一种新的蛋白质结构编码方法及其应用

基于四肽构象的可视化聚类的结果,提出了一种新的编码方法,由此可将蛋白质三维构象空间映射到一维编码空间,将蛋白质三维结构空间中的模式搜索和模式发现问题转化为一维编码空间中的相应问题。通过两个算法从模式检索以及模式发现两方面验证了编码的有效性;同时利用熵的概念探讨了序列、结构之间的相关度,得到了一些重要的序列．结构模式．实验结果表明,该编码方法能更加准确地反映四肽构象空间中的分布情况,其结果可解释性更强．     

Nat Biotechnol:科学家成功绘制出单细胞中短链RNA分子的图谱

正近日,刊登在国际杂志Nature Biotechnology上的一项研究报告中,来自瑞典卡罗琳学院的研究人员通过研究成功在单个胚胎干细胞中测定了短链非编码RNA序列的绝对数量。当基因中的信息被使用时,比如当其编码蛋白质时,首先DNA会转录成为信使RNA来作为蛋白质制造的范本,我们的机体细胞中包含有大量的短链非编码RNA序列,这些序列并不能制造蛋白质,而     

DNA序列信息的一种新的测度

根据信息理论给出了测度ＤＮＡ序列信息的一种新的方法,获得ＤＮＡ序列４个层次的信息量测度：Ｉｂ,Ｉｆ（１）,Ｉｆ（２）ａｎｄＩｆ（３）,这４种信息测度可分别用来测度ＤＮＡ的碱基序列、密码子序列、编码蛋白质序列和功能蛋白质序列的信息量。从Ｍ．ｅｄｕｌｉｓ的线粒体基因组中两个较短的编码蛋白质的ＤＮＡ序列和使用具有不同倍性的间并密码子组组成的模拟ＤＮＡ序列中所获得计算结果表明,这些信息测度确实能用来揭示所     

非编码DNA序列的功能及其鉴定

非编码DNA序列是指基因组中不编码蛋白质的DNA序列。这些序列可以结合调节因子、转录为功能性RNA、单独或协同地调节生理活动和病理过程。文章围绕基因表达调控作用, 总结了近几年非编码DNA序列的研究成果, 对其结构、功能和可能的作用机制进行了初步阐述, 介绍了目前鉴定非编码DNA序列中功能元件的计算方法和实验技术, 并对非编码DNA未来的研究进行了展望。     

细胞核的功能

真核细胞的显著特点之一是具有膜包裹着的细胞核,其主要功能是将基因的转录和信使核糖核酸指导合成蛋白质这2个过程在空间上分隔开。最初为蛋白质编码的RNA序列可能是被不为蛋白质编码的RNA序列所隔断的,这些非编码区后来成为DNA分子中基因里的内含子。原核细胞为了节省资源,已基本清除了基因中的内含子。而真核细胞则利用内含子,用同一个基因合成多种蛋白质,这就需要细胞核阻止含有内含子的m RNA与合成蛋白质的核糖体接触。     

基于统计CPG岛的基因预测方法

随着以功能基因组学和蛋白质组学为主要研究内容的后基因组时代的来临,人们面对着生物信息的数据呈指数增长,如何通过有效的计算方法由核酸和蛋白质的序列推导出它们的结构和功能,特别是识别DNA序列中编码蛋白质的基因预测问题是迫切需要解决的研究课题之一.本文在CpG岛对研究基因编码的特殊生物意义下,通过三种方法确定CpG岛的位置,并在此基础上,结合一种新的DNA序列字母向量,利用信息熵离散量预测基因序列,提高了识别基因编码的效率,而且计算的时间有显著的减少.     

美洲大蠊新基因Parcxpwxxq01的分析及功能预测

为进一步研究已发现的美洲大蠊新基因Parcxpwxxq01,我们采用BLASTp,ORF Finder,ProtScale,ScanProsite和Tmpred Server等软件或数据库进行相似性比较、开放读码框预测和编码蛋白质的功能等生物信息学方法对该序列进行特征分析和功能预测,以获得该基因及其编码的蛋白质的更多功能提示。结果发现得到的Parcxpwxxq01序列是该基因的全长序列,该基因编码的蛋白质是一碱性跨膜蛋白,该蛋白质可能为美洲大蠊的药用有效成分,有进一步研究的价值。     

非编码保守DNA序列形成与演化机制

作为一种系统进化足迹,基因组非编码保守DNA序列受到极大关注。由于非编码保守DNA序列很可能与转录因子或特异蛋白质相互作用,直接参与调控基因表达或稳定染色体结构等重要的生命活动。因此,它极有可能成为基因组研究的下一个新浪潮。在总结对生物非编码保守DNA序列的认识过程的基础上,详细阐述了非编码保守DNA序列形成与演化的模型及其分子生物学机制,进一步展望了非编码保守DNA序列在生物学研究中的应用前景。     

基于分组重量编码的蛋白质功能预测

从蛋白质序列出发,采用分组重量编码(Encoding Based on Grouped Weight,简记EBGW),并结合最近邻居算法对蛋白质功能进行预测。对酵母(Saccharomyces cerevisiae)蛋白质的1826条序列进行预测,整体预测准确率与其他基于序列信息的蛋白质功能预测方法相当。实验结果表明基于EBGW编码方案的新方法可有效地应用于蛋白质功能预测。     

鲑鱼泌乳素cDNA的分子克隆和序列分析

从太平洋切奴克鲑鱼的垂体制备cDNA文库。按照鲑鱼泌乳素的部分蛋白质序列所提供的信息合成寡聚脱氧核苷酸探针。用探针筛查泌乳素基因,识别出一个阳性克隆PRL-10。该克隆的硷基序列已被测出。PRL-10的总长为1.1kb,编码了含有211个氨基酸组成的泌乳素前体,其中包括了编码23个氨基酸的信号肽序列和编码188个氨基酸的成熟泌乳素序列。     

长角血蜱卵泡抑素相关蛋白的定性

参照GenBank中长角血蜱致病性Okayama株卵泡抑素基因的核苷酸序列(GenBank Accession No.DQ248886)设计合成一对引物,从本实验室保藏的单克隆洁净长角血蜱饥饿成蜱中快速提取总RNA,通过RT-PCR扩增出814bp的卵泡抑素基因,序列比对结果显示:与长角血蜱致病性Okayama株的核苷酸序列及氨基酸序列一致性分别为97.8%和99%,将其亚克隆到表达载体pGEX-4T-1中进行表达,GST融合重组蛋白预期分子量为57kD。表达重组蛋白经MagneGSTTM蛋白纯化系统纯化后作为抗原分别与抗不同发育阶段长角血蜱(卵、幼蜱、若蜱、成蜱)多克隆抗体作为一抗进行免疫印迹,结果表明:与长角血蜱卵制备的多克隆抗体有很强的免疫反应,而与其他发育阶段(幼蜱、若蜱、成蜱)饥饿长角血蜱制备的多克隆抗体反应性很弱。以上结果表明:长角血蜱卵泡抑素蛋白在长角血蜱产卵及卵成熟发育时期的表达水平较其他发育阶段(幼蜱、若蜱、成蜱)的蛋白表达水平高。     

Structure of the murine anion exchange protein

A full-length clone encoding the mouse erythrocyte anion exchange protein, band 3, has been isolated from a cDNA library using an antibody against the mature erythrocyte protein. The complete nucleotide sequence has been determined. Substantial homology is evident between the deduced murine amino acid sequence and published sequences of fragments of human band 3 protein. The amino-terminal 420 and the carboxy-terminal 32 residues constitute polar, soluble domains, while the intervening 475 amino acids are likely to be intimately associated with the lipid bilayer. Hydrophobic analysis of this sequence, together with structural studies on the human protein, suggests the possibility of at least 12 membrane spans, predicting that both the amino- and carboxy-termini are intracellular.     

The S-layer protein from Campylobacter rectus: sequence determination and function of the recombinant protein

The gene encoding the crystalline surface layer (S-layer) protein from Campylobacter rectus , designated slp , was sequenced and the recombinant gene product was expressed in Escherichia coli . The gene consisted of 4086 nucleotides encoding a protein with 1361 amino acids. The N-terminal amino acid sequence revealed that Slp did not contain a signal sequence, but that the initial methionine residue was processed. The deduced amino acid sequence displayed some common characteristic features of S-layer proteins previously reported. A homology search showed a high similarity to the Campylobacter fetus S-layer proteins, especially in their N-terminus. The C-terminal third of Slp exhibited homology with the RTX toxins from Gram-negative bacteria via the region including the glycine-rich repeats. The Slp protein had the same N-terminal sequence as a 104-kDa cytotoxin isolated from the culture supernatants of C. rectus . However, neither native nor recombinant Slp showed cytotoxicity against HL-60 cells or human peripheral white blood cells. These data support the idea that the N-terminus acts as an anchor to the cell surface components and that the C-terminus is involved in the assembly and/or transport of the protein.     

Structure and evolutionary origin of the gene encoding mouse NF-M, the middle-molecular-mass neurofilament protein

We describe the complete sequence of the gene encoding mouse NF-M, the middle-molecular-mass neurofilament protein. The coding sequence is interrupted by two intervening sequences which align perfectly with the first two intervening sequences in the gene encoding NF-L (the low-molecular-mass neurofilament protein); there is no intron in the gene encoding NF-M corresponding to the third intron in NF-L. Therefore, both the number of introns and their arrangement in the genes coding NF-L and NF-M contrast sharply with the number and arrangement of introns in the genes of known sequence, encoding other members of the intermediate filament multigene family (desmin, vimentin, glial fibrillary acidic protein and the acidic and basic keratins); with the exception of a single truncated keratin gene that lacks an encoded tailpiece, these genes all contain eight introns, of which at least six are placed at homologous locations. Assuming the existence of a primordial intermediate filament gene containing most (if not all) the introns found in contemporary non-neurofilament intermediate filament genes, it seems likely that an RNA-mediated transposition event was involved in the generation of an ancestral gene encoding the NF polypeptides. A combination of insertional transposition and gene-duplication events could then explain the anomalous number and placement of introns within these genes. Consistent with this notion, we show that the genes encoding NF-M and NF-L are linked.     

cDNA and deduced primary structure of rat protein B23, a nucleolar protein containing highly conserved sequences

Protein B23 (Mr/pI = 38,000/5.1) is a major RNA-associated nucleolar phosphoprotein which contains highly acidic segments and has a high affinity for silver ions. Using synthetic oligonucleotides as probes cloned cDNAs encoding protein B23 were isolated and characterized. One of the cDNAs, obtained from a rat brain library, contained an insert of 1232 base pairs of DNA encoding a polypeptide of 292 amino acid residues. Segments of the protein sequence were confirmed by partial sequencing of CNBr fragments from rat hepatoma protein B23. The protein contains a methionine-rich amino-terminal sequence and two highly acidic segments in the center of the sequence. The first acidic segment, in which 11 of the 13 residues are acidic, begins at residue 120 and contains a major phosphorylation site. In the second segment (residues 159-187) there are four copies of the sequence Asp-Asp-Glu, and all but two of the 29 residues have acidic side chains. When the sequence of the rat protein was compared with available sequences from other species a high degree of conservation was found; the 77-residue carboxyl-terminal sequence is identical with that of human protein B23 (Chan, P. K., Chan, W.-Y., Yung, B. Y. M., Cook, R. G., Aldrich, M. B., Ku, D., Goldknopf, I. L., and Busch, H. (1986) J. Biol. Chem. 261, 14335-24341), and about 63% of the residues are identical when the rat B23 sequence is compared with protein N038 from Xenopus laevis (Schmidt-Zachmann, M. S., Hügle-D?rr, B., and Franke, W. (1987) EMBO J. 6, 1881-1890). Except for the presence of highly acidic regions no significant similarities were found with protein C23 (nucleolin), the other major nucleolar protein.     

Identification of a gene encoding an immuno-reactive membrane protein from Campylobacter jejuni

A gene encoding a putative membrane protein has been identified from Campylobacter jejuni NCTC 11168 following an immuno-screen of a lambda ZAP II genomic DNA library with antiserum raised against glycine-extractable proteins. The nucleotide sequence of the entire genomic insert revealed six open reading frames, all but one of which have sequence homologues in the complete genome sequence of Helicobacter pylori. The gene encoding the immuno-reactive protein was further identified by independent expression of these reading frames in Escherichia coli. The gene encodes an integral membrane protein, expression of which in E. coli results in a profound filamentous phenotype.     

A cDNA encoding a putative lipid transfer protein expressed in sunflower seeds

Based on the N-terminal sequence of a sunflower antifungal protein, a full length cDNA (Ha-LTP5) encoding a putative lipid transfer protein from sunflower seeds was cloned using a RT-PCR based strategy. However, the sequence of the deduced protein is not identical to that of the antifungal protein previously isolated. The nucleotide sequence presents an ORF of 116 amino acids with a putative signal peptide, thus encoding a mature protein of 90 amino acids that is basic and hydrophobic. In contrast to the pattern of expression described for most LTP-like genes from dicots, Northern blot analyses detected constitutive expression of Ha-LTP5 in seeds, but not in aerial parts of sunflower plants.     

Structure and expression of the gene encoding ribosomal protein S1 from the cyanobacterium Synechococcus sp. strain PCC 6301: striking sequence similarity to the chloroplast ribosomal protein CS1

We isolated a 38 kDa ssDNA-binding protein from the unicellular cyanobacterium Synechococcus sp. strain PCC 6301 and determined its N-terminal amino acid sequence. A genomic clone encoding the 38 kDa protein was isolated by using a degenerate oligonucleotide probe based on the amino acid sequence. The nucleotide sequence and predicted amino acid sequence revealed that the 38 kDa protein is 306 amino acids long and homologous to the nuclear-encoded 370 amino acid chloroplast ribosomal protein CS1 of spinach (48% identity), therefore identifying it as ribosomal protein (r-protein) S1. Cyanobacterial and chloroplast S1 proteins differ in size from Escherichia coli r-protein S1 (557 amino acids). This provides an additional evidence that cyanobacteria are closely related to chloroplasts. The Synechococcus gene rps1 encoding S1 is located 1.1 kb downstream from psbB, which encodes the photosystem 11 P680 chlorophyll a apoprotein. An open reading frame encoding a potential protein of 168 amino acids is present between psbB and rps1 and its deduced amino acid sequence is similar to that of E. coli hypothetical 17.2 kDa protein. Northern blot analysis showed that rps1 is transcribed as a monocistronic mRNA.     

Structure and expression of the gene encoding ribosomal protein S1 from the cyanobacterium Synechococcus sp. strain PCC 6301: striking sequence similarity to the chloroplast ribosomal protein CS1

We isolated a 38 kDa ssDNA-binding protein from the unicellular cyanobacterium Synechococcus sp. strain PCC 6301 and determined its N-terminal amino acid sequence. A genomic clone encoding the 38 kDa protein was isolated by using a degenerate oligonucleotide probe based on the amino acid sequence. The nucleotide sequence and predicted amino acid sequence revealed that the 38 kDa protein is 306 amino acids long and homologous to the nuclear-encoded 370 amino acid chloroplast ribosomal protein CS1 of spinach (48% identity), therefore identifying it as ribosomal protein (r-protein) S1. Cyanobacterial and chloroplast S1 proteins differ in size from Escherichia coli r-protein S1 (557 amino acids). This provides an additional evidence that cyanobacteria are closely related to chloroplasts. The Synechococcus gene rps1 encoding S1 is located 1.1 kb downstream from psbB, which encodes the photosystem 11 P680 chlorophyll a apoprotein. An open reading frame encoding a potential protein of 168 amino acids is present between psbB and rps1 and its deduced amino acid sequence is similar to that of E. coli hypothetical 17.2 kDa protein. Northern blot analysis showed that rps1 is transcribed as a monocistronic mRNA.     

Human cellular retinol-binding protein gene organization and chromosomal location

The gene encoding the human cellular retinol-binding protein (CRBP) has been isolated from genomic libraries and its structure determined. Only one copy of the gene is present in the human genome. We have located the CRBP gene to segment 3p11-3qter on human chromosome 3 using hybridizations to mouse-human, rat-human and hamster-human cell hybrids. The gene harbors four exons encoding 24, 59, 33, and 16 amino acid residues respectively. The second intervening sequence alone occupies 19 kb of the 21 kb of the CRBP gene. The nucleotide sequence of the gene has been determined with the exception of the second intron. The positions of the introns agree with those in the rat CRBPII, the rat liver fatty-acid-binding protein and the mouse adipose P2 protein genes encoding molecules belonging to the same protein family as CRBP. In contrast to the other sequenced members of this family the promoter of the CRBP gene resembles those found in the 'housekeeping' genes in that it is (G + C)-rich, contains multiple copies of the CCGCCC sequence and lacks TATA box. A 9-bp homology containing the core sequence of the simian virus 40 enhancer repeat was found in the 5' upstream region. A genomic Southern blot probed with CRBP cDNA revealed hybridizing bands in restricted chicken and frog DNA.