Sense-Antisense Homology Boxes in Proteins: Structural Motifs Enconded in the DNA?

Carlos A. Del Carpio [1] (
Valentin Gogonea [2] (
Katsuhisa Yamaguchi [1] (
Makoto Takei [1] (
Kouji Nishimura [1] (

[1] Lab. for Informatics & AI in Molecular and Biological Science
Department of Ecological Engineering,
Toyohashi University of Technology.
Tempaku. Toyohashi 441, Japan
[2] Computer Chemistry Center,
Institute for Organic Chemistry
Erlangen-Nurnberg University, Nagelsbachstr.
25, D-91052 Erlangen, Germany


Experimental evidence implying that complementary DNA strands encode amino acids which exhibit complementary hydrophobic characteristics has led us to the inspection of sense-antisense homology in several hundreds of proteins recorded in the PDB. We present here partial results of this analysis which relate localized peculiar structural characteristics of proteins to the sense-antisense homology boxes found in the primary sequences. A further analysis is performed in order to determine whether these sense-antisense homology boxes,if existent within the protein, are encoded by unique sequences of codons in the DNA. We also make here a progress report about the methodology and the results obtained so far.