Program in Molecular Biophysics, Johns Hopkins University , Baltimore, Maryland 21218, United States.
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland 21205, United States.
J Phys Chem B. 2017 Nov 22;121(46):10436-10442. doi: 10.1021/acs.jpcb.7b06862. Epub 2017 Nov 9.
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are responsible for the majority of excitatory transmission at the synaptic cleft. Mechanically speaking, agonist binding to the ligand binding domain (LBD) activates the receptor by triggering a conformational change that is transmitted to the transmembrane region, opening the ion channel pore. We use fully atomistic molecular dynamics simulations to investigate the binding process in the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor, an iGluR subtype. The string method with swarms of trajectories was applied to calculate the possible pathways glutamate traverses during ligand binding. Residues peripheral to the binding cleft are found to metastably bind the ligand prior to ligand entry into the binding pocket. Umbrella sampling simulations were performed to compute the free energy barriers along the binding pathways. The calculated free energy profiles demonstrate that metastable interactions contribute substantially to the energetics of ligand binding and form local minima in the overall free energy landscape. Protein-ligand interactions at sites outside of the orthosteric agonist-binding site may serve to lower the transition barriers of the binding process.
离子型谷氨酸受体（iGluRs）是配体门控离子通道，负责突触间隙中大多数兴奋性传递。从力学上讲，激动剂与配体结合域（LBD）的结合通过触发构象变化来激活受体，该构象变化传递到跨膜区域，打开离子通道孔。我们使用全原子分子动力学模拟来研究α-氨基-3-羟基-5-甲基-4-异恶唑丙酸（AMPA）受体，一种 iGluR 亚型的结合过程。使用轨迹群的字符串方法来计算配体结合过程中谷氨酸可能经历的途径。发现结合裂缝周围的残基在配体进入结合口袋之前，以亚稳态结合配体。进行了伞状采样模拟，以计算结合途径上的自由能势垒。计算得到的自由能曲线表明，亚稳态相互作用对配体结合的能量有很大贡献，并在整体自由能景观中形成局部最小值。位于正位激动剂结合位点之外的蛋白质-配体相互作用可能有助于降低结合过程的跃迁势垒。
