Pruitt Margaret M, Lamm Monica H, Coffman Clark R
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
BMC Struct Biol. 2013 Sep 18;13:15. doi: 10.1186/1472-6807-13-15.
The arginine of the D/E/NRY motif in Rhodopsin family G protein-coupled receptors (GPCRs) is conserved in 96% of these proteins. In some GPCRs, this arginine in transmembrane 3 can form a salt bridge with an aspartic acid or glutamic acid in transmembrane 6. The Drosophila melanogaster GPCR Trapped in endoderm-1 (Tre1) is required for normal primordial germ cell migration. In a mutant form of the protein, Tre1sctt, eight amino acids RYILIACH are missing, resulting in a severe disruption of primordial germ cell development. The impact of the loss of these amino acids on Tre1 structure is unknown. Since the missing amino acids in Tre1sctt include the arginine that is part of the D/E/NRY motif in Tre1, molecular dynamics simulations were performed to explore the hypothesis that these amino acids are involved in salt bridge formation and help maintain Tre1 structure.
Structural predictions of wild type Tre1 (Tre1+) and Tre1sctt were subjected to over 250 ns of molecular dynamics simulations. The ability of the model systems to form a salt bridge between the arginine of the D/E/NRY motif and an aspartic acid residue in transmembrane 6 was analyzed. The results indicate that a stable salt bridge can form in the Tre1+ systems and a weak salt bridge or no salt bridge, using an alternative arginine, is likely in the Tre1sctt systems.
The weak salt bridge or lack of a salt bridge in the Tre1sctt systems could be one possible explanation for the disrupted function of Tre1sctt in primordial germ cell migration. These results provide a framework for studying the importance of the arginine of the D/E/NRY motif in the structure and function of other GPCRs that are involved in cell migration, such as CXCR4 in the mouse, zebrafish, and chicken.
视紫红质家族G蛋白偶联受体（GPCRs）中D/E/NRY基序的精氨酸在96%的此类蛋白中是保守的。在一些GPCRs中，跨膜3中的这个精氨酸可与跨膜6中的天冬氨酸或谷氨酸形成盐桥。果蝇GPCR被困在内胚层-1（Tre1）是正常原始生殖细胞迁移所必需的。在该蛋白的一种突变形式Tre1sctt中，八个氨基酸RYILIACH缺失，导致原始生殖细胞发育严重受损。这些氨基酸缺失对Tre1结构的影响尚不清楚。由于Tre1sctt中缺失的氨基酸包括Tre1中D/E/NRY基序的一部分精氨酸，因此进行了分子动力学模拟，以探讨这些氨基酸参与盐桥形成并有助于维持Tre1结构这一假说。
对野生型Tre1（Tre1+）和Tre1sctt进行了超过250纳秒的分子动力学模拟结构预测。分析了模型系统在D/E/NRY基序的精氨酸与跨膜6中的天冬氨酸残基之间形成盐桥的能力。结果表明，在Tre1+系统中可形成稳定的盐桥，而在Tre1sctt系统中，可能形成弱盐桥或不形成盐桥（使用另一个精氨酸）。
Tre1sctt系统中弱盐桥或无盐桥可能是Tre1sctt在原始生殖细胞迁移中功能受损的一种可能解释。这些结果为研究D/E/NRY基序的精氨酸在其他参与细胞迁移的GPCRs（如小鼠、斑马鱼和鸡中的CXCR4）的结构和功能中的重要性提供了一个框架。
