bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-dimensional structure of the peptide-binding domain of E.coli DnaK
Authors: Gething M -J 
Published: November 2023

Abstract
HSP70 proteins contain two major. domains - an N-terminal domain that contains the ATPase catalytic site, a (-terminal substrate binding domain - that com municate to regulate the affinity, duration of (poly)peptide binding (reviewed by McKay et al., 1993). The 3-dimensional structure of the isolated ATPase domain of the constitutively-expressed bovine cytosolic Hsc70 was reported some time ago (Flaherty et al., 1990), but the determination of the structure of the (-terminal domain of an HSP70 protein remained elusive. Intriguingly, two totally indepent approaches using struc ture prediction algorithms suggested that the peptide binding domain might resemble that of MHC class I anti gens (Flajnik et al., 1991; Rippmann et al., 1991).
Saccharomyces cerevisiae Ssb proteins
Authors: Ziegelhoffer T , Craig Christine Pfund, E A 
Published: November 2023

Abstract
The SSB1, SSB2 genes (initially known as YG101, YG103) were isolated by virtue of their high degree of similarity to Drosophila HSP70 genes (Ingolia et al., 1982; Craig, Jacobsen, 1985).
Mammalian a-Crystallins
Authors: Jong W W de , Boelens W C 
Published: November 2023

Abstract
α-Crystallin, comprising up to one-third of total lens protein in mammals, can be isolated in large quantities by gel filtration of aqueous lens extracts (Groenen et al., 1994). Lenticular a-crystallin is composed of acidic aA, more basic aB subunits, generally in a ratio of about 3:1. These can be separated by ion exchange chromatography under denaturing conditions, or by reverse-phase HPLC. The amino acid sequences of calf lens aA, aB, determined in the early 1970s, are 57% identical. aA, aB are 173, 175 residues in length, appear on SDS-PAGE as 20, 22 kDa bands, respectively. Both proteins are N-terminally acetylated.
Schizosaccharomyces pombe BiP
Authors: Armstrong J 
Published: November 2023

Abstract
A homologue of the BiP/Kar2p proteins of mammalian cells, budding yeast was identified in the fission yeast Schizosaccharomyces pombe (Pidoux, Armstrong, 1992). A portion of the gene was recovered by polymerase chain reaction using primers designed from sequences conserved between mammalian, 5. cerevisiae BiP. This fragment was used to isolate the complete gene by hybridization. A further S. pombe HSP70 homologue, which is probably located in the endoplasmic reticulum, has been identified from genome sequencing (protein accession number e212000) but no studies of this gene have been reported.
Mammalian thioredoxin
Authors: Nakamura H , Bjornstedt M , Holmgren A 
Published: November 2023

Abstract
Mammalian thioredoxin has been purified from several sources including rat Novikoff hepatoma, calf liver, rat liver, rabbit bone marrow, human placenta (Holmgren, 1985; Holmgren, Bjornstedt, 1995). A protein that was purified from the conditioned medium of human T cell lymphotropic virus type-l (HTLV-l)-trans-formed T cells, Epstein-Barr virus-transformed B cells.
Mammalian ERp72
Authors: Ferrari D , Soling H -D 
Published: November 2023

Abstract
ERp72 DNA/protein sequences have been reported from several sources [EMBL/SWISS-PROT accession numbers J05016/P13667 (human), S59335/P38659 (rat), J05186/ P15841 (mouse), L15188/P34329 (Caenorhabditis elegans)]. The DNA sequences are c. 1.9 kb long, encode an N-terminal signal sequence of around 20 amino acids that is cleaved to generate a highly conserved c. 625 amino acids protein (Mazzarella et a!.,
Escherichia coli cydophilins
Authors: Takahashi N 
Published: November 2023

Abstract
Although the peptidyl-prolyl cis-trans isomerase (PPIase) activities of most cyclophilins originating from eukaryotic cells are inhibited by the immunosuppressive drug cyclosporin A (CsA), the activity of Escherichia coli cyclophilins is essentially not sensitive to CsA. No definitive evidence for the physiological role of cyclophilins was identified in E. coli cells; however, they are believed to be involved in protein folding in the cell.
Saccharomyces cerevisiae cydophilin B /Cpr2/Cyp2
Authors: Cafferkey R , Stan R , Freeman K , Livi G P 
Published: November 2023

Abstract
Cyclophilin B belongs to the family of yeast cyclophilin-related peptidyl-prolyl cis-trans isomerases (PPIases), enzymes that catalyse the isomerization of prolyl-peptide bonds in vitro. The protein was originally identified as the deduced translation product of a gene cloned as a homolog of a human cyclophilin A-encoding cDNA. Yeast cyclophilin B is directed to the ER/secretory pathway by a 20 amino acid hydrophobic signal sequence, where it may function to catalyse the folding of secretory proteins. Cyclophilin B is also involved in the heat shock response. Although purified recombinant cyclophilin B protein possesses cyclosporin A (CsA)-sensitive PPIase activity in vitro, cyclophilin B does not play a role in CsA cytotoxicity in yeast, which is mediated instead by cytosolic cyclophilin A.
Saccharomyces cerevisiae mitochondrial cydophilin Cpr3
Authors: Matouschek A 
Published: November 2023

Abstract
CYP3 (McLaughlin et al., 1992), cyclophilin C (see Cafferkey et al. p. 373). The yeast mitochondrial cyclophilin gene was isolated as CPR3 from a S. cerevisiae genomic library by hybridization with a rat cyclophilin cDNA probe (Davis etal., 1992). Independently, yeast mitochondrial cyclophilin protein was purified from yeast extracts following cyclosporin A-sensitive peptidyl-prolyl cis-trans isomerase activity (McLaughlin etal., 1992). The corresponding gene (CYP3) was then isolated from S. cerevisiae genomic libraries by hybridization with a probe derived from the N-terminal protein sequence.
Neurospora crassa cydophilins
Authors: Tropschug M 
Published: November 2023

Abstract
Fungi like Neurospora crassa or Saccharomyces cerevisiae are ideal organisms to study the cellular roles of the different peptidyl-prolyl cis-trans isomerases (PPIases) and the molecular mechanisms of action of immunosuppressants like CsA, FK506 or rapamycin (reviewed by Kunz and Hall, 1993). These drugs were originally isolated as antifungal compounds. Three families of PPIases have been described. Two of these, the cyclophilins (Cyps) and FKBPs, have been known for some time (see reviews by Schreiber, 1992; Schmid, 1993; Fischer, 1994; Galat and Metcalfe, 1995; see also the overview in this volume, p. 359). Parvulins constitute a more recently defined family (Rahfeld etal., 1994; see overview p. 365). To date only members of the Cyp (this entry) and FKBP (see entry p. 416) families have been defined in N. crassa.
Drosophila melanogaster Hsc4p
Authors: Mehta A D , Rubin D M , Elefant F , Palter K B 
Published: November 2023

Abstract
The nucleotide sequence for Drosophila HSC4 was determined from a genomic clone [GenBank accession numbers M36114 (Perkins et al., 1990), L01500 (Rubin et al., 1993)]. Comparison of the genomic sequence with that of a cDNA clone revealed the presence of a 1.6-kb intron located 5’ of the initiating ATG (Perkins et al., 1990). The DNA sequence of HSC4 revealed an open reading frame of 1953 bp that would encode a protein of 651 amino acids with a molecular mass of 71 130 daltons.
Saccharomyces cerevisiae FKBP13
Authors: Parent S P , Neilsen J B 
Published: November 2023

Abstract
The yeast FKB2 gene encodes a single open reading frame of 135 amino acids (GenBank accession numbers M90767, M90646; Nielsen et al., 1992; Partaledis et al., 1992). At its start are two consecutive ATG initiator codons. Depending on which start site is used, there is a signal peptide of 16 or 17 amino acids, which is presumably removed by processing. The mature protein is 118 amino acids with a predicted molecular weight of 12 446 daltons. Among the FKBPs, it is most homologous to human FKBP13 (hFKBP13) (Jin etal., 1991), sharing 64% identity in the core regions of these proteins. Its identity with the major human cytosolic FKBP (hFKBP12) in the same region is 51%. The amino acid residues of hFKBP12 and yFKBPI 2, whose side chains interact with FK506, are conserved (Van Duyne etal., 1991; Rotonda et al., 1993).
Saccharomyces cerevisiae Npi46p
Authors: Shan X , Xue Z , Melese T 
Published: November 2023

Abstract
NPI46 was isolated by screening a AZAP yeast genomic expression library, using antiserum raised against yeast NLS-binding proteins (Shan et al., 1994). It encodes a protein of 411 amino acid residues with a molecular mass of 46 541 Da (Genbank accession number X79379). It was also identified as Fpr3, a protein that binds to FK520, a FK506-related immunosuppressant agent (Benton et al., 1994; Manning-Krieg etal., 1994). The C-terminal domain of Npi46p shares 45% identity with both human and yeast FKBP12. The N-terminal domain is highly charged, contains a bipartite NLS, and a number of acidic stretches with serine residues.
Mammalian FKBP12.6
Authors: Wiederrecht G J 
Published: November 2023

Abstract
Among the known mammalian members of the family of FK506-binding proteins, FKBP12.6 is the one most closely related to FKBP12. The affinities of FK506 and rapamycin for FKBP12.6 are equivalent to their affinities for FKBP12. Importantly, the FKBP12.6-FK506 complex is as potent an inhibitor of calcineurin as the FKBP12-FK506 complex, indicating that FKBP12.6 may be associated with some of the immunosuppressive or toxic side effects of FK506 therapy. The physiological function of FKBP12.6 is distinct from that of FKBP12. Whereas FKBP12 binds to and regulates the ryanodine receptor (RyR-1) of skeletal muscle sarcoplasmic reticulum, FKBP12.6 binds to and regulates the ryanodine receptor isoform (RyR-2) of cardiac muscle.
Saccharomyces cerevisiae Ess1
Authors: Hanes S D 
Published: November 2023

Abstract
The ESS1 gene was originally isolated by cross-hybridization with the simian sarcoma virus oncogene v-sis, known to promote the G1/S transition. However, Ess1 protein bears little similarity to p28s/s. ESS1 mapped to the right arm of chromosome 10 and was not allelic to any known yeast mutation (Hanes et al., 1989). PTF1 was identified in a screen for pre-mRNA processing mutants defective in 3’-end formation (Hani etal., 1995).
Transcriptional regulation of eukaryotic heat shock genes
Authors: Morimoto R I 
Published: November 2023

Abstract
Common to all organisms is an essential, highly conserved and exquisitely regulated cellular response to suboptimal physiological and environmental conditions that affect cell growth, maintenance of cellular activities, and development. The activation of heat shock genes is a highly regulated response to heat shock, oxidative stress, heavy metals, various toxic chemicals, bacterial and viral infection, and exposure to a number of acute and chronic disease states which results in the elevated synthesis of a family of stress-induced or heat shock proteins (Lindquist and Craig, 1988; Morimoto et al., 1990, 1994). This affords the cell a protective mechanism against acute exposure to stress which, if unchecked, leads to irreversible cell damage and cell death. Heat shock proteins, many of which have properties as molecular chaperones, have essential roles in the process of protein biosynthesis, specifically in the synthesis, folding, degradation, transport, and translocation of proteins (reviewed in Gething and Sambrook, 1992; Georgopoulos and Welch, 1993; Hendrix and Hartl, 1993; Craig et al., 1993; Morimoto et al., 1994).
Mammalian mitochondrial Hsp70
Authors: Hoogenraad N J , Hoj P B , Naylor D , Webster T 
Published: November 2023

Abstract
Grp 75 (Mizzen et al., 1989); P71 (Leustek et al., 1989); Pbp74 (Domanico et al., 1993); C3H strain specific antigen (CSA) (Michikawa et al., 1993); mortalin (Wadhwa et al., 1993) ;mthsp75 (Bhattacharyya etal., 1995).
Neurospora crassa Hsp88
Authors: Plesofsky-Vig N , Brambl R 
Published: November 2023

Abstract
We first identified Hsp88 in our search for proteins from heat shocked cells that interact with the small HSP of N. crassa. Two detectable proteins, Hsp70, Hsp88, were found to bind specifically to Hsp30 (N. Plesovsky-Vig, R. Brambl, unpublished results). Hsp88 was isolated by affinity chromatography, gel electrophoresis. After digestion of Hsp88 by trypsin, several peptides were N- terminally sequenced, leading to the design of conceptually coding oligonucleotides. An amplified gene fragment, produced by the polymerase chain reaction, was used to probe a N. crassa cDNA library,, a 2.6 kb cDNA was identified, sequenced.
Mammalian OSP94
Authors: Gullans S R , Kojima R 
Published: November 2023

Abstract
osp94 was identified during an analysis of mRNAs that are up-regulated by hyperosmotic stress in mouse inner medullary collecting duct (mlMCD3) cells (Kojima et al., 1996). APG-1 was identified during a search for germ cellspecific mRNAs in testes (Kaneko etal., 1997).
Mammalian Grp170
Authors: Easton D P , Subjeck ,J R 
Published: November 2023

Abstract
Chinese hamster Grp 170 is encoded as a 999 amino acid precursor with a 34 residue signal peptide (GenBank accession number U34206, Chen et al., 1996). The calculated molecular weight of the processed protein is 107 461 Da. Grp170 is a glycoprotein with a calculated Mrof 164 kDa, determined by SDS-gel electrophoresis. The peptide terminates in NDEL which serves as an ER retention signal.
HSP40 (DnaJ-related) proteins — an overview
Authors: Cyr D M 
Published: November 2023

Abstract
The purpose of this overview is to provide an introduction to the key features of the HSP40 or DnaJ family of proteins. General aspects of HSP40 function will be discussed, special features of individual family members will be highlighted. To limit overlap, the details of the functions of specific HSP40 proteins will be discussed in the entries on individual family members. At present there are a total of 219 entries in GenBank, some redundant, for proteins with homology to the progenitor of the HSP40 family, E. coli DnaJ. A limited number of HSP40 proteins from both E. coli, eukaryotic organisms whose sequence, function are known have been selected for detailed discussion below.
Saccharomyces cerevisiae Sisi
Authors: Arndt K T 
Published: November 2023

Abstract
The DNA sequence of SISI (GenBank accession number X58460) predicts a protein of 37.6 kDa with a pl of 9.15, a codon bias of 0.163 (Luke et al., 1991). The N-terminal third, the C-terminal third of Sislp are related to the corresponding regions of bacterial DnaJ. The middle third of Sislp is unrelated to DnaJ, contains a glycine/methionine-rich region.
Saccharomyces cerevisiae Zuotin
Authors: Cyr A M 
Published: November 2023

Abstract
Zuotin was purified from yeast nuclear matrix based on its ability to bind a Z-DNA affinity column (Zhang et al., 1992). The ZUO1 gene (GenBank accession number X63612) is located on yeast chromosome VII near ADE3, encodes a 433 residue protein that has predicted molecular weight of 49 kDa (Zhang et al., 1992). Zuotin is a basic protein with a pl of 8.8 and, based on sequence analysis, has a number of interesting features (Zhang etal., 1992).
Saccharomyces cerevisiae Mdjlp
Authors: Schwarz Schwarz 
Published: November 2023

Abstract
The nuclear gene for mitochondrial DnaJ (MDJ1) was identified during the sequence analysis of chromosome VI (GenBank accession number D50617x53). The MDJ1 open reading frame encodes a polypeptide of 511 residues (Rowley et al., 1994) that possesses all the features characteristic of a DnaJ protein: (i) an N-terminal J-domain of about 70 amino acid residues; (ii) a 60-residue segment rich in glycine, phenylalanine; (iii) four cysteine-containing repeats with the sequence motif: CXXCXGXG (with X being predominantly a polar or charged residue);, (iv) a C-terminal domain with little sequence conservation to other DnaJ proteins (for detailed reviews about the HSP40/DnaJ protein family see Caplan et al., 1993; Cyr et al., 1994;, the introductory overview to this section, p. 89).
Saccharomyces cerevisiae Scjlp
Authors: Craig E A 
Published: November 2023

Abstract
Saccharomyces cerevisiae DnaJ homologue (Blumberg, Silver, 1991). SCJ1 was originally identified by a genetic screen in yeast in which overexpression of candidate genes could result Brodsky, J.L., Schekman, R. (1993). A sec63-BiP complex from yeast is required for protein translocation in a reconstituted proteoliposome. J. Cell Biol. 123, 1355-1363.
Plant Anj1
Authors: Zhu J -K 
Published: November 2023

Abstract
The nucleotide sequence of ANJ1 cDNA cloned from the halophytic higher plant Atriplex nummularia (GenBank accession number L09124) predicts a polypeptide of 417 amino acids without signal sequence or transmembrane domain (Zhu et al., 1993a). At the N-terminus is a J-domain of approximately 70 amino acids which is conserved in all DnaJ-related proteins from both prokaryotes, eukaryotes (Caplan et al., 1993; Zhu et al., 1993a). J-domains are known to interact with HSP70 homologs (Schlenstedt et al., 1995). A glycine-rich motif (or G/F domain) (Wall et al., 1995) connects the J-domain to a putative ‘zinc finger’ which consists of four CXXCXGXG repeats (Caplan et al., 1993; Zhu et al., 1993a).
Escherichia coli GrpE
Authors: Buchberger A , Bukau B 
Published: November 2023

Abstract
The first grpE mutation, grpE280, was obtained upon selection for mutants resistant to lytic infection by bacteriophage A (Saito, Uchida, 1977). The grpE gene product was later shown to be identical to heat shock protein B25.3 (Ang etal., 1986).
Drosophila melanogaster Hsp83
Authors: Nathan D F , Lindquist S 
Published: November 2023

Abstract
Drosophila melanogaster HSP83 is a single copy gene positioned at cytogenic locus 63B (GenBank accession numbers X03810, K01685). Unlike the majority of Drosophila HSP genes, which do not contain intervening sequences, the HSP83 gene contains an intron just upstream of the translation start site (Hackett, Lis, 1983; Blackman, Meselson, 1986). The second exon encodes a 718 amino acid protein that is highly homologous to other members of the HSP90 family.
Plant Hsp90
Authors: Krishna P 
Published: November 2023

Abstract
Nucleotide sequence analysis of plant hsp90 genes (GenBank accession numbers M36960, M96549, M99431) predicts a molecular mass between 80, 82 kDa,, pls of 5.73, 5.76 in two cases, for the encoded proteins (Conner et al., 1990; Felsheim, Das, 1992; Koning et al., 1992; Takahashi et al., 1992; Marrs et al., 1993; Yabe et al., 1994).
The CPN60, CPN10 families — an overview
Authors: Hartl F U , Mayhew M 
Published: November 2023

Abstract
CPN60 (or chaperonin 60; Hemmingsen et al., 1988) family members are also called HSP60. CPN10 family members are also called chaperonin 10, HSP10 or cochaperonin. Sequence alignment of CPN60 family members reveals at least 70% similarity, 50-70% identity between any two members. Residues 86-91 of the CPN60 protein from Escherichia coli, GroEL, form part of the ATP-binding site that includes the consensus sequence GDGTT found in all chaperonins, which is similar to the sequence GXGXX(G) in the ATP-binding sites of many type I kinases (Kim et al., 1994). Finally, all CPN60 family members contain two or three GGM repeats at their extreme C-termini.
Thermus thermophilus GroEL, GroES
Authors: Taguchi H , Yoshida M 
Published: November 2023

Abstract
Thermus chaperonin means the chaperonin from T. thermophilus, consisting of 14 copies of GroEL homologues (T. th cpn60), seven copies of GroES homologues (T. th cpn10) (Taguchi etal., 1991; Amada etal., 1995).
The neuroendocrine polypeptide 7B2
Authors: Martens GJ 
Published: November 2023

Abstract
The 7B2 protein was first isolated from porcine, human pituitary glands by HPLC,, the first 50 (porcine), 77 (human) amino acid residues were determined by N-terminal amino acid sequence analysis (Hsi etal., 1982; Seidah etal., 1983).
CCTγ
Authors: Kubota A , Willison K 
Published: November 2023

Abstract
A temperature-sensitive mutant called bin2-1 shows abnormal actin, tubulin organization in budding yeast, disruption of the gene creates a recessive lethal phenotype (Chen et aL, 1994). A temperature-sensitive mutant of CCTy is lethal in combination with a temperature-sensitive mutant of either CCTa, CCT/3 or CCT5 (Chen etal., 1994).
Escherichia coli CIpX
Authors: Wawrzynow A , Zylicz M 
Published: November 2023

Abstract
The clpX gene (GenBank accession number 223278) together with the dpP gene forms a heat shock-regulated operon located upstream of the Ion gene at 10 minutes on the E. coli map (Gottesman et al., 1993). clpX can also be expressed independently from dpP using its own promotor (Yoo et al., 1994). The clpX gene encodes a protein of 424 amino acids (Gottesman et al., 1993). The clpX gene was identified following N-terminal sequence analysis of the ClpX (LopC) protein, which is the specificity component of CIpXP ATP-dependent protease (Wojtkowiak et al., 1993).
Ca2+ -ATPase (plasma membrane)
Authors: Celio Marco R 
Published: November 2023

Abstract
The plasma membrane Ca2+ ATPase (PMCA) or Ca2• pump is an integral membrane protein which is present in all mammalian cells. It belongs to the family of the P-type ATPases. The pump transports Ca2+ ions out of the cells, by using the energy stored in ATP and is essential in the control of the Ca2+ concentration in the cytosol.
α-Toxin (Staphylococcus aureus)
Authors: Menestrina G , Ferreras) M 
Published: November 2023

Abstract
Staphylococcal a-toxin is an exotoxin with hemolytic, cytotoxic, dermonecrotic, and lethal activity (Thelestam and Blomqvist 1988; Bhakdi and Tranum-Jensen 1991). It is secreted by most pathogenic strains of S. aureus (commonly Wood 46) as a water-soluble polypeptide of 33 kD (293 amino acid residues, sequence accession number to the Swiss Prot databank: P09616 HLA-STAAU; corrections were published (Walker et al. 1992)). Its relevance as a virulence factor has been firmly established, at least in animal models. As outlined in Fig. 1, this toxin oligomerizes on the surface of mammalian cells (and liposomes) to form a membrane-embedded oligomer of about 220 kD, which appears in the electron microscope as a hollow cylinder protruding from the plane of the bilayer. It forms crystalline 2D layers on lipid membranes of either natural or artificial origin. From such arrays, a low-resolution three-dimensional map of the oligomer was obtained (Olofsson et al. 1988), suggesting it was a hexamer. However, more recent low-resolution X-ray analysis of microcrystals (Gouaux et al. 1994) provided evidence that the oligomer is actually an heptamer like the one formed by aerolysin from Aeromonas hydrophila.
δ-Toxin (Staphylococcus aureus) and melittin (Apis mellifera)
Authors: Dufourcq J , Castano S 
Published: November 2023

Abstract
δToxin and melittin (Mel) are 26 residue long peptides, secreted by Staphylococcus aureus strains and representing about 50 per cent of the dry weight of bee venom, respectively. Both are pleiotropic toxins with no sequence homology, despite this they share most of their biological properties. The first target is the plasma membrane, but the toxins also act on a wide variety of intracellular elements whether membranes, proteins, or nucleic acids. Their behaviour is dominated by their amphipathic character, they are surface active, have rather nonspecific affinity for interfaces, and are classified as ‘membrane invading’ or ‘direct lytic’ peptides.