Principal component analysis of the conformational freedom within the EF-hand superfamily.
A database of nonredundant structures of EF-hand domains--i.e., pairs of helix-loop-helix motifs--has been assembled, and the six angles among the four helices re-determined. A principal component analysis of these angles allows us to use two such components (PC1 and PC2) to describe the system retaining 80% of the total variance. A PC2 against PC1 plot representation allows us to represent in a compact way the full range of structural diversity of EF-hand domains, their grouping into protein families, and the variation for each family upon calcium and peptide binding.
Babini
Elena
E
Department of Food Science, University of Bologna, 47023 Cesena, Italy.
Bertini
Ivano
I
Capozzi
Francesco
F
Luchinat
Claudio
C
Quattrone
Alessandro
A
Turano
Maria
M
D020816:Amino Acid Motifs; D000704:Analysis of Variance; D000818:Animals; D002118:Calcium / Q000737:chemistry; D002147:Calmodulin / Q000737:chemistry; D030562:Databases, Protein; D005998:Glycine / Q000737:chemistry; D006801:Humans; D008024:Ligands; D009218:Myosins / Q000737:chemistry; D010320:Parvalbumins / Q000737:chemistry; D025341:Principal Component Analysis; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D019209:Troponin C / Q000737:chemistry
D002147:Calmodulin; D008024:Ligands; D010320:Parvalbumins; D019209:Troponin C; D009218:Myosins; D002118:Calcium; D005998:Glycine