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. Keywords: EF-hand • principal component analysis • calcium binding • interhelical angle • structural analysis