We study the π$\pi$-stacking interaction between the chromophore and Tyr203 in the Yellow Fluorescent Protein (YFP) in order to (i) evaluate the contribution of the internal interaction energy of the isolated Chromophore-Tyrosine complex (E_int${\text{E}}_{\mathit{int}}$) to the 26 nm red shift observed from GFP to YFP, (ii) compare the effects of E_int${\text{E}}_{\mathit{int}}$ and of the proteic environment. To that end, we perform quantum mechanical and force field (ff) calculations of the isolated complex in S₀ and S₁ states on a large sample of geometries, together with molecular dynamics simulations and potential of mean force analysis. The calculated absorption wavelengths are found red shifted with respect to the isolated chromophore by 12-19 nm, that represents a large part of the GFP-YFP shift. We find that the effect of the protein is determinant on the dynamics of the complex while the error that results from using a classicalff is of limited effect.

中文翻译：

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π$\pi$S ₀和S ₁状态下YFP中的堆积相互作用，量子力学和力场评估

我们研究π$\pi$黄色荧光蛋白（YFP）中生色团与Tyr203之间的堆积相互作用，以便（i）评估分离的生色团-酪氨酸复合物的内部相互作用能的贡献（E _int${\text{E}}_{\mathit{整型}}$）到从GFP到YFP观察到的26 nm红移，（ii）比较E _int的影响${\text{E}}_{\mathit{整型}}$和蛋白质环境。为此，我们对大量几何样品进行S ₀和S ₁状态下的孤立复合物的量子力学和力场（ff）计算，以及分子动力学模拟和平均力分析的潜力。发现所计算的吸收波长相对于分离的生色团红移了12-19nm，这代表了GFP-YFP移位的很大一部分。我们发现蛋白质的作用决定了复合物的动力学，而使用经典ff导致的误差作用有限。