Substrate‐binding domains (SBD) are important structural elements of substrate transporters mediating the transport of essential molecules across the cell membrane. The SBD2 domain of the glutamine (GLN) transporter from bacteria consists of two domains D1 and D2 that bind GLN in the space between the domains in a closed conformation. In the absence of ligand, SBD2 adopts an open conformation with increased domain distance. In molecular dynamics (MD) simulations in the absence of ligands, no closing of the open conformation was observed on the MD time scale. Addition of GLN resulted in several reversible binding and unbinding events of GLN at the binding site on the D1 domain but did not induce domain closing indicating that binding and global domain closing do not occur simultaneously. The SBD2 structure remained in a closed state when starting from the GLN‐bound closed crystal structure and opened quickly to reach the open state upon removal of the GLN ligand. Free energy simulations to induce opening to closing indicated a barrier for closing in the absence and presence of ligand and a significant penalty for closing without GLN in the binding pocket. Simulations of a Leu480Ala mutation also indicate that an interaction of a C‐terminal D1‐tail_471‐484 with a D2‐helix_418‐427 (not contacting the substrate‐binding region) plays a decisive role for controlling the barrier of conformational switching in the SBD2 protein. The results allow us to derive a model of the molecular mechanism of substrate binding to SBD2 and associated conformational changes.

中文翻译：

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分子动力学模拟揭示了GlnPQ底物结合域2的配体结合和整体适应性

底物结合域（SBD）是底物转运蛋白的重要结构元素，介导必需分子跨细胞膜的转运。来自细菌的谷氨酰胺（GLN）转运蛋白的SBD2结构域由两个结构域D1和D2组成，两个结构域D1和D2以闭合构象结合结构域之间空间中的GLN。在不存在配体的情况下，SBD2采用具有增加的结构域距离的开放构象。在不存在配体的分子动力学（MD）模拟中，在MD时间尺度上未观察到开放构象的闭合。GLN的添加在D1域的结合位点上导致了GLN的几个可逆的结合和非结合事件，但没有诱导域关闭，表明结合和全局域关闭不是同时发生的。当从GLN结合的闭合晶体结构开始时，SBD2结构保持闭合状态，并在去除GLN配体后迅速打开以达到打开状态。诱导打开到闭合的自由能模拟表明在不存在和存在配体的情况下闭合的障碍，以及在结合口袋中没有GLN的闭合的显着损失。对Leu480Ala突变的模拟还表明，C末端D1尾巴的相互作用_471-484用D2-螺旋_418-427（不接触底物结合区域）起到用于控制的构象转换在SBD2蛋白阻挡决定性的作用。结果使我们能够得出底物与SBD2结合及相关构象变化的分子机制模型。