Prediction of structure and function of protein complexes

蛋白质复合物结构和功能的预测

基本信息

批准号：
13208010
负责人：
KIDERA Akinori
金额：
$ 41.22万
依托单位：
Yokohama City University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research on Priority Areas
财政年份：
2001
资助国家：
日本
起止时间：
2001 至 2004
项目状态：
已结题

项目摘要

Database analyses of protein structures(1)Structural classification of all B-proteins: A novel structural classification of all B-proteins is presented from the viewpoint of the ring-shaped structure and the zipper-like contact pattern, based on the fact that 92% and 60% of B proteins have the ring topology and the zippered contact pattern, respectively.(2)Probabilistic alignment method: We developed a method of generating probabilistic alignments for sequences and structures, by which the correspondence between pairs of residues is evaluated in a probabilistic manner. This method was applied to TIM-barrel and β-trefoil proteins.Simulation analyses of protein functions(1)Development of a molecular dynamics program on parallel computer: A partial rigid-body method of molecular dynamics simulations for proteins and membranes is presented. The standard NPT ensemble is extended to the membrane-specific ensembles, the NPAT and NPyT ensembles.(2)Molecular dynamics simulations of aquaporins: Molecular dynamics simulations were performed for four members of the aquaporin family (AQPl, AQPZ, AQPO, and GlpF) in the explicit membrane environment. The single channel water permeability was evaluated to be GlpF AQPZ > AQPl≫AQPO.(3)Linear response theory of protein structural change upon ligand binding: A simple formula based on linear response theory is proposed to explain and predict the structural change of proteins upon ligand binding. The results for three protein systems of various sizes are consistent with the observations in the crystal structures.Experimental analyses of protein dynamics(1)Development of analysis method for neutron scattering spectra: The origin of the Boson peak in the inelastic neutron scattering was clarified based on the dynamic structural transition of proteins at low temperature.

蛋白质结构的数据库分析(1)所有B蛋白的结构分类：基于92个事实，从环状结构和拉链状接触模式的角度提出了所有B蛋白的新结构分类%和60%的B蛋白分别具有环形拓扑结构和拉链式接触模式。(2)概率比对方法：我们开发了一种为序列和结构生成概率比对的方法，通过该方法，该方法适用于TIM-barrel和β-trefoil蛋白。蛋白质功能的模拟分析(1)并行计算机上分子动力学程序的开发：分子动力学模拟的部分刚体方法。提出了针对蛋白质和膜的标准NPT系综扩展到膜特异性系综、NPAT和NPyT系综。(2)水通道蛋白的分子动力学模拟：分子动力学模拟。对水通道蛋白家族的四个成员(AQPl、AQPZ、AQPO和GlpF)在显式膜环境中进行了单通道水渗透性评估，结果为GlpF AQPZ>AQPl≫AQPO。(3)蛋白质结构的线性响应理论。配体结合时的变化：提出了一个基于线性响应理论的简单公式来解释和预测配体结合时蛋白质的结构变化三种不同大小的蛋白质系统的结果。蛋白质动力学的实验分析(1)中子散射谱分析方法的发展：根据蛋白质在低温下的动态结构转变，阐明了非弹性中子散射中玻色子峰的起源。温度。