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 (PII) helices. In this work, we present side-chain conformational estimates for the three regular secondary structure types: α-helices, β-strands, and PII 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 PII 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.
Original language | English |
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Pages (from-to) | 411-420 |
Number of pages | 10 |
Journal | Proteins: Structure, Function and Genetics |
Volume | 62 |
Issue number | 2 |
DOIs | |
State | Published - Feb 1 2006 |
Keywords
- Monte Carlo simulations
- Polyproline II helices
- Protein folding
- Unfolded states
- α-helices
- β-strands
ASJC Scopus subject areas
- Structural Biology
- Biochemistry
- Molecular Biology