G Simon, R Paladini, S Tisminetzky, M Cserzö, Z Hátsági, A Tossi, S Pongor
{"title":"Improved detection of homology in distantly related proteins: similarity of adducin with actin-binding proteins.","authors":"G Simon, R Paladini, S Tisminetzky, M Cserzö, Z Hátsági, A Tossi, S Pongor","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>A novel and generally applicable method is described for the detection of homology in distantly related proteins using a new domain sequence database that contains over 20,000 protein sequence segments of known function. The use of the method is illustrated on distantly related domains shared by complement components C1S and C1R, calcium-dependent serine proteinase and bone morphogenetic protein 1. New homologies are shown between human adducin and the actin-binding domains of alfa-actinin and dystrophin.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"5 1","pages":"39-42"},"PeriodicalIF":0.0,"publicationDate":"1992-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12660938","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}
{"title":"Structural similarities in the repeat sequences of plasma apolipoproteins, A-I, A-IV, and E.","authors":"P K Ponnuswamy, S Selvaraj","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The presence of 22-residue repeats, each with a preferential potential to form an amphipathic alpha-helix, is a unique feature of the plasma apolipoproteins. There are 27 such repeats in the three human apolipoproteins A-I, A-IV, and E. The extent of similarities and differences among these repeats have been estimated by computing correlation coefficients, Dayhoff scores, secondary structure difference profiles, and discrete Fourier transforms. The results reveal that there is a high level of similarity among the repeats of apo A-IV, and a low level of similarity in the repeats of apo E. Within each protein, similarity among some specified repeat pairs is distinctively higher than the others. A high order of similarity is also found among certain segments of each protein with those in the other two. The repeats prefer a mostly alpha-helical structure that is amphipathic in nature. Among the repeats of the three proteins, those of apo E show a high level of divergence among themselves. A consensus alignment of the residues of the 27 repeats into a hydrophobic versus hydrophilic pattern brings to focus the possible specific structure-stabilizing factors, such as the leucine zipper and the salt bridge. The recently reported crystal structures of the human apolipoprotein E and locust apolipophorin-III support many of the predictions made in this study.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"5 1","pages":"47-56"},"PeriodicalIF":0.0,"publicationDate":"1992-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12660940","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}
G Wachinger, H Nitschko, M Wachinger, K von der Helm
{"title":"The p17 stretch at the N terminus of the HIV1-gag precursor and the intracellular part of HIV1-env gp41 have heptad repeat regions in their sequences that could bind to each other in a coiled coil.","authors":"G Wachinger, H Nitschko, M Wachinger, K von der Helm","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"375-6"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974135","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}
A Dlouha, A Lecroisey, A Henschen, P Rouger, B Keil
{"title":"Subgroup assignment of a human monoclonal anti-Rh(D) antibody.","authors":"A Dlouha, A Lecroisey, A Henschen, P Rouger, B Keil","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Variable subgroups of both chains of a human monoclonal anti-RH(D) IgG1 (kappa), QA37C3G6, were determined from their N-terminal sequences. Sequence comparison with corresponding chains of other human antibodies indicated that the light chain belongs to the third subgroup of human kappa-light chains while the heavy chain belongs to the second subgroup of human heavy chains.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"317-8"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974198","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}
{"title":"The N-terminal amino acid sequence of yeast transketolase.","authors":"P F Nixon, R G Duggleby","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"325-6"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974200","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}
C S Jone, N Kotani, K Aso, L Yang, I Enami, K Kondo, A Tsugita
{"title":"Amino acid sequence of the 8-kDa protein in photosystem I reaction center complex from a thermophilic cyanobacterium, Synechococcus elongatus.","authors":"C S Jone, N Kotani, K Aso, L Yang, I Enami, K Kondo, A Tsugita","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The 8-kDa protein in Photosystem I (PS I) reaction center complex was isolated from a thermophilic cyanobacterium, Synechococcus elongatus, by SDS-polyacrylamide gel electrophoresis using TRIS-Tricine buffer system. The complete amino acid sequence of the protein was determined. The 8-kDa protein consisted of 73 amino acid residues giving a calculated molecular weight of 7,472. No significant sequence homology were observed with the known other small subunits in PS I reaction center complex, except for the 6.5-kDa protein in PS I from another thermophilic cyanobacterium, S. vulcanus. The 8-kDa protein was characteristically rich in hydrophobic amino acid residues, especially the content of leucine. These suggest that the 8-kDa subunit is an intrinsic structure component in PS I core complex for stabilization of the reaction center.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"327-31"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974201","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}
{"title":"Sequence regions of Bacilli metalloproteinases that can affect enzyme thermostability.","authors":"A Strongin, S Kostrov, N Kaydalova","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>By a computer analysis of the five Bacilli metalloprotease sequences it was found that mesophilic Bacillus amyloliquefaciens and B. subtilis proteases had lost two Ca(2+)-binding sites due to the substitutions Asp----Ser 57, Asp----Thr 59, Asp----Pro 200, in comparison with the thermostable B. thermoproteolyticus thermolysin and B. stearothermophilus protease, which conserved three Ca(2+)-binding sites, and B. cereus protease with the intermediate thermostability, which had presumably lost only one site (Ile----Lys 197 substitution). The multiple substitutions within the sequence regions 91-101, 150-154, and 275-280 of the mesophilic enzymes also corresponded with the decrease in the proteinase thermostability value. On the known X-ray structure of thermolysin these sequence regions are spatially drawn together, being located near the central alpha-helix opposite the active site hole and providing the contact of the N- and C-terminal domains. It may be concluded that to increase the thermostability of the mesophilic Bacilli proteinases it is necessary to substitute the sequence regions 91-101, 150-154, 275-280 for the thermolysin ones and restore the Ca(2+)-binding sites of the enzymes.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"355-61"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974132","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}
A Dlouha, A Lecroisey, A Henschen, Y Ruttyn, P Rouger, B Keil
{"title":"Partial amino acid sequence of the light chain of human anti-Rh(D) monoclonal antibody H2D5D2F5.","authors":"A Dlouha, A Lecroisey, A Henschen, Y Ruttyn, P Rouger, B Keil","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Antibody H2D5D2F5 is a human monoclonal anti-Rh(D) IgG1 (lambda) produced by Epstein-Barr virus-immortalized B lymphocytes from a healthy donor. The complete amino acid sequence of the light (L) chain, with the exception of positions 94-97, was determined by Edman degradation of the intact chain, containing 30 residues, and derived tryptic and thermolytic peptides. Sequences of the peptides were aligned by comparison with the sequences of previously reported L chains. H2D5D2F5 L chain belongs to the first variable subgroup of human chains. Its sequence does not reveal striking differences when compared to those of other human lambda chains issued from myeloma or hybridoma.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"319-24"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974199","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}
A Meinke, N R Gilkes, D G Kilburn, R C Miller, R A Warren
{"title":"Bacterial cellulose-binding domain-like sequences in eucaryotic polypeptides.","authors":"A Meinke, N R Gilkes, D G Kilburn, R C Miller, R A Warren","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The catalytic domain of endoglucanase II of Trichoderma reesei and the spore germination-specific polypeptide 270-11 of Dictyostelium discoideum contain amino acid sequences which share identity with the sequences of the cellulose-binding domains of several bacterial beta-1,4-glycanases. This is the first report of the presence of such sequences in eucaryotic polypeptides.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"349-53"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974205","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}
M Kusunoki, D G George, K Namboodiri, N Pattabiraman
{"title":"PRENRL_3D: a computer program for an automatic creation of NRL_3D, protein sequence-structure database, from the Protein Data Bank.","authors":"M Kusunoki, D G George, K Namboodiri, N Pattabiraman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Recently, we have developed a sequence-structure database of protein information, NRL_3D, that is extracted from the Protein Data Bank (PDB) of the Brookhaven National Laboratory. NRL_3D provides a vehicle for the retrieval of the three-dimensional coordinates of protein fragments as identified by sequence properties. These data are formulated to allow access by standard sequence analysis programs such as those provided by the Protein Identification Resource (PIR). Because the PDB is updated four times per year, semimanual construction of NRL_3D in coordination with these updates becomes a time-consuming and inefficient task. Hence, we have developed a computer program (PRENRL_3D) in the \"C\" computer language that automatically extracts NRL_3D from the PDB. Although the program was developed in a VAX/VMS environment, care was taken to ensure its portability to other computer systems. Customized versions of the NRL_3D database can be created from the PDB entry files using various options available in PRENRL_3D, such as selection of entries determined at high resolution and with low R-value. The program has been developed modularly and it contains a number of generalized procedures for manipulating various information in the PDB.</p>","PeriodicalId":77336,"journal":{"name":"Protein sequences & data analysis","volume":"4 6","pages":"333-6"},"PeriodicalIF":0.0,"publicationDate":"1991-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"12974202","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}