title: Location of helical regions in tetrapyrrole-containing proteins by a helical hydrophobic moment analysis. Application to phytochrome.
abstract: Helical regions in many tetrapyrrole proteins are highly amphiphilic, one side interacting with a hydrophobic core and another side interacting with the polar solvent. The mean helical hydrophobic moment is a measure of amphiphilicity of a helix. Helical regions in myoglobin, the alpha and beta subunits of C-phycocyanin, and cytochrome c can be distinguished from nonhelical regions by use of a hydrophobic moment analysis. 24 of 27 (89%) of the helical regions in these proteins were located by this analysis. Calculations were also performed on chymotrypsin, ribonuclease, and papain, which do not possess as pronounced a hydrophobic core as the tetrapyrrole-containing proteins. Less than 50% of the helical regions were correctly located, indicating a lack of amphiphilicity in the helices of these proteins. The hydrophobic moment analysis was also used to predict helical regions in phytochrome, the ubiquitous photoreceptor in plants. Additionally, this analysis is used to quickly locate internal hydrophilic residues which may be functionally important. The distribution of hydrophobic moments from a random sequence was determined so that qualitative and to some extent quantitative comparisons between different amphiphilic helices may be made.
authors.affiliation: Department of Chemistry, University of Nebraska, Lincoln 68588.
authors.forename: W
authors.initials: W
authors.lastname: Parker
authors.forename: P S
authors.initials: PS
authors.lastname: Song
mesh_terms: D000595:Amino Acid Sequence; D003574:Cytochrome c Group / Q000737:chemistry*; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry*; D010798:Phycocyanin / Q000737:chemistry*; D010834:Phytochrome / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D011758:Pyrroles / Q000032:analysis / Q000737:chemistry*; D012689:Sequence Homology, Nucleic Acid; D045725:Tetrapyrroles
chemical_list: D003574:Cytochrome c Group; D046911:Macromolecular Substances; D009211:Myoglobin; D011758:Pyrroles; D045725:Tetrapyrroles; D010798:Phycocyanin; D010834:Phytochrome