CAREER: Computational Design of Fluorescent Proteins with Multiscale Excited State QM/MM Methods

在化学系生命过程化学（CLP）项目的支持下，来自韦恩州立大学的Alice步行者正在研究荧光蛋白传感器的计算机模拟设计，包括量子和经典物理。荧光蛋白被广泛用于观察和跟踪活细胞中的生物化学。然而，蛋白质的特定运动和结构之间的关系以及这与发色团的光催化运动之间的关系尚未完全理解。拟议的计算工作将提供深入了解这些关系的技术，模型的运动，整个荧光蛋白及其对光的反应。这一系列研究有望支持新的单体红色阴离子传感器、可调光开关二聚体的开发，并可能创造出广泛适用的合理设计原则来创建新的传感器。该项目包括本科生在计算化学方面的虚拟和基于课堂的研究经验。 该研究项目的目标是将计算化学应用于新的荧光蛋白（FP）传感器的理解和合理设计。FP在生化实验中被广泛使用，并作为化学生物学的工具，它们可以应用于成像分子或感兴趣的机制。新FP传感器的发展在很大程度上是实验性的-蛋白质结构的原子细节和FP发色团的物理学之间的关系还没有很好地理解。这种基本的知识差距使得有针对性的FP传感器的创建特别具有挑战性。我们的中心假设是，在基态的蛋白质结构集合和激发态的发色团运动之间存在物理关系，如果清楚地理解，可以帮助创建新的传感器。为了验证这一假设，步行者团队将使用经典分子动力学（MD），激发态非绝热量子力学/分子力学（QM/MM）动力学和机器学习（ML）的组合方法来研究特定的系统，目的是开发新的荧光探针并更普遍地建立FP传感器的合理设计原则。这项工作将表征表面突变对同源四聚体Dicosoma红色荧光蛋白与单体衍生物的影响，设计和研究新的负离子-该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查进行评估，被认为值得支持的搜索.

With the support of the Chemistry of Life Processes (CLP) program in the Division of Chemistry, Alice Walker from Wayne State University is investigating the design of fluorescent protein sensors with computer simulations, including quantum and classical physics. Fluorescent proteins are widely used to watch and track biochemistry in living cells. However, the relationship between specific motions and structures of the protein and how this relates to the light-catalyzed motion of the chromophore is not fully understood. The proposed computational work will provide insight into these relationships with techniques that model the motion of the entire fluorescent protein and its reaction to light. This line of research is expected to support the development of new monomeric, red anion sensors, tunable photoswitchable dimers, and potentially create broadly applicable rational design principles to create new sensors. This project includes virtual and classroom-based research experiences in computational chemistry for undergraduate students. The goal of this research project is to apply computational chemistry to the understanding and rational design of new fluorescent protein (FP) sensors. FPs are used ubiquitously in biochemical experiments and as tools in chemical biology, where they can be applied to image molecules or mechanisms of interest. The development of new FP sensors is largely empirical—the relationship between the atomic details of the protein structure and photophysics of FP chromophores is not well understood. This fundamental knowledge gap makes the creation of targeted FP sensors especially challenging. Our central hypothesis that there is a physical relationship between the structural ensemble of the protein on the ground state and the motion of the chromophore on the excited state that, if clearly understood, could aid in the creation of new sensors. To test this hypothesis, the Walker team will use a combined approach of classical molecular dynamics (MD), excited state nonadiabatic quantum mechanical/molecular mechanical (QM/MM) dynamics, and machine learning (ML) to investigate specific systems with the aims of developing new fluorescent probes and establishing rational design principles for FP sensors more generally. This work will characterize the impact of surface mutations on the homotetrameric Dicosoma red fluorescent protein vs monomeric derivatives, design and study new anion-specific red FP sensors based on NeonGreen and endeavor to determine the mechanism of action for photodissociative Dronpa dimers.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.