Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Science. 2010 Feb 19;327(5968):1014-8. doi: 10.1126/science.1183649. Epub 2010 Feb 4.
Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-to-proton distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that structures can be accurately determined without nuclear magnetic resonance (NMR) information on the side chains for proteins up to 25 kilodaltons by incorporating backbone chemical shifts, residual dipolar couplings, and amide proton distances into the Rosetta protein structure modeling methodology. These data, which are too sparse for conventional methods, serve only to guide conformational search toward the lowest-energy conformations in the folding landscape; the details of the computed models are determined by the physical chemistry implicit in the Rosetta all-atom energy function. The new method is not hindered by the deuteration required to suppress nuclear relaxation processes for proteins greater than 15 kilodaltons and should enable routine NMR structure determination for larger proteins.
传统的基于核磁共振数据的蛋白质结构测定严重依赖于侧链质子质子距离。然而，必要的侧链共振分配是劳动密集型的，容易出错。在这里，我们通过将骨架化学位移、残差偶极耦合和酰胺质子距离纳入 Rosetta 蛋白质结构建模方法，证明即使没有关于蛋白质侧链的核磁共振（NMR）信息，也可以准确地测定高达 25 千道尔顿的蛋白质结构。对于传统方法来说，这些数据过于稀疏，只能引导构象搜索朝着折叠景观中能量最低的构象进行；计算模型的细节由 Rosetta 全原子能量函数中隐含的物理化学决定。新方法不受抑制大于 15 千道尔顿的蛋白质中核弛豫过程所需的氘化的限制，应该能够为更大的蛋白质进行常规的 NMR 结构测定。
