静电和疏水效应对SARS冠状病毒3CL蛋白酶二聚体稳定性的影响

从TGEV3CL蛋白酶二聚体结构出发,研究了TGEV3CL蛋白酶二聚体单体之间的静电和疏水相互作用.蛋白质的静电相互作用通过有限差分方法求解Poisson-Boltzmann方程得到,疏水相互作用通过分析溶剂可及性表面模型得到.考察了不同pH值对SARS3CL蛋白酶二聚体静电和疏水相互作用的影响,在pH=5.5～8.5时,二聚体静电相互作用能、静电去溶剂化能和疏水自由能都具有较小的数值,表明在该条件下静电和疏水相互作用有利于二聚体的稳定存在.由于SARS3CL蛋白酶活性模式为二聚体,因此,在该pH值范围内,有利于蛋白酶保持活性.在pH=7.0条件下,蛋白酶单体之间具有最强的静电和疏水相互作用,从而使蛋白酶具有最强的活性,这与实验结果相一致.pH值对静电去溶剂化能的影响大于疏水自由能,表明静电作用是造成强酸或强碱条件下二聚体不能稳定存在的主要原因.     

SARS冠状病毒主要蛋白酶二聚体静电和疏水效应的研究

从三种冠状病毒主要蛋白酶SARS 3CL, HCoV 3CL和TGEC 3CL蛋白酶结构出发,着重研究了三种蛋白酶二聚体单体之间的静电和疏水相互作用.用连续介质模型有限差分方法计算得到三种蛋白二聚体界面处的静电势,发现三种蛋白酶单体和单体之间静电势分布具有明显的互补性,三种蛋白酶二聚体单体之间具有相同的静电相互作用能.用溶剂可及表面积模型分析了分子表面积及疏水性,发现三种蛋白酶具有相同的疏水分布,其中SARS 3CL蛋白酶疏水率为74%,驱动其单体聚合成二聚体.对三种蛋白酶的去溶剂化能疏水项的计算表明,三种蛋白酶二聚体单体之间具有相似的疏水相互作用能.     

SARS冠状病毒3CL蛋白酶及其抑制剂的理论研究

应用AutoDock程序将SARS冠状病毒3CL蛋白酶及其抑制剂配体和受体进行了对接,并用InsightⅡ中的Discover 3模块进行了分子动力学模拟,分析了蛋白酶活性口袋的形状,讨论了其亚基的氢键、静电、疏水等相互作用,为进一步设计药物提供了重要的参考信息.     

SARS 3CL蛋白酶同源二聚化与底物结合互为别构调控因素

研究了严重急性呼吸系统综合症(SARS)冠状病毒3C-Like蛋白酶(3CLpro)在存在底物或抑制剂时的二聚体形成情况. 通过测定酶活性随酶浓度的变化, 拟合出在底物存在下酶二聚体的解离常数约为0.94 μmol·L-1, 小于纯蛋白酶的二聚体解离常数(14.0 μmol·L-1), 表明底物对二聚体的形成具有增强作用. 选用与底物具有类似结合方式的靛红类抑制剂N-萘甲基靛红-5-甲酰胺(5f), 利用超速离心沉降速率方法定量测定了SARS 3CL蛋白酶单体和二聚体在不同浓度5f时的含量, 发现5f同样具有诱导二聚体形成的能力. 在3 μmol·L-1蛋白酶浓度下测定得到诱导二聚的EC50 值(半数有效浓度)约为1 μmol·L-1, 说明二聚体中只有一个单体与抑制剂结合. 研究结果表明, 随着底物浓度的升高, SARS 3CL蛋白酶会形成更多的二聚体, 而二聚体含量的提高又反过来提高酶的活性, 这种双向别构调控机制有可能是病毒用来调控多聚蛋白水解速率和组装时机的一种方法.     

固体的表面能及其亲水/疏水性

固体表面的亲水/疏水性质与表面分子与水之间的固/液界面相互作用自由能以及水介质中表面分子与空气之间的固/(液)/气界面相互作用自由能密切相关.水介质中固体表面与水之间存在范德华引力或疏水引力,与气泡之间存在范德华斥力、疏水引力以及静电斥力.在Lifshitz-范德华(LW)相互作用自由能、Lewis酸-碱(AB)相互作用自由能以及静电(EL)相互作用自由能3者之中,AB相互作用自由能比其它两者要大2～3个数量级以上.与固体表面能Lewis酸-碱分量相关的亲水指数√r_s~++√r_s~-可以成为衡量固体表面亲水/疏水性质的重要判据,水介质中固体表面疏水的必要条件是√r_s~++√r_s~-＜5mJ~(1/2)/m,指数大于或接近5mJ~(1/2)/m的表面必然是亲水的.     

苯、甲苯、联苯在水-叔丁醇混合溶剂中的溶解度和疏水作用

在283.15,288.15,293.15,298.15 K温度下,测定了苯、甲苯、联苯在水-叔丁醇混合溶剂中的溶解度,其中混合溶剂中叔丁醇的物质的量分数分别为0.000,0.010,0.020,0.030,0.040,0.045,0.050,0.060,0.080,0.100. 以此为基础计算了苯、甲苯、联苯在不同温度和溶剂组成条件下的标准溶解Gibbs自由能和相关过程的疏水相互作用Gibbs自由能,并从微观上讨论了溶剂结构对溶解度和疏水作用的影响.     

pH响应木质素基胶体球的制备和表征

以造纸制浆废液中的松木碱木质素（AL）为原料,通过季铵化改性,制备了季铵化碱木质素（QAL）.QAL与十二烷基苯磺酸钠（SDBS）通过静电作用形成QAL/SDBS复配物,将QAL/SDBS复配物在乙醇/水混合溶剂中进行自组装得到具有pH响应性的胶体球.采用X射线光电子能谱（XPS）、扫描电子显微镜（SEM）、透射电子显微镜（TEM）、元素分析和静态接触角研究了胶体球的形成过程和结构.研究结果表明,QAL/SDBS复配物通过疏水聚集作用形成具有较疏水的“核”和较亲水的“壳”结构的规整胶体球.在pH=3.0时,由于QAL与SDBS间的静电作用和疏水作用使胶体球能够稳定存在.当pH>7.5时,季铵化碱木质素上的羧基电离,由于静电斥力的作用使胶体球开始解聚,当pH=10.5时,季铵化碱木质素上的酚羟基的电离使得QAL与SDBS间的静电斥力增大,胶体球完全解聚.这种在酸性条件下稳定,中性条件下解聚的胶体球在药物缓释方面具有潜在的应用.     

沥青质杂环模型分子间相互作用及溶剂化效应的理论研究

重质油中沥青质组分易发生聚沉形成团簇,严重影响重质油的加工和利用效率,但目前对于沥青质聚沉的研究较少,其机理尚不明确。本文采用理论计算对沥青质杂环模型分子间相互作用和溶剂化效应进行研究,以此为重质油沥青质聚沉现象的研究及聚沉抑制剂的研发提供一定的数据和理论支持。(1)在M062X/6-31G(d)水平上,计算得到了11种由沥青质杂环分子片段组成的二元体系的全优化稳定构型,讨论分析了构型的几何结构、NBO电荷、Mulliken重叠布居、相互作用能和分子轨道能,得到了最稳定的两种构型。(2)在B3LYP/6-31G(d)水平上,运用SMD模型对沥青质大分子在13种溶剂中进行溶剂化效应的建模和理论计算,通过对静电溶剂化自由能(ΔGelec)、非静电溶剂化自由能(ΔGnonelec)、总溶剂化自由能(ΔGsolv)的分析可知,沥青质溶解性大小的关键在于溶剂对它的远程静电作用的大小。     

水及有机溶剂中离子溶剂化焓的理论计算

离子溶剂化热力学的理论研究是一项令人感兴趣的工作.在Born理论的基础上人们先后提出了多种较详细的计算离子溶剂化热力学量的模型或公式,并对离子在不同溶剂中的溶剂化自由能进行了理论计算.本文从离子-溶剂间的相互作用力出发,分别考虑了离子溶剂化过程中造腔作用、静电吸引、静电排斥及非静电相互作用对离子溶剂化焓的贡献,得到了一个具有一定意义的、计算离子溶剂化焓的理论公式。     

非平衡溶剂化的连续介质模型和超快过程溶剂效应

在连续介质理论基础上, 根据Jackson的能量积分公式导出非平衡态静电自由能和溶剂化能的正确表达式. 引入“弹簧能”概念, 对平衡态和非平衡态的静电能构成给出了合理解释, 即此能量由溶质自由电荷和溶剂极化电荷的自能、 两者之间的相互作用能和极化电荷的“弹簧能”构成. 对目前几种代表性的非平衡溶剂化理论进行了论证和比较, 指出其中存在的基本理论问题. 根据新的非平衡溶剂化能建立了电子转移反应溶剂重组能的双球模型、 光谱移动的单球孔穴点偶极模型, 多级展开方法和非平衡溶剂效应的数值解方法.在Poisson方程求解中引入类导体屏蔽模型, 建立了任意孔穴极化电荷数值解方法并应用到Closs-Miller电子转移体系, 得到与实验值吻合的溶剂重组能, 解决了传统非平衡溶剂化理论高估溶剂重组能的问题.     

Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 1. Approximate expression for the free energy of hydrophobic association based on a Gaussian-overlap model

A physics-based model is proposed to derive approximate analytical expressions for the cavity component of the free energy of hydrophobic association of spherical and spheroidal solutes in water. The model is based on the difference between the number and context of the water molecules in the hydration sphere of a hydrophobic dimer and of two isolated hydrophobic solutes. It is assumed that the water molecules touching the convex part of the molecular surface of the dimer and those in the hydration spheres of the monomers contribute equally to the free energy of solvation, and those touching the saddle part of the molecular surface of the dimer result in a more pronounced increase in free energy because of their more restricted mobility (entropy loss) and fewer favorable electrostatic interactions with other water molecules. The density of water in the hydration sphere around a single solute particle is approximated by the derivative of a Gaussian centered on the solute molecule with respect to its standard deviation. On the basis of this approximation, the number of water molecules in different parts of the hydration sphere of the dimer is expressed in terms of the first and the second mixed derivatives of the two Gaussians centered on the first and second solute molecules, respectively, with respect to the standard deviations of these Gaussians, and plausible analytical expressions for the cavity component of the hydrophobic-association energy of spherical and spheroidal solutes are introduced. As opposed to earlier hydration-shell models, our expressions reproduce the desolvation maxima in the potentials of mean force of pairs of nonpolar solutes in water, and their advantage over the models based on molecular-surface area is that they have continuous gradients in the coordinates of solute centers.     

Molecular origin of anticooperativity in hydrophobic association

The structuring of water molecules in the vicinity of nonpolar solutes is responsible for hydrophobic hydration and association thermodynamics in aqueous solutions. Here, we studied the potential of mean force (PMF) for the formation of a dimer and trimers of methane molecules in three specific configurations in explicit water to explain multibody effects in hydrophobic association on a molecular level. We analyzed the packing and orientation of water molecules in the vicinity of the solute to explain the effect of ordering of the water around nonpolar solutes on many-body interactions. Consistent with previous theoretical studies, we observed cooperativity, manifested as a reduction of the height of the desolvation barrier for the trimer in an isosceles triangle geometry, but for linear trimers, we observed only anticooperativity. A simple mechanistic picture of hydrophobic association is drawn. The free energy of hydrophobic association depends primarily on the difference in the number of water molecules in the first solvation shell of a cluster and that in the monomers of a cluster; this can be approximated by the molecular surface area. However, there are unfavorable electrostatic interactions between the water molecules from different parts of the solvation shell of a trimer because of their increased orientation induced by the nonpolar solute. These electrostatic interactions make an anticooperative contribution to the PMF, which is clearly manifested for the linear trimer where the multibody contribution due to changes in the molecular surface area is equal to zero. The information theory model of hydrophobic interactions of Hummer et al. also explains the anticooperativity of hydrophobic association of the linear trimers; however, it predicts anticooperativity with a qualitatively identical distance dependence for nonlinear trimers, which disagrees with the results of simulations.     

Complexation and chiral recognition thermodynamics of 6-amino-6-deoxy-beta-cyclodextrin with anionic, cationic, and neutral chiral guests: counterbalance between van der Waals and coulombic interactions

The stability constant (K), standard free energy (Delta G degrees), enthalpy (Delta H degrees), and entropy changes (T Delta S degrees) for the complexation of 6-amino-6-deoxy-beta-cyclodextrin with more than 50 negatively or positively charged as well as neutral guests, including 22 enantiomer pairs, have been determined in aqueous phosphate buffer (pH 6.9) at 298.15 K by titration microcalorimetry. The thermodynamic parameters obtained in this study and the relevant data for native beta-cyclodextrin indicate that the complexation and chiral discrimination behavior of the cationic host with charged guests are governed by the critical counterbalance between the electrostatic interactions of the charged groups in host and guest and the conventional intracavity interactions of the hydrophobic moiety of guest, such as hydrophobic, van der Waals, solvation/desolvation, and hydrogen-bonding interactions.     

Emission of thioflavin T and its off-on control in polymer membranes.

The absorption and emission spectral properties of thioflavin T (TFT+) in Nafion (Nf) and cellulose matrices have been studied. Formation of the emittive dimer is observed in both matrices. The monomer TFT+ emission is blueshifted in Nafion membrane (Nf), whereas it is red-shifted in cellulose membrane when compared with the emission in aqueous solution. The dimer emission of TFT+ in the Na+-Nf membrane undergoes off-on switching with acids and alkalis. The TFT+ molecule undergoes protonation in the H+-Nf and the protonated dye is fluorescent. The dimer emission of TFT+ is not observed in the dry H+-Nf membrane because of the protonation of the TFT+ molecule. The diffusion coefficient and the free energy of hydrophobic interaction for the TFT+ molecule in the Nf membrane are calculated. The TFT+ molecule experiences hydrophobic and electrostatic interactions in the Nf matrix, whereas it experiences a polar environment in the cellulose membrane. The 3D emission spectral studies support the formation of the emittive dimer in both Nf and cellulose matrices.     

Factors determining the enzyme catalytic power caused by noncovalent interactions: Charge alterations in enzyme active sites

Understanding the origin of the enormous catalytic power of enzymes is very important. Electrostatic interactions and desolvation are the phenomena that are most proposed to explain the catalysis of enzymes; however, they also decelerate enzymatic reactions. How enzymes catalyze reactions through noncovalent interactions is still not well-understood. In this study, we explored how enzyme-substrate noncovalent interactions affect the free energy barriers (ΔG³s) of reactions by using a theoretical derivation approach. We found that enzymes reduce ΔG³s of reactions by decreasing positive charges and/or increasing negative charges in the electron-donating centers and by decreasing negative charges and/or increasing positive charges in the electron-accepting centers of reactions. Enzyme-substrate noncovalent interactions are essential approaches through which the charge alterations lead to ΔG³ reductions. Validations with reported experimental data demonstrated that this charge alteration mechanism can explain the catalyses caused by diverse types of noncovalent interactions. Electrostatic interactions and desolvation are the most observed noncovalent interactions essential for ΔG³ reductions. This mechanism does not contradict any specific enzymatic catalysis and overcomes the shortages of the electrostatic interaction and desolvation mechanisms. This study can provide useful guidance in exploring enzymatic catalysis and designing catalyst.     

Origin of attraction and directionality of the pi/pi interaction: model chemistry calculations of benzene dimer interaction.

A model chemistry for the evaluation of intermolecular interaction between aromatic molecules (AIMI Model) has been developed. The CCSD(T) interaction energy at the basis set limit has been estimated from the MP2 interaction energy near the basis set limit and the CCSD(T) correction term obtained by using a medium size basis set. The calculated interaction energies of the parallel, T-shaped,and slipped-parallel benzene dimers are -1.48, -2.46, and -2.48 kcal/mol, respectively. The substantial attractive interaction in benzene dimer, even where the molecules are well separated, shows that the major source of attraction is not short-range interactions such as charge-transfer but long-range interactions such as electrostatic and dispersion. The inclusion of electron correlation increases attraction significantly. The dispersion interaction is found to be the major source of attraction in the benzene dimer. The orientation dependence of the dimer interaction is mainly controlled by long-range interactions. Although electrostatic interaction is considerably weaker than dispersion interaction, it is highly orientation dependent. Dispersion and electrostatic interactions are both important for the directionality of the benzene dimer interaction.     

The Effect of Surface Charge on Adsorption of a Cationic Polyelectrolyte

The regularities of adsorption of a cationic polyelectrolyte, poly(diallyldimethylammonium chloride), on the surface of fused quartz are studied at different values of solution pH by capillary electrokinetics. It is shown that the polyelectrolyte adsorption on a negatively charged surface depends on the value of the surface charge and increases with its growth. At a low charge value (pH 3.8), the polyelectrolyte adsorption increases the quartz surface charge. The driving forces of the adsorption are both electrostatic interaction and forces of nonelectrostatic nature, probably hydrophobic interactions and a change in entropy due to the displacement of counterions from a double layer. The adsorption of poly(diallyldimethylammonium chloride) on quartz from alkaline and neutral solutions is irreversible, which indicates the key role of the electrostatic interaction. At low values of the surface charge, the nonelectrostatic interactions play the main role, thereby resulting in polyelectrolyte desorption.     

Thermodynamics of molecular recognition of bile salts by 3,6'-(oligoethylenediamino-bridged) beta-cyclodextrin dimers

The molecular recognition behaviors of some representative bile salts by three 3,6'-bridged beta-cyclodextrin dimers with oligo(ethylenediamino) linkers in different lengths, i.e. 3,6'-(ethylenediamino-bridged) beta-cyclodextrin dimer (1), 3,6'-(diethylenetriamino-bridged) beta-cyclodextrin dimer (2), and 3,6'-(triethylenetetraamino-bridged) beta-cyclodextrin dimer (3), were investigated in aqueous phosphate buffer solution (pH 7.20) at 25 degrees C by means of 2D NMR spectroscopy and isothermal titration microcalorimetry. Owing to the cooperative host-linker-guest binding mode between host and guest, these 3,6'-bridged beta-cyclodextrin dimers showed significantly enhanced binding abilities and molecular selectivities as compared with native beta-cyclodextrin through the simultaneous contributions of hydrophobic, hydrogen bond, and electrostatic interactions. Thermodynamically, the inclusion complexations of these beta-cyclodextrin dimers with bile salts were mainly driven by large enthalpic gain, accompanied by slight to moderate entropic loss. An enthalpy-entropy compensation analysis demonstrated that these beta-cyclodextrin dimers experienced large conformational changes and extensive desolvation effect upon inclusion complexation with guest molecules.