Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.
Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.
复制标题
DOI：
10.1021/ja512062h
复制
发表时间：
2015-03-04
影响因子：
15
通讯作者：
Pappu, Rohit V.
中科院分区：
文献类型：
--
作者：
Holehouse, Alex S.;Garai, Kanchan;Lyle, Nicholas;Vitalis, Andreas;Pappu, Rohit V.
在含有高浓度化学变性剂（如尿素和氯化胍（GdmCl））的水溶液中，蛋白质膨胀以形成异质构象集合。这些变性环境被认为是通用蛋白质序列的良好溶剂，因为构象分布的性质与典型的无规卷曲的性质一致。先前的研究表明，水是多肽主链的不良溶剂，因此主链在水性溶剂中形成塌陷的球状结构。在这里，我们问多肽骨架是否可以在高浓度的尿素和GdmCl的水溶液中固有地进行必要的扩链。我们回答这个问题，使用分子动力学模拟和荧光相关光谱相结合。我们发现，在高浓度变性剂的水溶液中，骨架膨胀的程度是最小的。相反，多肽骨架样品的构象是变性剂特异性的螺旋和小球的混合物，具有对小球的持续偏好。因此，典型的变性环境不能归类为多肽骨架的良好溶剂。那么一般蛋白质序列在变性环境中是如何扩展的呢？为了回答这个问题，我们研究了侧链的影响，使用模拟的两个原型序列的氨基酸组成是带电的，疏水的，和极性基团的混合物。我们发现侧链降低了主链酰胺在水中的有效浓度，导致在不存在变性剂的情况下多肽主链的内在膨胀。通过与变性剂的优先相互作用实现骨架酰胺的有效浓度的额外稀释。这些影响导致在变性环境中的构象统计与那些典型的无规卷曲一致。我们的研究结果突出了侧链介导的相互作用的决定因素的构象性质的展开状态在水中，并在影响链扩张变性。
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 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 sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains 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 sidechain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation.
登录
查看更多内容
影响因子：
4.4
作者：
Bussi, Giovanni;Zykova-Timan, Tatyana;Parrinello, Michele
通讯作者：
Parrinello, Michele
DOI：
10.1073/pnas.94.5.1779
发表时间：
1997-03-04
影响因子：
11.1
作者：
Chan, CK;Hu, Y;Hofrichter, J
通讯作者：
Hofrichter, J
影响因子：
4.3
作者：
Daidone, Isabella;Neuweiler, Hannes;Smith, Jeremy C.
通讯作者：
Smith, Jeremy C.
影响因子：
2.9
作者：
Dunker, AK;Lawson, JD;Obradovic, Z
通讯作者：
Obradovic, Z
影响因子：
2.9
作者：
Diehl, Roger C.;Guinn, Emily J.;Record, M. Thomas, Jr.
通讯作者：
Record, M. Thomas, Jr.