Thermodynamic study of transthyretin association (wild‐type and senile forms) with heparan sulfate proteoglycan: pH effect and implication of the reactive histidine residue

The tetramer destabilization of transthyretin into monomers and its fibrillation are phenomena leading to amyloid deposition. Heparan sulfate proteoglycan (HSPG) has been found in all amyloid deposits. A chromatographic approach was developed to compare binding parameters between wild‐type transthyretin (wtTTR) and an amyloidogenic transthyretin (sTTR). Results showed a greater affinity of sTTR for HSPG at pH 7.4 compared with wtTTR owing to the monomeric form of sTTR. Analysis of the thermodynamic parameters showed that van der Waals interactions were involved at the complex interface for both transthyretin forms. For sTTR, results from the plot representing the number of protons exchanged vs pH showed that the binding mechanism was pH‐dependent with a critical value at a pH 6.5. This observation was due to the protonation of a histidine residue as an imidazolium cation, which was not accessible when TTR was in its tetrameric structure. At pH >6.5, dehydration at the binding interface and several contacts between nonpolar groups of sTTR and HSPG were also coupled to binding for an optimal hydrogen‐bond network. At pH <6.5, the protonation of the His residue from sTTR monomer when pH decreased broke the hydrogen‐bond network, leading to its destabilization and thus producing slight conformational changes in the sTTR monomer structure. Copyright © 2014 John Wiley & Sons, Ltd.     

与HBV X蛋白相互作用的细胞蛋白的筛选及其鉴定

参考GenBank核苷酸序列库中的HBV的核苷酸序列设计合成了一对对应于HBx基因的引物，从原发性肝癌(hepatocellular carcinoma，HCC)患者的血清中提取HBV基因组DNA作为模板，扩增HBx编码区并测定了核苷酸序列．将该编码区克隆到酵母双杂交系统的诱饵蛋白表达载体pGBKT7中，转入酵母细胞AH109，进行表型鉴定．然后通过Mating实验从已制备好用于酵母双杂交系统的肝cDNA表达文库中筛选与HBx相互作用的细胞蛋白，并用体外免疫共沉淀实验进一步验证．研究表明，分离得到的与HBx基因编码的蛋白相互作用的4种新的细胞蛋白，分别是醛缩酶B、C8α亚基、一种丝氨酸蛋白酶Hepsin和一种未知蛋白．     

Microstructure dependent dynamic fracture analyses of trabecular bone based on nascent bone atomistic simulations

Trabecular bone fracture is closely related to the trabecular architecture, microdamage accumulation, and bone tissue properties. Primary constituents of trabecular tissue are hydroxyapatite (HA) mineralized type-I collagen fibers. In this research, dynamic fracture in two dimensional (2-D) micrographs of ovine (sheep) trabecular bone is modeled using the mesoscale cohesive finite element method (CFEM). The bone tissue fracture properties are obtained based on the atomistic strength analyses of a type-I collagen + HA interfacial arrangement using molecular dynamics (MD). Analyses show that the presented framework is capable of analyzing the architecture dependent fracture in 2-D micrographs of trabecular bone.     

Self-Interactions of Strands and Sheets

Physical strands or sheets that can be modelled as curves or surfaces embedded in three dimensions are ubiquitous in nature, and are of fundamental importance in mathematics, physics, biology, and engineering. Often the physical interpretation dictates that self-avoidance should be enforced in the continuum model, i.e., finite energy configurations should not self-intersect. Current continuum models with self-avoidance frequently employ pairwise repulsive potentials, which are of necessity singular. Moreover the potentials do not have an intrinsic length scale appropriate for modelling the finite thickness of the physical systems. Here we develop a framework for modelling self-avoiding strands and sheets which avoids singularities, and which provides a way to introduce a thickness length scale. In our approach pairwise interaction potentials are replaced by many-body potentials involving three or more points, and the radii of certain associated circles or spheres. Self-interaction energies based on these many-body potentials can be used to describe the statistical mechanics of self-interacting strands and sheets of finite thickness.     

基于几何不变量的蛋白质三维分子结构比对

为了解决蛋白质三维结构比对需要处理大量的旋转、平移变换，直接用动态规划将变得十分繁琐这一问题，在保留蛋白质空间结构属性特征的基础上，对蛋白质三维数据进行了预先的处理．通过计算蛋白质结构在旋转和平移下的几何不变量，将蛋白质的三维结构坐标变换为具有旋转、平移不变性的一维序列．进一步给出了“距离”以及“相似得分”的定义．在此基础上采用动态规划方法给出了新的蛋白质结构比对算法．对专家分类的蛋白质结构数据库进行测试，结果显示准确、快速．     

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。