Holehouse Alex S, Garai Kanchan, Lyle Nicholas, Vitalis Andreas, Pappu Rohit V
Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis , One Brookings Drive, Campus Box 1097, St. Louis, Missouri 63130, United States.
J Am Chem Soc. 2015 Mar 4;137(8):2984-95. doi: 10.1021/ja512062h. Epub 2015 Feb 23.
In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones, and therefore, backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations of denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of side chains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that side chains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of side chain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation.
在含有高浓度化学变性剂（如尿素和氯化胍（GdmCl））的水溶液中，蛋白质会展开形成异质构象集合体。这些变性环境被认为是一般蛋白质序列的良溶剂，因为构象分布的特性与典型无规卷曲的特性相符。先前的研究表明，水对于多肽主链来说是不良溶剂，因此，主链在水性溶剂中会形成塌陷的球状结构。在这里，我们要问，在含有高浓度尿素和GdmCl的水溶液中，多肽主链是否能内在地经历必要的链扩张。我们通过分子动力学模拟和荧光相关光谱相结合的方法来回答这个问题。我们发现，在含有高浓度变性剂的水溶液中，主链的扩张程度极小。相反，多肽主链采样的构象是无规卷曲和球状的变性剂特异性混合物，并且一直偏好球状。因此，典型的变性环境不能被归类为多肽主链的良溶剂。那么，一般的蛋白质序列在变性环境中是如何展开的呢？为了回答这个问题，我们使用具有带电、疏水和极性基团混合物氨基酸组成的两个典型序列的模拟研究了侧链的影响。我们发现，侧链降低了水中主链酰胺的有效浓度，导致在没有变性剂的情况下多肽主链发生内在扩张。通过与变性剂的优先相互作用，进一步稀释了主链酰胺的有效浓度。这些效应导致变性环境中的构象统计与典型无规卷曲的构象统计一致。我们的结果突出了侧链介导的相互作用在决定水中未折叠状态的构象特性以及影响变性时链扩张方面的作用。
