Database Analysis of Acidic Proteins from Halophilic Species and Their Corresponding Basic Proteins from Non-halophilic Species

Abstract

Aims: To reveal which amino acid residues determine whether a protein is acidic or basic between orthologous pairs, acidic proteins from halophilic species and corresponding basic proteins from non-halophilic species were compared. Similarly acidic versus acidic protein pairs, and basic versus basic protein pairs were also analyzed. Place and Duration of Study: Department of Clinical Laboratory Science, Graduate Course of Medical Science and Technology, School of Health Sciences, Kanazawa University, Japan. Methodology: Halobacterium sp. NRC-1 was used as halophilic species and Gram-positive bacterium Bacillus subtilis, and radiation resistant bacterium Deinococcus radiodurans were used as non-halophilic species. The three species were selected because their proteins were closely related each other. The amino acid compositions were compared and the amino acid substitutions were counted for the orthologous protein pairs between Halobacterium and B. subtilis. Similar comparison was done for the proteins between Halobacterium and D. radiodurans. Results: The Asp and Glu residues are determinant whether a protein of Halobacterium sp. NRC-1 is acidic or basic. Amino acid substitutions to increase the Asp residues in the acidic proteins of Halobacterium from the corresponding proteins of non-halophilic species were almost identical whether the corresponding proteins were acidic or basic. This result suggested that the change of protein charges from basic proteins to acidic ones was same as from acidic proteins to acidic ones. The proteins of Halobacterium showed a tendency to have residues with smaller side chain than the proteins of B. subtilis / D. radiodurans.