Prediction of structure and function of protein complexes

蛋白质结构的数据库分析（1）B蛋白质的结构分类：基于B蛋白质中92%的B蛋白质具有环状拓扑结构，60%的B蛋白质具有拉链状接触模式，从环状结构和拉链状接触模式的角度提出了一种新的B蛋白质结构分类方法。（2）概率比对方法：我们开发了一种生成序列和结构的概率比对的方法，通过该方法，以概率的方式评估残基对之间的对应关系。蛋白质功能的模拟分析（1）并行计算机分子动力学程序的开发：提出了一种蛋白质和膜分子动力学模拟的部分刚体方法。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：在外显膜环境中对水通道蛋白家族的四个成员（AQP1、AQPZ、AQPO和GlpF）进行分子动力学模拟。单通道水渗透率被评估为GlpF AQPZ > AQPl> AQPO。（3）蛋白质结构变化对配体结合的线性响应理论：基于线性响应理论提出了一个简单的公式来解释和预测蛋白质结构变化对配体结合的影响。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来源。

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.