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At least 235 records · Page 13Linked to original sources
PubMed1991

Identification of proteins in sequence databases from amino acid composition data.

Having obtained the amino acid composition of a protein, chemists and molecular biologists may wish to identify the protein from this data alone. In general such data will have errors associated with them and the length of the protein may be known only approximately or not at all. In this paper a method is described which enables searching of protein sequence databases for sequences or fragments of sequences which have a composition similar to the one being sought. Such searches are generally quite discriminating as shown by the examples provided. This method has been implemented as part of the computer program Scrutineer and is being freely distributed. It is simple to use.

Algorithms↗
PubMed1976

An assessment of protein secondary structure prediction methods based on amino acid sequence.

Five of the several secondary structure prediction methods based on protein amino acid sequence has been computerized, allowing the calculation of joint prediction histograms which have been shown to be superior to any individual prediction. The known structures of about 40 proteins experimentally determined by X-ray crystallography are compared with the predictions resulting from calculated histograms. The accuracy of the predictions for helices is generally much better than for both beta-sheet regions and for turns. The overall agreement between prediction and observation within the amino terminal half of the protein molecules is clearly superior to that for the carboxyl half, suggesting an amino nucleating core. Predictions for smaller proteins and thermally stable proteins are generally good, indicating the sensitivity of the methods to short-range but not long-range interactions. In less than half the cases tested were the predictions useful; there was no way of knowing ahead of time if a favorable prediction would result. Given the lack of dramatic improvement with an increase in data base for the schemes and the generally poor agreement factors, it appears that a perfect predictive algorithm must include a consideration of energy minimization, thermalization, and long-range interactions. Extreme caution is suggested in applying present prediction routines to unknown protein structures.

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↗
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

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↗
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

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↗
PubMed1988

Unexpected divergence and molecular coevolution in yeast plasmids.

Four closely related species of yeast possess multicopy nuclear plasmids whose shared molecular architecture demonstrates a common ancestor, despite their lack of discernible DNA sequence homology. Each plasmid encodes three proteins which have equivalent essential functions in plasmid maintenance. These three groups of proteins show markedly different degrees of conservation, so that although we have successfully aligned sequences for two groups, members of the third group have diverged to such an extent that they cannot be aligned. All the proteins are sufficiently different that they function only in conjunction with their encoding plasmid. These proteins have therefore conserved their functional interactions with the relevant DNA sequences of their particular plasmids, despite lack of amino acid sequence conservation. The maintenance of function in the face of DNA sequence divergence is analogous to the coevolution of ribosomal DNA promoters and RNA polymerase I, and suggests that molecular drive may be an important force in the evolution of these plasmids. This view is reinforced by the inconsistent phylogenetic relationships determined from the two alignment sets, and by the contradiction that the two plasmids known to be the closest related taxonomically and by their host interchangeability are suggested to be the most distant by their sequences.

Amino Acid Sequence↗