Side-chain entropy effects on protein secondary structure formation

Loss of conformational entropy is one of the primary factors opposing protein folding. Both the backbone and side-chain of each residue in a protein will have their freedom of motion restricted in the final folded structure. The type of secondary structure of which a residue is part will have a significant impact on how much side-chain entropy is lost. Side-chain conformational entropies have previously been determined for folded proteins, simple models of unfolded proteins, α-helices, and a dipeptide model for β-strands, but not for polyproline II (P_II) helices. In this work, we present side-chain conformational estimates for the three regular secondary structure types: α-helices, β-strands, and P_II helices. Entropies are estimated from Monte Carlo computer simulations. β-Strands are modeled as two structures, parallel and antiparallel β-strands. Our data indicate that restraining a residue to the P_II helix or antiparallel β-strand conformations results in side-chain entropies equal to or higher than those obtained by restraining residues to the parallel β-strand conformation. Side-chains in the α-helix conformation have the lowest side-chain entropies. The observation that extended structures retain the most side-chain entropy suggests that such structures would be entropically favored in unfolded proteins under folding conditions. Our data indicate that the P _II helix conformation would be somewhat favored over β-strand conformations, with antiparallel β-strand favored over parallel. Notably, our data imply that, under some circumstances, residues may gain side-chain entropy upon folding. Implications of our findings for protein folding and unfolded states are discussed.