Hills Ronald D, Brooks Charles L
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC6, La Jolla, CA 92037, USA.
J Mol Biol. 2008 Oct 3;382(2):485-95. doi: 10.1016/j.jmb.2008.07.007. Epub 2008 Jul 11.
The folding of multidomain proteins often proceeds in a hierarchical fashion with individual domains folding independent of one another. A large single-domain protein, however, can consist of multiple modules whose folding may be autonomous or interdependent in ways that are unclear. We used coarse-grained simulations to explore the folding landscape of the two-subdomain bacterial response regulator CheY. Thermodynamic and kinetic characterization shows the landscape to be highly analogous to the four-state landscape reported for another two-subdomain protein, T4 lysozyme. An on-pathway intermediate structured in the more stable nucleating subdomain was observed, as were transient states frustrated in off-pathway contacts prematurely structured in the weaker subdomain. Local unfolding, or backtracking, was observed in the frustrated state before the native conformation could be reached. Nonproductive frustration was attributable to competition for van der Waals contacts between the two subdomains. In an accompanying article, stopped-flow kinetic measurements support an off-pathway burst-phase intermediate, seemingly consistent with our prediction of early frustration in the folding landscape of CheY. Comparison of the folding mechanisms for CheY, T4 lysozyme, and interleukin-1 beta leads us to postulate that subdomain competition is a general feature of large single-domain proteins with multiple folding modules.
多结构域蛋白质的折叠通常以分层方式进行，各个结构域彼此独立折叠。然而，一个大的单结构域蛋白质可能由多个模块组成，其折叠方式可能是自主的，也可能是相互依赖的，具体情况尚不清楚。我们使用粗粒度模拟来探索两结构域细菌应答调节蛋白CheY的折叠态势。热力学和动力学表征表明，该态势与另一种两结构域蛋白质T4溶菌酶所报道的四态态势高度相似。观察到在更稳定的成核结构域中形成的一条折叠途径上的中间体，以及在较弱结构域中过早形成的偏离途径接触中受阻的瞬态。在达到天然构象之前，在受阻状态下观察到局部解折叠，即回溯。非生产性受阻归因于两个结构域之间对范德华接触的竞争。在一篇配套文章中，停流动力学测量支持了一个偏离途径的爆发相中间体，这似乎与我们对CheY折叠态势中早期受阻的预测一致。对CheY、T4溶菌酶和白细胞介素-1β折叠机制的比较使我们推测，结构域竞争是具有多个折叠模块的大的单结构域蛋白质的一个普遍特征。
