824.
9
Probing microscopic origins of confined subdiffusion by first-passage observables.
Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5675-80. doi: 10.1073/pnas.0712158105. Epub 2008 Apr 7.
10
Counting the number of proteins coupled to single nanoparticles.
J Am Chem Soc. 2007 Oct 24;129(42):12592-3. doi: 10.1021/ja0731975. Epub 2007 Sep 29.

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