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At least 289 records · Page 16Linked to original sources
PubMed1990

Weighting aligned protein or nucleic acid sequences to correct for unequal representation.

Aligned sequences from the same family (e.g. the haemoglobins) are seldom representative of the entire family. This is because (1) the sequence databases are heavily skewed toward a small number of organisms and (2) only a minute fraction of all the different family members have been sequenced. For many applications, such as using alignments or profiles to perform database searches for distantly related family members, such unequal representation requires correction. An algorithm to perform appropriate weighting of individual sequences is presented along with examples illustrating its efficacy.

Algorithms↗
PubMed2001

Changes in plasma gonadotrophin and prolactin concentrations following castration of the pony stallion.

Concentrations of gonadotrophins and prolactin were recorded in pony stallions castrated during the early breeding season, to examine the regulatory role of the gonad at a time when testosterone has been postulated to exert positive feedback on LH secretion. Further, gonadotrophin concentrations in geldings are reported to return to values within the normal range of the entire stallion. In an attempt to characterize this species-specific reversal, the gonadotrophin concentrations of 6 male ponies castrated on 25 March were monitored for 4 months, and 4 stallions were used to generate control data. Blood samples were collected daily, from 3 d before to 10 d after castration (Day 0), and weekly thereafter until Day 122. The pituitary response to castration was immediate. Castration resulted in a previously unreported, dramatic (13-fold) but transient (3 d) surge in circulating concentrations of LH. Concentrations of LH and FSH increased in a logarithmically scaled (LH, R2 = 0.77; FSH, R2 = 0.93) manner over the subsequent 5 wk, during which temporal changes in concentrations of both hormones were strongly correlated (R2 = 0.97). The ratio of plasma gonadotrophin concentrations was consistent throughout (LH:FSH, 1.43 +/- 0.04). Maximal concentrations of LH (20.58 +/- 1.97 ng/mL, Day 34.8 +/- 3.2) were attained approximately 2 wk before the peak in FSH (16.99 +/- 1.97 ng/mL, Day 49.7 +/- 3.0). Plasma gonadotrophin concentrations exceeded those of entire stallions throughout the study. The equine testes inhibited LH secretion during the early breeding season, and no chronic decrease in plasma gonadotrophin concentrations was recorded. However, the LH surge evident for 3 d immediately afer castration, may be related to the dynamic seasonal interaction between gonadal steroids and the regulation of pituitary gonadotrophin release.

Animals↗
PubMed1997

Probing Flp: a new approach to analyze the structure of a DNA recognizing protein by combining the genetic algorithm, mutagenesis and non-canonical DNA target sites.

A topological and functional overview of a DNA recognition protein with unknown structure can be achieved by combining three different, but complementary approaches: modeling by the genetic algorithm, functional analysis of mutated variants, and testing the target DNA using non-canonical oligonucleotides. As an example we choose the Flp protein, a site-specific recombinase from Saccharomyces cerevisiae. We derive the topological outline including the DNA binding cleft, examine DNA binding regions by deletional and mutational analysis, and analyze the DNA binding site using 7-deazaadenine, 7-deazaguanine, inosine and 4-O-methylthymine as probes. The combined data offer a comprehensive sketch of a plausible protein architecture for Flp. The structure is detailed enough to verify the prediction accuracy for different peptide regions from pre-existing data and by new experimental design.

Binding Sites↗
PubMed1997

The future of protein secondary structure prediction accuracy.

BACKGROUND: The accuracy of secondary structure prediction for a protein from knowledge of its sequence has been significantly improved by about 7% to the 70-75% range by inclusion of information residing in sequences similar to the query sequence. The scientific literature has been inconsistent, if not negative, regarding chances for further improvement from the vast knowledge to be provided by genome sequencing efforts. RESULTS: By applying a prediction technique that is particularly sensitive to added sequence information to a standard set of query sequences with related primary structures taken from chronologically successive releases of the SWISS-PROT database, it is shown that prediction accuracy can be expected to reach 80-85% with a large 10-fold increase in present sequence knowledge. CONCLUSIONS: Even with present prediction approaches, improvement in prediction accuracy can still be expected, albeit limited to no more than 10%.

Algorithms↗
PubMed1997

Protein thermal stability: hydrogen bonds or internal packing?

Thermally stable proteins are of interest for several reasons. They can be used to improve the efficiency of many industrial processes and provide insight into the general mechanisms of protein folding and stabilization. Comparison of tertiary structural properties of several protein families with members of different thermostability should help to delineate the role of individual factors in achieving stability at high temperature. In this work, 16 protein families with at least one known thermophilic and one known mesophilic tertiary structure were examined for the number and type of hydrogen bonds and salt links, polar surface composition, internal cavities and packing densities, and secondary structural composition. The results show a consistent increase in the number of hydrogen bonds and in polar surface area fraction with increased thermostability.

Hydrogen Bonding↗
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↗
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↗
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↗
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↗
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↗
PubMed1977

Secondary-structure predictions of calcium-binding proteins.

The known tertiary structure of carp muscle parvalbumin is consistent with an "EF-hand" architecture (helix-loop-helix) for each calcium-ion binding site. Primary-sequence alignments have indicated four EF hands in rabbit skeletal muscle troponin C and in rabbit myosin alkali light chains. Five secondary-structure prediction methods, based on amino acid sequence only, have been fully computerized and used to calculate joint prediction histograms for several calcium-binding proteins. The joint histogram can suggest directly the extent and sequence of the helical- and loop-structural elements, as well as any secondary structural distortions or evolutionary developments. Since the histogram predicted well the length and sequence of secondary structural elements in carp muscle parvalbumin, it seemed reasonable to calculate the joint distribution for other proteins that might bind calcium through the EF-hand configuration. The histograms indicated the four EF-hand regions speculated fro rabbit skeletal muscle troponin C but suggested only three such hands in bovine cardiac muscle troponin C and with a distorted fourth hand. Considerable secondary structural distortion is postulated for the alkali light chains. Possible EF configurations consistent with the histogram results are speculated for Escherichia coli acyl-carrier protein and bovine prothrombin fragment 1, which have been shown to bind calcium. The secondary-structure-prediction algorithms appear to be a useful adjunct to sequence-alignment techniques, especially in cases where the primary sequence homology is weak or the evolutionary distance is large.

Amino Acid Sequence↗
PubMed1977

Convergence of active center geometries.

Comparisons have been made between the active center geometries of lactate dehydrogenase and glyceraldehyde-3-phosphate dehydrogenase, chymotrypsin and papain, and glyceraldehyde-3-phosphate dehydrogenase and papain. In the dehydrogenases, orientation of the nicotinamide ring about the glycosidic bond is determined by the substrate stereochemistry. The proper positioning of the carboxyamide moiety allows for the close approach of the C4 atom on the nicotinamide and the reactive carbon of the substrate. It follows that, once the conformation of the substrate or substrate intermediate has been established with respect to the functional groups in the enzyme, the A- or B-side specificity of the nicotinamide ring is predetermined. Hence, dehydrogenases which are divergently evolving from a common precursor must maintain the nicotinamide specificity if the protein fold of the catalytic domain is conserved. The tetrahedral intermediates produced during acylation of chymotrypsin and papain are found to be of opposite hand, while those of papain and glyceraldehyde-3-phosphate dehydrogenase can be regarded to be of the same hand. Thus the serine proteases, subtilisin and those of the chymotrypsin family, are of one hand while the cysteine enzymes, glyceraldehyde-3-phosphate dehydrogenase and papain, are of the other.

Binding Sites↗
PubMed2001

Reactivity of site-isolated metal clusters: propylidyne on gamma-Al2O3-supported Ir4.

To contrast the reactivity of supported metal clusters with that of extended metal surfaces, we investigated the reactions of tetrairidium clusters supported on porous gamma-Al2O3 (Ir4/gamma-Al2O3) with propene and with H2. Infrared, 13C NMR, and extended X-ray absorption fine-structure spectroscopy were used to characterize the ligands formed on the clusters. Propene adsorption onto Ir4/gamma-Al2O3 at 298 K gave stable, cluster-bound mu3-propylidyne. Propene adsorbed onto Ir4/gamma-Al2O3 at 138 K reacted at approximately 219 K to form a stable, highly dehydrogenated, cluster-bound hydrocarbon species approximated as CxHy (such as, for example, C3H2 or C2H). H2 reacted with Ir4/gamma-Al2O3 at 298 K, forming ligands (likely hydrides), which prevented subsequent reaction of the clusters with propene to form propylidyne. Propylidyne on Ir4 was stable in helium or H2 as the sample was heated to 523 K, whereupon it reacted with oxygen of the support to give CO. Propylidyne on Ir4 did not undergo isotopic exchange in the presence of D2 at 298 K. In contrast, the literature shows that propylidyne chemisorbed on extended metal surfaces is hydrogenated in the presence of H2 (or D2) and exchanges hydrogen with gaseous D2 at room temperature; in the absence of H2, it decomposes thermally to give hydrocarbon fragments at temperatures much less than 523 K. The striking difference in reactivities of propylidyne on clusters and propylidyne on extended metal surfaces implies the requirement of ensembles of more than the three metal surface atoms bonded to propylidyne in the surface reactions. The results highlight the unique reactivity of small site-isolated metal clusters.

Journal Article↗