Program System for Protein Electron Crystallography

蛋白质电子晶体学程序系统

基本信息

批准号：
09558092
负责人：
KIDERA Akinori
金额：
$ 5.38万
依托单位：
KYOTO UNIVERSITY
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
1997
资助国家：
日本
起止时间：
1997 至 1999
项目状态：
已结题

项目摘要

3D Structure determination of membrane bound proteins by electron diffraction from 2D crystal has a crucial importance in structural biology as a complementary method to X-ray diffraction. The purpose of this work is to develop a modeling and refinement tool for the electron crystallography. Through the research period, we have determined 3D structures of various proteins, and established the modeling and refinement techniques. The results of the technical development can be seen in the atomic resolution models of bacteriorhodopsin and aquaporin, which provide important pieces of information about the mechanism how their functions occur on the 3D structures. It has become clear from the analyses that the most fundamental characteristics in electron diffraction is in the information about the charged state of a protein. Electron is scattered by the electronic potential instead of electron density in X-ray scattering. Hence, the valence electron strongly affects the scattering behavior of electron. In other words, the electron diffraction depends on the charged state of the constituent atoms. We developed a method of treating charged state correctly by the following way. We carred out ab initio quantum chemical calculations of the electronic potentials of small model compounds, which constitute a protein molecule, in various charged states and solvation states, and calculated the atomic scattering factor for each charged and solvation state by the Fourier transformation of the potential function. In the application to the structural analysis, since the charge state has a certain distribution in a crystal, an optimal linear combination of the atomic scattering factors for various charge states will be calculated in the course of the refinement process.

从2D晶体中电子衍射对膜结合蛋白的3D结构在结构生物学中至关重要，作为X射线衍射的补充方法。这项工作的目的是为电子晶体学开发建模和改进工具。在整个研究期间，我们已经确定了各种蛋白质的3D结构，并确定了建模和改进技术。在细菌紫红素和水通道蛋白的原子分辨率模型中可以看到技术发展的结果，这些模型提供了有关其功能如何在3D结构上发生的重要信息。从分析中可以清楚地看出，电子衍射中最基本的特征在于有关蛋白质带电状态的信息。电子在X射线散射中被电子电位而不是电子密度散射。因此，价电子强烈影响电子的散射行为。换句话说，电子衍射取决于成分原子的带电状态。我们开发了一种通过以下方式正确处理充电状态的方法。我们从头量化的小型化合物的电子电位计算出量子化学计算，在各种带电状态和溶剂化状态下构成了蛋白质分子，并通过电势转换计算了每个带电的溶剂和溶剂化态的原子散射因子和溶剂化态的原子散射因子。功能。在对结构分析的应用中，由于电荷状态在晶体中具有一定的分布，因此将在改进过程的过程中计算各种电荷状态的原子散射因子的最佳线性组合。