Open AccessUnderlying order in protein sequence organization.
Author(s) -
Alexander L. Berman,
Eugene Kolker,
Edward N. Trifonov
Publication year - 1994
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.91.9.4044
Subject(s) - sequence (biology) , protein sequencing , biology , universality (dynamical systems) , computational biology , order (exchange) , sequence logo , peptide sequence , genetics , sequence alignment , evolutionary biology , physics , gene , finance , quantum mechanics , economics
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.