Tobramycin与16S rRNA A位点复合物的分子动力学模拟

采用分子动力学方法(Molecular dynamics, MD)对托普霉素(Tobramycin)与16S rRNA的A位点复合物的特异性识别机制进行了理论模拟研究, 模拟时间为3.6 ns. 结果表明, A位点中波动最大的部位是两个环外碱基A1492和A1493; tobramycin的环Ⅰ和环Ⅱ是其最保守的结构单元, 可能参与了Tobramycin与16S rRNA的A位点之间的特异性识别. 另外, 发现一个残存时间为3.6 ns的“结构化”水分子, 它桥接了Tobramycin环Ⅱ的N3与环Ⅰ的N6'之间的氢键, 稳定了Tobramycin的结构; Tobramycin周围水合密度较高的位点出现在环Ⅰ和环Ⅱ附近, 这也正是晶体结构中形成较多水媒介氢键及动力学模拟中结构化水分子出现的位置. 动力学模拟证实Tobramycin与16S rRNA间的结合是大量氢键及水分子相互作用的结果, 这有助于设计和开发以Tobramycin为基础, 具有高亲和力及特异性的16S rRNA抑制剂.     

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.     

模型分子筛对水分子的吸附

The adsorptive process of H2O molecule in model zeolite have been studied by PM3 semi empirical quantum chemistry method. The variation of heat of formation and O-H bond lengths with the adsorption distance have been calculated .The results show that there are two active adsorption site on the model zeolite. The average heats of adsorption is about -44 kJ•mol-1,in accordance with experiment results (-51 kJ•mol-1).     

铜铈协同作用对CuCeMgAl(O)催化活性的影响

ＦＣＣ(流化催化裂化)是炼厂生产汽油的主要方法之一.ＦＣＣ中ＮＯｘ的排放量约占空气中其总量的10%[1].ＦＣＣ再生器烟气中ＮＯｘ的浓度为0.005%0.05%(,体积分数,下同),主要是ＮＯ(约为90%),同时含有少量的ＮＯ2.此外,在烟气中还存在着Ｏ2、ＣＯ、Ｈ2Ｏ等气体.由于ＮＯｘ能形成酸雨和光化学烟雾,破坏臭氧层,损害人体健康.因此,近20年来人们对ＤｅＮＯｘ催化剂进行了广泛的研究.鉴于ＦＣＣ的烟气中存在着ＣＯ,用ＣＯ做还原剂是同时消除ＮＯ和ＣＯ的最佳途径.对于ＮＯ和ＣＯ反应,含铜催化剂有高的催化活性[2-5],遗憾的是所有这些催化剂都…     

甲硫氨酸-脑啡肽的活性位点

用ＡＭ１方法中计算静电势的ＰＭＥＰ子程序了甲硫氨酸－脑啡肽的活性位点。通过计算得到了整个分子的三维空间静电势分布和由静电势导出的各原子的电荷分布。进一步分析,确定模型分子活性位点为酪氨酸残在的叔氨原子和苯酚基、苯丙氨酸残基的苯基及部分氧原子。     

Sites are Separable in Garnets with ALCHEMI

 It is shown in this paper that – in contrast to the accepted belief in the literature – it is possible to determine if a minority component is located on the dodecahedral, octahedral or tetrahedral sites in a garnet single crystal. Previous literature regarded the dodecahedral sites indistinguishable form the tetrahedral sites. Our prediction about the separability is based upon dynamical Bloch-wave calculations and proved experimentally in a transmission electron microscope (TEM) on two different natural garnets (almandine and grossular). The crystallographic positions of the minority components are determined in an ALCHEMI experiment that makes use of the channeling of electrons in special directions of a single-crystal sample.     

The EC4 European Register for Clinical Chemists in relation to quality aspects

 The European Register for Clinical Chemists is founded and guarded by the European Communities Confederation of Clinical Chemistry (EC4). This register fits the current mind set of harmonization and globalization of occupations within the European Community. But in addition it enables and serves the continuing quest for quality assessment and improvement within the field of laboratory medicine. The content and position of clinical chemists in the European Union is described and the European Register outlined. Received: 10 July 2000 / Accepted: 20 July 2000     

对微环境敏感的系列双亲卟啉的光谱研究

研究了系列双亲卟啉(四苯酚基卟啉P₀及其烷氧基衍生物P₁,P₂,P₃)在不同微环境下的电子吸收光谱和荧光发射及荧光激发光谱.研究发现,卟啉在THF溶液中以单体形式存在,并且其侧链取代基对卟啉电子态的影响很小;然而卟啉在CTAB胶束溶液中的光谱特性却表现出很大差异,由此分析了不同侧链取代基对卟啉分子聚集行为和定位性质的影响,初步解释了卟啉在CTAB胶束溶液中随体系pH值改变而发生的荧光猝灭现象.     

十二烷基三甲基溴化铵在聚苯乙烯胶乳粒子上的吸附

实验测得C~1~2TAB在PS胶乳粒子表面的吸附等温线呈L型的二阶段吸附特征,这表明初始的C~1~2TA^+离子是将其季铵正电性头基吸引在PS链的负电性硫酸根端基上,并将碳氢链通过疏水相互作用吸附在PS链上。结合光子相关谱测得胶乳粒子流体力学半径R~H的变化,表明第I阶段围绕着这些初始吸附位的聚集吸附,产生平均聚集数为4.0的松散小聚集体,此时对应的浓度c/cmc=0.32是文献通常所指的临界表面胶团浓度csmc。其后的进一步聚集吸附最终生成了附着在PS链端基处且平均聚集数为19.5的球形吸附胶团。这一饱和吸附的结果增加了胶乳粒子在水溶液中的分散稳定性。     

牛血清白蛋白与十二烷基硫酸钠作用的机理

利用电动势法得到了牛血清白蛋白(BSA)与十二烷基硫酸钠(SDS)相互作用的结合等温线. 通过四阶导数紫外光谱法和荧光光谱法研究了相互作用过程中芳香族氨基酸残基微环境极性的变化. 通过研究发现, 随着SDS浓度的逐渐增大, SDS在BSA上的平均结合数(v)逐渐增大, 色氨酸(Trp)残基所处微环境的极性在减弱后保持基本不变, 酪氨酸残基所处微环境的极性在明显增强后稍有减弱, 苯丙氨酸残基所处微环境的极性略有增强. 结果表明, 当v由0增大到14时, SDS主要结合在BSA的Trp-213附近并逐渐形成聚集体, 从而诱导BSA由结构域ⅡA 开始逐渐展开. 此后, SDS呈正协同作用的特点与BSA 结合, v急剧增大. 当v约为302 时, SDS在BSA上的结合基本达到饱和, BSA的构象趋于稳定.