Prediction of folding equilibria of differently substituted peptides using 
one-step perturbation

Lin, Zhixiong; Kornfeld, Jörgen; Machler, Markus; van Gunsteren, Wilfred F.

doi:10.1021/ja100879k

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Prediction of folding equilibria of differently substituted peptides using one-step perturbation

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引用

Lin, Z., Kornfeld, J., Machler, M., & van Gunsteren, W. F. (2010). Prediction of folding equilibria of differently substituted peptides using one-step perturbation. Journal of the American Chemical Society, 132(21), 7276-7278. doi:10.1021/ja100879k.

引用: https://hdl.handle.net/21.11116/0000-0009-7648-2

要旨

Computer simulation using long molecular dynamics (MD) can be used to simulate the folding equilibria of peptides and small proteins. However, a systematic investigation of the influence of the side-chain composition and position at the backbone on the folding equilibrium is computationally as well as experimentally too expensive because of the exponentially growing number of possible side-chain compositions and combinations along the peptide chain. Here, we show that application of the one-step perturbation technique may solve this problem, at least computationally; that is, one can predict many folding equilibria of a polypeptide with different side-chain substitutions from just one single MD simulation using an unphysical reference state. The methodology reduces the number of required separate simulations by an order of magnitude.