Title: Evolution of bacterial ribosomal protein L1

Authors: William L. Duax; Robert Huether; David Dziak

Addresses: Department of Structural Biology, Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY 14203, USA. ' Department of Structural Biology, Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY 14203, USA. ' Department of Structural Biology, Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo, NY 14203, USA

Abstract: Search vectors composed of Gly, Ala, Arg, and Pro (GARP) residues retrieve 98% of each of the ribosomal proteins in prokaryotic species with no false hits. Different combinations of G, A, R and P and insertions differentiate each ribosomal protein from all others. Amino acids in two sequence positions separate Gram+ from Gram− bacteria. Specific residues separate proteins of cyanobacteria and chloroplasts from all other species. Structural information played an essential role in developing a GARP based technique to achieve perfect sequence alignment. It is possible to understand why GARP residues are 100% conserved in specific positions in families of proteins present in all species.

Keywords: molecular evolution; ribosomes; ribosomal protein L1; accurate alignment; GARP; Gly; Ala; Arg; Pro; genetic code evolution; gram positive bacteria; gram negative bacteria; bioinformatics; prokaryotic species; cyanobacteria; chloroplasts; protein separation; sequence alignment.

DOI: 10.1504/IJBRA.2012.045979

International Journal of Bioinformatics Research and Applications, 2012 Vol.8 No.1/2, pp.99 - 111

Published online: 05 Dec 2014 *

Full-text access for editors Full-text access for subscribers Purchase this article Comment on this article