Department of Chemistry , Lomonosov Moscow State University , Moscow 119991 , Russia.
Emanuel Institute of Biochemical Physics , Russian Academy of Sciences , Moscow 119334 , Russia.
J Phys Chem B. 2019 Jul 25;123(29):6133-6149. doi: 10.1021/acs.jpcb.9b00591. Epub 2019 May 10.
Remarkable success in engineering novel efficient biomarkers based on fluorescent and photoactive proteins provokes a question of whether computational modeling of their properties can contribute to this important field. In this Feature Article, we analyze selected papers devoted to computer simulations of three types of photoactive systems: the green fluorescent protein and its derivatives, the flavin-binding proteins, and the phytochrome domains. The main emphasis is on structures, optical spectra, and chemical reactions in the chromophore-containing pockets. Quantum chemistry, quantum mechanics/molecular mechanics, and molecular dynamics methods are effective tools in these simulations. We highlight both the success stories and the persisting challenges, discussing the ways of elevating theoretical approaches to the level of testable predictions.
在基于荧光和光活性蛋白的新型高效生物标志物的工程方面取得了显著成功，这引发了一个问题，即它们的性质的计算建模是否可以为这个重要领域做出贡献。在这篇专题文章中，我们分析了三篇专门讨论三种类型的光活性系统的计算机模拟的论文：绿色荧光蛋白及其衍生物、黄素结合蛋白和光敏色素结构域。主要重点是含发色团口袋中的结构、光学光谱和化学反应。在这些模拟中，量子化学、量子力学/分子力学和分子动力学方法是有效的工具。我们强调了成功案例和持续存在的挑战，讨论了将理论方法提升到可测试预测水平的方法。
