Proteins of the same fold and unrelated sequences have similar amino acid composition.
It is well established that there is a relationship between the amino acid composition of a protein and its structural class (i.e., alpha, beta, alpha + beta, or alpha/beta). Several studies have even shown the power of amino acid composition in predicting the secondary structure class of a protein. Herein, we show that significant similarity in amino acid composition exists not only between proteins of the same class, but even between proteins of the same fold. To test conjectural explanations for this phenomenon, we analyzed a set of structurally similar proteins that are dissimilar in sequence. Based on this analysis, we suggest that specific residues that are involved in intramolecular interactions may account for this surprising relationship between composition and structure.
Ofran
Yanay
Y
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA. yanay.ofran@columbia.edu
Margalit
Hanah
H
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D030562:Databases, Protein; D008958:Models, Molecular; D008962:Models, Theoretical; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
D000596:Amino Acids; D011506:Proteins