Identification of functionally conserved residues with the use of entropy-variability plots.
We introduce sequence entropy-variability plots as a method of analyzing families of protein sequences, and demonstrate this for three well-known sequence families: globins, ras-like proteins, and serine-proteases. The location of an aligned residue position in the entropy-variability plot correlates with structural characteristics, and with known facts about the roles of individual amino acids in the function of these proteins. The large numbers of known sequences in these families allowed us to introduce new filtering methods for variability patterns. The results are discussed in terms of a simple evolutionary model for functional proteins.
Oliveira
Laerte
L
Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
Paiva
Paulo B
PB
Paiva
Antonio C M
AC
Vriend
Gerrit
G
D000465:Algorithms; D000595:Amino Acid Sequence; D001665:Binding Sites; D017124:Conserved Sequence / Q000235:genetics; D030562:Databases, Protein; D019277:Entropy; D005914:Globins / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000737:chemistry / Q000235:genetics; D018631:ras Proteins / Q000737:chemistry / Q000235:genetics
D011506:Proteins; D005914:Globins; D012697:Serine Endopeptidases; D018631:ras Proteins