Statistical Mechanics of Helix Bundles Using a Dynamic Programming Approach
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- 作者：Adam Lucas ; Liang Huang ; Aravind Joshi ; Ken A. Dill
- 刊名：Journal of the American Chemical Society
- 出版年：2007
- 出版时间：April 11, 2007
- 年：2007
- 卷：129
- 期：14
- 页码：4272 - 4281
- 全文大小：258K
- 年卷期：v.129,no.14(April 11, 2007)
- ISSN：1520-5126
文摘
Despite much study, biomolecule folding cooperativity is not well understood. There arequantitative models for helix-coil transitions and for coil-to-globule transitions, but no accurate models yettreat both chain collapse and secondary structure formation together. We develop here a dynamicprogramming approach to statistical mechanical partition functions of foldamer chain molecules. We call itthe ascending levels model. We apply it to helix-coil and helix-bundle folding and cooperativity. For 14- to50-mer Baldwin peptides, the model gives good predictions for the heat capacity and helicity versustemperature and urea. The model also gives good fits for the denaturation of Oas's three-helix bundle Bdomain of protein A (F13W*) and synthetic protein 
3C by temperature and guanidine. The model predictsthe conformational distributions. It shows that these proteins fold with transitions that are two-state, althoughthe transitions in the Baldwin helices are nearly higher order. The model shows that the recently developedthree-helix bundle polypeptoids of Lee et al. fold anti-cooperatively, with a predicted value of 
ta.gif" BORDER=0 >HvH/ta.gif" BORDER=0 >Hcal =0.72. The model also predicts that two-helix bundles are unstable in proteins but stable in peptoids. Ourdynamic programming approach provides a general way to explore cooperativity in complex foldablepolymers.
3C by temperature and guanidine. The model predictsthe conformational distributions. It shows that these proteins fold with transitions that are two-state, althoughthe transitions in the Baldwin helices are nearly higher order. The model shows that the recently developedthree-helix bundle polypeptoids of Lee et al. fold anti-cooperatively, with a predicted value of ta.gif" BORDER=0 >HvH/ta.gif" BORDER=0 >Hcal =0.72. The model also predicts that two-helix bundles are unstable in proteins but stable in peptoids. Ourdynamic programming approach provides a general way to explore cooperativity in complex foldablepolymers.