De Jong Deborah, Riley Robert, Alonso Darwin O V, Daggett Valerie
Department of Medical Chemistry H165, School of Pharmacy, University of Washington, P.O. Box 357610, Seattle, WA 98195-7610, USA.
J Mol Biol. 2002 May 24;319(1):229-42. doi: 10.1016/S0022-2836(02)00212-7.
Previous molecular dynamics (MD) simulations of the thermal denaturation of chymotrypsin inhibitor 2 (CI2) have provided atomic-resolution models of the transition state ensemble that is well supported by experimental studies. Here, we use simulations to further investigate the energy landscape around the transition state region. Nine structures within approximately 35 ps and 3 A C(alpha) RMSD of the transition state ensemble identified in a previous 498 K thermal denaturation simulation were quenched under the quasi-native conditions of 335 K and neutral pH. All of the structures underwent hydrophobically driven collapse in response to the drop in temperature. Structures less denatured than the transition state became structurally more native-like, while structures that were more denatured than the transition state tended to show additional loss of native structure. The structures in the immediate region of the transition state fluctuated between becoming more and less native-like. All of the starting structures had the same native-like topology and were quite similar (within 3.5 A C(alpha) RMSD). That the structures all shared native-like topology, yet diverged into either more or less native-like structures depending on which side of the transition state they occupied on the unfolding trajectory, indicates that topology alone does not dictate protein folding. Instead, our results suggest that a detailed interplay of packing interactions and interactions with water determine whether a partially denatured protein will become more native-like under refolding conditions.
先前对胰凝乳蛋白酶抑制剂2（CI2）热变性的分子动力学（MD）模拟已经提供了过渡态系综的原子分辨率模型，该模型得到了实验研究的有力支持。在此，我们使用模拟来进一步研究过渡态区域周围的能量景观。在先前498K热变性模拟中确定的过渡态系综的约35皮秒和3埃Cα均方根偏差（RMSD）范围内的九个结构，在335K和中性pH的准天然条件下进行了淬火。所有结构都因温度下降而经历了疏水驱动的塌缩。比过渡态变性程度小的结构在结构上变得更像天然结构，而比过渡态变性程度大的结构则倾向于显示出天然结构的额外损失。过渡态紧邻区域的结构在变得更像或不太像天然结构之间波动。所有起始结构都具有相同的类天然拓扑结构，并且非常相似（在3.5埃Cα RMSD范围内）。这些结构都共享类天然拓扑结构，但根据它们在解折叠轨迹上位于过渡态的哪一侧，会分化为或多或少像天然结构的结构，这表明仅拓扑结构并不能决定蛋白质折叠。相反，我们的结果表明，堆积相互作用以及与水的相互作用之间的详细相互作用决定了部分变性的蛋白质在重折叠条件下是否会变得更像天然结构。
