Integrated Quantum, Molecules, Solvatoin, Charge State Simulations of Proteins

蛋白质的功能和反应性是其原子和电子结构、动力学及其辅助因子的产物。这项研究的目标是超越对某些反应如何发生的定量描述，到它为什么发生，到对事件的理解，在原子或官能团的水平上，以及在原理方面。该项目的核心主题是能量传导或耦合的概念，既是一个总体的解释原则，也是一个研究工具。新的测量和分析内部和外部斯塔克测量蛋白质（电能转化为蛋白质的变化）

A protein's function and reactivity is the product of its atomic and electronic structure, its dynamics, and its cofactors. The goal of this research is to go beyond quantitative descriptions of how some reaction occurs to why it occurs, to an understanding of the events, at both the level of atoms or functional groups and in terms of principles. The nucleating theme of the program project is the concept of energy transduction or coupling, both as an overarching explanatory principle, and as an investigative tool. Novel measurements and analysis of internal and external Stark measurements on proteins (transduction of electrical energy into changes in spectral transition energies) will probe the environment of protein cofactors, and the mechanisms by which these proteins modulate cofactor function and reactivity. Analysis of high resolution spectroscopy will be used to study the relationship between solvent and protein dynamics and the protein's energy landscape (How the energy of solvent and protein fluctuations is transduced into other activated and functional modes), using recently integrated simulation and theoretical tools. The first aim of project # 4 is to develop a coherent suite of simulation technologies that can span the range from quantum chemical calculations of cofactor electronic structure, via simulation of protein motions, through to long time scale solvent, electrostatic and charge transfer effects, by combining quantum chemical calculations, classical dynamics and finite difference Poisson-Boltzmann methods. The second aim of project # 4 is to apply this suite of simulation technologies to specific problems: The effect of protein and solvent on heme properties, quantitative characterization of protein dynamics, and the effect of internal electrostatic fields of proteins.