A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering
A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering
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DOI：
10.1073/pnas.0506202102
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发表时间：
2005-11-22
影响因子：
11.1
通讯作者：
Blackledge, M
中科院分区：
文献类型：
--
作者：
Bernadó, P;Blanchard, L;Blackledge, M
天然未折叠蛋白在正常和病理的生化过程中起着关键作用。尽管它们在功能上很重要，但由于其固有的构象异质性，这类蛋白质仍然超出了经典结构生物学的范围。我们描述了基于来自折叠蛋白质数据库环区的残基特定phi/psi倾向和简单体积排除的未折叠蛋白质的内在构象采样。这一方法被用来提出仙台病毒磷蛋白核衣壳结合域的57-AA天然无序区的结构模型。遵循这些简单的构象采样规则的结构系综被用来模拟平均剩余偶极耦合(RDC)和小角X射线散射数据。这种蛋白质特别有信息量，因为来自相同大小的折叠和未折叠结构域的RDC数据都报告了非结构化区域，从而允许对蛋白质这一部分存在的有序度进行定量分析。实验和模拟的RDC和小角X射线散射数据的密切一致验证了这一简单的构象采样模型，提供了对局部结构和动力学以及采样结构集合的平均维度的精确描述。来自两个尿素展开系统的RDC数据也被紧密复制。通过一组简单的规则可以根据初级序列准确地预测未折叠蛋白质的构象行为，这对于我们理解非结构状态的结构和动力学具有重要的意义。
Natively unfolded proteins play key roles in normal and pathological biochemical processes. Despite their importance for function, this category of proteins remains beyond the reach of classical structural biology because of their inherent conformational heterogeneity. We present a description of the intrinsic conformational sampling of unfolded proteins based on residue-specific phi/psi propensities from loop regions of a folded protein database and simple volume exclusion. This approach is used to propose a structural model of the 57-aa, natively disordered region of the nucleocapsid-binding domain of Sendai virus phosphoprotein. Structural ensembles obeying these simple rules of conformational sampling are used to simulate averaged residual dipolar couplings (RDCs) and small-angle x-ray scattering data. This protein is particularly informative because RDC data from the equally sized folded and unfolded domains both report on the unstructured region, allowing a quantitative analysis of the degree of order present in this part of the protein. Close agreement between experimental and simulated RDC and small-angle x-ray scattering data validates this simple model of conformational sampling providing a precise description of local structure and dynamics and average dimensions of the ensemble of sampled structures. RDC data from two urea-unfolded systems are also closely reproduced. The demonstration that conformational behavior of unfolded proteins can be accurately predicted from the primary sequence by using a simple set of rules has important consequences for our understanding of the structure and dynamics of the unstructured state.