Mateo-delaFuente Henar, Nogueira Juan J
Chemistry Department, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain.
IADCHEM, Institute for Advanced Research in Chemistry, Universidad Autónoma de Madrid, Calle Francisco Tomás y Valiente, 7, 28049, Madrid, Spain.
Photochem Photobiol Sci. 2024 Dec;23(12):2157-2171. doi: 10.1007/s43630-024-00654-y. Epub 2024 Nov 13.
The modeling of the bioluminescent system of fireflies is key to understand the binding mode of the oxyluciferin/luciferase complex and its photophysical properties with the aim of developing high-efficiency devices and techniques. In this work, we present the OLUFF force field, which is able to describe the interactions to sample the conformational space of the four possible oxyluciferin emitters in both ground and excited state. This force field has been parameterized to reproduce quantum mechanical (QM) energies and geometrical parameters. Moreover, it has been validated by comparing probability distribution functions, minimized structures, infrared spectra and normal mode analysis obtained from OLUFF-based molecular dynamic (MD) simulations with their QM counterparts. Additionally, ground state simulations have also been performed using the general amber force field (GAFF) and compared with the OLUFF. It has been demonstrated that the OLUFF not only reproduces well the QM properties, but also improves the results from the GAFF.
萤火虫生物发光系统的建模是理解氧化荧光素/荧光素酶复合物的结合模式及其光物理性质的关键,目的是开发高效的设备和技术。在这项工作中,我们提出了OLUFF力场,它能够描述相互作用,以采样四种可能的氧化荧光素发射体在基态和激发态下的构象空间。该力场已被参数化以重现量子力学(QM)能量和几何参数。此外,通过将基于OLUFF的分子动力学(MD)模拟获得的概率分布函数、最小化结构、红外光谱和正常模式分析与其QM对应物进行比较,对其进行了验证。此外,还使用通用琥珀力场(GAFF)进行了基态模拟,并与OLUFF进行了比较。结果表明,OLUFF不仅能很好地重现QM性质,还能改善GAFF的结果。