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.     

Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed     

Intrinsic Fluorescence of Actin

In this work actin is used to illustrate connection of protein fluorescence characteristics with its structure. On one hand, it has been demonstrated what kind of information about the contribution of each tryptophan residues to the bulk fluorescence spectrum can be obtained from the special analysis of protein three-dimensional structure. On the other hand, potentials of intrinsic fluorescence for elucidation of proteins structure, dynamics and processes of folding-unfolding are shown. In particular, using this method a new essentially unfolded kinetic intermediate state of actin was detected and characterized, and the place of inactivated actin and its kinetic predecessor in the process of folding-unfolding was determined. It has been revealed that inactivated actin is not intermediate state between the native and completely unfolded states, as it has been accepted before, but a result of protein misfolding. On the basis of the obtained data a new model of actin folding-unfolding pathway has been proposed.     

江浙蝮蛇蛇毒蛋白C激活因子基因的克隆及测序

从江浙蝮蛇毒腺中抽提总RNA，RT－PCR进行体外扩增，获得江浙蝮蛇蛇毒蛋白C激活因子基因，克隆至pGEX-5X-3载体中，对3个重组克隆分别作DNA全序列分析，通过遗传密码推导出相应的氨基酸序列，与其它已知的丝氨酸复白酶蛇毒蛋白的氨基酸作比较，其中许多上氨基酸有很强的同源性，该基因的成功克隆，不仅推导出江浙蝮蛇蛇毒蛋白C激活因子的蛋白质序列，也为进一步开展江浙蝮蛇蛇毒蛋白C激活因子蛋白质工程的研究工作打下良好的基础。     

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。     

复制缺陷型人泡沫病毒载体辅助质粒pΔGP的构建及转染小肠癌细胞的研究

在人泡沫病毒原病毒全长克隆pHRSV13的基础上,缺失突变gag和pol基因,并且用SV40polyA加尾信号替代人泡沫病毒的3′LTR,构建辅助质粒pΔGP.将复制缺陷型人泡沫病毒载体质粒pGPSNI EGFP和辅助质粒pΔGP分别转染和共转染小肠癌HIC细胞系,荧光显微镜检测发现共转染pGPSNI EGFP和pΔGP的HIC细胞能够强烈表达绿色荧光蛋白,转染有复制缺陷型人泡沫病毒载体质粒pGPSNI EGFP的HIC细胞能够表达少量的绿色荧光蛋白,而转染有辅助载体pΔGP的HIC细胞不表达绿色荧光.结果证明复制缺陷型人泡沫病毒载体的构建成功,表明人泡沫病毒env基因3′端的内部启动子IP具有弱启动子的活性,并且bel基因产生的调控蛋白能够反式激活人泡沫病毒内部启动子IP和5′LTR的启动子.     

Circadian synchrony in networks of protein rhythm driven neurons

The interaction between gene activation and cellular activity has recently emerged as a critical aspect of brain behavior, but the dynamics of networks incorporating these interactions are poorly understood. An interesting phenomena arises when the genetic activation oscillates endogenously and a network of such cells synchronize to a coherent rhythm, such as is the case with the suprachiasmatic nucleus. To explain this synchronization, we propose a model in which a mRNA/protein expression cycle drives neurons electrical activity, and synaptic activation shifts the phase of the protein rhythm. Using lattice networks, we demonstrate that these interactions are sufficient to generate coherent oscillation. © 2006 Wiley Periodicals, Inc. Complexity 12: 67–72, 2006     

海藻酸钠/大豆蛋白共混凝胶微球的结构

利用钙离子交联海藻酸钠／大豆分离蛋白共混溶液，制得海藻酸钠／大豆分离蛋共混凝胶微球．结果表明，海藻酸钠和大豆分离蛋白质量配比的不同以及各组分间相互作用的变化，微球呈现不同的微观结构．将微球干燥后置于水中溶胀，微球的尺寸无法回复到干燥前的尺寸，这是由于真空干燥处理使水分子挥发，促进微球内组分间形成了强的氢键作用所致．此外，用碱处理该共混微球，发现由于大豆分离蛋白溶解以及部分钙离子被置换析出，微球塌陷且内部形成了大孔．