Computer simulation of the proton transfer pathways at the extracellular side of bacteriorhodopsin and calculation of IR spectra of the photocycle intermediates

QM/MM技术将用于测定bR光循环中间体的结构和红外光谱。为了实现这一目标，我们将使用DFT方法以及重参数化DFTB方法，并通过计算Hessian矩阵以及通过速度和偶极子自相关函数的傅里叶变换来确定红外光谱。这些计算有助于解决原子（x射线）结构与实验红外光谱的分配问题，并有助于确定bR光循环的后期结构。特别令人感兴趣的是所谓的质子释放基团（PRG）的身份和结构。我们将测试这一组由细胞外一侧的质子化水团簇组成的建议，这一假设将解释实验红外光谱。PRG的测定为研究第二步和第五步质子转移、质子在M态从PRG向体体的释放以及Asp85和PRG在0和bR基态之间的最后一个质子转移步骤开辟了道路。在这里，最小路径搜索算法以及伞式采样技术将被应用。

QM/MM techniques will be used to determine structures and IR spectra of the bR photocycle intermediates. To achieve this goal, we will use DFT methods as well as a reparameterized DFTB method and determine the infrared spectra via calculation of the Hessian matrix as well as via Fourier transform of the velocity- and dipole- autocorrelation functions. These calculations may help resolving the assignment problem of atomic (X-ray) structures to experimental IR spectra and in the determination of the later structures of the bR photocycle. Of particular interest is the identity and structure of the so-called proton release group (PRG). We will test the suggestion that this group consists of a protonated water cluster at the extracellular side, a hypothesis which would explain the experimental IR spectra. The determination of the PRG opens the way for the investigation of the second and fifth proton transfer steps, the proton release from the PRG to the bulk in the M state and the last proton transfer step between Asp85 and the PRG between the 0 and bR ground state. Here, minimum pathway search algorithms as well as umbrella sampling techniques will be applied.