现代优化计算方法在蛋白质结构预测中的应用

现代优化计算方法在蛋白质结构预测中占有重要地位.简要地介绍了模拟退火算法,遗传算法,人工神经网络和图论算法在蛋白质结构预测中的应用.对国内外近年来应用这些算法,特别是在蛋白质构象搜索问题中,解决蛋白质结构预测的研究作了回顾,并分析、比较了这几种算法的效果和特点.     

Nonlinear Correlations of Protein Sequences and Symmetries of Their Structures

We investigate the nonlinear correlations of protein sequences by using the nonlinear prediction method developed in nonlinear dynamical theory. It is found that a lot of protein sequences show strong nonlinear correlations and have deterministic structures. Further investigations show that the strong nonlinear correlations of these protein sequences are due to the symmetries of their tertiary structures. Furthermore, the correlation lengths of the sequences are related to the degrees of the symmetries. These results support the duplication mechanism of protein evolution and also reveal one aspect how amino acid sequences encode their spatial structures.     

酵母蛋白质网络的动力学性质

蛋白质-蛋白质、蛋白质-DNA相互作用网络决定了细胞中各种关键功能的执行．基于芽殖酵母(budding yeast saccharomyces cerevisiae)的蛋白质-蛋白质相互作用网络数据和相关的实验文献，我们建立了调控细胞周期和生命周期(cell cycle and life cycle)的蛋白质网络，并利用离散模型研究了该网络的动力学性质，研究表明：细胞周期网络的动力学性质具有很强的稳定性，约94％的蛋白质初态将演化到对应于生物学G1基态的稳定态，使其成为惟一的全局吸引点；同时，绝大多数的初态的演化路径都通过由G1激发态到G1基态的细胞周期演化路径，使细胞周期路径成为全局性的“吸引”路径。     

在三通道α-螺旋蛋白质中传递生物能量的孤子的特性

用庞小峰先生提出的生物能量传递的新理论和 Runge-Kutta数值模拟方法,研究了三通道α-螺旋蛋白质中激发的孤子的动力学特性,求出在0K和300K温度下该孤子稳定地沿蛋白质链传递.由此可见,它能担任在蛋白质分子中传递生物能量的功能.从而再次证实了新理论的可利用性.     

Nonlinear Dynamics Approach to the Correlation Analysis of Protein Sequences

To clarify the randomness of protein sequences,we make a detailed analysis of a set of typical protein sequences representing each fold by using the nonlinear prediction method developed in nonlinear dynamics theory.No deterministic structures are found in these protein sequences and this implies that they behave as random chains.We also explain the controversial results obtained in previous investigations.     

巴旦杏中脂肪酸的测定

采用气相色谱仪进行定量分析，气－联质联用仪进行定性分析，巴旦杏中脂肪酸进行了测定，并探讨了样品处理方法和气－质联用仪的分析条件，得到了较为满意的分析结果。     

荧光光谱法研究蛋白质构象的电磁-温度协同效应

长期以来电磁生物效应受到人们普遍关注，近年来从各个角度进行了相关研究。电磁－温度协同效应是当前的热点。本研究通过电磁场及温度协同对蛋白质影响的研究，发现蛋白质在电磁场作用下的不可逆变性，而且这种变性也遵循Arrhenius规律，并进一步得出电磁－温度协同作用的蛋白质变性模型。本文从分子反应动力学的角度解释了电磁－温度协同效应，并对非热效应作了一定的探讨。     

Scaling Behaviour of Conserved Sites in Protein Families

Base on the database of families of structurally similar proteins, a statistical study is made on the scaling behaviour of occupying probabilities of conserved sites (Pc) in various protein families. A power-law decrease of Pc with the increasing protein-chain length Lf is found. This is related to the power-law scaling behaviour of the occurring probabilities of local contact interactions (Plocal) between residues. In addition, applying residue grouping, we find the same scaling behaviour when the number of residue types is more than 12, indicating that 12 residue types are enough to present the complexity of proteins.     

核酸识体的研究及应用

核酸识体(aptamer)是近年来发展起来的一类经体外人工进化程序筛选出的寡聚核苷酸。它能高效、特异地结合各种配体，在蛋白质的分析检测、医学诊断治疗、生物传感器和分子开关的开发等方面有很大的应用前景，文章对核酸识体的研究和应用进展进行了综述。     

Penta-Coordinate Phosphorus Intermediates Analysis on Phospho-related Proteins

In this paper, based on known crystal structures of square pyramid （SP） and trigonal bipyramid （TBP） penta coordinated phosphorus compounds containing amino acid side chains, such as amino, carboxyl, hydroxyl or thiol, a software for survey the P（5）-structure of phosphorylated proteins was derived. By this software, it was found that 382 of 398 phosphorus related kinases （96%） from current PDB could go through the penta-coordinated phosphorus transition state or intermediate.