Computational studies of membrane transport proteins

膜转运蛋白的计算研究

• 批准号: 10263049
• 负责人: Lucy Forrest
• 金额: $ 171.87万
• 依托单位: NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10263049
• 关键词: ATP Hydrolysis; Address; Annexins; Architecture; Aspartate; Back; Binding; Binding Sites; Biochemical; Biophysics; Calcium; Calcium Binding; Carrier Proteins; Cellular Membrane; Charge; Chemistry; Collaborations; Coupled; Crowding; Cryoelectron Microscopy; Cytoplasmic Granules; Data; Diabetes Mellitus; Electrostatics; Energy-Generating Resources; Environment; Event; Exhibits; Exposure to; Family; Free Energy; Frontotemporal Dementia; Genetic Transcription; Genome; Glutamates; Homologous Gene; Integral Membrane Protein; Ion Channel; Ions; Kinetics; Knowledge; Laboratories; Light; Lipid Bilayers; Lipids; Location; Lysosomes; Measurement; Membrane; Membrane Proteins; Membrane Transport Proteins; Mental Depression; Methodology; Molecular; Molecular Conformation; Morphology; Movement; Movement Disorders; National Heart, Lung, and Blood Institute; National Institute of Neurological Disorders and Stroke; Neurodegenerative Disorders; Neurons; Neurotransmitters; Nutrient; Organism; Pathway interactions; Pharmaceutical Preparations; Pharmacological Treatment; Physiological; Procedures; Process; Protein Conformation; Protein Family; Proteins; Protomer; Publications; RNA; Reporting; Retina; Role; Shapes; Side; Site; Sodium; Specificity; Structural Models; Structure; Surveys; TRP channel; Thermodynamics; Water; computer studies; cost; design; experience; experimental study; insight; interest; novel; novel therapeutics; protein structure; receptor; response; simulation; small molecule; structured data; symporter; three dimensional structure; uptake; ward

Secondary active transporters are a class of membrane proteins that utilize pre-existing molecular concentration gradients as an energy source for translocating another substrate, such as a nutrient or a neurotransmitter, against its concentration gradient. This process requires the protein to change conformations so as to expose a pathway to the substrate binding site(s) on one or other side of the membrane, in a cycle known as alternating access. Every organism expresses dozens of different secondary transporter proteins, and these exhibit a diverse set of architectures, albeit always with some form of internal structural symmetry. Unprecedented, ground-breaking insights have been garnered from three-dimensional structures obtained in the last decade. Nevertheless, a detailed understanding of the mechanism of each membrane transport protein requires knowledge of its structure in many more conformational states, including identification of the binding regions for the substrate or substrates. Moreover, those structures need to be placed into a context of dynamic ensembles on a thermodynamic landscape separated by kinetic barriers. Studies from our group over the last year have continued to investigate these issues in many membrane proteins. That transporters and other membrane proteins can influence the morphology of their surrounding membrane is increasingly recognized. Less appreciated is that the extent and free-energy cost of these deformations likely varies among different functional states of a protein, and thus, that they might contribute significantly to defining its mechanism. We considered the trimeric sodium-aspartate symporter GltPh, a homolog of an important class of neuronal transporters, the EAATs, whose mechanism entails one of the most drastic structural changes known. In collaboration with the Faraldo-Gomez lab (NHLBI), we carried out molecular simulations of GltPh which indicated that when the protomers become inward-facing, they cause deep, long-ranged, and yet mutually-independent membrane deformations. Using a novel simulation methodology, we estimated that the free-energy cost of this membrane perturbation is substantial, raising important new questions about the role of the membrane in neuronal glutamate uptake, especially in crowded environments such as that experienced by retinal EAAT proteins (Ref. 1). Membrane interactions are also critical for water-soluble proteins, for example, through calcium-dependent electrostatic interactions with charged lipids. In collaboration with the Ward lab (NINDS), we used structural modeling to predict calcium binding sites and resultant changes in electrostatic potential in the carboxy-terminal domain of annexin A11 (Ref. 2), a protein implicated in the neurodegenerative disease Frontotemporal Dementia. The amino-terminal segment of annexin A11, is associated with RNA granules, whose mechanism of long-distance movement around neurons remained to be identified. The structural models provided a testable mechanistic prediction of calcium-dependent attachment with lysosomes through annexin A11, a process that would enable to RNA granules to hitchhike to local sites of transcription. For many transporters and other membrane proteins such as channels, recent years have shown an unprecedented amount of structural data, in part due to studies using cryo-electron microscopy. One case of particular interest is the large and diverse transient receptor potential (TRP) family of ion channels, of which over one hundred structures have been reported in just a few years. This plethora of data requires a systematic approach to enable analysis of common features such as pathways and binding sites. We have previously developed structure alignment procedures that allow comparison of large numbers of membrane protein structures. In collaboration with the Swartz lab (NINDS), we adapted these procedures for the specific case of TRP channel structures, enabling a comprehensive, systematic survey that led to multiple, testable hypotheses (Ref. 3), and laid the groundwork for systematic analyses of other membrane protein families for which large numbers of structures become available. In summary, our publications this year reflect ongoing efforts to utilize computational approaches in close collaboration with experimental laboratories, and drive understanding of the mechanism of biomedically-important proteins in neuronal processes, including transporters, channels and other membrane-associated proteins.

二级活性转运蛋白是一类膜蛋白，它们利用已有的分子浓度梯度作为能量来源，针对其浓度梯度转运另一种底物，如营养物质或神经递质。这个过程需要蛋白质改变构象，以便在膜的一侧或另一侧暴露一条通往底物结合位点的途径，这是一个被称为交替进入的循环。每个生物体都表达几十种不同的二级转运蛋白，这些转运蛋白表现出不同的结构，尽管总是具有某种形式的内部结构对称。在过去的十年里，人们从三维结构中获得了前所未有的、突破性的见解。然而，要详细了解每种膜转运蛋白的机制，需要了解其在许多构象状态下的结构，包括鉴定底物或底物的结合区域。此外，这些结构需要被置于动力学屏障分隔的热力学景观上的动态集成环境中。在过去的一年里，我们的研究小组继续在许多膜蛋白中研究这些问题。