The HP Model, Designability and Alpha-Helices in Protein Structures
Abstract
Detailed analysis of the geometric properties of the HP model for protein structure shows that structures having the highest designabilities are those with close to the maximum number of surface-surface-core-core patterns that suggest $\alpha$-helices. Global comparison of model polypeptide sequences with concatenated protein sequences listed in the Protein Data Bank confirms that portions of protein sequences rich in $\alpha$-helices are most similar to model sequences folding into structures of high designability. This provides an explanation for the essentially simultaneous fast initial collapse of a polypeptide chain to a globular shape and formation of $\alpha$-helices.Keywords
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