Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
Biophys J. 2011 Jun 8;100(11):2764-72. doi: 10.1016/j.bpj.2011.03.056.
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states that lie energetically between folded and unfolded conformations. There are different ways to test for two-state cooperativity; however, most of these approaches probe indirect proxies of this depletion. Generalized-ensemble computer simulations allow us to unambiguously identify this transition by a microcanonical analysis on the basis of the density of states. Here, we present a detailed characterization of several helical peptides obtained by coarse-grained simulations. The level of resolution of the coarse-grained model allowed to study realistic structures ranging from small α-helices to a de novo three-helix bundle without biasing the force field toward the native state of the protein. By linking thermodynamic and structural features, we are able to show that whereas short α-helices exhibit two-state cooperativity, the type of transition changes for longer chain lengths because the chain forms multiple helix nucleation sites, stabilizing a significant population of intermediate states. The helix bundle exhibits signs of two-state cooperativity owing to favorable helix-helix interactions, as predicted from theoretical models. A detailed analysis of secondary and tertiary structure formation fits well into the framework of several folding mechanisms and confirms features that up to now have been observed only in lattice models.
二态协同性是蛋白质折叠中的一个重要特征。它是通过消耗位于折叠和未折叠构象之间的能量状态来定义的。有不同的方法来测试二态协同性；然而，这些方法中的大多数都探测了这种消耗的间接替代物。广义系综计算机模拟允许我们通过微正则分析基于态密度来明确识别这种转变。在这里，我们通过粗粒化模拟对几个得到的螺旋肽进行了详细的表征。粗粒化模型的分辨率水平允许研究从小α-螺旋到从头三螺旋束的真实结构，而不会使力场偏向蛋白质的天然状态。通过将热力学和结构特征联系起来，我们能够表明尽管短α-螺旋表现出二态协同性，但对于更长的链长，由于链形成多个螺旋成核位点，从而稳定了大量的中间状态，因此过渡类型会发生变化。由于有利的螺旋-螺旋相互作用，螺旋束表现出二态协同性的迹象，这与理论模型的预测一致。对二级和三级结构形成的详细分析很好地符合了几种折叠机制的框架，并证实了迄今为止仅在晶格模型中观察到的特征。
