Moritsugu Kei, Terada Tohru, Kidera Akinori
Graduate School of Medical Life Science, Yokohama City University , 1-7-29 Suehirocho, Tsurumi, Yokohama 230-0045, Japan.
Graduate School of Agricultural and Life Sciences, The University of Tokyo , 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan.
J Phys Chem B. 2017 Feb 2;121(4):731-740. doi: 10.1021/acs.jpcb.6b11696. Epub 2017 Jan 18.
Protein-ligand interactions are frequently coupled with protein structural changes. Focusing on the coupling, we present the free-energy surface (FES) of the ligand-binding process for glutamine-binding protein (GlnBP) and its ligand, glutamine, in which glutamine binding accompanies large-scale domain closure. All-atom simulations were performed in explicit solvents by multiscale enhanced sampling (MSES), which adopts a multicopy and multiscale scheme to achieve enhanced sampling of systems with a large number of degrees of freedom. The structural ensemble derived from the MSES simulation yielded the FES of the coupling, described in terms of both the ligand's and protein's degrees of freedom at atomic resolution, and revealed the tight coupling between the two degrees of freedom. The derived FES led to the determination of definite structural states, which suggested the dominant pathways of glutamine binding to GlnBP: first, glutamine migrates via diffusion to form a dominant encounter complex with Arg75 on the large domain of GlnBP, through strong polar interactions. Subsequently, the closing motion of GlnBP occurs to form ligand interactions with the small domain, finally completing the native-specific complex structure. The formation of hydrogen bonds between glutamine and the small domain is considered to be a rate-limiting step, inducing desolvation of the protein-ligand interface to form the specific native complex. The key interactions to attain high specificity for glutamine, the "door keeper" existing between the two domains (Asp10-Lys115) and the "hydrophobic sandwich" formed between the ligand glutamine and Phe13/Phe50, have been successfully mapped on the pathway derived from the FES.
蛋白质-配体相互作用常常伴随着蛋白质结构的变化。聚焦于这种耦合作用，我们展示了谷氨酰胺结合蛋白（GlnBP）与其配体谷氨酰胺的配体结合过程的自由能表面（FES），其中谷氨酰胺结合伴随着大规模的结构域闭合。全原子模拟是在显式溶剂中通过多尺度增强采样（MSES）进行的，MSES采用多拷贝和多尺度方案来实现对具有大量自由度的系统的增强采样。从MSES模拟得到的结构系综产生了耦合作用的FES，它以原子分辨率下配体和蛋白质的自由度来描述，并揭示了这两个自由度之间的紧密耦合。导出的FES导致确定了明确的结构状态，这表明了谷氨酰胺与GlnBP结合的主要途径：首先，谷氨酰胺通过扩散迁移，与GlnBP大结构域上的Arg75形成主要的相遇复合物，通过强极性相互作用。随后，GlnBP发生闭合运动，与小结构域形成配体相互作用，最终完成天然特异性复合物结构。谷氨酰胺与小结构域之间氢键的形成被认为是限速步骤，它诱导蛋白质-配体界面的去溶剂化以形成特异性天然复合物。为实现对谷氨酰胺的高特异性的关键相互作用，即两个结构域之间存在的“守门人”（Asp10-Lys115）以及配体谷氨酰胺与Phe13/Phe50之间形成的“疏水三明治”，已成功地映射到从FES导出的途径上。
