Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins,The Journal of Physical Chemistry B

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Improving the Design of the Triple-Decker Motif in Red Fluorescent Proteins
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2017-11-15 00:00:00 , DOI: 10.1021/acs.jpcb.7b07517
Maria G. Khrenova ₁ , Igor V. Polyakov ₁ , Bella L. Grigorenko _{1,

2} , Anna I. Krylov ₃ , Alexander V. Nemukhin _{1,

2}

Affiliation

We characterize computationally a red fluorescent protein (RFP) with the chromophore (Chro) sandwiched between two aromatic tyrosine rings in a triple-decker motif. According to the original proposal [ J. Phys. Chem. Lett. 2013, 4, 1743], such a tyrosine-chromophore-tyrosine π-stacked construct can be accommodated in the green fluorescent protein (GFP). A recent study [ ACS Chem. Biol. 2016, 11, 508] attempted to realize the triple-decker motif and obtained an RFP variant called mRojoA-VYGV with two tyrosine residues surrounding the chromophore. The crystal structure showed that only a tyrosine-chromophore pair was involved in π-stacking, whereas the second tyrosine was oriented perpendicularly, edge-to-face with respect to the chromophore. We propose a more promising variant of this RFP with a perfect triple-decker unit achieved by introducing additional mutations in mRojoA-VYGV. The structures and optical properties of model proteins based on the structures of mCherry and mRojoA are characterized computationally by QM(DFT)/MM. The electronic transitions in the protein-bound chromophores are computed by high-level quantum chemical methods. According to our calculations, the triple-decker chromophore unit in the new RFP variant is stable within the protein and its optical bands are red-shifted with respect to the parent mCherry and mRojoA species.

中文翻译：

改进红色荧光蛋白中的三层图案的设计

我们通过计算将红色荧光蛋白（RFP）与生色团（Chro）夹在两个三层装饰基序中的两个芳香族酪氨酸环之间进行表征。根据原始建议[ J. Phys。化学来吧 2013年， 4， [1743]，这种酪氨酸-发色团-酪氨酸π-堆叠的构建体可以容纳在绿色荧光蛋白（GFP）中。最近的一项研究[ ACS化学。生物学 2016年， 11， 508]试图实现三层基序，并获得了一个名为mRojoA-VYGV的RFP变体，在发色团周围有两个酪氨酸残基。晶体结构表明，只有一个酪氨酸-生色团参与π-堆积，而第二个酪氨酸相对于生色团是垂直，边对面取向的。我们建议通过在mRojoA-VYGV中引入其他突变来实现具有理想三层单元的该RFP的更有希望的变体。基于mCherry和mRojoA结构的模型蛋白的结构和光学性质通过QM（DFT）/ MM计算表征。通过高级量子化学方法计算结合蛋白质的发色团中的电子跃迁。根据我们的计算，

更新日期：2017-11-16

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