Brown Scott, Head-Gordon Teresa
Department of Bioengineering, 472 Donner Laboratory, University of California, Berkeley, Berkeley, CA 94720-1762, USA.
Protein Sci. 2004 Apr;13(4):958-70. doi: 10.1110/ps.03316004.
We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted beta-1 and beta-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third beta-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.
我们使用一个简约的蛋白质模型，并结合序列设计策略，来确定蛋白质L和G一级结构上的差异，这两种蛋白质通过截然不同的折叠机制进行折叠。我们发现蛋白质L和G的折叠与成核凝聚机制一致，其中每种机制分别被描述为螺旋辅助的β-1和β-2发夹形成。我们确定蛋白质G的模型展现出一个在折叠限速屏障之前的早期中间体，它将未对齐的二级结构元件聚集在一起，这些元件通过涉及第三条β链的疏水核心接触而稳定，并预示着后期过渡态，在该过渡态中这些相同二级结构元件的正确链对齐得以恢复。最后，通过将动力学数据拟合到一个两步一级可逆反应，分析了蛋白质G靶向中间体集合的有效性，证明蛋白质G折叠涉及一个在折叠途径上的早期中间体，并且应该可以通过实验进行富集并观察到。
