Computational Studies of Sodium Symporters

钠同向转运蛋白的计算研究

• 批准号: 8184353
• 负责人: Michael Grabe
• 金额: $ 28.38万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-30 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8184353
• 关键词: Adopted; Adsorption; Affinity; Amino Acid Neurotransmitters; Architecture; Binding; Binding Sites; Biological Assay; Biological Process; Blood; Cells; Chemistry; Computing Methodologies; Coupled; Coupling; Crystallization; Cytoplasm; DNA Sequence Rearrangement; Data; Dehydration; Deposition; Diabetes Mellitus; Disease; Docking; Drug Delivery Systems; Drug Design; Energy Metabolism; Engineering; Ensure; Environment; Event; Exhibits; Extracellular Space; Failure; Family; Free Energy; Galactose; Glucose; Goals; Homeostasis; Human; Ingestion; Intestines; Ions; Kidney; Lead; Ligands; Measurement; Mechanics; Mediating; Membrane; Mental Depression; Metabolism; Modeling; Mole the mammal; Molecular; Molecular Conformation; Movement; Mutation; Nature; Non-Insulin-Dependent Diabetes Mellitus; Oral Rehydration Therapy; Organelles; Patients; Play; Positioning Attribute; Proteins; Pump; Rehydrations; Resolution; Role; Sampling; Screening procedure; Simulate; Small Intestines; Sodium; Solutions; Structure; Testing; Thick; Thyroid Gland; Urea; Water; Work; blind; brush border membrane; cell type; computer studies; design; drug discovery; extracellular; improved; inhibitor/antagonist; member; mutant; operation; prevent; simulation; solute; sugar; symporter; tool; uptake

DESCRIPTION (provided by applicant): The ability of the cell to tightly regulate the temporal and spatial movement of molecules across membranes is central to its survival. This movement has to be done in a selective manner to ensure that the chemistry of the cytoplasm and other internal compartments is not disturbed. To carry out these tasks, membranes are studded with transporters and channels that are often specific to particular cell types or organelles. The primary objective of the current proposal is to use computational methods to examine the conformational changes and functional operation of the sugar transporter vSGLT. vSGLT is the bacterial member of the solute sodium symporter family of transporters responsible for adsorption of simple sugars in the small intestine and kidneys of humans. vSGLT is related to a very large superfamily of transporters called the five helix inverted repeat (5HIR) superfamily. An increased understanding of their molecular workings has the potential to help in treating disease states related to type 2 diabetes mellitus (T2DM) and the treatment of severe dehydration. In Aim 1, we will study the coupling of Na+ and sugar release into the cell. We hypothesize that Na+ exit allows blocking residues to move out of the way and allow sugar to escape, much like opening a gate with a key. All structures of 5HIR superfamily members exhibit these gates, so elucidating this step could be widely informative to other cotransporters. Computations in the Grabe lab will be aided by transport assays on mutant vSGLTs in the Abramson and Wright labs. Our goal in Aim 2 is to use computational drug discovery to design potent inhibitors to vSGLT and hSGLT2. hSGLT2 is a drug target for treating T2DM, so our efforts, coupled with screening in the Wright lab, could lead to new therapies. High-affinity inhibitors to vSGLT would provide a new tool for stabilizing and crystallizing the unknown, outward-facing structure of vSGLT. In Aim 3, we will use transition path sampling coupled with GPU-accelerated dynamics to generate the ensemble of paths between the outward-facing and inward-facing conformations. These simulations will reveal, in molecular detail, the mechanical escapement that allows the 5HIR superfamily to move substrates in the presence of a Na+ gradient. These studies will be guided by experimental SAXS/WAXS and DEER measurements in the Abramson lab. Finally, hSGLT1 plays a central role in the treatment of severe dehydration through the use of Oral Rehydration Therapy, which is estimated to save 1-3 millions lives per year since its inception. Treatment + consists of ingestion of a glucose/NaCl solution. The glucose and Na are absorbed across the brush border membrane by hSGLT1 in the intestine and subsequently deposited in the blood. Each transported mole of glucose is accompanied by 4-6 L of water. We will determine how and in which state(s) vSGLT allows water to permeate, and we will explore the effect of different sugars on water permeation. This final set of computations may suggest improved solutions to aid in rehydration of severally dehydrated patients. 1 PUBLIC HEALTH RELEVANCE: This study is to determine how vSGLT transports galactose across the membrane by harnessing the energy stored in sodium gradients. The results of our studies on vSGLT will impact our understanding of closely related human transporters including those involved in energy metabolism, thyroid metabolism, and depression. Our docking and ligand free energy simulations have the potential to aid in the design of human hSGLT2 inhibitors to treat type 2 diabetes mellitus. 1

描述（由申请人提供）：细胞严格调节分子跨膜的时间和空间运动的能力对其生存至关重要。这种移动必须以选择性的方式进行，以确保细胞质和其他内部区室的化学性质不被干扰。为了执行这些任务，膜上布满了通常针对特定细胞类型或细胞器的转运蛋白和通道。当前提案的主要目标是使用计算方法来检查糖转运蛋白 vSGLT 的构象变化和功能操作。 vSGLT 是溶质钠转运蛋白家族的细菌成员，负责人类小肠和肾脏中单糖的吸附。 vSGLT 与一个非常大的转运蛋白超家族相关，称为五螺旋反向重复 (5HIR) 超家族。加深对其分子运作的了解有可能有助于治疗与 2 型糖尿病 (T2DM) 相关的疾病状态和严重脱水的治疗。在目标 1 中，我们将研究 Na+ 和糖释放到细胞中的耦合。我们假设 Na+ 的退出可以让阻塞残基移开并让糖逸出，就像用钥匙打开大门一样。 5HIR 超家族成员的所有结构都具有这些门，因此阐明这一步骤可以为其他协同转运蛋白提供广泛的信息。 Grabe 实验室的计算将得到 Abramson 和 Wright 实验室突变 vSGLT 转运分析的帮助。我们的目标 2 是利用计算药物发现来设计 vSGLT 和 hSGLT2 的有效抑制剂。 hSGLT2 是治疗 T2DM 的药物靶点，因此我们的努力加上 Wright 实验室的筛选，可能会带来新的疗法。 vSGLT 的高亲和力抑制剂将为稳定和结晶 vSGLT 未知的外向结构提供新的工具。在目标 3 中，我们将使用过渡路径采样与 GPU 加速动力学相结合来生成向外和向内构象之间的路径集合。这些模拟将以分子细节揭示机械擒纵机构，该机械擒纵机构允许 5HIR 超家族在存在 Na+ 梯度的情况下移动基板。这些研究将以艾布拉姆森实验室的实验 SAXS/WAXS 和 DEER 测量为指导。最后，hSGLT1 在通过使用口服补液疗法治疗严重脱水方面发挥着核心作用，该疗法自推出以来估计每年可挽救 1-3 百万人的生命。治疗+包括摄入葡萄糖/氯化钠溶液。葡萄糖和Na在肠道中被hSGLT1穿过刷状缘膜吸收，随后沉积在血液中。每运输一摩尔葡萄糖都伴随着 4-6 升水。我们将确定 vSGLT 如何以及在何种状态下允许水渗透，并且我们将探讨不同糖对水渗透的影响。这最后一组计算可能会提出改进的解决方案，以帮助多次脱水的患者补液。 1 公共健康相关性：本研究旨在确定 vSGLT 如何利用钠梯度中存储的能量跨膜转运半乳糖。我们对 vSGLT 的研究结果将影响我们对密切相关的人类转运蛋白的理解，包括那些参与能量代谢、甲状腺代谢和抑郁症的转运蛋白。我们的对接和配体自由能模拟有可能有助于设计治疗 2 型糖尿病的人类 hSGLT2 抑制剂。 1