分子元素与功能核酸分子

 介绍了"分子元素"概念。论述了核酸适体的筛选及其作为大分子药物的应用价值,概述了人工碱基的合成及进展;探讨了脱氧核酶的作用原理,分析了分子信标、分子马达在生物传感、生物合成、生物药物研究等方面的应用前景,展望了核酸分子研究领域的前景及面临的挑战。     

酶催化功能混杂性研究进展

酶催化生物体内化学反应,是生命代谢形成运转的动力。与传统观点认为酶具有专一性催化功能相对,近年来生物信息与实验分析都证实了酶具有多种混杂催化功能是普遍存在的现象。在过去的几十亿年里,古老酶一直不断演化以适应变化的环境,形成现代功能多样的酶蛋白家族。基于独特底物结合模式和动态蛋白结构的催化功能混杂性是酶蛋白适应性演化的基础。酶的混杂活性有望被开发应用于药物酶法合成及环境修复领域。本文就酶催化功能混杂性的普遍性、分子机理、可进化性等方面的相关研究进展进行综述。     

Self-assembly of amphiphilic dendritic dipeptides into helical pores

Natural pore-forming proteins act as viral helical coats and transmembrane channels, exhibit antibacterial activity and are used in synthetic systems, such as for reversible encapsulation or stochastic sensing. These diverse functions are intimately linked to protein structure. The close link between protein structure and protein function makes the design of synthetic mimics a formidable challenge, given that structure formation needs to be carefully controlled on all hierarchy levels, in solution and in the bulk. In fact, with few exceptions, synthetic pore structures capable of assembling into periodically ordered assemblies that are stable in solution and in the solid state have not yet been realized. In the case of dendrimers, covalent and non-covalent coating and assembly of a range of different structures has only yielded closed columns. Here we describe a library of amphiphilic dendritic dipeptides that self-assemble in solution and in bulk through a complex recognition process into helical pores. We find that the molecular recognition and self-assembly process is sufficiently robust to tolerate a range of modifications to the amphiphile structure, while preliminary proton transport measurements establish that the pores are functional. We expect that this class of self-assembling dendrimers will allow the design of a variety of biologically inspired systems with functional properties arising from their porous structure.     

Recent development of peptide self-assembly

Amino acids are the building blocks to build peptides and proteins. Recent development in peptide synthesis has however enabled us to mimic this natural process by preparing various long and short peptides possessing different conformations and biological functions. The self-assembly of short designed peptides into molecular nanostructures is becoming a growing interest in nanobiotechnology. Self-assembled peptides exhibit several attractive features for applications in tissue regeneration, drug delivery, biological surface engineering as well as in food science, cosmetic industry and antibiotics. The aim of this review is to introduce the readers to a number of representative studies on peptide self-assembly.     

Recent development of peptide self-assembly

Amino acids are the building blocks to build peptides and proteins. Recent development in peptide synthesis has however enabled us to mimic this natural process by preparing various long and short peptides possessing different conformations and biological functions. The self-assembly of short designed peptides into molecular nanostructures is becoming a growing interest in nanobiotechnology. Self- assembled peptides exhibit several attractive features for applications in tissue regeneration, drug delivery, biological surface engineering as well as in food science, cosmetic industry and antibiotics. The aim of this review is to introduce the readers to a number of representative studies on peptide self-assembly.     

A metal complex that binds alpha-amino acids with high and predictable stereospecificity.

Molecular recognition is the key step in a wide range of controlled separation and chemical transformation processes, with enzymes performing this task with an unsurpassed degree of selectivity. Enzymes contain only 20 simple amino acids, yet it remains difficult to rationalize or even predict these stereospecific recognition events. Nonetheless, the rational design of receptors able to recognize amino acids stereospecifically is attracting considerable interest because therapeutic drugs, that may be developed from chiral amino acid intermediates, are increasingly required in enantiomerically pure form. Early work has stimulated the development of efficient receptors based on small molecules, but binding of amino acids with high and predictable stereospecificity remains difficult to achieve. Directed molecular evolution, on the other hand, does select for RNA sequences or antibodies that bind amino acids with high specificity, but typically without providing insights into the molecular recognition mechanisms involved. Here we show that a rationally designed metal complex formed from a trivalent cobalt ion and a tetradentate ligand binds natural amino acids, including the simple yet challenging amino acid alanine, with high and predictable regio- and stereospecificity. We expect that our approach will allow the binding as well as separation and stereospecific catalytic formation of its target amino acids.     

RNA-guided genetic silencing systems in bacteria and archaea

Clustered regularly interspaced short palindromic repeat (CRISPR) are essential components of nucleic-acid-based adaptive immune systems that are widespread in bacteria and archaea. Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids, including viruses and plasmids. However, the mechanism of RNA-based bacterial immunity is distinct from RNAi. Understanding how small RNAs are used to find and destroy foreign nucleic acids will provide new insights into the diverse mechanisms of RNA-controlled genetic silencing systems.     

Structure of recombinant human rheumatoid arthritic synovial fluid phospholipase A2 at 2.2 A resolution

Phospholipases A2 (PLA2s) may be grouped into distinct families of proteins that catalyse the hydrolysis of the 2-acyl bond of phospholipids and perform a variety of biological functions. The best characterized are the small (relative molecular mass approximately 14,000) calcium-dependent, secretory enzymes of diverse origin, such as pancreatic and venom PLA2s. The structures and functions of several PLA2s are known. Recently, high-resolution crystal structures of complexes of secretory PLA2s with phosphonate phospholipid analogues have provided information about the detailed stereochemistry of transition-state binding, confirming the proposed catalytic mechanism of esterolysis. By contrast, studies on mammalian nonpancreatic secretory PLA2s (s-PLA2s) have only recently begun; s-PLA2s are scarce in normal cells and tissues but large amounts are found in association with local and systemic inflammatory processes and tissue injury in animals and man. Such s-PLAs have been purified from rabbit and rat inflammatory exudate, from synovial fluid from patients with rheumatoid arthritis and from human platelets. Cloning and sequencing shows that the primary structure of the human s-PLA2 has about 37% homology with that of bovine pancreatic PLA2 and 44% homology with that of Crotalus atrox PLA2. The human s-PLA2 is an unusually basic protein, yet contains most of the highly conserved amino-acid residues and sequences characteristic of the PLA2s sequenced so far. Here we report the refined, three-dimensional crystal structure at 2.2 A resolution of recombinant human rheumatoid arthritic synovial fluid PLA2. This may aid the development of potent and specific inhibitors of this enzyme using structure-based design.     

甜菊钙调蛋白基因的克隆及结构分析

钙调蛋白（Calmodulin）是生物细胞内一种重要的调控蛋白，通过其与靶酶的相互作用控制细胞正常的生长发育及细胞对外界环境变化的反应，我们从甜菊顶芽和花芽中提取总RNA，逆转录合成cDNA第一链，以此为模板，参考GenBank上已发表植物的钙调蛋白基因序列合成5′端和3′端引物，利用多聚酶链式反应（PCR）扩增并克隆得到了甜菊钙调蛋白基因的两个异型基因，序列分析表明，它们均由450个核苷酸组成，编码148个氨基酸，在核苷酸序列上与迄今已知的多种植物钙调蛋白均有很高的同源性，同源率在83％以上，编码的氨基酸序列同源性更同，同源率高达95％以上，这两个基因之间存在差异，其核苷酸序列同源率为85％，编码区的氨基酸序列的同源率为99％，仅在第122个氨基酸由ALA代替了VAL。     

天人菊matK基因克隆及生物信息学分析

为了完善天人菊的遗传信息,丰富菊科植物分子生物学分析数据.通过PCR扩增、基因克隆获得天人菊matK基因的完整核苷酸序列,采用生物信息学方法分析天人菊matK蛋白的结构及性质,并与其他12种matK氨基酸序列进行对比,构建系统进化树.结果表明,天人菊matK基因全长1296 bp,可编码432个氨基酸,二级结构以α-螺...     

植物类黄酮的生理功能与抗菌机制

类黄酮是植物产生于不同部位的一大类次生代谢小分子,在植物各器官履行多种生理功能;对人类健康有广泛的药理和有益作用,包括抗氧化活性、自由基清除能力、预防冠心病、抗动脉粥样硬化、保肝、抗炎和抗癌活性,已获得医药及保健业的高度关注;研究表明:类黄酮还能通过破坏细菌细胞膜、抑制细菌脂肪酸、粘肽层、核酸与电子传递链和ATP合成、抑制细菌金属酶活性等,发挥抗菌抑菌作用;在细胞水平上可阻止细菌粘附到宿主受体,抑制细菌生物膜形成,不仅选择性地针对细菌细胞,也抑制毒性因子以及其他形式的微生物威胁;一些植物类黄酮能明显逆转抗生素的抗药性,提高其药效;开发和应用类黄酮药物,对抗生素耐药感染可能是一有前途的方法。     

生物大分子的分子动力学模拟过程在百万亿次集群上的部署优化

分子动力学模拟作为研究生物大分子功能和性质的新工具,已广泛应用于蛋白质和核酸等物质的分子动态学行为研究,但目前常规分子动力学模拟时间尺度较小,不能达到生物大分子分子动态行为的有效取样范围。温度副本交换分子动力学可同时运行多个独立模拟,明显提高模拟时间的可及尺度,但需要千核以至万核的计算资源,目前已发表的相关文献其模拟体系使用的计算资源均较小。本文利用国家超算济南中心的神威4000A百万亿次集群,首先进行单副本的分子动力学模拟,然后利用外切纤维素酶催化结构域的模拟体系(约5万原子)进行多达128个温度副本的分子动力学模拟,一次模拟任务最多成功利用6 720个CPU核心同时进行计算,最高总运算速度累计达到2 274 ns/d,这为分子动力学模拟利用上万核心进行计算提供了新的思路。     

Asymmetric spiroacetalization catalysed by confined Brønsted acids

Acetals are molecular substructures that contain two oxygen-carbon single bonds at the same carbon atom, and are used in cells to construct carbohydrates and numerous other molecules. A distinctive subgroup are spiroacetals, acetals joining two rings, which occur in a broad range of biologically active compounds, including small insect pheromones and more complex macrocycles. Despite numerous methods for the catalytic asymmetric formation of other commonly occurring stereocentres, there are few approaches that exclusively target the chiral acetal centre and none for spiroacetals. Here we report the design and synthesis of confined Br?nsted acids based on a C(2)-symmetric imidodiphosphoric acid motif, enabling a catalytic enantioselective spiroacetalization reaction. These rationally constructed Br?nsted acids possess an extremely sterically demanding chiral microenvironment, with a single catalytically relevant and geometrically constrained bifunctional active site. Our catalyst design is expected to be of broad utility in catalytic asymmetric reactions involving small and structurally or functionally unbiased substrates.     

Pathway complexity in supramolecular polymerization

Self-assembly provides an attractive route to functional organic materials, with properties and hence performance depending sensitively on the organization of the molecular building blocks. Molecular organization is a direct consequence of the pathways involved in the supramolecular assembly process, which is more amenable to detailed study when using one-dimensional systems. In the case of protein fibrils, formation and growth have been attributed to complex aggregation pathways that go beyond traditional concepts of homogeneous and secondary nucleation events. The self-assembly of synthetic supramolecular polymers has also been studied and even modulated, but our quantitative understanding of the processes involved remains limited. Here we report time-resolved observations of the formation of supramolecular polymers from π-conjugated oligomers. Our kinetic experiments show the presence of a kinetically favoured metastable assembly that forms quickly but then transforms into the thermodynamically favoured form. Quantitative insight into the kinetic experiments was obtained from kinetic model calculations, which revealed two parallel and competing pathways leading to assemblies with opposite helicity. These insights prompt us to use a chiral tartaric acid as an auxiliary to change the thermodynamic preference of the assembly process. We find that we can force aggregation completely down the kinetically favoured pathway so that, on removal of the auxiliary, we obtain only metastable assemblies.     

杂交型DNA电化学生物传感器研究进展

杂交型DNA电化学生物传感器是一类利用核酸互补配对杂交原理检测和分析特定DNA序列的电化学生物传感器.由于其具有快速简便、选择性好、灵敏度高等优点,在临床医学、遗传工程、环境检测、食品安全监测和生物科学等领域有着重要的应用价值.简述了杂交型DNA电化学生物传感器的一般原理,对共价键结合法、自组装法、生物素-亲和素法、电聚合法以及吸附法等单链DNA的固定方法和DNA杂交信号的直接和间接电化学转换机制的近期研究进展进行了深入探讨,并对其在医疗检测和转基因植物检测等基因检测方面的最新应用和发展趋势进行了论述.     

Homology between phosphotyrosine acceptor site of human c-abl and viral oncogene products

The human homologues of several independent viral oncogenes, each of which encodes tyrosine-specific protein kinases, have been identified. Of these, three (v-src, v-yes and v-fes/fps) are known to exhibit considerable sequence homology, particularly in the regions of their phosphorylation acceptor sites. In the present study, sequences encoding the tyrosine phosphorylation acceptor sites of the Abelson murine leukaemia virus oncogene, v-abl, and its human cellular homologue, c-abl, have been identified and their nucleic acid sequences determined. Our results establish extensive homology between this region of c-abl and acceptor domains of the v-src, v-yes and v-fes/fps family of viral oncogenes, as well as more distant relatedness to the catalytic chain of the mammalian cyclic AMP-dependent protein kinase. These findings suggest that, of the homologues of retroviral oncogenes with tyrosine protein kinase activity examined to date, all were probably derived from a common progenitor and may represent members of a diverse family of cellular protein kinases.     

Transposition of hAT elements links transposable elements and V(D)J recombination

Transposons are DNA sequences that encode functions that promote their movement to new locations in the genome. If unregulated, such movement could potentially insert additional DNA into genes, thereby disrupting gene expression and compromising an organism's viability. Transposable elements are classified by their transposition mechanisms and by the transposases that mediate their movement. The mechanism of movement of the eukaryotic hAT superfamily elements was previously unknown, but the divergent sequence of hAT transposases from other elements suggested that these elements might use a distinct mechanism. Here we have analysed transposition of the insect hAT element Hermes in vitro. Like other transposons, Hermes excises from DNA via double-strand breaks between the donor-site DNA and the transposon ends, and the newly exposed transposon ends join to the target DNA. Interestingly, the ends of the donor double-strand breaks form hairpin intermediates, as observed during V(D)J recombination, the process which underlies the combinatorial formation of antigen receptor genes. Significant similarities exist in the catalytic amino acids of Hermes transposase, the V(D)J recombinase RAG, and retroviral integrase superfamily transposases, thereby linking the movement of transposable elements and V(D)J recombination.     

金属-有机分子笼催化剂的近期研究进展

酶因在催化过程中展现出特异的选择性和活性而备受关注.在配位自组装过程中,通过调节金属结点的种类和有机配体结构,金属-有机分子笼（MOCs）的空腔可获得多种作用力协同的特殊环境.近年来,对于超分子反应器的研究显示,其空腔结构类似于生物酶,能在催化过程中展现出非常高的反应速率、空间和立体选择性,这一特性引起了科学家们的研究兴趣.文章就近两年MOCs在催化方面的应用研究进展进行了综述.     

胞嘧啶脱氨基酶APOBEC1研究进展

为全面理解载脂蛋白B mRNA(ApoB mRNA)编辑酶催化多肽-1(APOBEC1)的作用机制,介绍了APOBEC1和ApoB mRNA的蛋白及核酸序列,总结并绘制了APOBEC1与不同的辅助蛋白的结合模型,阐述了APOBEC1催化ApoB mRNA第6 666位的胞嘧啶(C_(6666))脱氨基化分子机制.列举了啮齿动物APOBEC1抑制多种逆转录病毒的研究报道,介绍了兔源APOBEC1结合人类免疫缺陷病毒1(HIV-1)的病毒粒子并编辑病毒基因组的机理.同时介绍了APOBEC1通过编辑胞嘧啶或与AU富集元件(ARE)结合来调控癌症等疾病相关的细胞因子表达.