麋鹿朊蛋白结构稳定性的分子动力学研究

朊蛋白病是一种致命且具有高度传染性的神经退行性疾病.糜鹿是目前已经报道的哺乳类动物中较易发生朊蛋白病的物种之一.作者使用分子动力学和操控式分子动力学模拟相结合的方法对糜鹿正常朊蛋白的结构稳定性进行了研究.发现了麋鹿朊蛋白结构中的不稳定结构域分布以及热动力学性质,揭示了糜鹿朊蛋白稳定性的分子结构基础以及力学特征.     

人类朊蛋白的动力学稳定性研究（英文）

朊蛋白病是一种能在人类或者动物之间传播的致命的神经退行性疾病.尤其是人类朊蛋白疾病在近几年蔓延迅速,已经威胁到人类的健康.在本文中,我们使用分子动力学(MD)和流体分子动力学(FMD)模拟相结合的方法研究了人类朊蛋白(hPrPc)的动力学稳定性.我们通过FMD模拟产生了两个典型的hPrPc的变性结构,并进一步研究了在自然状态下这两个变性结构重折叠的过程,从关键残基、二级结构、残基-残基相互作用图等方面详细讨论了hPrPc的解折叠和重折叠路径.研究发现hPrPc的三个α-螺旋结构组成了一个疏水核心,在蛋白质的解折叠和重折叠过程中发挥了重要的作用.刚性的疏水核心就像是脚手架一般为hPrPc的重折叠提供便利.在重折叠过程中,π-螺旋和310螺旋出现几率较高,并且β-折叠的延长也更多地出现在完全解折叠的hPrPc体系中.     

氯化钠对朊病毒结构稳定性影响的分子动力学研究

朊病毒疾病是由正常构象的PrPC转化为致病构象的PrPSc引起的一类可传染的蛋白质构象病.采用分子动力学模拟的方法研究了0～500mmol/L的NaCl溶液体系对人朊病毒构象影响并深入探讨了其分子机制.研究发现NaCl可以降低朊病毒的结构稳定性,并引起其α-螺旋含量的急剧降低.进一步的研究表明高浓度NaCl溶液体系能够显著破坏朊病毒螺旋1内部的重要盐桥Asp144-Arg148和Asp147-Arg151,同时明显降低其主要氢键Arg151 N:Asp147 O,Tyr150 N:Glu146 O,Tyr149 N:Tyr145 O和Arg148 N:Asp144 O的稳定性,并诱导朊病毒的疏水核心发生明显扩张,促使朊病毒整体稳定性的下降,这些可能是NaCl促进朊病毒构象转换的重要原因.     

多肽与朊蛋白相互作用研究

朊病毒病是一类累及多种动物和人类中枢神经系统退行性疾病,但至今针对这类疾病尚无有效的治疗方法.考虑到在180位的缬氨酸突变为异亮氨酸的180I突变蛋白的突变位点与朊蛋白181位的糖基化位点非常接近,其生物化学性质对朊病毒病的影响非常重要.本文针对180I突变蛋白的182-190段序列设计了KNFTK、KTDVE、EMMKE和EVVKK等四种αxyzβ型多肽.研究发现,四种多肽中只有EVVKK能稳定蛋白的构象,同时诱导β-折叠向α-螺旋的转变,而其他三种蛋白对180I的结构基本没有影响.该结论对于开发多肽药物并进一步用于临床治疗具有一定的借鉴作用.     

肝素诱导人细胞型朊蛋白构象变化的光谱表征

粘多糖在朊病毒病中所发挥的作用目前仍存在争议.以肝素钠作为粘多糖的代表,通过共振光散射光谱、荧光光谱和圆二色光谱的变化研究了肝素钠与人重组细胞型朊蛋白(rhPrPC23-231)的相互作用.结果表明,肝素钠与朊蛋白相互作用后光散射和荧光信号均得到增强,并且使朊蛋白的荧光寿命有一定程度的延长.圆二色光谱表明肝素钠能诱导朊蛋白从富含α-螺旋的构象向富含β-折叠的构象转变.     

谷朊蛋白的改性及应用

近20年来,利用动植物等可再生资源代替当前广泛使用的石化材料成为热门研究方向,是消除污染、保护环境、实现绿色化学、推进人类社会与环境和谐发展的唯一途径.谷朊蛋白是谷类淀粉加工的副产物,是植物代谢产生的天然植物蛋白,一种生物可降解、可再生的天然高分子.由于其独特的粘弹性、延伸性、薄膜成型性和热凝固性等,越来越受到人们的重视,不仅拓宽了在食品工业中的应用领域,还可作为价格适宜、性能优良的高分子材料应用于其它领域.本文介绍了有关谷朊蛋白的组成、近年来国内外改性原理和方法,及其潜在的应用.     

纳米结构表面浸润性质的分子动力学研究

采用分子动力学方法研究了氩纳米液滴在铂金属及其模型固体表面的浸润现象,获得了液滴在平滑表面和三角纳米结构阵列表面的接触角和展布特性.研究表明,液滴与壁面的势能作用较强时,液滴与纳米结构表面为均匀浸润,但是由于迟滞效应,接触角受表面纳米结构的影响不明显;势能作用较弱时,纳米结构间隙中存在类似蒸汽的低密度相,液滴与纳米结构表面为非均匀浸润,接触角受纳米结构的影响而增大;表面纳米结构可以使表面具有超疏水性.     

电解质溶液界面结构的分子动力学模拟研究

电解质溶液界面结构的研究不仅具有重要的理论意义, 而且具有一定的实用价值. 采用分子动力学模拟研究了LiCl, LiBr, LiI, NaI, KI, CsI水溶液中阴阳离子在1×105 Pa和300 K下的气液界面分布情况, 探讨离子水化与电解质溶液界面结构的关系, 并分析阳离子水化能力的强弱对共存阴离子在界面富集分布的影响. 通过对模拟结果的分析发现, 离子的水化能力越强, 就越能形成稳定的水化结构而处于本体相中, 水化能力越弱, 则越易在界面富集. 该机理合理地解释了离子在界面的分布现象, 阳离子水化能力一般较其共存阴离子强而处于本体相, 阴离子则趋向在界面处富集; 不同阴离子在界面的密度分布也与阴离子的水化能力相关, 阴离子水化能力越弱, 其在界面富集程度越高, 不同阴离子在界面的富集趋势为Cl－＜Br－＜I－; 阳离子水化能力的强弱也影响其共存阴离子在界面的富集程度, 阳离子的水化能力越弱, 其共存阴离子在界面的富集程度就越低.     

金属Ni熔化前后结构变化的分子动力学模拟

使用Tight-binding势函数, 对FCC-Ni升温熔化过程的结构变化进行了分子动力学模拟. 在定压条件下模拟得到的Ni的熔点在1850 K与1900 K之间. 计算得到了体系在各温度下的径向分布函数和配位数分布等静态结构信息以及动力学性质. 计算得出的液体Ni的扩散系数在1900 K时约为5.02×10−9 m2•s−1, 与实验数据相符. 对液态体系中FCC短程有序结构可能发生的畸变以及由此导致的H-A键型变化进行了分析, 结合配位体构型搜索和键对分析方法计算了各温度下不同短程有序结构的分布. 计算表明, Ni在熔化之后仍保留有部分晶态短程结构, 但发生了较大的畸变, 同时液态中有少量的缺陷二十面体结构存在. 而液体Ni中大多数的配位体的几何构型介于FCC与缺陷二十面体之间.     

三种金属硫蛋白动力学稳定性的理论研究

对三类金属硫蛋白（大鼠金属硫蛋白亚型Ⅱ,兔肝金属硫蛋白亚型Ⅰ和兔肝金属硫蛋白亚型Ⅱ）的单体和二聚体进行了水溶液条件下的分子动力学模拟。其中大鼠金属硫蛋白亚型Ⅱ的结构直接来自于晶体数据,兔肝金属硫蛋白亚型Ⅰ和Ⅱ的结构则通过同源蛋白模型搭建。动力学模拟的结果显示,这三种单体在水溶液中都具有相当大的柔性,柔性主要来源于柔性区的氨基酸残基。三类金属硫蛋白单体的动力学模拟均表明α结构域的动力学稳定性都要优于     

Steered molecular dynamics simulation of elastic behavior of adsorbed single polyethylene chains

We investigate the dynamics of the detachment of single polyethylene (PE) chains from a strongly adsorbing surface in vacuum using a united atom model. Various statistical properties, including the mean‐square end‐to‐end distance 〈R²〉, the mean‐square radii of gyration , , the shape factor , the torsion angle distribution, the average surface adsorption energy , the average total energy , and the average force , are analyzed. The relationship between the average force and the pulling velocity v shows two distinctive regions: a weakly dependence region at Å/ps and a strongly dependence region at Å/ps. Remarkably, the PE chain manifests force hysteresis under sequential stretching and releasing. These investigations may provide some insights into the elastic behavior of adsorbed polymer chains. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2322–2332, 2007     

Molecular dynamics simulation on HP1 protein binding by histone H3 tail methylation and phosphorylation

Trimethylation of histone H3 lysine 9 is important for recruiting heterochromatin protein 1 (HP1) to discrete regions of the genome, thereby regulating gene expression, chromatin packaging, and heterochromatin formation. Phosphorylation of histone H3 has been linked with mitotic chromatin condensation. During mitosis in vivo, H3 lysine 9 methylation and serine 10 phosphorylation can occur concomitantly on the same histone tail, whereas the influence of phosphorylation to trimethylation H3 tail recruiting HP1 remains controversial. In this work, molecular dynamics simulation of HP1 complexed with both trimethylated and phosphorylated H3 tail were performed and compared with the results from the previous methylated H3‐HP1 trajectory. It is clear from the 10‐ns dynamics simulation that two adjacent posttranslational modifications directly increase the flexibility of the H3 tail and weaken HP1 binding to chromatin. A combinatorial readout of two adjacent posttranslational modifications—a stable methylation and a dynamic phosphorylation mark—establish a regulatory mechanism of protein–protein interactions. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices

Here, an efficient method that predicts natural transition pathways between two endpoint states of an allosteric protein has been proposed. This method helps create structures that bridge these endpoints through multiple iterative and unbiased molecular dynamics simulations with explicit water. Difference distance matrices provide an approach for identifying states involving concerted slow motion. A series of structures are readily generated along the transition pathways of adenylate kinase. Predicted structures may be useful for an initial pathway to evaluate free energy landscapes via umbrella sampling and chain‐of‐states methods. © 2016 Wiley Periodicals, Inc.     

Theoretical study of the prion protein based on the fragment molecular orbital method

We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called “Parallelized ab initio calculation system based on FMO (PAICS)”. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Confinement effects on the thermal stability of poly(ethylene oxide)/graphene nanocomposites: A reactive molecular dynamics simulation study

Nonisothermal and isothermal decomposition of poly(ethylene oxide) (PEO) loaded with different concentrations of pristine graphene (PG) and graphene oxide (GO) nanoplatelets were investigated using reactive molecular dynamics simulation. The onset of nonisothermal decomposition of the PG‐loaded PEO system was the highest among all systems, suggesting that introducing PG to the polymer improves its thermal stability (an effect that increases with an increase in the PG concentration). At low concentration, introducing GO to the polymer brings about a deterioration of the thermal stability of the polymer consistent with experimental findings. On average, the activation energy for the isothermal decomposition of PG‐loaded PEO system increases by 60% over that of the neat PEO system, while it decreases by 40% for the GO‐loaded PEO system. A time‐dependent analysis of the through‐thickness decomposition profile of the above systems reveals that the polymer confined between the PG sheets exhibit a higher thermal stability compared to the bulk polymer. However, an opposite effect is observed with the polymer confined between the GO sheets. The latter observation is attributed to accelerated polymer chain scission in confined regions due to the ejection of reactive hydroxyl radicals from the GO surface during the early stages of thermal decomposition. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017 , 55, 1026–1035     

胰岛素六聚体在水溶液中的稳定性研究

用分子动力学（MD）模拟方法设计了两个模拟时间为600ps的对比计算机模拟 实验,研究了R6态的胰岛素六聚体在水溶液中的稳定性以及苯酚和锌离子对结构稳 定性的影响。通过对MD模拟所得到的轨迹的分析发现,在维系胰岛素六聚体稳定性 的因素中,静电相互作用和氢键起着主要的作用。对于包含锌离子和苯酚的体系。 胰岛素六聚体的稳定性得到了增强;对不含锌离子和苯酚的关系,胰岛素六聚体的 稳定性明显减弱,在这种情况下,胰岛素六聚体还表现出解聚的倾向。这些模拟结 果与实验观测结果相吻合。     

Effect of tacticity on conformation of p-tert-butylphenol acetaldehyde resins as studied by molecular simulation

p-tert-Butylphenol acetaldehyde resins can have isotactic, syndiotactic, and atactic sequences. Structural characteristics of the p-tert-butylphenol acetaldehyde resin with different tacticities were studied using molecular mechanics and molecular dynamics. Trimer–decamer isotactic and syndiotactic resins and 12 stereoisomers of a hexamer were calculated. In the p-tert-butylphenol acetaldehyde resin, the hydroxyl groups cluster in the center of the molecule through intramolecular hydrogen bonding and the tert-butyl groups are extended out. It has been found that the energy-minimized structures of the isotactic resin are more stable than those of the syndiotactic resin by 7–17 kcal/mol. From the results of molecular dynamics at 303, 373, 474, and 573 K for 300 ps, the isotactic resin was also found to be more stable than the syndiotactic resin. For atactic resins, the closer to isotactic their structures are, the more stable they are. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1355–1361, 1998     

IBIsCO: a molecular dynamics simulation package for coarse-grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse-grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe-Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse-graining. The reverse nonequilibrium molecular dynamics simulation method (Müller-Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.