The prediction and orientation of α-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules

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Abstract
Amino acid substitution tables are used to estimate the extent to which amino acids in families of homologous proteins are exposed to the solvent. The approach depends on the comparison of difference environment-dependent tables for solvent accessible/inaccessible residues with amino acid substitutions at each position in an aligned set of sequences. The periodicity in the predicted accessible/inaccessible residues is calculated using a Fourier transform procedure modified from that used to calculate hydrophobic moments. a-Helices are identified from the characteristic periodicities and the solvent accessible face of the helix is defined. The initial helix predictions are refined using rules for identifying the N- and C-termini of helices from sequence alignments. These rules have been defined from a study of protein structures. The combined method correctly predicts 79% of the residues in helices and incorrectly predicts only 12% of the nonhelical residues as helical. In addition, since the method is reliable at predicting the correct number of helices in the correct position in the sequence and since it also predicts the internal face of each helix, the results can be used to postulate 3-D arrangements of the secondary structure elements.