水分子通道蛋白的结构与功能

水分子穿越双磷脂生物膜的输运机理是生理学和细胞生物学中一个长期未能解决的重要问题.AQP1水通道蛋白的发现和鉴定使得人们确认出一个新的蛋白质家族--水通道蛋白家族.正是这一蛋白家族的存在,使得水分子可以进行快速的跨膜传输.由晶体学方法解出的哺乳动物AQP1水通道蛋白的原子结构,最终揭示了水通道蛋白只允许水分子快速传输而阻挡其他的小分子和离子(包括质子H+)的筛选输运机理.本文概述了水通道蛋白的发现和其对水分子的筛选传输机理.     

兔子朊蛋白结构稳定性的分子动力学研究(英文)

朊蛋白病是一种能够对人类和动物带来致命影响,并具有高度传染性的神经退行性疾病.兔子是目前已经报道的哺乳类动物中对朊蛋白病免疫的少数几个物种之一.我们将分子动力学和操控式分子动力学模拟相结合,研究了兔子正常朊蛋白的结构稳定性;同时讨论了蛋白结构的收敛性及刚性分布,并揭示了兔子朊蛋白中关键二级结构的动力学以及受力各向异性特征,证实了兔子朊蛋白结构的稳定性特征.     

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.     

细胞死亡蛋白的三维结构及活性位点的理论研究

利用同源模建和分子动力学模拟方法,构建了细胞死亡蛋白（CED-10）的三维结构,并预测了其可能的活性位点,为细胞死亡蛋白家族催化机理的深入研究提供了、重要的参考信息．     

胆固醇酯类化合物在混合溶剂中的簇集及其荧光光谱的特征

近年来,人们对长链脂肪族、芳香族化合物分子在二甲基亚砜/水(DMSO/H₂O)混合溶剂中发生簇集,形成聚集体进行了广泛研究指出:簇集的驱动力是疏水作用。     

Non-Condon效应对电子转移速率影响的理论模拟及其在有机半导体中的应用

随着Condon近似下各种电子转移理论的不断发展与完善和人们对non-Condon效应在电子转移过程中重要作用认识的逐步深入,已建立了几个理论模型来研究这种效应对电子转移速率的影响.本文主要总结了近两年来我们在non-Condon效应电子转移理论方面的工作,首先阐述了指数型、高斯型以及直线型non-Condon电子转移速率的全量子表达式,然后运用该理论模型以及分子动力学模拟计算了二噻吩四硫富瓦烯（DT-TTF）有机半导体的迁移率.此外,还进一步利用数值模拟详细研究了这三种线型的non-Condon效应在量子尺度上对电子转移速率的影响.     

蔗渣木聚糖微观结构的分子动力学模拟

在对木聚糖来源及其结构进行分类比较的基础上,采用分子动力学模拟方法及Materials Studio 4.0软件对蔗渣木聚糖及木糖单元等进行微观模拟计算.通过原子净电荷、电子密度和Fukui函数分析等分析方法,对蔗渣木聚糖的木糖单元进行结构优化,得到了蔗渣木聚糖的木糖单元优化构型的键长、键角和电荷密度.木糖单元原子的Hirshfeld净电荷与Fukui函数分析数据表明,木糖单元的活性中心主要在C(3)上的羟基位置,且羟基氧原子易受亲电试剂的攻击,羟基氢原子易受亲核试剂的攻击.对蔗渣木聚糖单分子链及无定形结构进行模拟,得到了蔗渣木聚糖的微观结构模型,显示蔗渣木聚糖分子具有链状结构,大致呈螺旋状.获得了蔗渣木聚糖的最优化无定形结构,并通过计算得到了其最优化无定形结构的X射线衍射图谱.研究结果为系统探讨蔗渣木聚糖及其衍生物的结构与性能关系奠定了基础.     

透射电子显微镜在聚合物不同层次结构研究中的应用

聚合物材料的性能与功能取决于各级结构,其中化学结构决定材料的基本功能与性能,而不同层次聚集态结构能够改变材料的性能和赋予材料特殊功能,如高取向超高分子量聚乙烯的模量比相应非取向样品提高3个数量级,聚偏氟乙烯的β和γ结晶结构则能赋予其压电、铁电等特殊功能.因此,明确聚合物不同层次聚集态结构的形成机制、实现各层次结构的精准...     

固有无序超嗜热菌FlgM蛋白在两种不同温度下的构象变化特征

基于分子动力学模拟方法比较了超嗜热菌FlgM 蛋白在常温(293 K)和生理温度(358 K)下的结构特征.基于GROMACS软件包, 采用OPLS-AA分子力场和TIP3P水模型, 对超嗜热菌FlgM 蛋白在293 和358 K进行了2组独立的长时间分子动力学模拟, 每组体系模拟时间为1500 ns. 主要分析了两种温度下超嗜热菌FlgM蛋白的二级结构特征、整体构象变化及半无序化区域和结构化区域的构象特征. 研究结果表明: 在常温下, N端具有一定程度的螺旋成分, 但在生理温度下, 超嗜热菌FlgM 蛋白的结构变得松散, 螺旋结构减少, 构象稳定性减弱, H1 螺旋散开, FlgM 蛋白构象灵活性增强, 不稳定程度增加. 这些不同温度的结构变化说明: 半无序化区域(N端)在非结合状态下有一定的螺旋结构, 但该段螺旋的稳定性随温度升高而降低. 超嗜热菌FlgM蛋白会通过增加结构的无序程度使结构更加灵活, 以适应高温, 从而使该类固有无序蛋白更好地行使其功能, 如提高同其他成分的结合速率等.     

分子动力学模拟方法研究结构水在糖原合成酶激酶-3β中的作用

用分子动力学模拟的方法揭示了结构水分子在糖原合成酶激酶-3β(GSK-3β)中的作用.如果没有结构水,ATP嘌呤环的结合位置将发生偏移以填补结构水留下的空间;ATP结合口袋中的氢键网络将被破坏,保守残基Lys85与ATP的磷酸根侧链只能形成一个保守氢键,无法维持磷酸根转移所需的线性关系;由于失去了氢键网络的稳定作用,Glu97和Lys85会向远离ATP的方向移动,并导致Arg96的侧链发生偏转,使Arg96无法保持与Arg180和Lys205之间正常的相对位置,最终影响GSK-3β与底物的结合.     

Synthesis and Evaluation of the Analogues of Penicillide against Cholesterol Ester Transfer Protein

A series of penicillide analogues, with modifications at C‐3 and C‐9 positions, are synthesized as potential cholesteryl ester transfer protein (CETP) inhibitors. The preliminary in vitro inhibition assay provided some valuable structure‐activity relationship information about penicillide.     

荧光素蒽醌甲酯分子内光诱导电子转移及电荷分离态的检测

合成了以荧光素为光敏剂的电子给体-受体二元化合物荧光素蒽醌甲酯(FL-AQ),用吸收光谱、荧光光谱、荧光寿命研究了该化合物在乙醇溶液中的光物理性质,并首次用纳秒级瞬态吸收光谱检测了此化合物分子内光诱导电子转移所形成的电荷分离态.在溶液中激发FL,电子可从FL有效地转移到AQ,其速率常数为3.95×10⁹s^-1,效率为95%.但由于电荷分离态寿命较短,瞬态吸收信号弱,若在此溶液中加入二氧化钛(TiO₂)纳米胶体,使FL-AQ吸附在胶体上,电荷分离态信号明显增强.480nm处FL^+·的寿命为11.1μs;560nm处AQ^-·的寿命为8.93μs.     

MgO掺杂阿利特的结构演变及其调制结构表征

利用X射线衍射(XRD)和透射电子显微镜(TEM)对不同MgO掺量的阿利特结构演变进行了研究。结果表明:当MgO掺量为0.5wt%时,T1和M1型共存;当MgO掺量为1.0wt%时,稳定为M1型;当MgO掺量在1.5wt%以上时,稳定为M3型。基于XRD数据计算得到了不同晶型阿利特的伪六方亚晶胞参数,结果显示各晶型的亚晶胞参数值非常接近。通过选区电子衍射(SAED)和高分辨透射电子显微像(HRTEM)对各晶型中的调制结构进行了观察。结果表明:各晶型阿利特中的超晶胞反射斑点坐标均可用相应的线形表达式描述,调制结构可以在HRTEM像中观察到,并以波状衬度的形式展现,其方向平行于亚晶胞中相应的晶面。     

Allosteric Control of Naphthalene Diimide Encapsulation and Electron Transfer in Porphyrin Containers: Photophysical Studies and Molecular Dynamics Simulation

The complexation processes of N,N’-dibutyl-1,4,5,8-naphthalene diimide ( NDI ) into two types of π-electron-rich molecular containers consisting of two Zn(II)-porphyrins connected by four flexible linkers of two different lengths, were characterized by means of absorption and emission spectroscopies and molecular dynamics simulation. Notably, the addition of NDI leads to a strong quenching of the fluorescence of both cages only when they are in an open conformation suitable for guest encapsulation, a situation triggered by silver(I) ions binding to the lateral triazoles. Molecular dynamics simulations confirm the fast binding of NDI , likely assisted by NDI -silver(I) interactions. Upon NDI complexation, the two porphyrin macrocycles get closer, with an optimized face to face orientation, suggesting an induced-fit mechanism through π–π interactions with the NDI aromatic cycle. Ultrafast transient absorption experiments allowed to identify the process of quenching of the Zn-porphyrin fluorescence as an efficient photoinduced electron transfer reaction between the cage porphyrin and the included NDI guest. The process occurs on fast and ultrafast time scales in the two complexes (1.5 ps and ≤300 fs) leading to a short-lived charge separated state (charge recombination lifetimes in the order of 30–40 ps). The combined computational and experimental approach used here is able to furnish a reliable model of the NDI -cage complexation mechanism and of the corresponding electron transfer reaction, attesting the allosteric control of both processes by the silver(I) ions.     

Surface‐Tuned Electron Transfer and Electrocatalysis of Hexameric Tyrosine‐Coordinated Heme Protein

Molecular modeling, electrochemical methods, and quartz crystal microbalance were used to characterize immobilized hexameric tyrosine‐coordinated heme protein (HTHP) on bare carbon or on gold electrodes modified with positively and negatively charged self‐assembled monolayers (SAMs), respectively. HTHP binds to the positively charged surface but no direct electron transfer (DET) is found due to the long distance of the active sites from the electrode surfaces. At carboxyl‐terminated surfaces, the neutrally charged bottom of HTHP can bind to the SAM. For this “disc” orientation all six hemes are close to the electrode and their direct electron transfer should be efficient. HTHP on all negatively charged SAMs showed a quasi‐reversible redox behavior with rate constant k_s values between 0.93 and 2.86 s^?1 and apparent formal potentials ${E{{0{^{\prime }}\hfill \atop {\rm app}\hfill}}}$ between ‐131.1 and ‐249.1 mV. On the MUA/MU‐modified electrode, the maximum surface concentration corresponds to a complete monolayer of the hexameric HTHP in the disc orientation. HTHP electrostatically immobilized on negatively charged SAMs shows electrocatalysis of peroxide reduction and enzymatic oxidation of NADH.     

A Molecular Magnet Confined in the Nanocage of a Globular Protein

The effect of confinement and energy transfer on the dynamics of a molecular magnet, known as a model system to study quantum coherence, is investigated. For this purpose the well‐known polyoxovanadate [V₁₅As₆O₄₂(H₂O)]^6? (V₁₅) is incorporated into a protein (human serum albumin, HSA) cavity. Due to a huge overlap of the optical absorption spectrum of V₁₅ with the emission spectrum of a fluorescence center of HSA (containing a single tryptophan residue), energy transfer is induced and probed by steady‐state and time‐resolved fluorescence. The geometrical coordination and the distance of the confined V₁₅ to the tryptophan moiety of HSA are investigated at various temperatures. This effect is used as a local probe for the thermal denaturation of the protein at elevated temperatures.     

Excited‐State Proton Transfer Can Tune the Color of Protein Fluorescent Markers

We show by quantum mechanical/molecular mechanical (QM/MM) simulations that phenylbenzothiazoles undergoing an excited‐state proton transfer (ESPT) can be used to probe protein binding sites. For 2‐(2′‐hydroxy‐4′‐aminophenyl)benzothiazole (HABT) bound to a tyrosine kinase, the absolute and relative intensities of the fluorescence bands arising from the enol and keto forms are found to be strongly dependent on the active‐site conformation. The emission properties are tuned by hydrogen‐bonding interactions of HABT with the neighboring amino acid T766 and with active‐site water. The use of ESPT tuners opens the possibility of creating two‐color fluorescent markers for protein binding sites, with potential applications in the detection of mutations in cancer cell lines.