Sato Satoshi, Fersht Alan R
MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.
J Mol Biol. 2007 Sep 7;372(1):254-67. doi: 10.1016/j.jmb.2007.06.043. Epub 2007 Jun 22.
The B domain of protein A (BdpA) is a popular paradigm for simulating protein folding pathways. The discrepancies between so many simulations and subsequent experimental testing may be attributable to the protein being highly symmetrical: changing experimental conditions could perturb the subtle interplay between the effects of symmetry in the native structure and the effects of asymmetry from specific interactions in a given sequence. If the protein folds via multiple pathways, perturbations, such as temperature, denaturant concentration, and mutation, should change the flux of micro pathways, leading to changes in the bulk properties of the transition state. We tested this hypothesis by conducting a Phi-analysis of BdpA as a function of temperature from 25.0 degrees C to 60.0 degrees C. The Phi-values had no significant dependence on temperature and the values at 55.0 degrees C (denaturing conditions) are very similar to those at 25.0 degrees C (folding conditions), indicating the structure of the transition state does not significantly change although the experimental conditions are considerably altered. The results suggest that BdpA folds via a single dominant folding pathway.
蛋白 A 的 B 结构域（BdpA）是模拟蛋白质折叠途径的一个常用范例。众多模拟结果与后续实验测试之间的差异可能归因于该蛋白质具有高度对称性：改变实验条件可能会扰乱天然结构中对称性效应与给定序列中特定相互作用的不对称性效应之间的微妙相互作用。如果蛋白质通过多种途径折叠，那么诸如温度、变性剂浓度和突变等扰动应该会改变微观途径的通量，从而导致过渡态整体性质的变化。我们通过对 BdpA 在 25.0℃至 60.0℃温度范围内进行 Φ 分析来检验这一假设。Φ 值对温度没有显著依赖性，并且在 55.0℃（变性条件）下的值与在 25.0℃（折叠条件）下的值非常相似，这表明尽管实验条件发生了很大改变，但过渡态的结构并没有显著变化。结果表明，BdpA 通过单一主导折叠途径进行折叠。
