Validation of depth-dependent fluorescence quenching in membranes by molecular dynamics simulation of tryptophan octyl ester in POPC bilayer.
Validation of depth-dependent fluorescence quenching in membranes by molecular dynamics simulation of tryptophan octyl ester in POPC bilayer.
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DOI：
10.1021/jp310638f
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发表时间：
2013-05-02
影响因子：
3.3
通讯作者：
Ladokhin, Alexey S.
中科院分区：
文献类型：
--
作者：
Kyrychenko, Alexander;Tobias, Douglas J.;Ladokhin, Alexey S.
深度依赖的荧光猝灭是研究蛋白质和肽渗透到脂质双分子层的重要工具。然而，从猝灭数据中提取定量信息的复杂性在于：(1)实验中可用的猝灭剂数量有限；(2)由于猝灭剂和荧光团的横向位置分布广泛，导致热无序。在这里，我们验证和完善了一种通用的方法来确定沿双分子层正常的淬火数据荧光探针的位置，基于分子动力学（MD）模拟模型化合物，色氨酸辛基酯（TOE），在1-棕榈酰-2-油酰- pn -甘油-3-磷脂胆碱（POPC）双分子层。发现TOE环位于双层内较深（最可能的位置为13.3 Å，离双层中心的重心分布为14.8 Å），分布较广（深度分布宽度为9 Å），与前人实验观察结果一致。通过将POPC脂酰基链的碳原子作为“伪猝灭剂”，并计算与TOE的吲哚原子的适当横向重叠和碰撞率，模拟了深度相关的猝灭曲线。这些模拟的淬火曲线通过深度的高斯函数很好地拟合，就像对分布分析程序中的实验数据所做的那样（方法酶，1997,278,462-473）。将碰撞伪淬火剖面与TOE的吲哚部分的实际剖面进行比较，可以检验数据分析的有效性，并确定根据淬火数据计算膜穿透深度时可能的误差来源。
Depth-dependent fluorescence quenching is an important tool for studying the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information from quenching data is, however, complicated by (1) a limited number of experimentally available quenchers and (2) by thermal disorder resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Here we validate and refine a general approach to determining the location of a fluorescent probe along the bilayer normal from quenching data, based on a molecular dynamics (MD) simulation of a model compound, tryptophan octyl ester (TOE), in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. The TOE ring was found to lie deeply within the bilayer (most probable position of 13.3 Å and center-of-weight of the distribution of 14.8 Å from the bilayer center) and it was very broadly distributed (with 9 Å depth distribution width), which is consistent with previous experimental observations. The depth-dependent quenching profiles were simulated by treating carbon atoms of the lipid acyl chain of POPC as “pseudo-quenchers” and calculating appropriate transverse overlaps and collision rates with indole atoms of TOE. These simulated quenching profiles were well fitted by a Gaussian function of depth, as is routinely done with experimental data subjected to the Distribution Analysis procedure (Methods Enzymol. 1997, 278, 462–473). Comparison of the collisional pseudo-quenching profiles with the actual profiles of the indole moiety of TOE allows tests of the validity of the data analysis and identification of the possible sources of error in calculating depths of membrane penetration from quenching data.
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影响因子：
3.3
作者：
Kyrychenko, Alexander;Wu, Feiyue;Thummel, Randolph P.;Waluk, Jacek;Ladokhin, Alexey S.
通讯作者：
Ladokhin, Alexey S.
影响因子：
5.6
作者：
LANDOLTMARTICORENA, C;WILLIAMS, KA;REITHMEIER, RAF
通讯作者：
REITHMEIER, RAF
DOI：
10.3390/molecules16075437
发表时间：
2011-06-27
期刊：
Molecules (Basel, Switzerland)
影响因子：
--
作者：
Loura LM;Ramalho JP
通讯作者：
Ramalho JP
影响因子：
4.1
作者：
Kalé, L;Skeel, R;Schulten, K
通讯作者：
Schulten, K
影响因子：
3.9
作者：
Grossfield, A;Woolf, TB
通讯作者：
Woolf, TB