Prediction of homology and divergence in the secondary structure of polypeptides.
A quantitative procedure is described for the comparison of secondary structure of homologous proteins. Standard predictive methods are used to generate probability profiles from pairs of homologous amino acid sequences; correlation coefficients (R) are then computed between each pair of amino acids for alpha-helix (R alpha), extended structure (R beta), turn (R(t)), and coil (R(c)). R values are >0.2 for correctly aligned homologous sequences. Unrelated or incorrectly aligned sequences give R values near zero. Lack of correlation for a segment of otherwise well-correlated sequences is used to identify structural divergence, which is then evaluated graphically by using difference profiles. A combination of these techniques correctly predicts secondary structural differences between melittin or beta-endorphin and their respective synthetic analogs. The method is potentially useful to describe evolutionary changes in protein secondary structure as well as in the design of peptide analogs.
Pongor
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Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA.
Szalay
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AA
D000595:Amino Acid Sequence; D008433:Mathematics; D008555:Melitten / Q000737:chemistry; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry; D017386:Sequence Homology, Amino Acid; D001615:beta-Endorphin / Q000737:chemistry
D008555:Melitten; D001615:beta-Endorphin; D012273:Ribulose-Bisphosphate Carboxylase