基于疏水性小波分析的膜蛋白结构预测

膜蛋白在细胞膜上具有重要的生理功能,大部分膜蛋白在药物设计、转运蛋白和免疫识别等方面起着关键的作用,从分子水平上预测这类蛋白质的结构具有非常重要的意义.本文提出一种基于氨基酸疏水性小波变换技术预测膜蛋白跨膜区段数目和位置的新方法.以代码为upkb-bovin的膜蛋白为例,对跨膜螺旋区数目和位置的预测分析进行了描述.从膜蛋白数据库中随机抽取36个蛋白质(含跨膜螺旋区232)作为测试集检验小波分析的预测方法,其中226个跨膜螺旋区能被准确预测,准确率为96.8%.结果表明,这种预测方法具有较高的预测准确性.     

膜蛋白跨膜区段的预测分析

将连续小波变换技术的时频局部化特点和氨基酸的疏水特性相结合,提出了一种用于预测膜蛋白跨膜区段数目和位置的新方法,以代码为1YST的膜蛋白为例,对小波尺度和疏水值的种类进行了选择,同时描述了该法对跨膜螺旋区数目和位置的预测分析过程.从膜蛋白数据库中随机抽取36个蛋白质(含跨膜螺旋区232)作为测试集,采用该方法对其跨膜螺旋区进行预测,其中222个跨膜螺旋区能被准确预测,准确率为96.1%.结果表明,该法具有较高的预测准确性.     

基于氨基酸模糊聚类分析的跨膜区域预测

跨膜蛋白在进化过程中，序列保守性较差，即使是同源蛋白序列的一致性程度也较低，因而在跨膜区预测算法中，通过序列的一致性程度来选取训练集并不能有效地消除预测结果对训练集的过度适应性．本文提出了一种基于氨基酸模糊聚类分析的预测算法，通过氨基酸在各个区域分布的相似性程度进行模糊聚类，从而根据一类氨基酸的分布特性而不是各个氨基酸的分布特性进行跨膜区预测．结果表明，该方法能在一定程度上消除训练集的选取对测试结果的影响，提高跨膜蛋白拓扑结构预测的准确度，特别是提高对目前知之甚少的跨膜蛋白的预测准确度．     

应用连续小波变换预测蛋白质的二级结构

将代码为lgca蛋白质的氨基酸序列映射为疏水值序列，在合适的尺度下，通过 连续小波变换法分别对其α螺旋,α螺旋和β折叠之间的连接多肽(即部分规则和无 规则二级结构)进行预测，准确率分别为76．5％和85．7％．从PDBsum数据库中随 机抽取100个蛋白质作为测试对象，其中全α螺旋、全β折叠、α／β以及α+β蛋 白质各25个．在100个蛋白质中共有1618个连接多肽和747个α螺旋.本法预测到的 连接多肽共有1536个，其中1308个与实际结构一致，平均预测准确率为85.2％；预 测到的α螺旋有770个，其中581个与实际结构一致，平均预测准确率为75．5％． 结果表明：该法可较好地预测蛋白质的α螺旋、连接多肽，具有极大的发展前景．     

基于分子动力学模拟的TRPM8通道门控特性分析

TRPM8通道的温度感知等生理功能依赖于正常的门控, 但现有晶体结构中S6跨膜螺旋C末端形成的门控结构存在氨基酸缺失, 所以其门控特性未能揭晓. 本文基于已有的晶体结构和AlphaFold算法构建了 11个完整不同构象的TRPM8通道, 发现其S6跨膜螺旋C末端构成的门控存在回环和螺旋2种构象. 在回环构象中, 多个氨基酸参与形成阻碍离子通透的孔道区; 而在螺旋构象中, 仅有关键氨基酸V956发挥门控作用. 由于回环构象的柔性大于螺旋构象, 导致回环构象参与阻碍离子通透的关键氨基酸构象和数量变化多样. 二级结构预测与模建结果表明, S6跨膜螺旋C末端存在回环构象向螺旋构象的转变, 此过程中柔性的回环构象结构域向胞外侧上移, 关键氨基酸向孔道衬外扭转, 增强了与相邻跨膜螺旋S5的相互作用以及S5与TRP螺旋之间的相互作用, 进而形成刚性、 稳定且有序的螺旋构象. 这增加了TRPM8通道各结构域间的协同性, 使能量信息更高效地传递到门控结构域, 为TRPM8通道开启蓄势.     

SARS冠状病毒E蛋白的结构研究及功能预测

结合生物信息学方法及分子模拟手段,选择较高准确度的方法,预测了SARSE蛋白的分子结构并探讨其潜在的生物学活性和功能.研究结果表明,SARSE蛋白跨膜区25个疏水的氨基酸形成α-螺旋结构,包埋于病毒外壳磷脂双分子层中;N端10个氨基酸残基位于膜外;C端41个残基则附着于磷脂双分子膜内侧.同时发现,C端由9个氨基酸组成的劈裂是一个可能的活性部位.对分子进行进一步静电势分析证实,E蛋白C端可能的活性部位具有较大的静电势,可能的活性残基具有最大电荷密度,故有较强的结合受体或与其它蛋白相互作用的能力.     

基于复小波能量谱的蛋白质活性位点识别新方法

蛋白质活性位点的识别对于理解蛋白质的功能及计算机辅助药物设计具有重要的意义. 基于复小波能量谱建立蛋白质活性位点识别新方法, 采用Morlet复小波对数字化的蛋白质序列进行一维连续小波变换. 结果表明, 通过时-频分析, 能量集中区域往往与蛋白质的活性位点具有密切联系, 并且同源蛋白质序列的复小波能量最大值通常分布于相同的频率处, 表明小波功率谱在预测蛋白质活性位点方面具有广阔的应用前景.     

Slc11a2第六跨膜区在十二烷基磷酰胆碱胶束中的结构

采用圆二色谱和核磁共振波谱研究了Slc11a2第六跨膜区在十二烷基磷酰胆碱(DPC)膜模拟环境中的结构和定位.结果表明,Slc11a2第六跨膜区在DPC胶束中N端和C端各形成一小段α螺旋,两段螺旋中间通过高度灵活的区域连接,整个肽插入到DPC胶束中.H267A突变使螺旋长度变长,H272A突变使螺旋长度略有变短,突变后结构的变化可能和蛋白功能缺失相关.     

人红细胞摄取环己二胺合铂(Ⅱ)配合物的手性选择性研究

合成了六种以不同手性的1,2-环己二胺(1,2-dach)作为载体配体的铂(Ⅱ)配合物,用元素分析、红外及分子图形方法对其组成和结构进行了表征.测定了它们跨人红细胞膜的一级反应动力学常数.用膜蛋白巯基滴定、荧光标记、自旋标记ESR谱等方法研究了它们与膜蛋白、膜脂的相互作用;用脂质体模拟了这些配合物的细胞摄入.结果表明:这些配合物主要通过简单扩散进入红细胞,其跨膜速率对环己二胺的手性具有明显的选择性.这种选择性主要来源于配合物与膜脂作用过程中的手性识别。     

多尺度分子模拟研究来自于无类囊体蓝藻的五聚体门控离子通道门控机理

五聚体门控离子通道是一个重要膜蛋白家族, 在生理学过程中起到重要作用. 我们以来自无类囊体蓝藻(Gloebacter violaceus: GLIC)的五聚体门控离子通道X-ray结构为模型, 进行总共1.05 μs的粗粒化分子模拟, 并结合原子级分子模拟方法, 观察到其离子通道的闭合和相应的四级结构扭转. 我们发现其位于跨膜区组成通道的M2螺旋通过倾斜-旋转(指向通道中心)的协调运动来完成通道闭合. 进一步分析并结合前人的实验结果, 我们提出了该离子通道门控过程的可能的“连锁反应”机理: 由单独亚基的M2螺旋前部构象变化引发, 使该亚基发生整体的构象变化, 并且将这种变化传递到了邻近的亚基, 进而带动整个通道的构象变化, 最终完成通道的闭合.     

α-Amino acid derived enaminones and their application in the synthesis of N-protected methyl 5-substituted-4-hydroxypyrrole-3-carboxylates and other heterocycles

A new and simple synthesis of novel N-protected methyl 5-substituted-4-hydroxypyrrole-3-carboxylates, which exist in equilibrium with their 4-oxo tautomers, has been developed in two steps starting from N-protected α-amino acids. The key intermediates are enaminones, which can also be isolated, characterized, and used for the construction of other functionalized heterocycles, before they spontaneously decompose to pyrrole products. 4-Hydroxypyrroles are prone to partial aerial oxidation but can be efficiently alkylated or reduced to stable polysubstituted pyrrolidine derivatives.     

Specific intramolecular aromatic CH insertion of diazosulfonamides

The chemoselectivity in the intramolecular CH insertion of various diazosulfonamides has been experimentally studied. The results reveal that the aliphatic 1,4-, 1,5-, or 1,6-C(sp³)?H insertions of diazosulfonamides are not accessible, while the aromatic 1,5-C(sp²)?H insertion can be realized specifically by adjusting the diazo-adjacent group. In addition, the general chemoselectivities in the intramolecular CH insertions of diazosulfonyl compounds are summarized. Generally, diazosulfones undergo both aromatic 1,5-C(sp²)?H and aliphatic 1,5- and 1,6-C(sp³)?H insertions, while diazosulfonates undergo aliphatic 1,5- and 1,6-C(sp³)?H insertions. However, diazosulfonamides only undergo aromatic 1,5-C(sp²)?H insertion.     

N-Heterocyclic carbene-palladacyclic complexes: synthesis,characterization and their applications in the C-N coupling and α-arylation of ketones using aryl chlorides

N-Heterocyclic carbene-palladacyclic complexes 3 were successfully achieved in a one-pot procedure under mild conditions. The structure of 3a was unambiguously confirmed by X-ray single crystal diffraction and it was an active catalyst in the Buchwald-Hartwig amination and α-arylation of ketones even at very low catalyst loadings (0.01?mol%).     

Iodine-mediated oxidative Pictet-Spengler reaction using terminal alkyne as the 2-oxoaldehyde surrogate for the synthesis of 1-aroyl-β-carbolines and fused-nitrogen heterocycles

An efficient iodine-mediated oxidative Pictet-Spengler reaction in dimethyl sulphoxide (DMSO) using terminal alkynes as the 2-oxoaldehyde surrogate for the synthesis of aryl (9H-pyrido[3,4-b]indol-1-yl)methanones is described. The scope of the protocol includes the total synthesis of Fascaplysin, Eudistomins Y₁ and Y₂. The methodology is extended for preparing pyrrolo[1,2-a]-quinoxaline and indolo[1,5-a]quinoxaline derivatives. The utility of 1-aroyl-β-carbolines was demonstrated by performing palladium-catalyzed β-carboline directed ortho-C(sp2)-H functionalization of the phenyl ring with thiomethyl (SMe) group using DMSO as source and for accessing 4-aryl-canthin-6-ones.     

Facile synthesis of bicyclic 1-arylpyrazol-5-ones

In this Letter, we described a facile method for constructing fused bicyclic 1-arylpyrazol-5-one ring system. We employed various methylene-containing carboxylic acids as the substrates and proved that the pyrazolone ring closure requires activated methylene group in intermediate II. Accordingly, a series of structurally diversified, fused bicyclic 1-arylpyrazol-5-ones was prepared in moderate to high yields using the requisite substrates.     

Synthesis of pyrrolo[1,2-a]pyrazines and pyrazino[1,2-a]indoles by Curtius reaction in Morita-Baylis-Hillman derivatives

Synthesis of substituted pyrrolo[1,2-a]pyrazines and pyrazino[1,2-a]indoles from the Morita-Baylis-Hillman derivatives of acrylates via saponification followed by Curtius reaction is described.     

正丁胺对激光染料荧光谱影响的研究

用正丁胺作为碳源,采用射频辉光放电制备碳膜,选用激光染料R6G和聚乙二醇混合液作为蒸气源,采用单源热蒸发,在蒸发室与染料同时沉积得到混合膜,用拉曼光谱和红外光谱分析了碳膜的结构和键合方式,分析表明:碳膜中存在胺基团和氢原子.混合膜的荧光谱测量结果表明,认为正丁胺对染料荧光谱的影响是因为胺基和氢原子的存在.     

Cu0-catalysed 1,3-dipolar cycloadditions of α-amino acid derived N,N-cyclic azomethine imines to ynones

A series of 20 CuAIAC reactions between eight 4-acylamino substituted pyrazolidine-3-one-1-azomethine imines and four terminal ynones were performed using Cu⁰ as catalyst. The corresponding fluorescent cycloadducts were obtained in very high yields upon simple workup. Thus, Cu-metal turned out to be a better catalyst than Cu^I in terms of yield and ease of isolation. Availability of azomethine imines, mild reaction conditions, and simple workup enable a “click” access to libraries of densely substituted 2,3-dihydro-1H,5H-pyrazolo[1,2-a]pyrazol-1-ones. Reactivity of differently substituted dipoles was evaluated experimentally and by quantum chemical methods (DFT).     

Synthesis and antioxidative/anti-inflammatory activity of novel fullerene–polyamine conjugates

(E)-4-(Fullerenopyrrolidin-1-yl)-3-methylbut-2-enoic acid and its corresponding succinimidyl ester, readily obtained through Prato-type modification of C₆₀, were used for the selective N-acylation of polyamines. The thus obtained conjugates were evaluated for their antioxidative and anti-inflammatory activity and their cytotoxicity was determined. Members of this family of compounds showed interesting anti-lipid peroxidation, anti-lipoxygenase and anti-inflammatory activity and comparable cytocompatibility to spermidine.