Cyan fluorescent protein: Molecular dynamics, simulations, and electronic absorption spectrum
Cyan fluorescent protein: Molecular dynamics, simulations, and electronic absorption spectrum
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DOI：
10.1021/jp054656w
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发表时间：
2005-12-22
影响因子：
3.3
通讯作者：
Lévy, B
中科院分区：
文献类型：
--
作者：
Demachy, I;Ridard, J;Lévy, B
用1 ns的分子动力学（MD）模拟方法研究了绿色荧光蛋白（GFP）的突变体--增强型青色荧光蛋白（ECFP）的动力学和电子吸收光谱.考虑了ECFP的两种X射线构象A'和B'。假定发色团是中性的，并且所有可滴定的残基在中性pH下处于其标准质子化状态。将蛋白质包埋在水分子（和抗衡离子）的盒子中。第一个结果是发现两种构象A'和B'在整个沿着模拟过程中是稳定的。然后，氢键网络的分析表明，在发色团的吲哚部分的氮原子周围的两种构象之间的强烈差异。这部分是由于His 148残基附近的13桶中的缺陷，其允许构象A '的蛋白质内的一个溶剂分子进入。最后，使用TDDFT方法对每5 ps提取的MD轨迹的160个快照进行蛋白质和溶剂水分子的电荷云中的发色团的电子跃迁能的量子力学计算。发现构象A'和B'尽管涉及发色团的氢键网络不同，但表现出非常相似的光谱。这种相似性与电子跃迁中涉及的弱电荷转移和由ECFP在发色团附近产生的弱静电场有关，在本模拟中所作的假设内。
The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A' and B' of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A' and B' are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the 13 barrel near the His 148 residue, which allows the access of one solvent molecule inside the protein in conformation A'. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A' and B' exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.