TY - DATA T1 - Statistical Mechanics of Helix Bundles Using a Dynamic Programming Approach PY - 2007/04/11 AU - Adam Lucas AU - Liang Huang AU - Aravind Joshi AU - Ken A. Dill UR - https://acs.figshare.com/articles/journal_contribution/Statistical_Mechanics_of_Helix_Bundles_Using_a_Dynamic_Programming_Approach/3013540 DO - 10.1021/ja067153s.s001 L4 - https://ndownloader.figshare.com/files/4714852 KW - 13W KW - foldamer chain molecules KW - protein α3 C KW - transition KW - Dynamic Programming ApproachDespite KW - cooperativity KW - bundle KW - programming approach KW - model N2 - Despite much study, biomolecule folding cooperativity is not well understood. There are quantitative models for helix-coil transitions and for coil-to-globule transitions, but no accurate models yet treat both chain collapse and secondary structure formation together. We develop here a dynamic programming approach to statistical mechanical partition functions of foldamer chain molecules. We call it the ascending levels model. We apply it to helix-coil and helix-bundle folding and cooperativity. For 14- to 50-mer Baldwin peptides, the model gives good predictions for the heat capacity and helicity versus temperature and urea. The model also gives good fits for the denaturation of Oas's three-helix bundle B domain of protein A (F13W*) and synthetic protein α3C by temperature and guanidine. The model predicts the conformational distributions. It shows that these proteins fold with transitions that are two-state, although the transitions in the Baldwin helices are nearly higher order. The model shows that the recently developed three-helix bundle polypeptoids of Lee et al. fold anti-cooperatively, with a predicted value of ΔHvH/ΔHcal = 0.72. The model also predicts that two-helix bundles are unstable in proteins but stable in peptoids. Our dynamic programming approach provides a general way to explore cooperativity in complex foldable polymers. ER -