title: Structure model of core proteins in photosystem I inferred from the comparison with those in photosystem II and bacteria; an application of principal component analysis to detect the similar regions between distantly related families of proteins.
abstract: A principal component analysis based on the physico-chemical properties of amino acid residues is developed to assign similar regions between distantly related families of proteins, taking account of the species diversities in respective families. The most important advantage of this analysis should be that it reflects different physico-chemical properties and thus can predict more detailed structural properties, including the transmembrane helices, than the hydropathy analysis. Its first application reconfirms the similarity between the core proteins of photosynthetic reaction center in purple bacteria and those of photosystem II, indicating that the low percentage of identical amino acid residues estimated previously between them is due to much allowance for amino acid substitutions in purple bacteria. The application of this analysis to the core proteins of photosystem I reveals that any of these proteins includes two domains, each showing high similarity to the amino acid sequences of core proteins in photosystem II and purple bacteria. A core structure model of A1 and A2 proteins folded into four layers of sheets of transmembrane helices is proposed to provide a molecular basis for the electron pathway suggested by spectroscopic experiments as well as for the interaction sites with plastocyanin, 9 kDa protein and LHC proteins.
authors.affiliation: Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, Noda, Japan.
authors.forename: J
authors.initials: J
authors.lastname: Otsuka
authors.forename: H
authors.initials: H
authors.lastname: Miyachi
authors.forename: K
authors.initials: K
authors.lastname: Horimoto
mesh_terms: D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D045322:Photosynthetic Reaction Center Complex Proteins / Q000378:metabolism*; D045331:Photosystem I Protein Complex; D045332:Photosystem II Protein Complex; D011487:Protein Conformation; D012689:Sequence Homology, Nucleic Acid
chemical_list: D045322:Photosynthetic Reaction Center Complex Proteins; D045331:Photosystem I Protein Complex; D045332:Photosystem II Protein Complex