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P Argos

Publications and source records attributed to P Argos.

At least 145 records · Page 8Linked to original sources
PubMed1985

Protein-RNA interactions in belladonna mottle virus investigated by laser Raman spectroscopy.

Raman difference spectroscopy of the belladonna mottle virus (BDMV) and its separated RNA and protein components indicates that molecular interaction occurs between the single-stranded RNA genome and capsid subunits. The molecular interactions that stabilize the virion at pH 5.0 are altered or eliminated at pH 8.0, even though release of the RNA from the capsid is prevented by the addition of divalent metal cations (Ca2+). From the perturbations that occur to Raman lines of cytosine and adenine rings of the encapsidated RNA molecule between pH values of 5.0 and 8.0, it is concluded that cytosines are protonated in significant numbers at the conditions which maintain the native virus structure and that the stacking of adenines is altered by changes in pH. The degree of protonation of RNA bases can be reduced by elevation of the pH to 8.0 for encapsidated RNA or by release of the RNA from the capsid at pH 5.0. Although the protein groups that interact with the viral RNA cannot be identified unambiguously from the Raman spectra, it is apparent that the molecular environments of aromatic amino acid side chains are altered with the same changes in pH (from 5.0 to 8.0) that perturb the cytosine and adenine ring structures. No significant change in secondary structures of the capsid subunit can be detected with changes in pH or with RNA release. On the other hand, the characteristic Raman lines of the phosphate groups of packaged RNA differ from those of naked RNA at all pH values examined, most likely as a result of specific electrostatic binding of divalent cations to RNA phosphates within the virus shell.

Capsid↗
PubMed1985

Structural similarity between legumin and vicilin storage proteins from legumes.

The primary structures for several members of both the vicilin and legumin families of storage proteins were examined using a computer routine based on amino acid physical characteristics. The comparison algorithm revealed that sequences from the two families could be aligned and share a number of predicted secondary structural features. The COOH-terminal half of the subunits in both families displayed a highly conserved core region that was largely hydrophobic and in which a high proportion of the residues were predicted to be in beta-sheet conformations. The central region of the molecules which contained mixed areas of predicted helical and sheet conformations showed more variability in residue selection than the COOH-terminal regions. The NH2-terminal segments of subunits from the two different families could not be aligned though they characteristically had a high proportion of residues predicted to be in helical conformations. The feature which most clearly distinguished subunits between the two families was an inserted span in the legumin group with a high proportion of acidic amino acids located between the central and COOH-terminal domains. Residues in this insertion were predicted to exist mainly in helical conformation. Since considerable size variation occurs in this area amongst the legumin subunits, alterations in this region may have a minimal detrimental effect on the structure of the proteins.

Amino Acid Sequence↗
PubMed1985

Evidence for a repeating domain in type I restriction enzymes.

The primary structures of the recognition subunit (hsdS) in type I restriction enzymes from three isolates of Escherichia coli were compared and aligned by use of amino acid physical properties. A repeating domain was found in each of the subunits suggesting a pseudo-dimeric structure. Secondary structure predictions delineated two helical regions in each domain which suggested that the recognition subunits may act in a fashion similar to that proposed for repressor and activator molecules; namely, interaction with double-stranded DNA through helices and in two successive major grooves on the same DNA side. One helical motif could provide the specific recognition site and the other, the restriction site.

Amino Acid Sequence↗
PubMed1985

The release of growth arrest by microinjection of adenovirus E1A DNA.

The induction of DNA synthesis in growth-arrested mouse fibroblasts (NIH 3T3) was studied by microinjection of different constructs of adenovirus DNA using SV40 DNA and plasmid DNA as positive and negative controls. The E1A region of adenovirus types 2 and 12 appears to be sufficient to induce cellular DNA synthesis after growth arrest in approximately 30% of the cells and both 13S and 12S cDNA constructs mediate this effect. The presence of the E1A protein products as assayed by immunofluorescence does not strictly correlate with the induction of DNA synthesis in microinjected cells in contrast to the SV40 large T-antigen. Microinjection of truncated fragments of the Ad12 E1A region suggests, however, that the protein products of 12S and 13S may be involved in the induction process. A sequence comparison of the SV40 T-antigen and the adenovirus E1A products identified a region of significant homology providing a basis for a hypothesis concerning the evolution of T-antigen genes in DNA viruses.

Adenoviruses, Human↗
PubMed1984

Human adenosine deaminase. cDNA and complete primary amino acid sequence.

A previously cloned partial adenosine deaminase cDNA insert (0.8 kilobase) was used to clone additional nucleotide sequences from human HPB ALL cDNA libraries. cDNA encompassing the entire coding, and 3'-untranslated regions as well as nearly all of the 5'-untranslated region was obtained. The complete amino acid sequence of the enzyme deduced from the cDNA sequence and protein sequencing consists of 362 amino acids, excluding the initiator Met, and accounts for Mr = 40,638. Secondary structure predictions assign adenosine deaminase to the alpha/beta class of proteins. Northern blot analysis with a cDNA probe showed adenosine deaminase mRNA to be present in normal to above normal amounts in B-lymphoblasts derived from adenosine deaminase-deficient patients with severe combined immunodeficiency disease. Knowledge of the cDNA and primary amino acid sequence of adenosine deaminase will be pivotal in further defining the genetic abnormality and its functional consequences in adenosine deaminase expression defects.

Adenosine Deaminase↗
PubMed1984

Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families.

The amino acid sequences deduced from the nucleic acid sequences of several animal picornaviruses and cowpea mosaic virus (CPMV), a plant virus, were compared. Good homology was found between CPMV and the picornaviruses in the region of the picornavirus 2C (P2-X protein), VPg, 3C pro (proteinase) and 3D pol (RNA polymerase) regions. The CPMV B genome was found to have a similar gene organization to the picornaviruses. A comparison of the 3C pro (proteinase) regions of all of the available picornavirus sequences and CPMV allowed us to identify residues that are completely conserved; of these only two residues, Cys-147 and His-161 (poliovirus proteinase) could be the reactive residues of the active site of a proteinase with analogous mechanism to a known proteinase. We conclude that the proteinases encoded by these viruses are probably cysteine proteinases, mechanistically related, but not homologous to papain.

Amino Acid Sequence↗
PubMed1984

Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses.

Possible alignments for portions of the genomic codons in eight different plant and animal viruses are presented: tobacco mosaic, brome mosaic, alfalfa mosaic, sindbis, foot-and-mouth disease, polio, encephalomyocarditis, and cowpea mosaic viruses. Since in one of the viruses (polio) the aligned sequence has been identified as an RNA-dependent polymerase, this would imply the identification of the polymerases in the other viruses. A conserved fourteen-residue segment consisting of an Asp-Asp sequence flanked by hydrophobic residues has also been found in retroviral reverse transcriptases, a bacteriophage, influenza virus, cauliflower mosaic virus and hepatitis B virus, suggesting this span as a possible active site or nucleic acid recognition region for the polymerases. Evolutionary implications are discussed.

Animals↗
PubMed1984

Rhodopsin's protein and carbohydrate structure: selected aspects.

A topographic model for rhodopsin has been constructed based upon evaluation of rhodopsin's sequence by a secondary structure prediction algorithm as well as chemical and enzymatic modification of rhodopsin in the membrane [Hargrave et al. (1983) Biophys. Struct. Mech. 9, 235-244]. The non-uniform distribution of several amino acids in the primary structure and within the topographic model is discussed. The seven predicted helices were evaluated and each helix was found to have one surface which is much more hydrophobic than the other. Stereoscopic views of a three dimensional model with a functional color-coding scheme incorporating these features are presented. The amino acid sequence of rhodopsin has been compared to other proteins in the Dayhoff Protein Data Bank. No obvious relationship to any other protein sequenced was found. High resolution proton magnetic resonance spectroscopy was used to reinvestigate the structure and relative proportions of rhodopsin's major and minor oligosaccharide chains. One major (Man3GlcNAc3) and two minor (Man4GlcNAc3 and Man5GlcNAc3) were observed.

Amino Acid Sequence↗
PubMed1984

Residue contacts in protein structures and implications for protein folding.

The preferential association of amino acid side groups with specific side chain atoms are examined in 44 known protein structures. The resulting association potentials among residue side groups are used to detect structural homology in proteins displaying little or no homology in their primary sequences. Suggestions are also made regarding the nature of the protein folding process. They are based on statistical observations that delineate the extent of short and long range interactions and that display side group bias in association with other side chain atoms on their N-terminal side.

Amino Acid Sequence↗
PubMed1983

Structural homology of lens crystallins. III. Secondary structure estimation from circular dichroism and prediction from amino acid sequences.

Circular dichroism spectra (196-240 nm) of calf alpha-, beta H-, beta L- and gamma-crystallins were measured and analyzed over the entire wavelength range with five curve-fitting procedures for estimating protein secondary structure. For gamma-crystallin the estimates are in good agreement with the X-ray structure. For all four crystallins the estimates are very similar: 0-9% alpha-helix and 51-68% beta-sheet. This is in accordance with the three-dimensional homology of beta Bp- and gamma 2-crystallin polypeptide chains as postulated from their 30% sequence homology, and suggests that alpha A- and alpha B-crystallin chains may also have a corresponding structure. Secondary structure elements in the four amino acid sequences were predicted using two different comprehensive prediction methods. For gamma 2-crystallin the predictions of beta-sheet are in good agreement with the X-ray structure and with circular dichroism estimates. For beta Bp-crystallin only the C-terminal domain secondary structure predictions are considered satisfactory, which possibly relates to the proposed role of the N-terminal domain in subunit interactions. The combined predictions for alpha A- and alpha B-chains (3% helix, 49% sheet) are in excellent agreement with circular dichroism. Moreover, the good alignment of predicted beta-sheet segments in alpha-crystallin chains with known beta-sheet strands in gamma 2- (and presumably beta Bp-) crystallin strongly supports a similar 4-motif folding pattern in all four calf crystallin chains.

Amino Acid Sequence↗
PubMed1983

Nucleotide and amino acid sequence comparisons of preprosomatostatins.

The amino acid and nucleotide sequences have been aligned for five preprosomatostatins: two from catfish, two from anglerfish, and one from rat. The physical characteristics of the aligned residues as well as substitutions in the nucleotide sequences suggest considerable mutability in one of the catfish and anglerfish precursors while three of the preprohormones which give rise to somatostatins-14 are closely related. Although there is a considerable number of amino acid substitutions within the aligned somatostatin-14 precursors, there is a high degree of structural relatedness among them. These results suggest that additional physiological roles for the amino acid sequences outside of the hormone region are likely. The predicted secondary structures of the three somatostatin-14 precursors are dominated by helical and turn configurations which are correlated with observed co- and post-translational processing of the preprohormones.

Amino Acid Sequence↗
PubMed1983

A possible nucleotide-binding domain in the tertiary fold of phosphoribosyltransferases.

Comparison of the primary structures of three phosphoribosyltransferases (human hypoxanthine-guanine, Salmonella typhimurium ATP, and Escherichia coli glutamine) showed no significant amino acid sequence homology except for a 35-residue span in hypoxanthine-guanine and glutamine phosphoribosyltransferases. However, comparison of smoothed plots of amino acid physical characteristics thought to control protein folding with amino acid sequence number resulted in a substantial correlation for a 120-residue stretch in each of the phosphoribosyltransferases. A secondary structure prediction analysis of the regions indicated a dinucleotide-binding fold with its characteristic beta alpha beta secondary structural pattern. Furthermore, the physical parametric correlation analysis suggested a common catalytic domain fold for hypoxanthine-guanine and glutamine phosphoribosyltransferases which was consistent with the register of the sequence homology. A possible binding mode of the phosphoribosyltransferase substrates is discussed. The physical parametric approach to protein sequence comparison may be generally applicable for distantly related proteins which maintain similar structural folds without any apparent sequence homology.

ATP Phosphoribosyltransferase↗
PubMed1983

Structural homology of lens crystallins. A method to detect protein structural homology from primary sequences.

The X-ray crystallographic structure of bovine gamma-crystallin shows four similar folding motifs each composed of about 42 residues arranged as four topologically sequential, anti-parallel beta-strands. Since the beta and gamma-crystallin sequences show good homology, proposals for a four-motif beta-crystallin model have been made. The other bovine eye-lens protein species, alpha-crystallins, are not homologous to beta or gamma-crystallin in primary structure. In the present work, smoothed plots of amino acid sequence number versus a residue characteristic (e.g. hydrophobicity) were calculated for the various crystallins. Cross-correlation coefficients were then determined between pairs of crystallin plots for various registers of the curves. The correlation plots were then combined for several characteristics and for pairwise comparisons between beta or gamma-crystallin and the alpha-crystallins. The resulting plots showed four peaks separated by about 42 residues for the alpha-crystallins, suggesting that they also possess a four-motif beta-barrel structure. The physical parameter comparison technique appears generally applicable in suggesting a structural and functional relationship amongst proteins that show no primary sequence homology.

Amino Acid Sequence↗
PubMed1983

The structure of bovine rhodopsin.

We have isolated 16 peptides from a cyanogen bromide digest of rhodopsin. These cyanogen bromide peptides account for the complete composition of the protein. Methionine-containing peptides from other chemical and enzymatic digests of rhodopsin have allowed us to place the cyanogen bromide peptides in order, yielding the sequence of the protein. We have completed the sequence of most of the cyanogen bromide peptides. This information, in conjunction with that from other laboratories, forms the basis for our prediction of the secondary structure of the protein and how it may be arranged in the disk membrane.

Amino Acid Sequence↗
PubMed1982

Structural prediction of membrane-bound proteins.

A prediction algorithm based on physical characteristics of the twenty amino acids and refined by comparison to the proposed bacteriorhodopsin structure was devised to delineate likely membrane-buried regions in the primary sequences of proteins known to interact with the lipid bilayer. Application of the method to the sequence of the carboxyl terminal one-third of bovine rhodopsin predicted a membrane-buried helical hairpin structure. With the use of lipid-buried segments in bacteriorhodopsin as well as regions predicted by the algorithm in other membrane-bound proteins, a hierarchical ranking of the twenty amino acids in their preferences to be in lipid contact was calculated. A helical wheel analysis of the predicted regions suggests which helical faces are within the protein interior and which are in contact with the lipid bilayer.

Amino Acid Sequence↗
PubMed1982

A structural model for maize zein proteins.

With the knowledge of the amino acid sequences of two maize zein proteins (apparent molecular weights of 19,000 and 22,000), a structural model is proposed for their molecular conformation. The circular dichroic spectrum taken in the 190-240 nm range for a zein protein mixture in methanol solution showed the zein secondary structure to be largely helical. The polar, hydrophobic, and turn characteristics of the zein residues, as well as the homologous repeat units in their primary sequences, suggested a structure with nine adjacent, topologically antiparallel helices clustered within a distorted cylinder. Polar residues distributed along the helical surfaces allowed intra- and intermolecular hydrogen bonding such that the zein molecules could be arranged in planes. The proposed glutamine-rich turns located between the helices and at the cylindrical caps would favor side chain interactions resulting in stacking of the molecular planes. Physical properties observed for the zein proteins are explained by the model.

Amino Acid Sequence↗
PubMed1982

Amino acid distribution in protein secondary structures.

The compositional distribution of the twenty amino acids was examined for particular positions within secondary structures (alpha-helices, beta-strands, and turns) taken from a 44-protein sample. Correlation coefficients calculated between positional composition of the amino acids and various of their physico-chemical characteristics indicated considerable asymmetry in the properties of the residues comprising regions within and adjacent to secondary structures, modes of helix formation, physical parameters most sensitive to the buriedness of residues in beta-strands, and possible improvements in the accuracy of secondary structure prediction methodologies.

Amino Acids↗