Seshasayee Aswin Sai Narain
Centre for Biotechnology, Anna University, Chennai 600025, India.
Theor Biol Med Model. 2005 Mar 11;2:7. doi: 10.1186/1742-4682-2-7.
Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns.
High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg) and Root Mean Square Deviation (RMSD) have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles.
Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE), shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here.
色氨酸笼是一种最近构建的快速折叠小蛋白。它由一个短螺旋、一个3,10螺旋和一个C端多脯氨酸组成，该多脯氨酸堆积在α螺旋中的一个色氨酸上。已知它能在4纳秒内折叠。
使用GROMACS程序中包含的OPLS-AA力场，在显式水中对色氨酸笼小蛋白进行了高温展开分子动力学模拟。回转半径（Rg）和均方根偏差（RMSD）已被用作跟踪展开过程的序参量。Rg的分布用于识别系综。
可以识别出三个系综。虽然天然态系综显示出的Rg分布略有偏斜，但第二个系综，推测为过渡态系综（TSE），显示出极佳的拟合。变性系综显示出较大的波动，但可以拟合出一条高斯曲线。这意味着展开过程是两态的。这里展示了这些系综中每个系综的代表性结构。
