Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles.

ABSTRACT: The loss of conformational entropy is the largest unfavorable quantity affecting a protein's stability. We calculate the reduction in the number of backbone conformations upon folding using the distribution of backbone dihedral angles (ϕ,ψ) obtained from an experimentally validated denatured state model, along with all-atom simulations for both the denatured and native states. The average loss of entropy per residue is TΔS(BB)(U-N) = 0.7, 0.9, or 1.1 kcal·mol(-1) at T = 298 K, depending on the force field used, with a 0.6 kcal·mol(-1) dispersion across the sequence. The average equates to a decrease of a factor of 3-7 in the number of conformations available per residue (f = Ω(Denatured)/Ω(Native)) or to a total of f(tot) = 3(n)-7(n) for an n residue protein. Our value is smaller than most

SUBMITTER: Baxa MC 

PROVIDER: S-EPMC3464005 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature