Universal regularities in protein primary structure: preference in bonding and periodicity.

Utilizing the whole protein data base as well as parts of it (groups and individual representatives), the universal character of the regularities in protein primary structure - preference in bonding (self-ordering) and periodicity - is shown by means of an improved procedure of checking statistical significance. In the vast majority of the cases there is a preference in bonding with the same or with very similar amino acid. Taken as a whole, both regularities show a universal character. The results obtained provide evidence in favour of the conception about the priority of proteins as information polymers.

The structural periodicity of E. coli ribosomal proteins.

It is established that the sequences of all different proteins from E. coli ribosome as well as two protein biosynthesis initiation factors, two ribosome-associated DNA-binding proteins, and the elongation factor EF-Tu from the same source possess a periodicity expressed more weakly and different from that found earlier for a number of proteins representatives of 18 superfamilies. The statistical significance of the periodicity observed was checked by comparing the area below the periodicity curve of every protein examined with that of computer generated sequences having the same amino acid composition and length. The results concerning the proteins from small and large ribosomal subunit are compared. The conclusions support and supplement the concept about the presence of a trend in protein molecular evolution from universal (Gly, Ala) to specialized (Phe, Tyr, Trp, Cys) amino acids.

A study of the interaction of glycine and its oligohomopeptides with formaldehyde and acetaldehyde under possible primitive earth conditions.

It is established that glycine and glycine oligohomopeptides interact with formaldehyde and acetaldehyde in a homogeneous weak acid medium (pH 3.3-3.7) at mild temperatures (60-80 degrees C) in the absence of inorganic solid substances. Together with the expected serine and threonine, the formation of alanine, glutamic and aspartic acid, norvaline and isoleucine, as well as four non-protein amino acids is also established. It is suggested that the non-protein amino acids are hydroxymethylserine, hydroxymethylthreonine, hydroxymethylaspartic acid and gamma-amino-delta-hydroxyvaleric acid. The modes of formation of all protein and non-protein amino acids are discussed. These results strengthen the probability that similar processes may have been one of the pathways for the prebiotic synthesis of amino acids on primitive Earth.

Some evidence for the universality of structural periodicity in proteins.

A new simple and sensitive method for detecting small periodicity (repetition of a small segment along the chain) in proteins is developed, based on the repetition of identical residues. 38 proteins from organisms representing different levels of evolutionary development have been tested for small periodicity. The same is done with the nodal ancestors of 25 of them. The results are presented graphically (the periodicity curves). The statistical significance of the observed periodicity is confirmed by a modified version of the chi-square test. All the results obtained support the conception that the small periodicity of the contemporary proteins is a reflection of their evolutionary history and that the most ancient proteins have arisen through a polycondensation of short peptides or through transcription and translation of satellite-type repeat sequence DNA.

Application of the 'profiles of relationship' method to distantly related proteins.

An analysis is made of the applicability of the recently published 'profiles of relationship' method for establishing evolutionary relatedness among proteins by using the distantly related proinsulin and neurotoxin protein sequences as a test object. The method is based on a simultaneous group analysis of both the frequency of acceptance of mutations and their genetic code interchangeability. Regularities in the patterns of the profiles, which reflect decreased similarity with the passage of time, are established for typical cases of closely related, distantly related and unrelated proteins. This makes it possible to distinguish distantly related from unrelated proteins without extensive statistical randomization procedures. New evidence is stated in favour of a previously suggested definition of interchangeability which does not consider the third base in the codon. The applicability of the profiles of relationship method is examined on the distant relationship between proinsulin and the snake and scorpion neurotoxins which has been established previously by means of conventional approaches.