Presence of repeating sub-sequences and symmetry patterns in proteins

Protein signatures--a novel way to classify proteins

A method is developed to classify proteins by establishing their familial identity based on the presence and the absence of characteristic signature dipeptides. It is hoped that this method will lead to the establishment of a theoretical basis for the determination of interrelationships among proteins.

Relationships between alpha and beta secondary structures and amino-acid pseudosymmetrical arrangements

A total of 51 polypeptides of known amino acid sequence and secondary structure have been screened for the presence of symmetrical arrangements of amino acids. Similarity between amino acids was derived by using a genetic test (minimum mutation distance) or a structural test (relative frequencies of amino acids substitutions in families of related proteins). It is shown that the frequency of proteins displaying symmetrical arrangements of amino acids is slightly higher than predicted by chance. In contrast, when the analysis is restricted to protein subregions displaying identical types of secondary structure, the frequency of proteins in which the alpha and beta subregions exhibit symmetrical arrangements of amino acids is significantly higher than predicted by chance. On the other hand, it is observed that more discriminatory results are always obtained when the structural test is used as a criterion for amino acid similarity. These data suggest that symmetrical arrangements of amino acids could result from structural constraints imposed either by the alpha or beta secondary structures. It is postulated that the regular alternation in hydrophobicity which is generally observed in the amino acid sub-sequences displaying alpha or beta secondary structures may be responsible for the occurrence of symmetrical arrangements of amino acids.

Attempts at simulating evolution by a computer: I. evolution of proteins under prebiotic conditions

The effect of random mutations of five identical pentapeptides that have been inserted arbitrarily along a 100 amino acid-long protein chain has been studied by computer simulation. The method used was the application of mutation probability matrix for 2 PAMs of Dayhoff (1972) repeatedly to obtain the desired length of time. The results indicated that, given sufficient length of time, even the identical peptides could become drastically altered and in order to recognise them as stemming from the same origin one has to use reasonable statistical significance thresholds.

Structural analysis of the molecular evolution of some gastro-entero-pancreatic hormones

By means of a statistical analysis of the occurrence of amino-acid residues in the polypeptide chains of several gastro-entero-pancreatic (GEP) hormones an investigation was undertaken to determine whether any of these hormones might be related to each other--possibly from an evolutionary point of view. Particular interest was paid to the occurrence of small charged segments, i.e. those with acidic or basic amino acid residues, since such segments can be presumed to play a role in hormonal receptor binding mechanisms. By this method hormonal relationships were suggested by the observation that these small charged amino-acid sequences, contained in the hormonal structures, match as a result of non-randomness. It was found that hagfish and human insulin were related on a molecular level not only to the newly discovered (avian, bovine, human) pancreatic polypeptide (PP) but also to some other GEP hormones (VIP, GIP, glucagon) as well as to calcitonin and to the alpha-subunit of the glycoprotein hormones. Interpretation of the statistical data suggests that all these peptide hormones are related by a common hexapeptide sequence which contributed, at an evolutionary point, to their molecular architecture. A hexapeptide segment of APP is statistically related to a sequence of equal size in the carboxy terminal region of the A-chain of both hagfish and human insulin, providing the first instance of their structural similarity. Correlations between PP, insulin, glucagon, VIP, and calcitonin provide a tentative basis for predicting the production of one or more of these peptide hormones by immature or de-differentiated cells of neoplasms and non-neoplastic pathologic lesions of the GEP endocrine system.

Symmetry patterns in trypsinogen

When the primary structure of bovine trypsinogen is searched for the existence of regularities, according to Greller & Erhan (1974), one finds eight pairs of peptides, arranged in a symmetrical pattern along the molecule. These peptides cover 49% of the length of the molecule-112 of the 227 amino acids-and each pair folds in a similar way. This observation is in agreement with the observation that "Trypsin folds into two halves, each of which contains a pseudo-cylindrical arrangement of hydrogen bonds...", Stroud et al. (1971). Thus the above mentioned method is capable not only of detecting regulatities along the primary structure but also of predicting the folding of a protein.