%0 Journal Article
%A Barney, Brett M.
%D 2006
%T Classification of Proteins Based on Minimal Modular Repeats:
Lessons from Nature in Protein Design
%U https://acs.figshare.com/articles/journal_contribution/Classification_of_Proteins_Based_on_Minimal_Modular_Repeats_Lessons_from_Nature_in_Protein_Design/3235252
%R 10.1021/pr050103m.s003
%2 https://ndownloader.figshare.com/files/5069317
%K protein
%K sequential characteristics
%K organism Nitrosomonas europaea
%K Several databases
%K searches prokaryotic genomes
%K Protein Design Proteins
%X Proteins containing internal repeats within their primary sequence have received increased attention
recently, as the extent of their presence in various organisms is recognized more fully, and their role
in evolution is more thoroughly studied. Presented here is a technique used to detect and classify
proteins based on a modular evolutionary phenomenon that results in a series of small internal repeats.
The parameters chosen are based on a minimum segment of seven residues that result in simple
functional scaffolds. The genomes and corresponding proteomes of a variety of eubacteria and archaea
have been analyzed using an algorithm that searches prokaryotic genomes for proteins containing
small conserved repeats assembled in a modular fashion similar to a recently characterized protein
from the organism Nitrosomonas europaea. This analysis has revealed additional proteins present in
N. europaea with similar modular characteristics. A further survey of a variety of organisms
demonstrates that this evolutionary pathway has been utilized in other organisms as well, to yield a
broad assortment of small modular proteins. A thorough description of the sequential characteristics
of these modular proteins follows, along with a selection and discussion of the various proteins
uncovered through this expanded search and analysis. Several databases of the proteins uncovered
from this work and the program used to perform the search are available.
Keywords: internal protein repeats • modular design • algorithm • small proteins • database
%I ACS Publications