Abstract
In simple models side chains are often represented implicitly (e.g., by
spin-states) or simplified as one atom. We study side chain effects using
square lattice and tetrahedral lattice models, with explicitly side chains of
two atoms. We distinguish effects due to chirality and effects due to side
chain flexibilities, since residues in proteins are L-residues, and their side
chains adopt different rotameric states. Short chains are enumerated
exhaustively. For long chains, we sample effectively rare events (eg, compact
conformations) and obtain complete pictures of ensemble properties of these
models at all compactness region. We find that both chirality and reduced side
chain flexibility lower the folding entropy significantly for globally compact
conformations, suggesting that they are important properties of residues to
ensure fast folding and stable native structure. This corresponds well with our
finding that natural amino acid residues have reduced effective flexibility, as
evidenced by analysis of rotamer libraries and side chain rotatable bonds. We
further develop a method calculating the exact side-chain entropy for a given
back bone structure. We show that simple rotamer counting often underestimates
side chain entropy significantly, and side chain entropy does not always
correlate well with main chain packing. Among compact backbones with maximum
side chain entropy, helical structures emerges as the dominating
configurations. Our results suggest that side chain entropy may be an important
factor contributing to the formation of alpha helices for compact
conformations.