Demachy Isabelle, Ridard Jacqueline, Laguitton-Pasquier Hélène, Durnerin Elodie, Vallverdu Germain, Archirel Pierre, Lévy Bernard
Laboratoire de Chimie Physique, UMR 8000 CNRS-Université de Paris-Sud, 91405 Orsay Cedex, France.
J Phys Chem B. 2005 Dec 22;109(50):24121-33. doi: 10.1021/jp054656w.
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 beta barrel near the His148 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.
通过1纳秒的分子动力学（MD）模拟，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'。假设发色团呈中性，所有可滴定残基在中性pH下处于其标准质子化状态。蛋白质被嵌入水分子（和抗衡离子）的盒子中。第一个结果是，在整个模拟过程中发现两种构象A'和B'都是稳定的。然后，对氢键网络的分析表明，在发色团吲哚部分氮原子周围的两种构象之间存在很大差异。这部分是由于His148残基附近β桶的不完善，这使得一个溶剂分子能够进入构象A'的蛋白质内部。最后，使用TDDFT方法对MD轨迹每5皮秒提取的160个快照进行了发色团在蛋白质和溶剂水分子电荷云中的电子跃迁能量的量子力学计算。结果发现，尽管涉及发色团的氢键网络不同，但构象A'和B'表现出非常相似的光谱。在本模拟所做的假设范围内，这种相似性与电子跃迁中涉及的弱电荷转移以及ECFP在发色团附近产生的弱静电场有关。
