University Chemical Laboratories, Cambridge, UK.
Curr Opin Struct Biol. 2010 Feb;20(1):3-10. doi: 10.1016/j.sbi.2009.12.011. Epub 2010 Jan 22.
Kinetic transition networks can now be calculated for small proteins using geometry optimisation to characterise minima, transition states and pathways, and unimolecular rate theory to supply rate constants corresponding to each transition state. The networks can be visualised by constructing disconnectivity graphs, revealing striking differences between good structure-seeking systems and a model glass former. The glassy landscape contains competing low-lying minima separated by high barriers, providing a more extreme example of the frustration previously characterised for model proteins. Free energy projections that preserve barriers and rates can be obtained from the network representation, and global kinetics can be addressed on the experimental time scale.
现在可以使用几何优化来计算小分子蛋白的动力学转变网络,以描述最小势能点、转变态和途径,以及使用单分子速率理论来提供与每个转变态相对应的速率常数。通过构建不连通图可以将网络可视化,揭示出良好的结构寻求系统和模型玻璃形成体之间的显著差异。玻璃态景观包含由高势垒隔开的竞争的低能最小势能点,为之前针对模型蛋白所描述的挫折提供了更极端的例子。可以从网络表示中获得保留势垒和速率的自由能投影,并且可以在实验时间尺度上解决全局动力学问题。