The boundary structure in the analysis of reversibly interacting systems by sedimentation velocity.
The boundary structure in the analysis of reversibly interacting systems by sedimentation velocity.
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DOI：
10.1016/j.ymeth.2011.01.010
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发表时间：
2011-05
期刊：
影响因子：
4.8
通讯作者：
Schuck, Peter
中科院分区：
文献类型：
--
作者：
Zhao, Huaying;Balbo, Andrea;Brown, Patrick H.;Schuck, Peter
关键词：
异质相互作用系统的沉降速度（SV）实验表现出通常可以很容易识别和量化的特征边界结构。对于缓慢相互作用的系统，边界代表大分子物质的浓度，并且可以用仅基于质量作用定律的群体模型直接解释它们。对于快速反应，迁移和化学反应是耦合的，并且出现不同但同样容易辨别的边界结构。然而，由于缺乏直观且计算简单的模型，这些特征尚未普遍用于数据分析。最近引入的有效粒子理论（EPT）提供了一个合适的框架。在这里，我们回顾了EPT的动机和理论基础，并探讨了其应用的实践方面。我们在软件 SEDPHAT 中引入了一种基于 EPT 的设计工具，用于异质相互作用的 SV 实验。作为数据分析第一步的实用工具，我们描述了如何通过对先前单独研究的分子之间异质相互作用的情况进行最大熵正则化的贝叶斯调整来进一步提高 c(s) 中的边界分辨率。这可以通过将 c(s) 及其组装集成为等温线作为总负载浓度的函数来提取特征边界特征，这些等温线在第二阶段与 EPT 相匹配。讨论了解决等温线浓度误差的方法。最后，在 α-胰凝乳蛋白酶与大豆胰蛋白酶抑制剂相互作用的实验模型系统中，我们表明 EPT 很好地描述了快速相互作用系统的实验沉降边界结构。
Sedimentation velocity (SV) experiments of heterogeneous interacting systems exhibit characteristic boundary structures that can usually be very easily recognized and quantified. For slowly interacting systems, the boundaries represent concentrations of macromolecular species and they can be interpreted directly with population models based solely on the mass action law. For fast reactions, migration and chemical reactions are coupled, and different, but equally easily discernable boundary structures appear. However, these features have not been commonly utilized for data analysis, for the lack of an intuitive and computationally simple model. The recently introduced effective particle theory (EPT) provides a suitable framework. Here, we review the motivation and theoretical basis of EPT, and explore practical aspects for its application. We introduce an EPT-based design tool for SV experiments of heterogeneous interactions in the software SEDPHAT. As a practical tool for the first step of data analysis, we describe how the boundary resolution can be further improved in c(s) with a Bayesian adjustment of maximum entropy regularization to the case of heterogeneous interactions between molecules that have been previously studied separately. This can facilitate extracting the characteristic boundary features by integration of c(s) and their assembly into isotherms as a function of total loading concentrations, which are fitted with EPT in a second stage. Methods for addressing concentration errors in isotherms are discussed. Finally, in an experimental model system of alpha-chymotrypsin interacting with soybean trypsin inhibitor, we show that EPT provides an excellent description of the experimental sedimentation boundary structure of fast interacting systems.
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影响因子：
11.4
作者：
Barda-Saad, Mira;Shirasu, Naoto;Samelson, Lawrence E.
通讯作者：
Samelson, Lawrence E.
DOI：
10.1007/s00249-009-0514-1
发表时间：
2009-10
影响因子：
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作者：
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通讯作者：
Schuck, Peter
影响因子：
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作者：
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通讯作者：
Schuck, Peter
影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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