Helix Probability Profiles of Denatured Proteins and Their Correlation with Native Structures

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Abstract
The Zimm-Bragg formulation for the one-dimensional Ising model is applied to denatured proteins in order to compute helix probability profiles with different sigma and s parameters for the various amino acids; the latter are in principle determinable from melting curves for helix-coil transitions in random copolymers of amino acids. Using a tentative assignment of sigma and s values, we found a correlation for the propensity of a residue to be helical in the denatured protein and its occurrence in a helical region in the globular structure of the corresponding native protein. Thus, these incipient helical regions in the denatured chain may serve to nucleate the folding to form the native protein. Short-range interactions appear to determine the tendency for a residue to be helical or not, whereas long-range interactions may serve to carry out the nucleation and refolding processes.