Finke John M, Cheung Margaret S, Onuchic José N
The Center for Theoretical Biological Physics and the Department of Physics, University of California, San Diego, La Jolla, California 92093, USA.
Biophys J. 2004 Sep;87(3):1900-18. doi: 10.1529/biophysj.104.041533.
Modeling the structure of natively disordered peptides has proved difficult due to the lack of structural information on these peptides. In this work, we use a novel application of the host-guest method, combining folding theory with experiments, to model the structure of natively disordered polyglutamine peptides. Initially, a minimalist molecular model (C(alpha)C(beta)) of CI2 is developed with a structurally based potential and captures many of the folding properties of CI2 determined from experiments. Next, polyglutamine "guest" inserts of increasing length are introduced into the CI2 "host" model and the polyglutamine is modeled to match the resultant change in CI2 thermodynamic stability between simulations and experiments. The polyglutamine model that best mimics the experimental changes in CI2 thermodynamic stability has 1), a beta-strand dihedral preference and 2), an attractive energy between polyglutamine atoms 0.75-times the attractive energy between the CI2 host Go-contacts. When free-energy differences in the CI2 host-guest system are correctly modeled at varying lengths of polyglutamine guest inserts, the kinetic folding rates and structural perturbation of these CI2 insert mutants are also correctly captured in simulations without any additional parameter adjustment. In agreement with experiments, the residues showing structural perturbation are located in the immediate vicinity of the loop insert. The simulated polyglutamine loop insert predominantly adopts extended random coil conformations, a structural model consistent with low resolution experimental methods. The agreement between simulation and experimental CI2 folding rates, CI2 structural perturbation, and polyglutamine insert structure show that this host-guest method can select a physically realistic model for inserted polyglutamine. If other amyloid peptides can be inserted into stable protein hosts and the stabilities of these host-guest mutants determined, this novel host-guest method may prove useful to determine structural preferences of these intractable but biologically relevant protein fragments.
由于缺乏关于这些肽的结构信息，对天然无序肽的结构进行建模已被证明是困难的。在这项工作中，我们使用了主客体方法的一种新应用，将折叠理论与实验相结合，来对天然无序的聚谷氨酰胺肽的结构进行建模。最初，利用基于结构的势能开发了CI2的极简分子模型（CαCβ），并捕捉了许多通过实验确定的CI2的折叠特性。接下来，将长度不断增加的聚谷氨酰胺“客体”插入物引入CI2“主体”模型中，并对聚谷氨酰胺进行建模，以使其与模拟和实验之间CI2热力学稳定性的最终变化相匹配。最能模拟CI2热力学稳定性实验变化的聚谷氨酰胺模型具有：1）β-链二面角偏好，以及2）聚谷氨酰胺原子之间的吸引力能量是CI2主体Go接触之间吸引力能量的0.75倍。当在不同长度的聚谷氨酰胺客体插入物下正确模拟CI2主客体系统中的自由能差异时，这些CI2插入突变体的动力学折叠速率和结构扰动在模拟中也能被正确捕捉，而无需任何额外的参数调整。与实验一致，显示结构扰动的残基位于环插入物的紧邻区域。模拟的聚谷氨酰胺环插入物主要采用伸展的无规卷曲构象，这是一种与低分辨率实验方法一致的结构模型。模拟与实验在CI2折叠速率、CI2结构扰动和聚谷氨酰胺插入物结构方面的一致性表明，这种主客体方法可以为插入的聚谷氨酰胺选择一个物理上现实的模型。如果其他淀粉样肽可以插入稳定的蛋白质主体中，并确定这些主客体突变体的稳定性，那么这种新的主客体方法可能被证明有助于确定这些难以处理但具有生物学相关性的蛋白质片段的结构偏好。
