二维NOESY核磁共振波谱结合全原子分子动力学模拟研究肌肽在水溶液中的构象变化

采用二维NOESY核磁共振波谱结合全原子分子动力学模拟研究了肌肽在水溶液中的构象变化和相互作用. 以分子内距离、回转半径、RMSD以及溶剂可接触表面积等性质进行表征. 分子动力学模拟显示肌肽分子在水溶液中表现出了较高的柔性,其构象在伸展、折叠之间互相转换,大部分情况下是以伸展的构象为主导的,而折叠构象较少. 二维NOESY核磁共振实验证实了模拟的结果,实验与理论得到很好的吻合.     

纳米粒子在自吸附半柔性高分子诱导下成有序的环形结构

采用动态蒙特卡洛方法研究了自吸附半柔性高分子及其自吸附半柔性高分子与纳米粒子组成的混合物的构象行为.自吸附半柔性高分子的构象行为的研究,结果显示通过自吸附参数和弯曲能使高分子从一个线团状构象转变成一个紧密螺绕环状构象.紧密螺绕环状构象的折叠过程分为三个阶段:(i)几个分立的螺绕环(ii)一个松散的螺绕环(iii)一个紧密螺绕环.自吸附半柔性高分子与纳米粒子组成的混合物的构象行为的研究,结果表明可以采用具有紧密螺绕环结构的高分子有效地调控纳米粒子的空间排列.另外观察到一个非常有趣的现象,纳米粒子排列成一个环形结构.     

HIV蛋白酶多肽抑制剂的理论研究

艾滋病病毒的发现距今已有二十多年的历史了.它仍然以很快的速度在全球范围速蔓延.研发抗艾滋病药物是当代药学的重大课题之一.在以往研究的基础上,我们利用分子叠合和分子对接这两种分子模拟手段,把从PDB数据库中得到的与HIV蛋白酶结合的12个肽类分子和已经上市的抗艾滋病的药物Saquinavir做比较.根据结构相同或相近的分子具有相同的活性原理,运用分子叠合初部判断分子活性,特别是药效团的特征比对揭示了分子活性的原因,为进一步的药物设计奠定了良好的基础.进而采用分子对接的分子模拟方法对这12个肽类分子的活性构象进行了深入的分析,预测出了这12个分子对HIV病毒蛋白酶的不同抑制作用.研究发现:P01、P05、P09、P12可能与已知药物Saquinavir在与HIV蛋白酶结合时具有相似的活性,其中P9的活性最强,有望成为抗HIV药物的理想前体,为下一步的HIV药物的设计研究提供了理论依据.     

高压NMR在蛋白质结构和动力学研究中的应用

与温度一样,压力是基本的热力学变量.蛋白质在溶液中是多种构象的热力学平衡体.在不同的温度和压力等条件下,蛋白质包括折叠构象、变性构象以及各种中间体在内的不同构象的存在频率各不相同.当用压力作为扰动时,由于这些构象的偏摩尔体积不同,它们的存在频率便会因而发生变化,加压可将平衡向具有较小偏摩尔体积的方向移动.因此,利用高压核磁共振(NMR)技术,不仅可以研究高压对蛋白质结构和动力学的影响,还可以通过改变压力,在更为广泛的构象空间研究蛋白质结构和动力学.例如,利用平衡体系在加压时向体积小的构象方向移动这一特性,能够对在常压下因其存在频率低而难于检测、但在高压下因其体积小而存在频率增加了的构象进行深入研究,而这些构象往往与蛋白质的功能密切相关.该篇综述首先介绍了高压在蛋白质科学研究中的历史、有关概念和高压NMR技术;其次,结合实例,阐述高压NMR技术在蛋白质结构、折叠以及动力学研究中的应用;最后,对高压NMR技术在蛋白质研究中的应用前景进行展望.     

六硝基六氮杂三环十二烷的结构和性能——HEDM分子设计

用密度泛函理论B3LYP方法,在631G基组水平下设计和计算了高能量密度化合物六硝基六氮杂三环十二烷的结构和性质.由分子总能量、前线轨道能级和键集居数等电子结构参数,判别船式(α)比椅式(β)构象稳定.求得其IR谱频率和强度并作归属,报道了200～800K体系的热力学性质.基于理论计算密度和生成热,运用Kamlet公式预示了标题物的爆速和爆压,α构象的爆速和爆压分别为9.46km/s和41.74GPa,β构象则稍低些,分别为9.34km/s和40.02GPa.     

利用乙醇音速计算其它热力学性质

光散射法音速测量的适用温度范围较广,且有时高温比定压热容相对于密度而言更容易获得实验数据.基于此,提出了一个由较高温度比定压热容推算得到较高温度密度的迭代算法.以乙醇为例,利用高温热力学性质推算模型得到298.15～418.15 K、1.0 MPa下乙醇的密度,与Schroeder状态方程的计算结果进行对比,二者的平均绝对相对偏差为0.0119％,最大偏差为0.0298％.此外,沿1.0 MPa等压线测量了298.45～423.02 K温度范围内乙醇的液相音速,测量的拓展相对不确定度为0.9％(置信因子取2).与Schroeder状态方程相比,298.15～418.15K、1.0～9.0 MPa下乙醇密度和比定压热容计算值的平均相对偏差分别为0.0072％和0.0067％,最大偏差分别为0.0298％和0.0290％.可以看出,高温热力学性质推算模型的密度计算精度与实验测量精度相当.     

用于真实蛋白质结构预测的一种新的优化方法

用“相对熵”作为优化函数 ,提出了一个有效快速的折叠预测优化算法 .使用了非格点模型 ,预测只关心蛋白质主链的走向 .其中只用到了蛋白质主链上的两两连续的Cα 原子间的距离信息以及 2 0种氨基酸的接触势的一个扩展形式 .对几个真实蛋白质做了算法测试 ,预测的初始结构都为比较大的去折叠态 ,预测构象相对于它们天然结构的均方根偏差 (RMSD)为 5～ 7 .从原理上讲 ,该方法是对能量优化的改进 .     

EPR和NMR自旋标记法研究部分折叠蛋白质构象

部分折叠蛋白质的特征是在溶液中有部分二级结构,但是三级结构接触比较松散或者较少,其意义可能是蛋白质折叠过程的中间态,或者有重要的生理功能. 利用EPR和NMR波谱可以表征其构象特征,从而构建其二级结构、三级结构、四级结构以及构象变化的结构模型. 利用分子生物学的点突变技术可以在蛋白质主链上插入1个或2个半胱氨酸残基,然后把顺磁自旋标记物特异地共价结合在半胱氨酸的侧链巯基上来制备自旋标记样品. 位点特异性自旋标记电子顺磁共振（SDSL-EPR）波谱是通过测定2个自旋标记间的偶极相互作用,从而推测2个硝基氧自由基间的距离. 核磁共振（NMR）波谱则是通过测定单个自旋标记中心对周围原子核驰豫效应增强（PRE）的效应,推测出顺磁中心相对于周围原子核的距离. 连续波EPR和NMR自旋标记方法可以测定2.5 nm左右的偶极相互作用距离,属于长程的距离约束,这对于确定部分折叠蛋白质的构象至关重要. 该文将就蛋白质部分折叠态研究的生物学意义,自旋标记方法以及EPR和NMR方法研究其构象特征举例描述.     

高温高压下碳化钨晶体的结构、力学、电子、光学以及热力学性能的第一性原理计算

本文利用密度泛函理论中的广义梯度近似对碳化钨晶体的三种结构(碳化钨相、闪锌矿相以及纤锌矿相)进行了优化,得到能量最低的稳定构型,并在此基础上计算了它的力学、电子、光学和高温高压下的热力学性质.研究表明:在0～300 GPa压力范围内,碳化钨相具有最高的稳定性.同时,高压下碳化钨相的弹性常数满足Born-Huang准则,且0 GPa和300 GPa下的声子色散没有虚频,证明了高压下碳化钨相的静力学稳定性和动力学稳定性.电子性质表明了碳化钨的金属性.光学性质表明碳化钨在高能区很难吸收光.热力学性质的研究表明:体积比V/V_0对压强的变化更敏感;高温时C_V曲线近似一条直线;给定压强下热膨胀系数α在600 K温度以上增长非常缓慢;压强对德拜温度Θ_D的影响较大;在低压下格林艾森系数γ的变化较大.     

B-到Z-DNA结构转变特性的理论研究

本文给出了B-到Z-DNA的结构转变模型,研究了盐浓度和外力矩对B-Z结构转变特性的影响,得到了折叠角的几率分布、B-Z转变的临界扭矩和转变能随盐浓度的变化规律.结果表明:在没有外力和外力矩的情况下,盐浓度达到2.3 mol/L时,Z构象开始出现,与实验结果一致.随盐浓度的增加,Z构象存在的几率增大,B-Z转变所需的扭转力矩减小.     

Gonadal steroids differentially modulate neurotoxicity of HIV and cocaine: testosterone and ICI 182,780 sensitive mechanism

Background  

HIV Associated Dementia (HAD) is a common complication of human immunodeficiency virus (HIV) infection that erodes the quality of life for patients and burdens health care providers. Intravenous drug use is a major route of HIV transmission, and drug use is associated with increased HAD. Specific proteins released as a consequence of HIV infection (e.g., gp120, the HIV envelope protein and Tat, the nuclear transactivating protein) have been implicated in the pathogenesis of HAD. In primary cultures of human fetal brain tissue, subtoxic doses of gp120 and Tat are capable of interacting with a physiologically relevant dose of cocaine, to produce a significant synergistic neurotoxicity. Using this model system, the neuroprotective potential of gonadal steroids was investigated.     

N-acetylcysteine prevents HIV gp 120-related damage of human cultured astrocytes: correlation with glutamine synthase dysfunction

Background  

HIV envelope gp 120 glycoprotein is released during active HIV infection of brain macrophages thereby generating inflammation and oxidative stress which contribute to the development of the AIDS-Dementia Complex (ADC). Gp120 has also been found capable to generate excitotoxic effect on brain tissue via enhancement of glutamatergic neurotransmission, leading to neuronal and astroglial damage, though the mechanism is still to be better understood.     

A Euclidean perspective on the unfolding of azurin: spatial correlations

We investigate the stability to structural perturbation of Pseudomonas aeruginosa azurin using a previously developed geometric model. Our analysis considers Ru(2,2′,6′,2^″-terpyridine)(1,10-phenanthroline)(His83)-labelled wild-type azurin and five variants with mutations to Cu-ligating residues. We find that in the early stages of unfolding, the β-strands exhibit the most structural stability. The conserved residues comprising the hydrophobic core are dislocated only after nearly complete unfolding of the β-barrel. Attachment of the Ru-complex at His83 does not destabilize the protein fold, despite causing some degree of structural rearrangement. Replacing the Cys112 and/or Met121 Cu ligands does not affect the conformational integrity of the protein. Notably, these results are in accord with experimental evidence, as well as molecular dynamics simulations of the denaturation of azurin.     

Signalling crosstalk in FGF2-mediated protection of endothelial cells from HIV-gp120

Background  

The blood brain barrier (BBB) is the first line of defence of the central nervous system (CNS) against circulating pathogens, such as HIV. The cytotoxic HIV protein, gp120, damages endothelial cells of the BBB, thereby compromising its integrity, which may lead to migration of HIV-infected cells into the brain. Fibroblast growth factor 2 (FGF2), produced primarily by astrocytes, promotes endothelial cell fitness and angiogenesis. We hypothesized that treatment of human umbilical vein endothelial cells (HUVEC) with FGF2 would protect the cells from gp120-mediated toxicity via endothelial cell survival signalling.     

Contributions of polar and apolar groups to the thermodynamic stability of azurin

Summary All denaturational thermodynamic changes (ΔH, ΔS, ΔG) were calculated for the thermal unfolding of azurin fromPseudomonas Aeruginosa. DSC data could not be directly studied in terms of classical thermodynamics, because the thermal unfolding of azurin is an irreversible process. However, a mathematical extrapolation of heat capacity curves to infinite scan rate allowed us to obtain the denaturational enthalpy change and the melting temperature related to the reversible step. The denaturational heat capacity change (ΔC _p ), together with all the relevant contributions of polar and apolar groups to the thermodynamic parameters of azurin were calculated according to an approach taking into account the common features of protein unfolding and dissolution of model compounds. A comparison between the experimental and the expected denaturational thermodynamic values was briefly discussed.     

Folding of lattice protein model chains with fixed ends

Using Monte Carlo simulations, we have studied the folding dynamics and thermodynamics of geometricall yconstrained lattice protein model chains. The constraints are realized by fixing one or both terminals of the chains. By comparing the results with that of the free-end chains, we find that the folding behaviours of the end-constralned chains are not completely similar to that of the free-end chains. Both kinds of constraints on the chain ends affect the folding dynamics of the chains: i.e., the folding rate, but not the thermodynamics. The thermodynamic behaviour of the one-end-fixed chains shows less difference from that of the free-end chains, while the thermodynamic behaviour of the two-end-fixed chains has obvious difference from that of the free-end chains. The origin of these differences comes from the differences of the ergodicitv of the chains in the conformational space.     

Molecular Modeling of Polyisobutylene. Application of the Modified Rotational Isomeric States Model for Polymers Comprising Four Rotational Isomeric States

Due to the presence of two alternating bond angles in the backbone of the polymeric chains, polyisobutylene (PIB) possesses four different rotational isomeric states. Accordingly, conformations of PIB could be represented by a four-state rotational isomeric scheme with only one adjustable statistical weight parameter. Rotational isomeric states (RIS) were determined at +25°, ?25°, +120°, ?120°. Conformations were divided into a “+class” and “?class,” with bond conformations tended to be followed by those from the same class and with changes from one class to the other rare. Since the configurational and thermodynamic properties of PIB depend to a great deal on the conformational characteristics of the polymer, a modified rotational isomeric state approximation was used to generate the initial configurations of the polymeric chains without allowing for any segment-segment overlap. Attempts were made to test the configurational properties of these systems against those determined experimentally to ensure that these configurations do represent realistically the polymeric system. Furthermore, these configurations were used to perform subsequent molecular dynamics runs to elucidate the effect of the molecular weight of the polymer and the temperature on some of its important thermodynamic properties, such as self-diffusion coefficient, thermal pressure coefficient, heat capacity, and dielectric constant.     

Association of polyethylene friction and thermal unfolding of interfacial albumin molecules

Under the articulation of artificial joints, ultra-high molecular weight polyethylene (UHMWPE) acts as a bearing surface under the lubrication of synovial fluid containing various proteins. Albumin is the most abundant composition and acts as the interfacial molecule in the boundary lubrication regime. The dissipated energy including thermal energy from the tribological process may lead to the conformational change of albumin molecules.In this study, a series of experiments were designed and carried out to investigate the association of thermal unfolding albumin and the frictional characteristics of highly-crosslinked UHMWPE (x-UHMWPE). An accelerated oxidation experiment was used to prepare x-UHMWPE with an oxidized surface. Analysis of the albumin protein by circular dichroism (CD) spectroscopy was performed to detect the conformational changes during a thermal process. In addition, a molecular simulation was performed to understand the structural change of albumin at various temperatures and the exposed hydrophobic contact areas. Linear reciprocating frictional tests were carried out to obtain the start-up friction coefficients. The results indicate that a decrease of α-helix content and an unfolding of the secondary structure of albumin were observed with increasing temperatures which may come from the frictional heat of joint articulation process. The conformational change of albumin differentiates the frictional characteristics for x-UHMWPE with different oxidation levels. A model, describing that the properties of the lubricating molecules and articulating surfaces may affect the adsorption of the boundary lubrication thin film which is critical to the tribological behavior, is proposed.     

Thermodynamics and effective temperatures in sheared granular matter and emulsions

Recent theories postulate that the non-equilibrium behavior of systems experiencing jamming or structural arrest could be described by equilibrium thermodynamic concepts. If a thermodynamic framework can describe the behavior of systems far from equilibrium, then an effective temperature with a true thermodynamic meaning exists as a key parameter in characterizing the material's properties. In order to examine the validity of the thermodynamics for jammed systems, we perform a numerical experiment with a realistic granular matter model specially conceived to be reproducible in the laboratory. The results strongly support the thermodynamic picture.