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• W2025582173 abstract "Abstract 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. Proteins 2006. © 2005 Wiley‐Liss, Inc." @default.
• W2025582173 created "2016-06-24" @default.
• W2025582173 creator A5054972279 @default.
• W2025582173 creator A5091162249 @default.
• W2025582173 date "2005-11-28" @default.
• W2025582173 modified "2023-10-16" @default.
• W2025582173 title "Side-chain entropy effects on protein secondary structure formation" @default.
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• W2025582173 doi "https://doi.org/10.1002/prot.20766" @default.
• W2025582173 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/16315271" @default.
• W2025582173 hasPublicationYear "2005" @default.
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