Three-body interactions improve the prediction of rate and mechanism in protein folding models.
Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained Calpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Gō-like Hamiltonian with native pairwise interactions only, we have found (i) a significantly increased correlation with experimental phi values and folding rates, (ii) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is approximately 20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin inhibitor than in the other proteins studied.
Ejtehadi
M R
MR
Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada V6T 1Z1. ejtehadi@physics.ubc.ca
Avall
S P
SP
Plotkin
S S
SS
D046911:Macromolecular Substances; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D010940:Plant Proteins; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D046911:Macromolecular Substances; D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; C093336:chymotrypsin inhibitor 2