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：从环形结构的角度出现所有B蛋白的新结构分类和所有B蛋白的新结构分类，并且基于92％和60％的B蛋白具有环形拓扑和zipperative Align Align agimign Align imign Align imign Align imigillistion：2）。序列和结构，以概率方式评估残差对之间的对应关系。该方法应用于Tim-Barrel和β-Trefoil蛋白。蛋白质功能的仿真分析（1）在平行计算机上开发分子动力学程序：一种分子动力学模拟蛋白质和膜的部分刚体方法。标准的NPT集合扩展到膜特异性合奏，NPAT和NPYT集合。（2）在素材上，对水普通道蛋白的分子动力学模拟：Aquaporin家族的四个成员（AQPZ，AQPZ，AQPZ，AQPO和GLPF）进行了分子动力学模拟。评估单道通道水的渗透率为GLPF AQPZ> AQPL≫AQPO。（3）提出了基于线性响应理论的简单公式来解释和预测配体结合的蛋白质的结构变化。各种大小的三种蛋白质系统的结果与晶体结构中的观察结果一致。蛋白质动力学的实验分析（1）基于低温下蛋白质的蛋白质的动态结构过渡，阐明了中子散射光谱的分析方法：玻色子峰的起源。