Grabarek Dawid, Andruniów Tadeusz
Advanced Materials Engineering and Modelling Group, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
J Chem Theory Comput. 2020 Oct 13;16(10):6439-6455. doi: 10.1021/acs.jctc.0c00602. Epub 2020 Sep 21.
We systematically investigate an impact of the size and content of a quantum (QM) region, treated at the density functional theory level, in embedding calculations on one- (OPA) and two-photon absorption (TPA) spectra of the following fluorescent proteins (FPs) models: green FP (avGFP) with neutral (avGFP-n) and anionic (avGFP-a) chromophore as well as Citrine FP. We find that amino acid (a.a.) residues as well as water molecules hydrogen-bonded (h-bonded) to the chromophore usually boost both OPA and TPA processes intensity. The presence of hydrophobic a.a. residues in the quantum region also non-negligibly affects both absorption spectra but decreases absorption intensity. We conclude that to reach a quantitative description of OPA and TPA spectra in multiscale modeling of FPs, the quantum region should consist of a chromophore and most of a.a. residues and water molecules in a radius of 0.30-0.35 nm ( 200-230 atoms) when the remaining part of the system is approximated by the electrostatic point-charges. The optimal size of the QM region can be reduced to 80-100 atoms by utilizing a more advanced polarizable embedding model. We also find components of the QM region that are specific to a FP under study. We propose that the F165 a.a. residue is important in tuning the TPA spectrum of avGFP-n but not other investigated FPs. In the case of Citrine, Y203 and M69 a.a. residues must definitely be part of the QM subsystem. Furthermore, we find that long-range electrostatic interactions between the QM region and the rest of the protein cannot be neglected even for the most extensive QM regions ( 350 atoms).
我们系统地研究了在密度泛函理论水平下处理的量子（QM）区域的大小和内容，在嵌入计算中对以下荧光蛋白（FPs）模型的单光子吸收（OPA）和双光子吸收（TPA）光谱的影响：具有中性（avGFP-n）和阴离子（avGFP-a）发色团的绿色荧光蛋白（avGFP）以及柠檬黄荧光蛋白。我们发现，与发色团形成氢键的氨基酸（a.a.）残基以及水分子通常会增强OPA和TPA过程的强度。量子区域中疏水a.a.残基的存在也对两种吸收光谱有不可忽略的影响，但会降低吸收强度。我们得出结论，为了在FPs的多尺度建模中对OPA和TPA光谱进行定量描述，当系统的其余部分由静电点电荷近似时，量子区域应包括发色团以及半径为0.30 - 0.35 nm（200 - 230个原子）内的大多数a.a.残基和水分子。通过使用更先进的极化嵌入模型，QM区域的最佳大小可以减少到80 - 100个原子。我们还发现了所研究的特定FPs的QM区域的组成部分。我们提出，a.a.残基F165在调节avGFP-n的TPA光谱方面很重要，但对其他研究的FPs则不然。对于柠檬黄荧光蛋白，a.a.残基Y203和M69肯定必须是QM子系统的一部分。此外，我们发现即使对于最大的QM区域（350个原子），QM区域与蛋白质其余部分之间的长程静电相互作用也不能被忽略。
