甘蓝型油菜过氧化物酶的生物信息学分析

目的 分析甘蓝型油菜的过氧化物酶(Peroxiredoxin, PRDX)家族成员的生物学信息，以期为油菜及相近植物中PRDX的酶学特征及植物抗氧化的分子机制研究提供依据.方法 利用生物信息学方法，分析NCBI(National Center for biotechnology information)数据库中注册的7种油菜PRDX蛋白质的理化性质、信号肽、磷酸化位点、糖基化位点、蛋白质二级结构、三级结构及系统进化特点.结果 甘蓝型油菜PRDX蛋白质比较稳定；氨基酸序列中无信号肽，且不是分泌蛋白；该家族蛋白质中存在较多潜在糖基化位点和磷酸化位点；蛋白质二级结构、三级结构预测结果显示其结构具有极大相似性，且主要以α-螺旋和无规则卷曲为主；系统进化树将该家族成员分为了两个亚家族.结论 本研究为进一步探索植物PRDX家族的生物学功能提供了参考依据.     

大麦黄花叶病毒抗性突破株系的分子变异

通过大麦黄花叶病毒(BaYMV)抗性突破株系的核酸RNA1全序列分析并与野生株系比较表明.抗性突破株系在病毒复制酶或转运蛋白区域(6K2)和核酸RNA复制酶区域(NIb)存在二个变异位点.在这二个位点上抗性突破株系核酸分子编码的氨基酸分别为脯氨酸(Pro)和苏氨酸(Fhr),而野生株系分别为缬氨酸(Val)和丙氨酸(Ala).对该两种酶蛋白质二级结构分析显示,氨基酸的变异可能导致了蛋白质的结构、功能与性质的改变,并且此种变异与抗BaYMV冬大麦中抗性基因ym4的功能丧失有关,同时也说明了大麦品种田间致病性的差异与病毒核酸分子中的点突变关系密切.     

大麦黄花叶病毒抗性突破株系的分子变异

通过大麦黄花叶病毒 (Ba YMV)抗性突破株系的核酸 RNA1全序列分析并与野生株系比较表明 ,抗性突破株系在病毒复制酶或转运蛋白区域 (6K2 )和核酸 RNA复制酶区域 (NIb)存在二个变异位点 .在这二个位点上抗性突破株系核酸分子编码的氨基酸分别为脯氨酸 (Pro)和苏氨酸 (Thr) ,而野生株系分别为缬氨酸(Val)和丙氨酸 (Ala) .对该两种酶蛋白质二级结构分析显示 ,氨基酸的变异可能导致了蛋白质的结构、功能与性质的改变 ,并且此种变异与抗 Ba YMV冬大麦中抗性基因 ym4的功能丧失有关 ,同时也说明了大麦品种田间致病性的差异与病毒核酸分子中的点突变关系密切 .     

人SEPT9蛋白同源建模和活性位点分析

利用生物信息学在线软件预测了人SETP 9蛋白质的二级结构和模体信息,同时对其三级结构进行同源建模和模建结果质量评价,其次预测了该蛋白质的活性位点信息,旨在从蛋白质序列特征和分子结构水平理解其在人类生理病理过程中的作用.结果表明,模建的SEPT 9蛋白结构品质较高,具有7段α-螺旋和2组β-折叠结构,是一个典型的α/β类蛋白,表面呈弱正电势分布;人SEPT 9蛋白具有8个不同模体,可能参与不同生化反应或执行不同的功能.搜寻获得了人SEPT 9蛋白配基结合位点有10个,其中位点1可能是该蛋白的活性位点.这些研究结果对理解人SEPT 9蛋白功能以及配基结合位点定位非常重要,也为针对SEPT 9蛋白的分子对接和药物从头设计提供了理论基础.     

通过构建蛋白质结构域功能模版库做基于氨基酸序列的蛋白质功能位点预测(英文)

由蛋白质序列预测蛋白质功能位点对于理解蛋白质功能具有重大的意义,它同时也为生物学实验提供了重要依据.长期以来,基于知识库的方法一直是预测蛋白质功能位点的可靠方法.通过适当修改蛋白质结构分类库SCOP构建了一个附带功能注释的结构域模版库(fDPD),其中每个模版都包含一组序列和结构都非常相近的已知的蛋白质成员.fDPD通过隐马尔可夫模型方法HMMER由未知蛋白质的序列预测其功能位点.为了考察本方法的效果我们检测了两个通用的酶催化位点数据库,一个由约1 500个序列构成的钙离子结合蛋白数据库和从CASP9中提取出的数条蛋白质序列.我们的方法对于配体结合位点以及钙结合位点的预测取得了较高的精度和覆盖率,其催化位点的预测效果仅次于目前已知的最好的方法.我们的计算结果表明,结构上相似的蛋白质其功能位点倾向于出现在蛋白质表面上相似的位置.     

计算变异学创立背景及其用途

为了克服生物信息学和计算生物学中字母或数字不受序列长度、氨基酸组成和位置、相邻氨基酸影响的缺陷,根据自然界普遍存在的随机性原理,创立计算变异学。计算变异学用氨基酸对可预测性、氨基酸分布概率和变异概率3种方法量化整个蛋白质及每个氨基酸,用活的、动态的测量指标量化分析蛋白质。计算变异学方法可以应用于研究蛋白质进化、遗传病定量诊断,分析蛋白质结构与功能、药物设计和病毒变异预测等领域。     

马铃薯GDP-L-半乳糖磷酸化酶类1基因的生物信息学初步分析

本文根据马铃薯GDP-L-半乳糖磷酸化酶类1基因的EST序列,运用多种生物信息学方法,对其进行初步的生物信息学分析.电子克隆获得了该基因的全长,结果表明:该序列全长1 742 bp,共编码357个氨基酸,有多个限制性酶切位点,有多个磷酸化位点,属于亲水性氨基酸,无信号肽,有膜穿透性.通过蛋白质二级结构功能域的预测,发现该序列中含有11个功能位点.通过蛋白质同源序列比对,发现该基因与番茄GDP-L-半乳糖磷酸化酶基因相似度极高,暗示该基因与番茄GDP-L-半乳糖磷酸化酶基因具有相似的生物学功能.以上结果可以为进一步研究该基因在马铃薯中特别是在抗青枯病分子育种中的功能提供相关依据.     

梅花鹿骨形态发生蛋白BMP4基因的克隆与序列分析

通过提取梅花鹿肝脏总RNA以及采用RT-PCR技术,成功克隆梅花鹿骨形态发生蛋白BMP4基因序列,并对其核酸序列、蛋白质序列,功能保守区、亲疏水性进行生物信息学分析,同时构建序列进化树以及部分结构的三维模型.该序列已提交Genbank(索取号:HQ877675).该研究可为日后通过基因工程手段表达重组梅花鹿BMP蛋白并探究其药理作用提供基础.     

实用生物信息科学

本书为《核酸和分子生物学》丛书的第15卷，至今这是唯一一本沟通生物信息学家和分子生物学家，即沟通生物数据分析计算法的开发者和使用者的一本书，本书从蛋白质序列的研究和预测结构的计算法开始，直接利用实验室获得的数据改进功能预测的方法，包括一系列在实验研究中，应用不同类型的生物信息科学法。     

马鹿mtDNA Cyt b基因的生物信息学分析

基于NCBI数据库获取马鹿（Cervus elaphus）Cyt b基因序列，应用生物信息学方法对马鹿Cyt b基因编码的蛋白质进行理化性质、结构和相关功能的预测分析，了解马鹿mtDNA Cyt b基因的结构、功能和表达特性.结果表明：马鹿Cyt b编码的蛋白质为疏水性蛋白质，推测相互作用的蛋白质包括LOC100524873,UQCRC1,UQCRQ,ND1,MT-ND2,COX1,COX2,COX3,ND4H和CYC，功能与电子运输、耦合质子运输以及泛醌-细胞色素c还原酶活性有关；二级结构主要为无规则卷曲，有2个潜在的N-糖基化位点和34个磷酸化位点，9个跨膜螺旋结构域，定位于内质网和细胞质膜；马鹿与梅花鹿（Cervus nippon）的亲缘关系较近.这对于马鹿种质鉴定分子标记的筛选及其与梅花鹿的渐渗杂交具有理论意义.     

The molecular evolution of genes and proteins: a tale of two serines

The advent of techniques for cloning and rapidly sequencing DNA has produced an explosive increase of sequence information for nucleic acids and their inferred proteins. Careful study of this large store of data might give us new insights into the relations between the linear sequences of genes and their functions embodied in the three-dimensional structure of proteins, and also illuminate the origin and evolution of the structural complexity of present-day proteins. Here I argue from such a study that the active site sequences of enzymes that have analogous essential serine residues lie in fact on two lines of descent from an ancient ancestral enzyme which had a cysteine instead of serine in its active site. This is based on the assumption that the two codon types which define the separate lines of descent and which have different bases in two positions could not interconvert by single mutations.     

适用于空间环境的核酸杂交芯片技术研究

核酸杂交芯片是一种目前已经被广泛应用的核酸分析技术手段.在空间微重力条件下,利用小型化低功耗的检测设备,实现核酸杂交芯片功能,获得准确可信的核酸杂交检测结果,是一项非常具有挑战性的课题.本文对核酸杂交芯片在空间条件下的应用方法进行了探索,采用新型核酸杂交芯片结构、改变核酸杂交芯片反应条件、串联核酸PCR芯片系统等手段,开发出一套小型化低功耗的空间核酸杂交分析芯片,芯片系统整体功耗小于25 W,实现了对目标核酸序列的快速检测(检测周期90 min),并初步实现与空间聚合酶链式反应(PCR)等技术的联合应用,提高了核酸杂交芯片检测技术的检测灵敏度.     

Functional proteins from a random-sequence library

Functional primordial proteins presumably originated from random sequences, but it is not known how frequently functional, or even folded, proteins occur in collections of random sequences. Here we have used in vitro selection of messenger RNA displayed proteins, in which each protein is covalently linked through its carboxy terminus to the 3' end of its encoding mRNA, to sample a large number of distinct random sequences. Starting from a library of 6 x 1012 proteins each containing 80 contiguous random amino acids, we selected functional proteins by enriching for those that bind to ATP. This selection yielded four new ATP-binding proteins that appear to be unrelated to each other or to anything found in the current databases of biological proteins. The frequency of occurrence of functional proteins in random-sequence libraries appears to be similar to that observed for equivalent RNA libraries.     

鸭梨授粉前后子房核酸和蛋白质代谢的变化

本文以微量分析法对鸭梨授粉前后子房中核酸、蛋白质、核酸降解酶、蛋白水解酶的动态进行了测定分析。结果显示，花后８日内经授粉的子房中的ＤＮＡ、ＲＮＡ含量、蛋白质含量明显高于未授粉子房；核酸降解酶、水解蛋白酶的活性显著增强。表明授粉、受精作用引起子房中核酸，慢白质的旺盛合成，以及活跃的转录，翻译过程。     

两种快速的密码子检索方法

许多生物信息学软件涉及将核苷酸序列翻译成对应的氨基酸序列的操作.密码子检索表的结构及检索算法强烈地影响蛋白质翻译的速度.本文提出了2种快速的密码子检索方法.一是平均检索长度约为7,最大检索长度为9的分块检索;二是没有空间冗余和地址冲突的哈希表检索,其平均检索长度和最大检索长度均为3.对几种密码子检索方法的检索效率进行比较,结果表明哈希表的检索速度最快.     

A ribozyme that lacks cytidine

The RNA-world hypothesis proposes that, before the advent of DNA and protein, life was based on RNA, with RNA serving as both the repository of genetic information and the chief agent of catalytic function. An argument against an RNA world is that the components of RNA lack the chemical diversity necessary to sustain life. Unlike proteins, which contain 20 different amino-acid subunits, nucleic acids are composed of only four subunits which have very similar chemical properties. Yet RNA is capable of a broad range of catalytic functions. Here we show that even three nucleic-acid subunits are sufficient to provide a substantial increase in the catalytic rate. Starting from a molecule that contained roughly equal proportions of all four nucleosides, we used in vitro evolution to obtain an RNA ligase ribozyme that lacks cytidine. This ribozyme folds into a defined structure and has a catalytic rate that is about 10(5)-fold faster than the uncatalysed rate of template-directed RNA ligation.     

Programming biomolecular self-assembly pathways

In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a 'reaction graph' abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular 'tree', and autonomous locomotion of a bipedal walker.     

High resolution structure of the RNA duplex [U(U-A)6A]2

RNA is involved in many biological functions, ranging from information storage and transfer to the catalysis of reactions involving both nucleic acids and proteins. Previous crystallographic studies on RNA oligomeric chains provide only averaged structures or information limited in resolution. The oligomer [U(U-A)6A]2 was chosen for the study of protein-RNA interactions in viruses. Its size and base composition mimic portions of the genomic RNA in alfalfa mosaic virus that bind to the amino terminus of the viral subunit. The actual sequence was designed to guarantee the formation of a single species of duplex and to facilitate the production of the pure oligomer in large quantities. The molecular structure, derived from the 2.25 A resolution X-ray diffraction data, allows the most detailed analysis of an A-RNA helix reported to date. Two kinks are observed that divide the duplex into three blocks, each close to a canonical A-helical conformation. A few intermolecular hydrogen bonds involving 2'-hydroxyl groups stabilize this peculiar conformation of the RNA, which may be related to the temperature used for the crystallization (35 degrees C). The structure demonstrates both the plasticity of the RNA molecule and the role of the 2'-hydroxyl groups in intermolecular interactions.     

粉尘螨Der f4基因的克隆和蛋白分子特征分析

从深圳地区采集粉尘螨纯培养,提取总RNA,根据香港中文大学合成的尘螨基因序列并设计的引物,RT-PCR扩增出Der f4基因,克隆到pUC57载体后测序和进行生物信息学分析.将该目的基因克隆到pET-28a表达载体上得到重组质粒pET-28a-Der f4.用生物软件分析尘螨变应原Der f4序列. RT-PCR获得目的基因Der f4 cDNA全长为1593 bp.推测编码蛋白由526个氨基酸组成,生物信息学分析表明,Der f4具有多种磷酸化位点,含有信号肽,为疏水性蛋白,包含淀粉酶抑制剂功能结构域.获得Der f4基因全长,其编码的细胞外疏水性蛋白可能具有淀粉酶抑制剂活性.