Master's Program in Biology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
Phys Chem Chem Phys. 2021 Sep 22;23(36):20398-20405. doi: 10.1039/d1cp02876f.
Taste receptors are important sensors for the detection of nutrient concentrations in animals. Tastes are recognized by interactions between chemical substances and taste receptors. Recently, the high-resolution X-ray crystal structure of the extracellular ligand-binding domains (LBDs) of medaka fish () taste receptor type 1 (T1r) complexed with ligands (amino acids) was determined. Medaka fish T1r is a heterodimer composed of two different LBDs, T1r2aLBD and T1r3LBD. In this study, we performed all-atom molecular dynamics (MD) simulations on this heterodimer (T1r2aLBD-T1r3LBD) to address mutational effects on key residues near each ligand-binding pocket in recognizing one of the ligands (L-Gln). For T1r2aLBD, Ser165 is important in ligand recognition due to its direct hydrogen bonding with the ligand. After mutating Ser165 to Ile or Ala, the direct hydrogen bonds between the ligand and the binding pocket were weakened, which destabilized the ligand-binding form of T1r2aLBD. For T1r3LBD, Ser300 is important in ligand recognition. The water-mediated hydrogen bond with the side-chain hydroxyl group of Ser300 is a single interaction that maintains the ligand-binding form of T1r3LBD. After mutating Ser300 to Glu or Ala, both mutant systems almost maintained their ligand-binding form. As a mechanism for maintaining the binding form of T1r3LBD, alternative hydrogen bonds were formed as direct interactions instead of the indirect water-mediated interactions found in the wild-type system, which stabilized the binding form of T1r3LBD. Judging from our mutational analyses, T1r2aLBD was structurally destabilized by the amino acid mutations. Therefore, it might be required that the ligand-binding pocket of T1r2aLBD is composed of a set of specific residues to maintain its ligand-binding form. On the contrary, T1r3LBD was robust enough to withstand the amino acid mutations. These different ligand-binding abilities of both LBDs provide multiple binding modes, which might be helpful for discriminating various taste substances or detecting concentrations of nutrients efficiently.
味觉受体是动物检测营养浓度的重要传感器。味觉是通过化学物质与味觉受体之间的相互作用来识别的。最近，确定了离体配体结合域（LBD）与配体（氨基酸）结合的鱼类（）味觉受体 1（T1r）复合物的高分辨率 X 射线晶体结构。鱼类 T1r 是由两个不同的 LBD 组成的异二聚体，即 T1r2aLBD 和 T1r3LBD。在这项研究中，我们对这个异二聚体（T1r2aLBD-T1r3LBD）进行了全原子分子动力学（MD）模拟，以研究关键残基的突变效应对识别配体之一（L-Gln）的每个配体结合口袋的影响。对于 T1r2aLBD，由于其与配体的直接氢键作用，Ser165 对于配体识别很重要。将 Ser165 突变为异亮氨酸或丙氨酸后，配体与结合口袋之间的直接氢键减弱，从而使 T1r2aLBD 的配体结合形式不稳定。对于 T1r3LBD，Ser300 对于配体识别很重要。Ser300 侧链羟基的水介导氢键是维持 T1r3LBD 配体结合形式的单一相互作用。将 Ser300 突变为谷氨酸或丙氨酸后，两个突变系统几乎都保持了其配体结合形式。作为维持 T1r3LBD 结合形式的机制，替代氢键形成了直接相互作用，而不是野生型系统中发现的间接水介导相互作用，从而稳定了 T1r3LBD 的结合形式。从我们的突变分析来看，T1r2aLBD 的结构由于氨基酸突变而不稳定。因此，可能需要 T1r2aLBD 的配体结合口袋由一组特定的残基组成，以维持其配体结合形式。相反，T1r3LBD 足够坚固，可以承受氨基酸突变。这两个 LBD 的不同配体结合能力提供了多种结合模式，这可能有助于区分各种味觉物质或有效地检测营养物质的浓度。
