ExiFRET: flexible tool for understanding FRET in complex geometries
ExiFRET: flexible tool for understanding FRET in complex geometries
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DOI：
10.1117/1.jbo.17.1.011005
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发表时间：
2012-01-01
影响因子：
3.5
通讯作者：
Corry, Ben
中科院分区：
文献类型：
--
作者：
Deplazes, Evelyne;Jayatilaka, Dylan;Corry, Ben
荧光共振能量转移 (FRET) 可用于通过报告分子的接近度或测量分子间和分子内距离来获得低分辨率结构信息。该方法利用了能量转移的概率与荧光分子之间的分离有关的事实。对于一对荧光团，这种关系得到了很好的描述，但在包含两个以上荧光团的系统中，这种关系很复杂。在这里，我们提出了一种蒙特卡罗计算方案，该方案通过一个名为 ExiFRET 的用户友好的基于网络的程序来实现，该程序可用于确定各种荧光团排列中的 FRET 效率。 ExiFRET 可用于对随机分布在二维或三维中的单个荧光团、成对连接或以规则几何形状排列（有或没有预定义化学计量）的荧光团进行 FRET 建模。 ExiFRET 可以模拟均匀分布和聚集在簇中的荧光团。我们演示了如何使用该工具来了解标记效率对 FRET 效率的影响，估计分子间和分子内 FRET 的相对贡献，研究多聚体蛋白质、化学计量和寡聚体的结构，并帮助研究膜环境中脂质和蛋白质聚集的实验。我们还提出了一个扩展，可用于研究荧光团具有受限方向的情况。 (c) 2012 年光电仪器工程师协会 (SPIE)。 [DOI：10.1117/1.JBO.17.1.011005]
Fluorescence resonance energy transfer (FRET) can be utilized to gain low-resolution structural information by reporting on the proximity of molecules or measuring inter- and intramolecular distances. This method exploits the fact that the probability of the energy transfer is related to the separation between the fluorescent molecules. This relationship is well described for a single pair of fluorophores but is complicated in systems containing more than two fluorophores. Here, we present a Monte Carlo calculation scheme that has been implemented through a user-friendly web-based program called ExiFRET that can be used to determine the FRET efficiency in a wide range of fluorophore arrangements. ExiFRET is useful to model FRET for individual fluorophores randomly distributed in two or three dimensions, fluorophores linked in pairs or arranged in regular geometries with or without predefined stoichiometries. ExiFRET can model both uniform distributions and fluorophores that are aggregated in clusters. We demonstrate how this tool can be employed to understand the effect of labeling efficiency on FRET efficiency, estimate relative contributions of inter- and intramolecular FRET, investigate the structure of multimeric proteins, stoichiometries, and oligomers, and to aid experiments studying the aggregation of lipids and proteins in membrane environments. We also present an extension that can be used to study instances in which fluorophores have constrained orientations. (c) 2012 Society of Photo-Optical Instrumentation Engineers (SPIE). [DOI: 10.1117/1.JBO.17.1.011005]