Devore Matthew S, Gull Stephen F, Johnson Carey K
Department of Chemistry, University of Kansas, Lawrence, Kansas, 66045, United States.
Chem Phys. 2013 Aug 30;422. doi: 10.1016/j.chemphys.2012.11.018.
We analyze single molecule FRET burst measurements using Bayesian nested sampling. The MultiNest algorithm produces accurate FRET efficiency distributions from single-molecule data. FRET efficiency distributions recovered by MultiNest and classic maximum entropy are compared for simulated data and for calmodulin labeled at residues 44 and 117. MultiNest compares favorably with maximum entropy analysis for simulated data, judged by the Bayesian evidence. FRET efficiency distributions recovered for calmodulin labeled with two different FRET dye pairs depended on the dye pair and changed upon Ca binding. We also looked at the FRET efficiency distributions of calmodulin bound to the calcium/calmodulin dependent protein kinase II (CaMKII) binding domain. For both dye pairs, the FRET efficiency distribution collapsed to a single peak in the case of calmodulin bound to the CaMKII peptide. These measurements strongly suggest that consideration of dye-protein interactions is crucial in forming an accurate picture of protein conformations from FRET data.
我们使用贝叶斯嵌套采样分析单分子荧光共振能量转移（FRET）猝发测量数据。MultiNest算法可从单分子数据中生成准确的FRET效率分布。针对模拟数据以及在第44位和第117位残基处标记的钙调蛋白，比较了通过MultiNest和经典最大熵方法恢复的FRET效率分布。根据贝叶斯证据判断，对于模拟数据，MultiNest与最大熵分析相比具有优势。用两种不同的FRET染料对标记的钙调蛋白所恢复的FRET效率分布取决于染料对，并在钙结合时发生变化。我们还研究了与钙/钙调蛋白依赖性蛋白激酶II（CaMKII）结合域结合的钙调蛋白的FRET效率分布。对于这两种染料对，在钙调蛋白与CaMKII肽结合的情况下，FRET效率分布都集中到一个单峰。这些测量结果有力地表明，在从FRET数据形成蛋白质构象的准确图像时，考虑染料 - 蛋白质相互作用至关重要。
