三种金属硫蛋白聚合物静电效应的研究

考察了三种金属硫蛋白(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、二聚体和三聚体在pH为5.6-8.5和10.6两种缓冲条件下的静电势分布。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。三种金属硫蛋白的静电势通过有限差分方法求解Poisson-Boltzmann方程得到。对于三种金属硫蛋白的二聚体,pH为5.6-8.5时,单体和单体之间的静电势分布具有明显的互补性;但pH≥10.6时,这种互补性会大大削弱。对于三种金属硫蛋白的三聚体,单体和二聚体之间主要表现为静电排斥,而且pH在10.6下的静电排斥力明显强于pH为5.6-8.5时的静电排斥。     

大鼠金属硫蛋白晶体堆积形式的理论研究

考虑到蛋白质在结晶过程中溶液和晶体之间的动态平衡，蛋白质在溶液中的聚合状态决定了晶体堆积的最小单元。通过动态光散射实验以及计算机模拟，对大鼠金属硫蛋白亚型Ⅱ和兔肝金属硫蛋白亚型Ⅰ和Ⅱ的聚合物形式进行了比较，可以确定大鼠金属硫蛋白亚型Ⅱ在结晶条件下的缓冲液中应该以四聚体而不是二聚体形式存在。通过考察晶体的模型也可以发现，晶体的确可以通过四聚体的形式堆积得到，用四聚体堆积模型可以对晶体堆积作出更为合理的解释。     

金属硫蛋白聚合中阳离子作用机制的研究

蛋白质数据库 (ＰｒｏｔｅｉｎＤａｔａＢａｎｋ,ＰＤＢ)中有大鼠及几个其它种属动物的金属硫蛋白的结构 ,但其中只有大鼠金属硫蛋白亚型Ⅱ的晶体结构是完整的单体［１］,核磁共振溶液构象均只是金属硫蛋白被蛋白酶降解后的单一α或 β结构域．从大鼠金属硫蛋白亚型Ⅱ的晶体结构的堆积形式上看 ,二聚体可能是晶体生长过程中最小的堆积单元 ,因此Ｒｏｂｂｉｎｓ和Ｓｔｏｕｔ等人认为 ,大鼠金属硫蛋白亚型Ⅱ分子在溶液中也是以二聚体形式存在［２］．在晶体生长过程中 ,蛋白质在溶液中的构象会直接影响晶体的堆积．因此 ,对于大鼠金属硫蛋白…     

大鼠肝脏金属硫蛋白的分离纯化和金属硫蛋白亚型-Ⅱα结构域片段的制备及其核磁共振鉴定

Wistar雄性大鼠经腹腔注射CdCl_2诱导其肝脏合成金属硫蛋白。取鼠肝,先经匀浆、热变性、乙醇-氯仿萃取、丙酮沉淀等步骤,后由Sephadex G-75、DEAE-52柱层析,得金属硫蛋白的两亚型Ⅰ和Ⅱ。经原子吸收光谱测定每蛋白分子含有5个镉和2个锌。用枯草杆菌酶割法制备并分离了金属硫蛋白亚型Ⅱ的α结构域片段。还用NMR研究了金属硫蛋白的两个亚型及所得的α结构域片段。     

金属硫蛋白溶液聚合状态的研究

通过动态光散射实验首次证明了兔肝金属硫蛋白亚型 和 在不同的缓冲体系中不仅仅是以二聚体的形式 ,而且是以多种聚合形式存在[1] .深入考察金属硫蛋白在溶液中的聚合形式对于研究金属硫蛋白的结构和功能都具有非常重要的意义 .我们通过计算机模拟 [1] 比较系统地研究了各种因素对金属硫蛋白聚合的影响 .结果表明 ,在溶液聚合的分子识别过程中可由多种因素共同调控金属硫蛋白 ,这些因素主要包括静电相互作用、疏水性相互作用和溶液中阴阳离子等 .通过这些因素的综合分析 ,首次对兔肝金属硫蛋白在溶液中多种聚合形式的形成机制及相应的分子…     

铂(Ⅱ)配合物与金属硫蛋白结合反应的动力学

通过对顺铂及相关配合物与兔肝金属硫蛋白(MT)反应平衡产物的组成分析表明.铂(Ⅱ)化硫蛋白中角分子MT可以结合7.0当量Pt(Ⅱ),而且结构不同的顺. 反铂和四氯铂酸钾对应有相同的化学计量关系,研究了这些配合物与兔肝Zn~7,MT~2反应的动力学,发现Pt(Ⅱ)与MT的反应为三个速度不同的控制步骤,求得了相应的表观一级反应速率常数K~Ⅰ.K~Ⅱ和K~Ⅲ首次观测到在相同条件下,反铂与MT 的反应速度比顺铂大3-5倍,初始反应速度常数K~Ⅰ与Pt(Ⅱ)的存在形式及有效浓度有很强的依赖关系,而同一种配合物在不同pH和浓度下.K~Ⅱ和K~Ⅲ无明显变化.提出了铂(Ⅱ) 配合物与MT反应的动力学机理,并根据顺.反铂与MT反应动力学性质的不同, 对它们抗癌活性及毒性差异的原因进行了讨论.     

金属硫蛋白异构体及亚型异构体的液相色谱分离与质谱鉴别

建立了金属硫蛋白(MT)异构体及亚型异构体的色谱分离与质谱鉴别方法。将金属硫蛋白混合物通过弱阴离子DEAE Sephadex A-25离子交换柱,结合离线电感耦合等离子体质谱(ICP-MS)对锌诱导金属硫蛋白的两个异构体MT-1和MT-2进行分离和检测;利用Sephadex G-25凝胶排阻色谱柱对得到的两个金属硫蛋白异构体进行脱盐;探索脱盐后的金属硫蛋白异构体在不同色谱条件下的C18反相色谱柱上的保留行为,进而实现各个亚型异构体的分离;通过在线电喷雾质谱检测实现了对金属硫蛋白各个亚型异构体的鉴别。结果表明,通过优化色谱条件,由离子交换色谱及凝胶排阻色谱得到的金属硫蛋白各亚型异构体在酸性条件下均得到了良好的分离,质谱检测结果与前人的文献报道结果一致。该方法可使金属硫蛋白各异构体均达到最佳的分离效果。     

兔肝金属硫蛋白亚型异构体的高效液相色谱分离与ESI-MS,MALDI-TOF-MS鉴定

由于金属硫蛋白(MT)基因的多态性,决定不同亚型的MT异构体的存在,MT亚型异构体的结构是MT功能研究的基础.通过离子交换柱可将MT分成MT-1和MT-2两个异构体,用不同条件的反相高效液相色谱(RP-HPLC)可将MT-1和MT-2分成不同的亚型异构体,并利用MALDI-TOFMS和LC-ESI-MS对比确定了它们的分子量.结果表明,兔肝MT在不同的pH条件下分离得到不同分子量的亚型异构体.在酸性条件下,MT-1可分为2个主要亚型异构体,分子量分别为6149.0和6244.5,而MT-2主要分为3个亚型异构体,分子量分别为6149.0,6244.0和6127.0.MT-1和MT-2有2个亚型异构体分子量相同的异构体存在.在酸性条件下,MT-1的2个异构体及MT-2分子量为6127的亚型异构体可稳定存在.     

金属硫蛋白家族内的结构域拼接

金属硫蛋白(Metallothioneins,MTs)由结构独立且功能明显区别的β,α两个结构域组成。神经生长抑制因子(NeuronalGrowthInhibitoryFactor,GIF)双名金属硫蛋白-Ⅲ(MT-Ⅲ),是神经系统中第一个被鉴定的具有神经元生长抑制功能的蛋白,而β－结构域为其功能结构域。为深入系统地研究MTs,尤其是GIF及其结构域的结构与功能,我们构建了金属硫蛋白家族内结构域拼接体βGIF-αMT-1(βⅢ-αⅠ)和βMT-1-αGIF(βⅠ-αⅢ):PCR扩增得各个结构域的cDNA序列,酶切后克隆入原核表达载体pGEX-4T-1,经发酵、诱导表达、亲和层析、凝血酶切和进一步纯化,得率约为80mg蛋白/L菌液。测其电泳行为、氨基酸组成、质谱、金属巯基含量等,证明得到了目的蛋白。紫外吸收图谱和圆二色性图谱显示,结构域拼接体拥有金属硫蛋白家族成员的特征金属巯基簇结构域,初步功能实验表明,βⅢ－αⅠ也具有抑制神经元生长的功能。     

同位素示踪SEC-ICP-MS研究大鼠体内镉的形态

通过建立凝胶排阻色谱分离紫外与电感耦合等离子体质谱在线检测的联用技术,研究了灌喂低浓度镉富集同位素后大鼠各器官中镉与蛋白结合的形态.结果发现,镉主要在肝、肾、睾丸中与硫蛋白结合形成金属硫蛋白.与传统方法相比.该法危害性小、具有更接近慢性中毒、能将重金属来源分为天然来源和人为引入等特点.     

Evaporation of Lennard-Jones fluids

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.     

Infrared spectra of homogeneous and heterogeneous proton-bound dimers in the gas phase

Infrared multiphoton dissociation spectra of three homogeneous and two heterogeneous proton-bound dimers were recorded in the gas phase. Comparison of the experimental infrared spectra recorded in the fingerprint region of the proton-bound dimers with spectra predicted by electronic structure calculations shows that all modes which are observed contain motion of the proton oscillating between the two monomers. The O-H-O asymmetric stretch for the homogeneous dimers is shown to occur at around 800 cm-1. As expected, the O-H-O asymmetric stretching modes for the heterogeneous proton-bound dimers are observed to shift to significantly higher energy with respect to those for the homogeneous proton-bound dimers due to the asymmetry of the O-H-O moeity. This shift is shown to be predictable from the difference in proton affinities between the two monomers. Density functional predictions of the infrared spectra based on the harmonic oscillator model are demonstrated to predict the observed spectra of the homogeneous proton-bound dimers with reasonable accuracy. Calculations of the structure and infrared spectrum of protonated diglyme at the B3LYP/6-31+G** level and basis also agree well with an infrared spectrum recorded previously. For both heterogeneous proton-bound dimers, however, the predicted spectra are blue-shifted with respect to experiment.     

Exciton coherence lifetimes from electronic structure

We model the coherent energy transfer of an electronic excitation within covalently linked aromatic homodimers from first-principles. Our results shed light on whether commonly used models of the bath calculated via detailed electronic structure calculations can reproduce the key dynamics. For the systems we model, the time scales of coherent transport are experimentally known from time-dependent polarization anisotropy measurements, and so we can directly assess whether current techniques are predictive for modeling coherent transport. The coupling of the electronic degrees of freedom to the nuclear degrees of freedom is calculated from first-principles rather than assumed, and the fluorescence anisotropy decay is directly reproduced. Surprisingly, we find that although time-dependent density functional theory absolute energies are routinely in error by orders of magnitude more than the coupling energy between monomers, the coherent transport properties of these dimers can be semi-quantitatively reproduced from these calculations. Future directions which must be pursued to yield predictive and reliable models of coherent transport are suggested.     

Thermodynamics of beta-amyloid fibril formation

Amyloid fibers are aggregates of proteins. They are built out of a peptide called beta-amyloid (Abeta) containing between 41 and 43 residues, produced by the action of an enzyme which cleaves a much larger protein known as the amyloid precursor protein (APP). X-ray diffraction experiments have shown that these fibrils are rich in beta-structures, whereas the shape of the peptide displays an alpha-helix structure within the APP in its biologically active conformation. A realistic model of fibril formation is developed based on the 17 residues Abeta12-28 amyloid peptide, which has been shown to form fibrils structurally similar to those of the whole Abeta peptide. With the help of physical arguments and in keeping with experimental findings, the Abeta12-28 monomer is assumed to be in four possible states (i.e., native helix conformation, beta-hairpin, globular low-energy state, and unfolded state). Making use of these monomeric states, oligomers (dimers, tertramers, and octamers) were constructed. With the help of short, detailed molecular dynamics calculations of the three monomers and of a variety of oligomers, energies for these structures were obtained. Making use of these results within the framework of a simple yet realistic model to describe the entropic terms associated with the variety of amyloid conformations, a phase diagram can be calculated of the whole many-body system, leading to a thermodynamical picture in overall agreement with the experimental findings. In particular, the existence of micellar metastable states seem to be a key issue to determine the thermodynamical properties of the system.     

On the relative propensities of ether and methylene linkages for liquid crystal formation in calamitics

The nematic-isotropic transition temperatures for aromatic calamitic compounds with terminal alkyl chains attached via a methylene group are usually found to be lower than those with an ether link. This difference is generally attributed to the higher anisotropy of the molecular polarizability expected for an ether linkage in comparison with a methylene group. However these two modes of attachment for the chain also differ in their geometry and here we show, using a molecular field theory for flexible molecules, that this also results in higher transition temperatures for nematogens, both monomers and dimers, with the alkyl chains attached through ether rather than methylene linkages.     

Self consistent tight binding model for dissociable water

We report results of development of a self consistent tight binding model for water. The model explicitly describes the electrons of the liquid self consistently, allows dissociation of the water and permits fast direct dynamics molecular dynamics calculations of the fluid properties. It is parameterized by fitting to first principles calculations on water monomers, dimers, and trimers. We report calculated radial distribution functions of the bulk liquid, a phase diagram and structure of solvated protons within the model as well as ac conductivity of a system of 96 water molecules of which one is dissociated. Structural properties and the phase diagram are in good agreement with experiment and first principles calculations. The estimated DC conductivity of a computational sample containing a dissociated water molecule was an order of magnitude larger than that reported from experiment though the calculated ratio of proton to hydroxyl contributions to the conductivity is very close to the experimental value. The conductivity results suggest a Grotthuss-like mechanism for the proton component of the conductivity.     

Structural and Material Properties of Amyloid Aβ40/42 Fibrils

In this study, structural and mechanical properties of a series of models of Aβ₄₂ (one‐ and two‐fold) and Aβ₄₀ (two‐ and three‐fold) fibrils have been computed by using all‐atom molecular dynamics simulations. Based on calculations of the twist angle (θ) and periodicity (v=360d/θ), oligomers formed by 20, 11, and 13 monomers were found to be the smallest realistic models of three‐fold Aβ₄₀, one‐fold Aβ₄₂, and two‐fold Aβ₄₂ fibrils, respectively. Our results predict that the Aβ₄₀ fibrils initially exist in two staggered conformations [STAG(+2) and STAG(+1)] and then undergo a [STAG(+2)→STAG(+1)] transformation in a size‐dependent manner. The length of the loop region consisting of the residues 23–29 shrinks with the elongation of both Aβ₄₀ and Aβ₄₂ fibrils. A comparison of the computed potential energy suggests that a two‐fold Aβ₄₀ aggregate is more stable than its three‐fold counterpart, and that Aβ₄₂ oligomers can exist only in one‐fold conformation for aggregates of more than 11 monomers in length. The computed Young′s modulus and yield strengths of 50 GPa and 0.95 GPa, respectively, show that these aggregates possess excellent material properties.     

A DFT study on the dimerization of C62, H2-C62, and F2-C62

On the basis of calculations using the density functional theory, we show that C(62), a recently synthesized nonclassical fullerene, will presumably undergo dimerization with various isomers at elevated temperatures. This is shown by calculating the dimerization energy and the activation barrier of the dimerization. Eight possible isomers of the dimer were identified, all of which are more stable than the two isolated monomers. The relative stability of various isomers depends upon the kind of C=C bonds within the four-membered carbon ring involved in the dimerization. In addition, similar calculations were performed for the monomers and dimers of H(2)-C(62) and F(2)-C(62). Six isomers were identified for each of the dimers. Although less pronounced than the case of the C(62) dimer, all isomers of the H(2)-C(62) dimer are appreciably more stable than the individual monomers. Although a large steric repulsion due to F atoms significantly reduces the stability of F(2)-C(62) dimer, its two isomers are still more stable than separate monomers.