Zamparo Marco, Pelizzola Alessandro
Dipartimento di Fisica, CNISM Unità di Torino and INFN, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
J Chem Phys. 2009 Jul 21;131(3):035101. doi: 10.1063/1.3170984.
The folding pathways of the B domain of protein A have been the subject of many experimental and computational studies. Based on a statistical mechanical model, it has been suggested that the native state symmetry leads to multiple pathways, highly dependent on temperature and denaturant concentration. Experiments, however, have not confirmed this scenario. By considering four nearly symmetrical proteins, one of them being the above molecule, here we show that, if contact energies are properly taken into account, a different picture emerges from kinetic simulations of the above-mentioned model. This is characterized by a dominant folding pathway, which is consistent with the most recent experimental results. Given the simplicity of the model, we also report on a direct sampling of the transition state.
蛋白质A的B结构域的折叠途径一直是许多实验和计算研究的主题。基于统计力学模型，有人提出天然态对称性会导致多种途径，高度依赖于温度和变性剂浓度。然而，实验并未证实这种情况。通过考虑四种近乎对称的蛋白质，其中一种是上述分子，我们在此表明，如果适当考虑接触能，上述模型的动力学模拟会呈现出不同的情况。其特征是存在一条主导折叠途径，这与最新的实验结果一致。鉴于该模型的简单性，我们还报告了过渡态的直接抽样情况。
