组蛋白H1序列固有无序特性分析

组蛋白H1对于高阶染色质结构的形成和基因表达调控具有重要作用。为了揭示组蛋白H1在染色质结构形成中的生物学机制,本文对组蛋白H1三个结构域C-terminal domain (CTD)、N-terminal domain(NTD)和Globular domain (GD) 及各区域连接位点对应序列氨基酸偏好、复杂度等序列特征进行了系统对比研究,并对各区域进行了固有无序蛋白有序区/无序区预测分析。结果表明,组蛋白H1三个结构中,中间的球状结构域（GD）中的氨基酸序列是非常保守的,NTD富含疏水氨基酸,CTD末端富含碱性氨基酸。进一步的研究表明, CTD和NTD两个结构域普遍具有固有无序特性,因此这些区域具有较大的柔性结构,对其在染色质形成中行使的重要生物学功能具有重要意义。     

MRG15与甲基化组蛋白H3K36相互作用研究

人源转录调控因子MRG15（MORF4 related gene on chromosome 15）是在胚胎发育,细胞增殖和衰老过程中具有重要作用的蛋白质. 在分子水平上,MRG15的chromo结构域能够与组蛋白H3甲基化的肽段H3K36me3相互作用. 为了确定二者的作用位点和方式,利用液体核磁共振的方法对MRG15 chromo结构域和H3K36me3多肽进行了研究. 对MRG15 chromo结构域进行归属,用化学位移扰动的方法研究了其与H3K36me3肽段的相互作用,确定了相互作用位点的关键氨基酸为H21,Y46,W49和W53,并计算了解离常数约为1 mmol/L. 研究结果对于阐明MRG15与组蛋白H3的结合和相互作用机制提供了重要的线索.     

基于片段的核磁共振筛选方法识别NSD1 SET结构域的全新苗头化合物（英文）

包含SET结构域的核受体结合蛋白1(NSD1)是一种组蛋白甲基转移酶,它能够特异性的甲基化组蛋白H3赖氨酸第36位(H3K36).异常表达的NSD1主要发现于Sotos综合症患者体内,但它同样也能导致其他多种人类疾病的发生.目前已有靶向组蛋白甲基转移酶DOT1L和EZH2的小分子抑制剂报道,然而,靶向NSD1的化学探针分子尚未被发现.本文使用基于片段的核磁共振(NMR)筛选方法寻找到3个以NSD1蛋白作为靶点的苗头化合物,利用化学位移扰动分析技术测定了这些化合物与NSD1的结合亲和力.另外,利用分子对接方法选择获得苗头化合物与NSD1蛋白的最可能的结合模型.结果显示苗头化合物1结合于NSD1天然底物S-腺苷酸甲硫氨酸(SAM)的结合口袋中.我们的研究成果为进一步以结构为指导的从苗头化合物到先导化合物的衍化奠定了基础.     

蛋白质INSM1中的锌指结构域ZF (4-5)的表达、纯化与表征

胰岛素瘤相关蛋白1（INSM1）是一类转录调节蛋白,通过其C-端的锌指结构域（氨基酸250-510）来识别序列特异性的DNA分子.INSM1的C-端包含有5个串联的锌指结构域,然而这些结构域的结构及其如何识别DNA的分子机制目前仍不清楚.通过重组构建的质粒pET-32m-INSM1（424-497）表达的蛋白质（氨基酸424-497）包含了最后两个锌指结构域4和5,简称为ZF（4-5）.该文详细研究了蛋白质ZF（4-5）的诱导表达条件,得到了较高产率的纯化蛋白.核磁共振（NMR）谱和圆二色谱（CD）揭示了Zn²⁺对稳定锌指蛋白结构的必要性,以及C2H2-Zn²⁺结合的组氨酸呈现为δ-异构方式.     

形成素结合蛋白C-端FF结构域的1H和15N NMR谱峰归属和结构分析

FF结构域广泛存在于与信号传导相关的蛋白质中,我们选择形成素结合蛋白11 (formin-binding protein 11, FBP11)中所含的一个FF结构域,通过在H₂O和D₂O中采集的COSY,TOCSY,NOESY等二维核磁共振谱,识别了FF-结构域的氨基酸残基的质子自旋系统,通过解析二维和三维NOESY谱中的d_αN、d_NN和d_βN等NOE相关完成了序列专一性归属;二级结构分析表明FF-结构域包含三段α 螺旋.      

内禀无序蛋白构象与带电氨基酸残基排布关系——以精氨酸和天冬氨酸组成的随机多肽为例

内禀无序蛋白的结构特征与其氨基酸序列有着密切的联系.其中一个核心问题是正负带电氨基酸残基的排列如何影响无序蛋白或者多肽的构象?为了回答这一问题,本研究以天冬氨酸和精氨酸两种带电残基组成的随机多肽为研究对象,利用全原子蒙特卡罗模拟和温度副本交换采样方法,研究了随机多肽的电荷排布与结构之间的定性关系.结果表明:正负带电残基在序列上混合均匀时,由于肽链内部的静电吸引和排斥相互抵消,肽链倾向于形成无规卷曲的构象;正负带电残基分离时,由于长程静电相互吸引,多肽倾向于形成类β-发卡的形状.     

基于片段的核磁共振筛选方法识别NSD1 SET结构域的全新苗头化合物

包含SET结构域的核受体结合蛋白1（NSD1）是一种组蛋白甲基转移酶,它能够特异性的甲基化组蛋白H3赖氨酸第36位（H3K36）.异常表达的NSD1主要发现于Sotos综合症患者体内,但它同样也能导致其他多种人类疾病的发生.目前已有靶向组蛋白甲基转移酶DOT1L和EZH2的小分子抑制剂报道,然而,靶向NSD1的化学探针分子尚未被发现.本文使用基于片段的核磁共振（NMR）筛选方法寻找到3个以NSD1蛋白作为靶点的苗头化合物,利用化学位移扰动分析技术测定了这些化合物与NSD1的结合亲和力.另外,利用分子对接方法选择获得苗头化合物与NSD1蛋白的最可能的结合模型.结果显示苗头化合物1结合于NSD1天然底物S-腺苷酸甲硫氨酸（SAM）的结合口袋中.我们的研究成果为进一步以结构为指导的从苗头化合物到先导化合物的衍化奠定了基础.     

靶向肿瘤因子c-MYC基因启动区G4-DNA的小分子药物设计及核磁共振研究进展

肿瘤基因MYC在人类70%癌细胞中高表达,抑制其转录是治疗肿瘤的有效手段.c-MYC启动子区P1近端的核酸酶超敏元件Ⅲ₁(NHE Ⅲ₁)控制MYC基因近90%的转录激活.NHE Ⅲ₁区域富含碱基G序列并且形成G-四链体(G4),调控c-MYC基因转录,是抗肿瘤药物靶标.但G4-DNA和G4-RNA的三维结构高度相似,小分子与其他G4(如端粒G4、mRNA G4、c-Kit G4等)的非特异性作用会产生小分子药物“脱靶”效应,同时小分子药物会诱导其他G4形成从而干扰正常细胞的功能,造成靶向c-MYC G4抗癌药物设计困难.本文综述了近些年靶向肿瘤因子c-MYC G4-DNA的小分子药物研究进展,及核磁共振(NMR)技术在G4-DNA和G4-RNA结构确定中的作用,为靶向c-MYC G4-DNA的小分子药物设计等相关研究工作提供参考.     

波谱学杂志总目次

第23卷第1期2006年3月形成素结合蛋白C-端FF结构域的1H和15N NMR谱峰归属和结构分析…………………………………………………………吴昌琳,宋国强,胡红雨(1-10)一种具有数字预加重的磁共振成像梯度波形发生器………………………………………………………………………徐勤,王鹤,     

二维介观环中持续电流的梯度无序效应

基于紧束缚模型,考虑无序的梯度衰减,研究了无序-有序二维介观环体系中无序梯度及结构尺寸等因素对持续电流的影响.在表面无序区无梯度衰减时,持续电流随无序度的变化先减小后增大,观察到类弹道和局域性的转变.当存在梯度衰减时,无序区部分区域无序度相应减小,对有序区产生较强散射,典型电流比没有无序衰减时偏小.有趣的是,当无序度指数衰减时,上述类弹道和局域性的转变却消失了,揭示了介观实验中能否观察到该转变与无序的梯度分布密切相关.此外,计算表明表面无序渗透的深度和环的宽度对持续电流也有重要影响,呈现奇异的量子尺寸效应.这不同于以前的理论预言. 关键词： 介观环 梯度无序 持续电流     

MUSIC and aromatic residues: amino acid type-selective (1)H-(15)N correlations, III.

Amino acid type-selective experiments can help to remove ambiguities in automated assignment procedures for (15)N/(13)C-labeled proteins. Here we present five triple-resonance experiments that yield amino acid type-selective (1)H-(15)N correlations for aromatic amino acids. Four of the novel experiments are based on the MUSIC coherence transfer scheme that replaces the initial INEPT transfer and is selective for CH(2). The MUSIC sequence is combined with selective excitation pulses to create experiments for Trp (W-HSQC) as well as Phe, Tyr, and His (FYH-HSQC). In addition, an experiment selective for Trp H(epsilon1)-N(epsilon1) is presented. The new experiments are recorded as two-dimensional experiments and their performance is demonstrated with the application to a protein domain of 115 amino acids.     

Adsorption of amino acids on indium arsenide (1 0 0) surfaces: Assessment of passivation capabilities

Angle-Resolved X-ray Photoelectron Spectroscopy (ARXPS) was used to examine amino acid bonding and oxide removal on InAs(1 0 0) surfaces. Five amino acids were studied, including cysteine, lysine, aspartic acid, glutamic acid and arginine. Observations on the ability of specific functional groups to prevent oxide formation were made by examining the thickness of oxide films on the functionalize surfaces. Amino acids that possessed more than one functional group having resonance were shown to most effectively affect oxide formation. The influence of these groups on the electronic structure of InAs(1 0 0) provides insight into how multifunctional passivation strategies could be beneficial, as well as showing how biological molecules might affect detection when InAs(1 0 0) is used as a platform.     

Structural characterization and angiotensin-converting enzyme (ACE) inhibitory mechanism of Stropharia rugosoannulata mushroom peptides prepared by ultrasound

To reveal the structural characteristics and angiotensin-converting enzyme (ACE) inhibition mechanism of Stropharia rugosoannulata mushroom peptides prepared by multifrequency ultrasound, the peptide distribution, amino acid sequence composition characteristics, formation pathway, and ACE inhibition mechanism of S. rugosoannulata mushroom peptides were studied. It was found that the peptides in S. rugosoannulata mushroom samples treated by multifrequency ultrasound (probe ultrasound and bath ultrasound mode) were mainly octapeptides, nonapeptides, and decapeptides. Hydrophobic amino acids were the primary amino acids in the peptides prepared by ultrasound, and the amino acid dissociation of the peptide bonds at the C-terminal under the action of ultrasound was performed mainly to produce hydrophobic amino acids. Pro and Val (PV), Arg and Pro (RP), Pro and Leu (PL), and Asp (D) combined with hydrophobic amino acids were the characteristic amino acid sequence basis of the active peptides of the S. rugosoannulata mushroom. The docking results of active peptides and ACE showed that hydrogen bond interaction remained the primary mode of interaction between ACE and peptides prepared by ultrasound. The peptides can bind to the amino acid residues in the ACE active pocket, zinc ions, or key amino acids in the domain, and this results in inhibition of ACE activity. Cation–pi interactions also played an important role in the binding of mushroom peptides to ACE. This study explains the structural characteristics and ACE inhibition mechanism used by S. rugosoannulata mushroom peptides prepared by ultrasound, and it will provide a reference for the development and application of S. rugosoannulata mushroom peptides.     

Tubuliform silk protein: A protein with unique molecular characteristics and mechanical properties in the spider silk fibroin family

Orb–web weavers can produce up to six different types of silk and a glue for various functions. Tubuliform silk is unique among them due to its distinct amino acid composition, specific time of production, and atypical mechanical properties. To study the protein composing this silk, tubuliform gland cDNA libraries were constructed from three orb–weaving spiders Argiope aurantia, Araneus gemmoides, and Nephila clavipes. Amino acid composition comparison between the predicted tubuliform silk protein sequence (TuSp1) and the corresponding gland protein confirms that TuSp1 is the major component in tubuliform gland in three spiders. Sequence analysis suggests that TuSp1 shares no significant similarity with its paralogues, while it has conserved sequence motifs with the most primitive spider, Euagrus chisoseus silk protein. The presence of large side-chain amino acids in TuSp1 sequence is consistent with the frustrated β-sheet crystalline structure of tubuliform silk observed in transmission electron microscopy. Repeat unit comparison within species as well as among three spiders exhibits high sequence conservation. Parsimony analysis based on carboxy terminal sequence shows that Argiope and Araneus are more closely related than either is to Nephila which is consistent with phylogenetic analysis based on morphological evidence. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. PACS 61.41; 87.14 Ee; 87.15 Cc     

20种氨基酸近红外光谱及其分子结构的相关性

旨在研究20种氨基酸的分子结构与其近红外光谱的相关性,为氨基酸近红外光谱在动物科学、食品和医药等方面的推广应用奠定一定的理论基础。应用岛津傅里叶变换红外光谱仪IRPrestige-21及其近红外附件FlexIRTM Near-Infrared Fiber Optics module,采集20种氨基酸标准物质在1 000～2 502 nm波长范围内的近红外光谱,分辨率8 cm-1,每个样品扫描3次,每次扫描50遍,取其平均值为氨基酸标准品的近红外光谱。根据氨基酸侧链基团的不同,分别比较脂肪族氨基酸、芳香族氨基酸和杂环氨基酸中各氨基酸分子结构与其近红外光谱的相关性。研究表明,20种氨基酸在1 000～2 502 nm区域有非常明显的近红外光谱吸收且差异显著。分子量较大的脂肪族氨基酸其近红外光谱受侧链基团的影响较大,而甘氨酸近红外光谱受羧基和氨基的影响较大;两种芳香族氨基酸近红外光谱的差异主要来自于苯环,酪氨酸苯环上的—OH基团降低了苯分子的对称性,导致更多振动吸收峰的出现;杂环氨基酸因其侧链上杂环分子基团构成不同,其近红外光谱在1 600～1 800 nm区域差异较大。综上,20种氨基酸主要存在4个特征光谱区：第1特征光谱区为1 050～1 200 nm主要由C—H基团的二级倍频构成;第2特征光谱区为1 300～1 500 nm主要由C—H基团的组合频构成;因侧链基团分子构成不同,在第3特征光谱区1 600～1 850 nm和第4特征光谱区2 000～2 502 nm表现出差异较大的特征吸收峰。因此,可以利用此4个近红外光谱特征区域对氨基酸进行定量和定性分析,提高氨基酸近红外光谱模型预测的准确性。     

The coevolution theory of the origin of the genetic code

A review of the coevolution theory of the origin of the genetic code is presented. This theory maintains that the origin of the code should be sought in the biosynthetic relationships between amino acids. In particular, some amino acids, the precursors, occupied the structure of the genetic code early on. As the product amino acids developed from these precursors, part or all of the codon domain of the precursor amino acid was ceded to the product amino acids, which resulted in the structuring of the genetic code. This paper therefore reviews the evidence in favour of this theory. The existence of some molecular fossils representing the biosynthetic pathways on which the coevolution theory suggests biosynthetic transformations took place (precursor amino acid → product amino acid) seems to be a strong corroboration of this theory. A generalisation imposed by this theory on the ancestral metabolic state is then discussed and, finally, the main prospects that seem to stem from the coevolution theory are presented.     

氨基酸官能团的太赫兹振动模式研究

对比于氨基酸的红外分析法,太赫兹波的电子能量更低,可实现无损检测。氨基酸分子内原子振动、分子间氢键的作用、以及晶体中晶格的低频振动均处于太赫兹波段,使其在太赫兹波段具有吸收峰,且不同的氨基酸分子太赫兹吸收峰不同,故可用氨基酸在太赫兹波段的这种“指纹特性”实现氨基酸类物质的定性分析。量子化学分析方法可以应用量子力学的基本原理和方法,研究稳定和不稳定分子的结构、性能及其之间的关系,还可以针对分子与分子间的相互作用、相互碰撞及相互反应等问题进行研究。通过量子化学计算方法计算氨基酸分子的太赫兹吸收谱,可以为氨基酸分子的太赫兹吸收峰匹配分子振动模式,对氨基酸定性分析有一定参考性与指向性,并为实验获取的样品太赫兹时域光谱提供理论支撑,在实验获得太赫兹吸收谱的基础上进行量子化学计算,还能为实验结果进行验证。首先利用太赫兹时域光谱技术获取了谷氨酰胺、苏氨酸、组氨酸的太赫兹吸收谱,分别构建这三种氨基酸样品在实物中以两性离子形式存在的单分子构型,利用量子化学计算方法在完成结构优化后进行太赫兹吸收谱模拟计算。计算结果表明三种氨基酸单分子的太赫兹吸收谱计算结果与实验获取的太赫兹吸收谱差异较大,但在高频段吸收峰峰位基本吻合。通过GaussView分别查看了这三种氨基酸分子在太赫兹段内的吸收峰对应频率处的振转情况,发现在高频段内三种氨基酸分子官能团均只发生转动而未见振动,并且转动模式基本一致。通过对氨基酸官能团的太赫兹吸收谱进行量子化学计算,将官能团在高频段内吸收峰对应频率处的振转模式与三种氨基酸分子在该段内吸收峰对应频率处的振转模式做了对比。研究表明,在氨基酸单分子构型下由量子化学方法计算所得的太赫兹吸收谱中,高频段内计算得出的模拟吸收峰与实验获取的太赫兹吸收峰基本吻合;振转模式分析发现,谷氨酰胺、苏氨酸、组氨酸在太赫兹高频段内的氨基酸官能团振转模式相同,三种氨基酸分子在高频段内的吸收峰主要来源于氨基酸官能团。因此,结合量子化学计算与太赫兹吸收谱可以实现氨基酸类物质的定性分析。