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

细菌视紫红质胞外质子转移途径的计算机模拟和光循环中间体的红外光谱计算

• 批准号: 15479448
• 负责人: Professor Dr. Sandor Suhai
• 金额: --
• 依托单位: Abteilung für Theoretische Chemische Biologie
• 依托单位国家: 德国
• 项目类别: Research Units
• 财政年份: 2005
• 资助国家: 德国
• 起止时间: 2004-12-31 至 2008-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/15479448?language=en
• 关键词: Computer; simulation; proton; transfer; pathways

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.

QM/MM技术将用于确定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方法以及重新参数化的DFTB方法，并通过计算海森矩阵以及通过速度和偶极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)结构对实验红外光谱的指认问题，并有助于确定BR光循环的后期结构。特别感兴趣的是所谓的质子释放群(PRG)的身份和结构。我们将测试这一组由细胞外侧的质子化水团组成的假设，这一假说可以解释实验的红外光谱。PRG的确定为研究第二和第五质子转移步骤、从PRG向处于M态的块体的质子释放以及Asp85和PRG之间0和Br基态之间的最后质子转移步骤铺平了道路。在这里，最小路径搜索算法以及伞形抽样技术将被应用。