Prediction of Protein Domain Boundaries from Statistics of Appearance of Amino Acid Residues

摘要

A database of 452 two-domain proteins with less than 25% homology was constructed.One half of the database was used to obtain statistics on the appearance of amino acid residues at domain boundaries.Small and hydrophilic residues(proline,glycine,asparagine,glutamic acid,arginine,etc.)occurred more often at domain boundaries than in total proteins.Hydrophobic residues(tryptophan,methionine,phenylalanine,etc.)were rarer at domain boundaries than in total proteins.Probability scales of amino acid appearance in boundary-flanking regions were constructed with these statistics and used to predict the domain boundaries in proteins of the other half of the database.The probability scale obtained by averaging the appearance of amino acids over an 8-residue region(±4 residues from the real domain boundaries)yielded the best results:domain boundaries were predicted within 40 residues of the real boundary in 57% of proteins and within 20 residues of the real boundary in 41% of proteins.The probability scale was used to predict the domain boundaries in proteins with unknown structures(CASP6).