Secondary-structure predictions of calcium-binding proteins

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Abstract
The known tertiary structure of carp muscle parvalbumin is consistent with an EF-hand architecture (helix-loop-helix) for each Ca-ion binding site. Primary-sequence alignments have indicated 4 EF hands in rabbit skeletal muscle troponin C and in rabbit myosin alkali L chains. Five secondary-structure prediction methods, based on amino acid sequence only, have been fully computerized and used to calculate joint prediction histograms for several Ca-binding proteins. The joint histogram suggested directly the extent and sequence of the helical- and loop-structural elements and any secondary structural distortions or evolutionary developments. Since the histogram predicted well the length and sequence of secondary structural elements in carp muscle parvalbumin, it seemed reasonable to calculate the joint distribution for other proteins that might bind Ca through the EF-hand configuration. The histograms indicated the 4 EF-hand regions speculated for rabbit skeletal muscle troponin C but suggested only 3 such hands in bovine cardiac muscle troponin C with a distorted 4th hand. Considerable secondary structural distortion is postulated for the alkali L chains. Possible EF configurations consistent with the histogram results are speculated for Escherichia coli acyl-carrier protein and bovine prothrombin fragment 1, which bind Ca. The secondary-structure-prediction algorithms seem to be a useful adjunct to sequence-alignment techniques, especially in cases where the primary sequence homology is weak or the evolutionary distance is large.