Search PubMed⌕ Search

Biomedical subjects

P Argos

Publications and source records attributed to P Argos.

At least 163 records · Page 9Linked to original sources
PubMed1982

Protein secondary structure. Studies on the limits of prediction accuracy.

A secondary structure prediction technique is proposed which includes nucleation site determination through multiplication of conformational preference parameters as well as weighting factors to represent structurally stabilizing short range interactions. The prediction accuracy of the method is calculated using data bases categorized according to the four protein structural classes and with differing assignments of secondary structural regions. The results indicate that nearest neighbor prediction techniques (a) are insensitive to various assignment criteria for the secondary structural spans, (b) have nearly achieved their upper limit of prediction accuracy, and (c) can be somewhat improved through the use of stereochemical weighting factors and conformational parameters derived from the four structural groups.

Chemical Phenomena↗
PubMed1981

Structural stability of halophilic proteins.

An examination of halobacterial amino acids exchanges as they appear in the known Spirulina platensis [2Fe-2S] ferredoxin tertiary structure indicated that most of the additional acidic residues of the halophiles occurred on the external surface of the alga structure; however, further negative changes were not placed in the ferredoxin active site region. A statistical investigation of the amino acid compositions of seven halophile and nonhalophile protein counterparts indicated that the bulkiness of amino acids used by halophiles is considerably reduced and that the overall hydrophobicity of halophilic and non halophilic molecules was essentially the same. It is suggested that the principal mode of structural stabilization for halophilic proteins is effective competition with the cytoplasmic salt for water through utilization of many external carboxyl groups of glutamic and aspartic acids. A reduction is residue bulkiness would prevent inactivation in the presence of the high molarity, antichaotropic KCl. Halophilic functionality is preserved through avoidance of additional negative charge at the active site surface.

Amino Acid Sequence↗
PubMed1981

Structural prediction of sugar-binding proteins functional in chemotaxis and transport.

Comparisons of the D-galactose- and D-ribose-binding protein amino acid sequences and secondary structure predictions with the known primary and three-dimensional structure of L-arabinose-binding protein suggest that the three proteins have similar molecular structures. These studies also indicate an evolutionary relationship among the proteins. One region of striking homology between the galactose- and ribose-binding proteins suggests that this may be th protein-protein contact site for interaction with the membrane-bound chemotaxis receptor. The ligands and the geometry of the galactose binding site are also predicted.

Amino Acid Sequence↗
PubMed1981

Protein folding.

After some general remarks on protein structure, there follows a discussion on primary, secondary, and tertiary organization. The account of primary structure includes a discussion of the conformation of disulfide bonds. Types of helices, sheets, and turns are described in the section on secondary structure, followed by a discussion of super-secondary structure and the effects of metals and prosthetic groups of protein fold. The crux of the review lies in an examination of tertiary structure, or specifically of domains that are defined, in part, as functional units within a polypeptide chain. An assembly of domains can in turn result in a protein whose function is quite sophisticated. Some consideration of domain recognition is given in the section on taxonomy and in the appendix. The key part of the tertiary structure section concentrates on a taxonomic protein classification dependent not only on structure but also on function. A discussion of the requirements by quaternary structure on a fold are omitted in this review. Finally, no review of this kind can escape a discussion of evolutionary convergence and divergence.

Amino Acid Sequence↗
PubMed1980

The secondary structure of staphylococcal enterotoxins A, B and C.

The circular dichroism (CD) of staphylococcal enterotoxins A, B and C was measured. The CD of enterotoxins B and C were almost identical from 250 to 320 nm, but differed from the CD of enterotoxin A. The spectrum of enterotoxin A in this wavelength region contained the same bands with respect to both location and sign, but with significant differences in intensity. The CD spectra of enterotoxins B and C were also much more alike from 190 to 250 nm. Although all three enterotoxins had a major negative extremum at 215--218 nm, its magnitude was equal in enterotoxins B and C, but was substantially decreased in enterotoxin A. The secondary structure of the enterotoxins contained little alpha-helix as analyzed with CD models. A secondary structure of entertoxin B compured from a scheme based on a joint prediction histogram of five separate methods, placed 29 residues in alpha-helices, 71 in beta-pleated sheets, 88 in beta-turns and 55 in aperiodic conformation.

Chemical Phenomena↗
PubMed1980

The relationship between coding sequences and function in some heme binding proteins.

It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochrome c and cytochrome b5 chains (Argos and Rossmann 1979), it can be inferred that the cytochrome c gene will contain only one coding sequence while the cytochrome b5 gene will be composed of three exons as found in the globin gene.

Amino Acid Sequence↗
PubMed1980

A structural comparison of concanavalin A and tomato bushy stunt virus protein.

Significant structural equivalence has been found among the polypeptide folds of the two tomato bushy stunt virus (TBSV) subunit domains and concanavalin A. This suggests gene duplication in the TBSV coat protein and leads to speculation on common functional properties of concanavalin A and viral coat proteins.

Chemical Phenomena↗
PubMed1980

Prediction of secondary structural elements in glycerol-3-phosphate dehydrogenase by comparison with other dehydrogenases.

The secondary structure of glycerol-3-phosphate dehydrogenase was predicted from its amino acid sequence. The pattern of helices and sheets within the first half of the polypeptide as well as specific marker residues were consistent with the properties of the NAD binding domain in other dehydrogenases. The second half of the sequence shows similarities with the catalytic domain of glyceraldehyde-3-phosphate dehydrogenase. The resulting two-domain structure of glycerol-3-phosphate dehydrogenase allows the correct environment for the B specificity of the nicotinamide ring and the L-glycerol 3-phosphate substrate.

Alcohol Oxidoreductases↗
PubMed1979

Thermal stability and protein structure.

Amino acid sequences have been compared for thermophilic and mesophilic molecules of ferredoxin, glyceraldehyde-3-phosphate dehydrogenase, and lactate dehydrogenase. It is shown that Gly, Ser, Ser, Lys, and Asp in mesophiles are generally substituted by Ala, Ala, Thr, Arg, and Glu, respectively, in thermophiles. These exchanges suggest that thermal stability can be achieved by the addition of many small changes throughout the molecule without significant change in the backbone conformation. Their overall effect is primarily to increase internal and decrease external hydrophobicity as well as to favor helix stabilizing residues in helices. These substitutions minimize interruption of function or internal residue packing arrangements. Although the analysis has been confined to the above-mentioned molecules, the observed stabilizing principles may be more generally applicable.

Amino Acid Sequence↗
PubMed1979

Structural comparisons of heme binding proteins.

Of the 82 three dimensionally characterized residues of cytochrome c551, 49 are found to be structurally and topologically equivalent to the globin fold and 41 are equivalent to the cytochrome b5 fold, with a respective root mean square separation of 3.5 and 4.9 A between equivalenced Calpha atoms. The common fold represents a central heme binding core, corresponding to the middle exon of certain globin genes. After superposition of the protein folds, the heme irons are found to be separated by 5.4 and 1.6 A, while their heme normals are inclined by 6 degrees and 32 degrees, respectively. Furthermore, the heme "face", determined by the asymmetric attachment of the vinyl and propionyl side chains, is directed similarly in all three heme proteins. The heme itself is rotated by 72 degrees and 116 degrees about its normal, respectively. The minimum base change per codon for the three pairwise comparisons corresponds to the expected value of random sequence comparisons. While all three heme proteins may have diverged from a common ancestor, their similarity may have arisen from the requirements of heme binding or the utilization of a particularly stable fold. Known structures within commonly accepted divergent families were superimposed in order to discriminate better between convergence and divergence. Minimum base changes per codon, number of deletions and insertions, percentage of equivalenced residues, precision of heme superposition, and root mean square separation of equivalenced Calpha atoms were tested as measures of evolutionary relationships.

Cytochrome c Group↗
PubMed1978

The taxonomy of binding sites in proteins.

Conservation of polypeptide fold and mode of ligand binding is frequently found within proteins of related function. Examples illustrating this phenomenon are taken from NAD linked enzymes, nucleotide binding proteins, polysaccharide binding proteins, heme binding proteins and enzymes with essential Fe--S complexes or zinc atoms.

Amino Acid Sequence↗