Underlying order in protein sequence organization.

The idea of a possible standard modular structure of proteins has been known since 1929 when it was introduced by Svedberg. It still remains an idea with no quantitative confirmation of universality of such hypothetical organization. From a large collection of nonredundant protein sequences representing > 100 eukaryotic and prokaryotic species, we have obtained the protein sequence length distributions. Mere inspection of these distributions, as well as spectral analysis, shows that 15-30% of proteins, depending on species and sequence types, indeed appear to be made of sequence units with characteristic lengths of approximately 125 aa for eukaryotes and approximately 150 aa for prokaryotes. This underlying order in protein sequence organization is shown to be universal--that is, the weak regularity observed is not caused by a particular dominant species or protein group. Possible mechanisms are discussed that may be responsible for the observed regularity, including a hypothesis about the recombinational nature of such protein sequence organization.