Isolation and primary structure of rat secretin

A major form of rat secretin was purified to homogeneity from small intestine, being detected with a porcine secretin radioimmunoassay throughout 7 chromatographic steps. The sequence of the heptacosapeptide amide H-S-D-G-T-F-T-S-E-L-S-R-L-Q-D-S-A-R-L-Q-R-L-L-Q-G-L-V-NH2 shows that rat secretin has a glutamine residue in position 14 instead of arginine as in pig secretin.     

Analysis of the structure and subcellular location of filamentous phage pIV.

The gene IV protein of filamentous bacteriophages is an integral membrane protein required for phage assembly and export. A series of gene IV::phoA fusion, gene IV deletion, and gene IV missense mutations have been isolated and characterized. The alkaline phosphatase activity of the fusion proteins suggests that pIV lacks a cytoplasmic domain. Cell fractionation studies indicate that the carboxy-terminal half of pIV mediates its assembly into the membrane, although there is no single, discrete membrane localization domain. The properties of gene IV missense and deletion mutants, combined with an analysis of the similarities between pIVs from various filamentous phage and related bacterial export-mediating proteins, suggest that the amino-terminal half of pIV consists of a periplasmic substrate-binding domain that confers specificity to the assembly-export system.     

Codon preference and primary sequence structure in protein-coding regions

The stochastic complexity of a data base of 365 protein-coding regions is analysed. When the primary sequence is modeled as a spatially homogeneous Markov source, the fit to observed codon preference is very poor. The situation improves substantially when a non-homogeneous model is used. Some implications for the estimation of species phylogeny and substitution rates are discussed.     

Spatial structure of secretin molecule

By conformational analysis and circular dichroism the structure of peptide hormone secretin and its shortened N-terminal fragments in different solvents (water, aqueous solutions of alpha-L-phosphatidic acid and sodium dodecyl sulfate) have been studied. The results obtained by the two methods are compared.     

Identification and primary structure of calmodulin binding domains in the phosphorylase kinase holoenzyme

Fast twitch skeletal muscle phosphorylase kinase was isolated and incubated with a radioactive, bifunctional, photoactivable, and cleavable cross-linker conjugated to calmodulin. Incubation of the holoenzyme only resulted in the labeling of the alpha-subunit in the presence of Ca2+. After cleavage with CNBr (and subdigestion with Asp-N protease), a sequence was identified (residues 1069-1087) in the alpha-subunit which had the predominant basic character and the propensity to form an amphiphilic helix like other calmodulin binding domains. If cross-linked calmodulin was incubated with the isolated subunits of phosphorylase kinase, radioactivity was recovered in seven CNBr peptides: three came from the alpha-subunits, one of them corresponding to the sequence labeled in the holoenzyme. Three came from the beta-subunit, and one came from the gamma-subunit. The latter contained the two adjacent calmodulin binding domains recently identified in the gamma-subunit (Dasgupta, M., Honeycutt, T., and Blumenthal, D. K. (1988) J. Biol. Chem. 264, 17156-17163).     

Structure of the filamentous phage pIV multimer by cryo-electron microscopy

The homo-multimeric pIV protein constitutes a channel required for the assembly and export of filamentous phage across the outer membrane of Escherichia coli. We present a 22 A-resolution three-dimensional reconstruction of detergent-solubilized pIV by cryo-electron microscopy associated with image analysis. The structure reveals a barrel-like complex, 13.5 nm in diameter and 24 nm in length, with D14 point-group symmetry, consisting of a dimer of unit multimers. Side views of each unit multimer exhibit three cylindrical domains named the N-ring, the M-ring and the C-ring. Gold labeling of pIV engineered to contain a single cysteine residue near the N or C terminus unambiguously identified the N-terminal region as the N-ring, and the C-terminal region was inferred to make up the C-ring. A large pore, ranging in inner diameter from 6.0 nm to 8.8 nm, runs through the middle of the multimer, but a central domain, the pore gate, blocks it. Moreover, the pore diameter at the N-ring is smaller than the phage particle. We therefore propose that the pIV multimer undergoes a large conformational change during phage transport, with reorganization of the central domain to open the pore, and widening at the N-ring in order to accommodate the 6.5 nm diameter phage particle.     

Identification and primary structure of the cardiolipin-binding domain of mitochondrial creatine kinase

It was recently shown that the mitochondrial isozyme of heart creatine kinase binds to cardiolipin on the outer half of the inner membrane [Müller, M., et al. (1985) J. Biol. Chem. 260, 3839-3843]. The enzyme has now been extracted and purified to homogeneity from rat heart mitochondria, and cleaved with CNBr. The fragments have been separated on an FPLC system using a Mono Q HR 5/5 column. Only one of these binds to cardiolipin-containing liposomes and has thus been identified as the cardiolipin-binding domain of the enzyme. Its amino acid sequence has been determined. The fragment contains 25 amino acids and corresponds to the N-terminal region of the protein. The binding of the fragment of cardiolipin-containing liposomes was inhibited by adriamycin. Another and larger CNBr fragment could be specifically labelled with periodate-oxidized (di-aldehyde) ATP and has thus been identified as the ATP-binding domain. Chemical modification of the basic amino acids Lys and Arg of the enzyme abolished its binding to cardiolipin.     

Identification of potential conserved RNA secondary structure throughout influenza A coding regions

Influenza A is a negative sense RNA virus of significant public health concern. While much is understood about the life cycle of the virus, knowledge of RNA secondary structure in influenza A virus is sparse. Predictions of RNA secondary structure can focus experimental efforts. The present study analyzes coding regions of the eight viral genome segments in both the (+) and (-) sense RNA for conserved secondary structure. The predictions are based on identifying regions of unusual thermodynamic stabilities and are correlated with studies of suppression of synonymous codon usage (SSCU). The results indicate that secondary structure is favored in the (+) sense influenza RNA. Twenty regions with putative conserved RNA structure have been identified, including two previously described structured regions. Of these predictions, eight have high thermodynamic stability and SSCU, with five of these corresponding to current annotations (e.g., splice sites), while the remaining 12 are predicted by the thermodynamics alone. Secondary structures with high conservation of base-pairing are proposed within the five regions having known function. A combination of thermodynamics, amino acid and nucleotide sequence comparisons along with SSCU was essential for revealing potential secondary structures.     

Identification of ten additional nucleotides in the primary structure of yeast 18S rRNA

The ten-nucleotide-long sequence have been omitted while sequencing the 18S rRNA gene from yeast Saccharomyces cerevisiae [Rubtsov et al., Nucl. Acids Res. 8 (1980) 5779-5794]. This GAAGAUGAUC sequence and some other minor corrections are reintroduced into the yeast 18S rRNA primary structure.     

Identification of similar regions of protein structures using integrated sequence and structure analysis tools

Background  

Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have developed a web site and an API of web services that enables users to submit protein structures and identify statistically significant neighbors and the underlying structural environments that make that match using a suite of sequence and structure analysis tools. To do this, we have integrated S-BLEST, PSI-BLAST and HMMer based superfamily predictions to give a unique integrated view to prediction of SCOP superfamilies, EC number, and GO term, as well as identification of the protein structural environments that are associated with that prediction. Additionally, we have extended UCSF Chimera and PyMOL to support our web services, so that users can characterize their own proteins of interest.     

Identification of an ion channel-forming motif in the primary structure of tetanus and botulinum neurotoxins.

Synthetic peptides with amino acid sequences corresponding to predicted transmembrane segments of tetanus toxin were used as probes to identify a channel-forming motif. A peptide denoted TeTx II, with sequence GVVLLLEYIPEITLPVIAALSIA, forms cation-selective channels when reconstituted in planar lipid bilayers. The single channel conductance in 0.5 M NaCl or KCl is 28 +/- 3 and 24 +/- 2 pS, respectively. In contrast, a peptide with sequence NFIGALETTGVVLLLEYIPEIT, denoted as TeTx I, or a peptide with the same amino acid composition as TeTx II but with a randomized sequence, do not form channels. Conformational energy calculations show that a bundle of four amphipathic alpha-helices is a plausible structural motif underlying observable pore properties. The identified functional module may account for the channel-forming activity of both tetanus toxin and the homologous botulinum toxin A.     

Identification of immunodominant regions of transforming growth factor alpha. Implications of structure and function

Human transforming growth factor alpha (TGF alpha) is a 50-residue mitogenic peptide with a compact structure restrained by three disulfide bonds. Sequential and overlapping synthetic peptides were made to identify epitopes of TGF alpha using a panel of murine monoclonal antibodies and rabbit polyclonal antibodies. Antibodies were raised against human TGF alpha from different preparations obtained from either chemical synthesis or recombinant DNA techniques. Two related methodologies were used in these experiments. In the first method, probes were synthesized as peptides immobilized on polyethylene pins by the method of Geysen et al. (Geysen, H. M., Meloen, R. H., and Barteling, S. J. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 3998-4002). Three sets of sequentially overlapping tetrapeptides, hexapeptides, and octapeptides covering the entire length of the human TGF alpha sequence were synthesized. In the second method, a set of overlapping 8-residue synthetic peptides, freely soluble in solution, were used as probes. By both methods, the nonneutralizing monoclonal antibodies, i.e. those that did not inhibit TGF alpha in mitogenic assays, recognized two immunodominant regions represented by the NH2-terminal segment (residues 1-9) and the most prominent beta-sheet of the molecule (residues 22-31). The NH2 terminus and the beta-sheet-(22-31) are in the same face of the molecule as determined by the solution structure. These two immunodominant regions were also recognized by the polyclonal antibodies as well as regions in the COOH terminus as minor epitopes. However, none of the neutralizing monoclonal antibodies recognized any synthetic peptides. Thus, our results suggest that the receptor-binding surface of TGF alpha does not involve the face represented by the NH2-terminal fragment and the major beta-sheet of residues 22-31, but rather, that the opposite face represented by two loops formed by residues 12-20 and 34-43 may be involved in TGF alpha binding to its receptor.     

Different actions of secretin and Gly-extended secretin predict secretin receptor subtypes

Only one secretin receptor has been cloned and its properties characterized in native and transfected cells. To test the hypothesis that stimulatory and inhibitory effects of secretin are mediated by different secretin receptor subtypes, pancreatic and gastric secretory responses to secretin and secretin-Gly were determined in rats. Pancreatic fluid secretion was increased equipotently by secretin and secretin-Gly, but secretin was markedly more potent for inhibition of basal and gastrin-induced acid secretion. In Chinese hamster ovary cells stably transfected with the rat secretin receptor, secretin and secretin-Gly equipotently displaced (125)I-labeled secretin (IC(50) values 5.3 +/- 0.5 and 6.4 +/- 0.6 nM, respectively). Secretin, but not secretin-Gly, caused release of somatostatin from rat gastric mucosal D cells. Thus the equipotent actions of secretin and secretin-Gly on pancreatic secretion appear to result from equal binding and activation of the pancreatic secretin receptor. Conversely, secretin more potently inhibited gastric acid secretion in vivo, and only secretin released somatostatin from D cells in vitro. These results support the existence of a secretin receptor subtype mediating inhibition of gastric acid secretion that is distinct from the previously characterized pancreatic secretin receptor.     

Identification of highly polymorphic DNA regions in tomato

Summary This paper describes the use of oligonucleotide probes to reveal highly polymorphic DNA regions in pomato. With a (GATA)₄ probe the level of polymorphism detected is high enough to identify all 15 tomato cultivars used in this study. Individual plants of one cultivar all showed the same cultivar-specific DNA-finger-print. In an F₂-population of self-fertilized cv. Sonatine, GATA-containing loci segregated in a Mendelian (31) fashion. Experiments with in-vitro propagated plant material showed that the DNA-fingerprints are not affected by tissue-culture procedures. This indicates that changes in the genetic integrity, which often accompany in-vitro propagation (somaclonal variation), are not extended to the DNA detected with the (GATA)₄ probe. The relative high stability and the Mendelian segregation of (GATA)₄-derived DNA-fingerprints make them ideally suited for identification of tomato cultivars.     

Identification of four highly conserved regions in DNA-PKcs

The gene for the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) is responsible for severe combined immune deficiency (SCID) and its products associate with Ku70/Ku86 autoantigens, c-Abl, and other factors to exert its roles. Investigations to date suggest that DNA-PKcs comprises several regions which specifically interact with these known and other as yet unidentified factors. Nevertheless, the relationship between the structure and function of the DNA-PKcs molecule is poorly understood. Here we report cloning of the entire DNA-PKcs cDNA from chicken and Xenopus laevis. Comparative study of the DNA-PKcs polypeptides from four different vertebrates revealed at least three novel conserved regions in addition to the carboxyl-terminal region containing the phosphatidylinositol-3 kinase domain. We also demonstrated that the four vertebrates share the common genomic organization between a licensing factor, MCM4, and DNA-PKcs, both of which locate in a head-to-head manner within a few kilobase intervals. These data provide useful clues for the further genetic study of this huge multifunctional enzyme.