Quantifying protein sequences with reference to the genetic code

Although the analysis of protein molecules is extensive, their primary sequences have yet to be quantified like their mass or size. The composition and particular arrangement of amino acids in proteins confers the distinct biochemical functionality, but it remains unclear why only a tiny proportion of possible character combinations are potentially functional. Here, I offer a simple but effective technique, utilizing the assignment of codons in the genetic code, that permits the quantification of polypeptide sequences and establishes statistical parameters through which they can now be numerically compared. Two main tests were conducted, one analyzing the composition and the other the specific order of the amino acids within the primary sequence. The results confirm that natural proteins are significantly different to random heteropolymers of equivalent size, although this is much more marginal in the case of the arrangement than it is for the composition. Moreover, they reveal that there are key patterns that have hitherto not been identified, relevant to the the study of the evolution of proteins, and which raise doubts about the plausibility of some purported cases of the de novo origination of protein-coding genes from intergenic DNA. Despite the fact that the applicability of quantification to the design of novel proteins is probably limited, it nonetheless provides a useful guideline that could complement much more precise methods.