Secondary Structure of Proteins and Beyond

The requirements for hydrogen bond preservation in the folded structure result in the cooperative formation of hydrogen-bonded secondary structure regions in proteins. The secondary structure specifies regular polypeptide chain folding patterns of helices, sheets, coils and tnms that are combined/folded into tertiary structure. Studies of two-state structural transition suggest that a statistical method can be developed to predict the 

In the statistical method of Chou and Fasman (Chou and Fasman, 1978), the propensities for a residue type to adopt three structural states a-helix ( P ), p-sheet ( Pp ) and turn ( Pt ) conformations are calculated for all of the 20 amino acids according to 

Assign heUx and sheet propensity values and symbols (H, h, I, i, B, b for strong versus weak formers, indifferences and breakers). 

Resolution of simultaneous helix-sheet assignments For the same residues predicted to be a and P nucleation sites, calculate the average Pa and Pp for these residues. The nucleation site is assigned to a or p with higher probability. 

Propagation Extend helix and sheet from the nucleation sites in both directions until the average probability of the end tetrapeptide falls below 1.0. End residues, which are breakers, are not to be included in the secondary structure. 

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