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P Argos

Publications and source records attributed to P Argos.

At least 127 records · Page 7Linked to original sources
PubMed1987

Analysis of sequence-similar pentapeptides in unrelated protein tertiary structures. Strategies for protein folding and a guide for site-directed mutagenesis.

From the most recent Brookhaven Protein Co-ordinate Databank, 229 sequence-identical pentapeptide pairs, each found in two unrelated protein structures, were collected; 9115 such pairs differing in only one residue were also gathered. For both samples the main-chain fold was conserved about 20% of the time, despite the different atomic environments presented by the unrelated protein architectures. An analysis of the substituted residues as well as the composition of the sequence-similar pentapeptides allowed several suggestions regarding protein folding mechanisms. An examination of the most frequently observed residue substitutions and their correlation with structural changes in the oligopeptide pairs yields a possible guide for site-directed mutagenesis experiments, especially when no tertiary structural information is at hand.

Amino Acid Sequence↗
PubMed1987

Repeating structure of chick tropoelastin revealed by complementary DNA cloning.

A cDNA library was constructed from chick aorta poly(adenylic acid)-containing RNA in the expression vector pEX1. Several clones were identified by screening the library with a polyclonal antiserum raised against chick tropoelastin and confirmed by DNA sequencing. Analysis of the deduced amino acid sequence, corresponding to the mature tropoelastin and most of the signal peptide, revealed that the molecule is composed of at least 8, and possibly 13, repeating units. The common features of each unit include an N-terminal region composed largely of alanines and lysines and ending with an aromatic amino acid, followed by a GAG span and then a C-terminal region consisting mostly of valines, prolines, and glycines often present in several copies of the sequence (VPGV). This structure is discussed in terms of the functional properties of the molecule.

Amino Acid Sequence↗
PubMed1987

A sensitive procedure to compare amino acid sequences.

Methods are discussed that provide sensitive criteria for detection of weak sequence homologies. They are based on the Dayhoff relatedness odds amino acid exchange matrix and certain residue physical characteristics. The search procedure uses several residue probe lengths in comparing all possible segments of two protein sequences, and search plots are shown with peak values displayed over the entire search length. Alignments are automatically effected using the highest search matrix values and without the necessity of gap penalties. Tests for significance are derived from actual protein sequences rather than a random shuffling procedure.

Alcohol Dehydrogenase↗
PubMed1987

Is Sindbis a simple picornavirus with an envelope?

A three-dimensional image reconstruction was performed from cryo-electron micrographs of isolated Sindbis (SNV) nucleocapsids. The isolated capsid is a smooth but fenestrated T = 3 structure. Comparison with the nucleocapsid seen within the whole virion indicated that the structure resembles the swollen forms which some non-enveloped viruses adopt after removal of divalent cations. A sensitive comparison method was used to align SNV capsid protein sequences with those of picornavirus vp3 capsid proteins whose high resolution structures display an eight-stranded beta-barrel fold found in many icosahedral viruses. The alignment predicted a similar folding for the Sindbis protein which juxtaposes several sets of residues known to be essential for its serine proteolytic activity. These results suggest that the capsid proteins of the enveloped alphaviruses and the non-enveloped picornaviruses may have arisen through divergent evolution from a simple, vp3-like ancestor.

Amino Acid Sequence↗
PubMed1986

Cloning of the human cDNA for the U1 RNA-associated 70K protein.

Anti-RNP sera were used to isolate a cDNA clone for the largest polypeptide of the U1 snRNP, a protein of mol. wt 70 kd designated 70K, from a human liver cDNA library constructed in the expression vector pEX1. The cro-beta-galactosidase-70K fusion protein reacted with various anti-RNP patient sera, a rabbit anti-70K antiserum, as well as with a monoclonal antibody specific for this protein. The sequences of four 70K peptides were determined and they match parts of the deduced amino acid sequence of the 1.3 kb insert of p70.1 indicating that it is a genuine 70K cDNA. Screening of a new cDNA library constructed from polysomal mRNA of HeLa cells with the p70.1 clone yielded an overlapping clone, FL70K, which was 2.7 kb long and covered the complete coding and 3'-untranslated sequence of the 70K protein in addition to 680 nucleotides upstream of the putative initiation codon, The predicted mol. wt of the encoded protein is approximately 70 kd. Amino acid analysis of the purified HeLa 70K protein yielded values close or identical to those deduced from the nucleotide sequence of the full-length cDNA. The 70K protein is rich in arginine (20%) and acidic amino acids (18%). Extremely hydrophilic regions containing mixed-charge amino acid clusters have been identified at the carboxyl-terminal half of the protein, which may function in RNA binding. A sequence comparison with two recently cloned RNA binding proteins revealed homology with one region in the U1 RNP 70K protein. This domain may also be responsible for RNA binding.

Amino Acid Sequence↗
PubMed1986

Human adenine phosphoribosyltransferase. Complete amino acid sequence of the erythrocyte enzyme.

We defined the amino acid sequence of adenine phosphoribosyltransferase isolated from human erythrocytes. Peptide fragments formed by cleavage at arginine, lysine, glutamic acid, and methionine were purified by high pressure liquid chromatography and sequenced by manual Edman degradation. The complete primary structure of human adenine phosphoribosyltransferase was established by sequence analysis of 19 peptide fragments. Presumed homology between the human and rodent enzymes was used to order fragments that had inadequate overlapping sequences. The enzyme has 179 residues with a calculated subunit molecular weight of 19,481. Mass spectrometry indicated that the NH2-terminal residue is acetylated. Human adenine phosphoribosyltransferase has sequence homology with xanthine-guanine phosphoribosyltransferase from Escherichia coli in 110-amino acid region encompassing the NH2-terminal section of the enzyme.

Adenine Phosphoribosyltransferase↗
PubMed1986

Sequence analysis and characterization of a maize gene encoding a high-sulfur zein protein of Mr 15,000.

We have isolated a gene coding for a sulfur-rich zein protein from a maize genomic library. The nucleotide sequence of this gene predicts a protein composed of 180 amino acids, including a 20-amino acid signal peptide. As is true of other zeins, there are no intervening sequences in the gene. Comparison of the nucleotide sequence of this gene with that of a homologous cDNA clone revealed only a single difference resulting in a valine/alanine substitution. The Mr 15,000 zein contains no repetitive nucleotide sequences and shows no homology with genes encoding the Mr 22,000 and 19,000 zeins. Circular dichroism analysis of the Mr 15,000 zein protein revealed that it is composed primarily of beta and turn structures. This gene has a short region of nucleotide sequence homology to the cysteine-rich domain of the Mr 27,000 zein, as well as the cysteine-containing barley B-hordein.

Amino Acid Sequence↗
PubMed1986

A conformational preference parameter to predict helices in integral membrane proteins.

Assignments were made for helical regions in several integral membrane proteins using an algorithm devised to delineate the transmembrane helices in bacteriorhodopsin (Eur. J. Biochem. 182 (1982) 565-575). A new conformational preference parameter for membrane-buried helices was obtained. The use of this parameter to predict helices in membrane proteins is discussed. When applied to the L and M subunits of Rhodopseudomonas sphaeroides, five helices were predicted, which is consistent with the three-dimensional X-ray crystal structure. Data on signal sequences and amino acid exchanges in membrane proteins are also analysed and discussed

Adenosine Triphosphatases↗
PubMed1986

The integrase family of site-specific recombinases: regional similarities and global diversity.

A combination of two methods for detecting distant relationships in protein primary sequences was used to compare the site-specific recombination proteins encoded by bacteriophage lambda, phi 80, P22, P2, 186, P4 and P1. This group of proteins exhibits an unexpectedly large diversity of sequences. Despite this diversity, all of the recombinases can be aligned in their C-terminal halves. A 40-residue region near the C terminus is particularly well conserved in all the proteins and is homologous to a region near the C terminus of the yeast 2 mu plasmid Flp protein. This family of recombinases does not appear to be related to any other site-specific recombinases. Three positions are perfectly conserved within this family: histidine, arginine and tyrosine are found at respective alignment positions 396, 399 and 433 within the well-conserved C-terminal region. We speculate that these residues contribute to the active site of this family of recombinases, and suggest that tyrosine-433 forms a transient covalent linkage to DNA during strand cleavage and rejoining.

Amino Acid Sequence↗
PubMed1986

The chicken oestrogen receptor sequence: homology with v-erbA and the human oestrogen and glucocorticoid receptors.

A chicken oviduct cDNA clone containing the complete open reading frame of the oestrogen receptor (ER) has been isolated and sequenced. The mol. wt of the predicted 589-amino acid protein is approximately 66 kd which is very close to that of the human ER. Comparison of the human and chicken amino acid sequences shows that 80% of their amino acids are identical. There are three highly conserved regions; the second and third of which probably represent the DNA- and hormone-binding domains of the receptor. The putative DNA-binding domain is characterised by its high cysteine and basic amino acid content, and the hormone-binding domain by its overall hydrophobicity. These two domains of homology are also present in the human glucocorticoid receptor (GR) and the product of the avian erythroblastosis virus (AEV) gene, v-erbA, indicating that c-erbA, the cellular counterpart of v-erbA, belongs to a multigene family of transcriptional regulatory proteins which bind steroid-related ligands. The first highly conserved ER region is not present in the truncated v-erbA gene, but shares some homology with the N-terminal end of the GR. The function of the v-erbA gene product is discussed in relation to its homology with the ER and GR sequences.

Amino Acid Sequence↗
PubMed1986

Primary structural relationships may reflect similar DNA replication strategies.

The primary structures of several proteins of bacterial and viral origin involved in the initiation of DNA synthesis and its subsequent elongation were compared. It was found that the known sequences of DNA polymerases and the single-stranded DNA binding proteins from phage T7 and Escherichia coli aligned well. Furthermore, segmental homologies were found in the phage phi 29 and adenovirus polymerases as well as in their DNA binding proteins. These results suggest similar mechanisms of DNA synthesis for E. coli and T7 on the one hand and for phi 29 and adenovirus on the other.

Adenoviruses, Human↗
PubMed1985

Homologies and anomalies in primary structural patterns of nucleotide binding proteins.

In searches for homology among nucleotide binding proteins, recent reports have described primary structure alignments for stretches of 30 or so amino acid residues among a variety of proteins including the ras and src oncogene products. The significance of these sequence matches has been tested by searching in available data banks for certain conserved residue patterns resulting from the alignments. The tests suggest that alignments over these limited stretches are not necessarily justifiable and any implications for residues involved in nucleotide binding must be viewed with caution.

Amino Acid Sequence↗
PubMed1985

Turnip yellow mosaic virus and its capsid have thermal stabilities with opposite pH dependence: studies by differential scanning calorimetry and 31P nuclear magnetic resonance spectroscopy.

In the differential scanning calorimetry (DSC) scans of turnip yellow mosaic virus (TYMV) or its capsid a single endotherm was observed. The endotherm was attributed to disruption of the virion or capsid structure with accompanying protein denaturation. At pH 4.5 the thermal stabilities of the TYMV virion and capsid were similar. With increasing pH, the capsid stability increased while the virion stability decreased. At neutral pH the capsid disrupted at 83.5 degrees, and the virion disrupted at 69 degrees. Our results suggest that packaging of viral RNA in the TYMV capsid imparts instability. The pHmid for disruption of the TYMV capsid is 5.7, which is in the pKa range expected for histidine side chains. Hence repulsive interactions involving one or more of the three histidines of the TYMV coat protein may explain the decreased stability of the TYMV capsid at low pH. This conclusion is supported further by the observation that belladonna mottle virus (BDMV) capsid (BDMV and TYMV belong to the tymo virus group), which contains no histidine in its coat protein, did not exhibit pH-dependent stability. The size of the cooperative unit in the disruption of TYMV capsid was estimated to be approximately that of a dimer of the coat protein, at pH 7.0, but a larger oligomer at low pH. Several reports implicate pH-dependent protein-RNA interactions with a pHmid near 7 as important in stabilizing tymovirus virions. Both DSC and 31P nuclear magnetic resonance linewidth analyses of the TYMV virion showed a transition midpoint at pH 7.0.

Calorimetry, Differential Scanning↗
PubMed1985

The primary structure of transcription factor TFIIIA has 12 consecutive repeats.

Analysis of the amino acid sequence of transcription factor TFIIIA from Xenopus laevis reveals the presence of 12 repeating structures, each about 30 residues in length. These segments have been aligned and their secondary structure predicted. The repeats each contain two invariant cysteines and two invariant histidines, perhaps to coordinate a zinc cation. Possible nucleic acid interaction modes are discussed.

Amino Acid Sequence↗
PubMed1985

The primary structure of human hemopexin deduced from cDNA sequence: evidence for internal, repeating homology.

We have cloned and analyzed a cDNA containing the coding sequence for human hemopexin. We have first identified, by immunological screening of 30.000 colonies of a liver cDNA library in the expression vector pEX1, a clone carrying an insert 1170 base pairs long that shows 100% homology with a known human hemopexin peptide. The complete sequence coding for hemopexin was isolated from a liver cDNA library in the vector pAT218. The DNA insert of 1523 base pairs shows an open reading frame coding for 439 amino acids, a 3' noncoding region of 159 nucleotides long, followed by a poly(A) tail. The insert spans the entire coding region and from which the primary structure of the protein was deduced. By computer assisted analysis of the amino acid sequence, it was possible to recognize a core unit, of about 45 amino acids, which is repeated 8 or possibly even 10 fold along the polypeptide chain. This feature suggests that the gene might have evolved through a series of duplications. This characteristic, together with prediction of secondary structure, suggest a rough model for the tridimensional folding that allows some speculations on the function of hemopexin. Blot hybridization of total RNA from human liver with nick translated hemopexin cDNA detected a message of about 1600 nucleotides. Southern blot experiments to identify the hemopexin gene (s) suggest that it is not a large multi-gene family, but that there is only one or at most a few genes in the human genome.

Amino Acid Sequence↗
PubMed1985

Identification of a trpG-related glutamine amide transfer domain in Escherichia coli GMP synthetase.

An improved method was developed to align related protein sequences and search for homology. A glutamine amide transfer domain was identified in an NH2-terminal segment of GMP synthetase from Escherichia coli. Amino acid residues 1-198 in GMP synthetase are homologous with the glutamine amide transfer domain in trpG X D-encoded anthranilate synthase component II-anthranilate phosphoribosyltransferase and the related pabA-encoded p-aminobenzoate synthase component II. This result supports a model for gene fusion in which a trpG-related glutamine amide transfer domain was recruited to augment the function of a primitive NH3-dependent GMP synthetase. Sequence analyses emphasize that glutamine amide transfer domains are thus far found only at the NH2 terminus of fused proteins. Two rules are formulated to explain trpG and trpG-related fusions. (i) trpG and trpG-related genes must have translocated immediately up-stream of genes destined for fusion in order to position a glutamine amide transfer domain at the NH2 terminus after fusion. (ii) trpG and trpG-related genes could not translocate adjacent to a regulatory region at the 5' end of an operon. These rules explain known trpG-like fusions and explain why trpG and pabA are not fused to trpE and pabB, respectively. Alignment searches of GMP synthetase with two other enzymes that bind GMP, E. coli amidophosphoribosyltransferase and human hypoxanthine-guanine phosphoribosyltransferase, suggest a structurally homologous segment which may constitute a GMP binding site.

Amidophosphoribosyltransferase↗
PubMed1985

Primary structural comparison of the preprohormones cholecystokinin and gastrin.

The nucleotide and amino acid sequences of rat preprocholecystokinin and porcine preprogastrin have been aligned and their secondary structures predicted. Both precursors are predicted to be largely in turn and helical configurations. The sequence homology and position of an intron which splits the preprohormones suggest their evolution from a common ancestral protein.

Amino Acid Sequence↗