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Protein sequences & data analysis最新文献

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The following protein sequences were reprinted from the: protein sequence database of the Protein Identification Resource (PIR). 以下蛋白质序列转载自protein Identification Resource (PIR)的蛋白质序列数据库。
Protein sequences & data analysis Pub Date : 1989-04-01
W C Barker, L T Hunt, D G George, L S Yeh, H R Chen, M C Blomquist, E I Seibel-Ross, A Elzanowski, J K Bair, D A Ferrick
{"title":"The following protein sequences were reprinted from the: protein sequence database of the Protein Identification Resource (PIR).","authors":"W C Barker, L T Hunt, D G George, L S Yeh, H R Chen, M C Blomquist, E I Seibel-Ross, A Elzanowski, J K Bair, D A Ferrick","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 3","pages":"193-282"},"PeriodicalIF":0.0,"publicationDate":"1989-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13894815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein databases and software on BIONET. BIONET上的蛋白质数据库和软件。
Protein sequences & data analysis Pub Date : 1989-02-01
S Maulik
{"title":"Protein databases and software on BIONET.","authors":"S Maulik","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>BIONET provides databases, software, and networking/communications tools to over 2500 molecular biologists worldwide. Software for the analysis of nucleic acid and protein sequence data is provided by both IntelliGenetics and academic contributors. BIONET is currently implementing dedicated high speed servers for searching protein databases, as well as providing more flexible tools for protein structure recognition and prediction. In this review, protein databases and analysis software available on the BIONET resource are described, and progress in providing new tools for structure prediction, comparative sequence analysis, and pattern recognition using Artificial Intelligence (AI) techniques are summarized.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 2","pages":"111-4"},"PeriodicalIF":0.0,"publicationDate":"1989-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13795467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Amino acid composition is correlated with protein abundance in Escherichia coli: can this be due to optimization of translational efficiency? 大肠杆菌中氨基酸组成与蛋白质丰度相关:这是由于翻译效率的优化吗?
Protein sequences & data analysis Pub Date : 1989-02-01
E G Shpaer
{"title":"Amino acid composition is correlated with protein abundance in Escherichia coli: can this be due to optimization of translational efficiency?","authors":"E G Shpaer","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Amino acid occurrence frequencies were found for four groups of Escherichia coli proteins with different abundance levels in the cell. These frequencies decrease with increasing protein abundance for amino acids whose codons are translated by tRNAs present at low concentrations (e.g., Cys, Trp, Ser, etc.); the opposite tendency was observed for amino acids translated by abundant tRNAs (Lys, Val, etc.). The efficiency (rate and accuracy) of codon translation is expected to be proportional to the concentration of the cognate tRNA. Therefore, the observed constraints on amino acid composition may be explained as resulting from evolutionary pressure optimizing the translational efficiency of a gene (the same pressure is responsible for the nonrandom choice of synonymous codons).</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 2","pages":"107-10"},"PeriodicalIF":0.0,"publicationDate":"1989-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13795466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA. 真核5S rRNA茎区碱基错配的快速进化修复。
Protein sequences & data analysis Pub Date : 1989-02-01
K Horimoto, J Otsuka, T Kunisawa
{"title":"Rapid evolutionary repair of base mispairings in stem regions of eukaryotic 5S rRNA.","authors":"K Horimoto,&nbsp;J Otsuka,&nbsp;T Kunisawa","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>An extensive set of 216 eukaryotic 5S rRNA sequences are compared and the previous observations, that (i) invariable base positions are located primarily in loop regions and (ii) stem regions are more variable but the number of mispairings is kept small, are confirmed. On the basis of a comparison of the contemporary sequences, evolutionary processes of base substitutions in stem regions are discussed. It is found that there is no evident selective pressure to keep a particular kind of base pair in stem regions and individual bases may change freely as long as mispairings are kept few. It is also found that the secondary structure of 5S rRNA has been maintained stable by an equilibrium between base pair formation- and destruction-substitutions and that the low occurrence of mispairings in stem regions is attributable to a high value (ca. 90) of the equilibrium constant. The present analyses suggest a structure-function relationship of the eukaryotic 5S rRNA; stem regions structurally help loop regions to interact well with other ribosomal components and therefore, there is a marked selection pressure to maintain the secondary structure under the evolutionary noise of mutation.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 2","pages":"93-9"},"PeriodicalIF":0.0,"publicationDate":"1989-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13852310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evolution of the DNA invertase Gin of phage Mu and related site-specific recombination proteins. 噬菌体Mu DNA转化酶Gin及相关位点特异性重组蛋白的进化。
Protein sequences & data analysis Pub Date : 1989-02-01
B Stern, D Kamp
{"title":"Evolution of the DNA invertase Gin of phage Mu and related site-specific recombination proteins.","authors":"B Stern,&nbsp;D Kamp","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The relationship between site-specific recombination enzymes has been studied by computer analysis of nucleotide and amino acid sequences. A phylogenetic tree for two types of these enzymes has been constructed. DNA resolvases of Tn3-related transposable elements and DNA invertases form a superfamily which can be divided into four families of resolvases and one family of invertases comprising the Gin, Cin, Pin and Hin proteins. The DNA invertase genes descend from the tnpR branch that is represented by Tn917. Although TnpR 917 and Gin are almost 50% identical in their amino acid sequence, no gin-complementing activity of Tn917 could be measured. Within the family of DNA invertases, Gin and Pin are the closest relatives. The degree of sequence relatedness of the various invertases compared to Gin correlates with the biological relatedness tested in a gin complementation assay. A relationship between the inversion enzymes FimB and FimE and the super-family of site-specific recombinases could not be detected by these methods.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 2","pages":"87-91"},"PeriodicalIF":0.0,"publicationDate":"1989-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13684260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Striking sequence similarity among sialic acid-binding lectin, pancreatic ribonucleases, and angiogenin: possible structural and functional relationships. 唾液酸结合凝集素、胰腺核糖核酸酶和血管生成素之间惊人的序列相似性:可能的结构和功能关系。
Protein sequences & data analysis Pub Date : 1989-02-01
M T Lewis, L T Hunt, W C Barker
{"title":"Striking sequence similarity among sialic acid-binding lectin, pancreatic ribonucleases, and angiogenin: possible structural and functional relationships.","authors":"M T Lewis,&nbsp;L T Hunt,&nbsp;W C Barker","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We found that a sialic acid-binding lectin (SABL) from bullfrog egg bears a remarkable degree of similarity with human angiogenin and the pancreatic ribonucleases (EC 3.1.27.5). Based on (1) the conservation of several disulfide bond-forming cysteines, (2) a cluster of nonpolar residues, and (3) a number of active-site residues of bovine ribonuclease, we propose that SABL has essentially the same secondary and tertiary structures and very likely has ribonuclease activity. Other possible physiological roles are discussed.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 2","pages":"101-5"},"PeriodicalIF":0.0,"publicationDate":"1989-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13852308","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural and functional consequences of amino acid substitutions in hemoglobin as manifested in natural and artificial mutants. 天然和人工突变血红蛋白中氨基酸取代的结构和功能后果。
Protein sequences & data analysis Pub Date : 1989-02-01
K Imai, D T Shih, J Tame, K Nagai, G Miyazaki
{"title":"Structural and functional consequences of amino acid substitutions in hemoglobin as manifested in natural and artificial mutants.","authors":"K Imai,&nbsp;D T Shih,&nbsp;J Tame,&nbsp;K Nagai,&nbsp;G Miyazaki","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Compiled data for more than 440 natural human hemoglobin mutants with single amino acid substitutions indicate that molecular properties (oxygen binding, structural stability, ease of autooxidization, etc.) of more than half of them are altered in some way and that the mode of alteration is closely related to the region within the hemoglobin molecule in which the substitution takes place. The present study gives a quantitative basis for the correlations. By means of protein engineering, including site-directed mutagenesis, several artificial mutants of human hemoglobin were prepared and their oxygen binding properties were studied to investigate the functional consequences of the amino acid substitutions which have not yet been isolated in natural mutants. These artificial mutants gave straight-forward information regarding the major factors regulating the oxygen affinity of heme and the identification of a Bohr group in the alpha chain. On the other hand the mutants, which were designed to test some hypotheses for the molecular evolution in hemoglobin, did not necessarily give the results predicted from accumulated structure-function data obtained from the study of natural mutants and X-ray crystallographic analyses.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 2","pages":"81-6"},"PeriodicalIF":0.0,"publicationDate":"1989-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13852309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Amino acid sequence analysis of the glutamate synthase enzyme from Escherichia coli K-12. 大肠杆菌K-12谷氨酸合成酶的氨基酸序列分析。
Protein sequences & data analysis Pub Date : 1989-01-01
G Gosset, E Merino, F Recillas, G Oliver, B Becerril, F Bolivar
{"title":"Amino acid sequence analysis of the glutamate synthase enzyme from Escherichia coli K-12.","authors":"G Gosset,&nbsp;E Merino,&nbsp;F Recillas,&nbsp;G Oliver,&nbsp;B Becerril,&nbsp;F Bolivar","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The amino acid sequence for the two subunits of the glutamate synthase of Escherichia coli K-12 was compared to the protein sequences compiled in the National Biomedical Research Foundation databank. Similarities were detected between the small glutamate synthase subunit and three members of the flavin-containing pyridine nucleotide-disulphide oxidoreductase superfamily, and also with three members of a lactate dehydrogenase family. Two segments in this glutamate synthase subunit showed similarity to regions previously proposed as part of dinucleotide-binding sites in some members of these two families. Similarity can be extended if the predicted secondary structure is considered. Based on these data, residues 148-260 and 289-409 in the small GOGAT subunit are proposed as dinucleotide-binding regions. Comparison of the amino acid sequence of the large glutamate synthase subunit with the glutamine phosphoribosylamine:pyrophosphate phosphoribosyltransferases of B. subtilis and E. coli revealed a significant similarity between the amino termini of these three enzymes. In these last two amidotransferases, the glutamine-binding site has been located in their amino-terminal region. The comparison with a second group of glutamine amidotransferases did not show any significant global similarity with the large glutamate synthase subunit. However, this polypeptide contains a small segment that shares similarity with a 13-amino acid segment proposed as part of the glutamine-binding site in this second group of amidotransferases.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 1","pages":"9-16"},"PeriodicalIF":0.0,"publicationDate":"1989-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"13785389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Three-dimensional structures of proteins in solution by nuclear magnetic resonance spectroscopy. 用核磁共振波谱分析溶液中蛋白质的三维结构。
Protein sequences & data analysis Pub Date : 1989-01-01
A M Gronenborn, G M Clore
{"title":"Three-dimensional structures of proteins in solution by nuclear magnetic resonance spectroscopy.","authors":"A M Gronenborn,&nbsp;G M Clore","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Nuclear magnetic resonance (NMR) spectroscopy has emerged in recent years as a powerful method for the determination of three dimensional structures of small proteins in solution. Major cornerstones towards these advances were the introduction of two dimensional NMR experiments in combination with high field superconducting magnets, as well as the development of computational procedures to convert NMR derived distances into a 3D structure. This article outlines the methodology employed and illustrates its applicability based on a variety of examples.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"1989-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14047391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Creation of a nuclear magnetic resonance data repository and literature database. 建立核磁共振资料库及文献资料库。
Protein sequences & data analysis Pub Date : 1989-01-01
E L Ulrich, J L Markley, Y Kyogoku
{"title":"Creation of a nuclear magnetic resonance data repository and literature database.","authors":"E L Ulrich,&nbsp;J L Markley,&nbsp;Y Kyogoku","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We believe the need exists for an organized and accessible repository of protein nuclear magnetic resonance data. The structure and dynamics of hundreds of proteins are being investigated by NMR. NMR data currently are spread throughout the world and often are not published for lack of journal space. Difficulties in locating, obtaining, and correlating these data with protein structures limits their usefulness to the scientific community. In time, the data may become lost or ignored. To provide a collection point for the results of protein NMR studies and a uniform means of distributing these data, we propose that a data bank be created consisting of two databases: a comprehensive and thoroughly indexed database for the NMR literature and a data repository for the storage of extensive protein NMR data sets. Our current specifications for the types of information to be stored in the NMR databases and their organization for dissemination are defined. The design is intended to be flexible, capable of expanding to include new techniques, new forms of data, and biopolymers other than proteins. This is a proposal to the community of NMR spectroscopists. Only through the active cooperation and support of those in the field of NMR spectroscopy can the proposed data bank succeed.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"2 1","pages":"23-37"},"PeriodicalIF":0.0,"publicationDate":"1989-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"14047393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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