Mechanistic analysis of dynamic scaffolding in a cellular signaling network

细胞信号网络中动态支架的机制分析

• 批准号: 8132339
• 负责人: RAMA RANGANATHAN
• 金额: $ 34.97万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-01 至 2013-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8132339
• 关键词: Address; Afferent Neurons; Allosteric Regulation; Biological Models; Calcium; Calcium ion; Cell model; Cells; Characteristics; Chronic; Collecting Cell; Complex; Coupled; Data; Defect; Dependence; Development; Disease; Drosophila genus; Event; Eye; Feedback; Goals; Invertebrates; Knowledge; Lead; Left; Light; Macromolecular Complexes; Malignant Neoplasms; Measures; Mechanics; Mediating; Methods; Modeling; Molecular Conformation; Organelles; Output; Performance; Phosphorylation; Phosphorylation Site; Photons; Photoreceptors; Physiological; Physiological Processes; Process; Property; Protein Dynamics; Protein Isoforms; Proteins; Regulation; Research; Research Personnel; Role; Scaffolding Protein; Series; Shapes; Signal Transduction; Signaling Molecule; Specificity; Speed; Stimulus; Structure; System; TRP channel; Tertiary Protein Structure; Testing; Time; Transgenic Organisms; Vision; Visual; Work; absorption; compound eye; design; disease characteristic; disulfide bond; in vivo; information processing; millisecond; mutant; programs; protein complex; quantum; research study; response; scaffold; small molecule

Cells collect and process information about the external world through elaborate networks of proteins and small molecules that we call the signal transduction machinery. The functional capability of the transduction machinery is often prodigious; weak input signals can be selectively amplified and filtered for optimal sensing of physiological stimuli, and layers of feedback control provide for complex regulatory characteristics and protection against output saturation. For example, sensory neurons of the eye can generate reliable electrical responses to the absorption of single photons under dark adapted conditions, but can also adjust the gain to continue operating in bright daylight conditions without response saturation. The overall goal of our research program is to understand how signaling systems provide for such functional characteristics, and how disease processes arise from defects in the underlying mechanisms. In this application, we propose to mechanistically understand a specific macromolecular complex that is required for visual function in Drosophila. The complex is assembled by a multi-PDZ domain protein called InaD, and our recent work shows that rather than acting as a passive scaffold, this protein is a dynamic machine that undergoes light-dependent conformational changes at the time scale of visual signaling. In the course of the experiments proposed here, we will (1) understand the exact physiological processes controlled by InaD dynamics, (2) define how light-signaling is coupled to the conformational switching of InaD, (3) define how the conformational change regulates the visual output, and (4) carry out studies to see if InaD organizes spatial gradients of signaling molecules. InaD has already served as a classic model system for understanding macromolecular organization of signaling systems. We expect that this work will expose new mechanisms of InaD function, and will help resolve current models for scaffolding in general. Scaffolding is thought to enhance the efficiency and specificity of signaling events in many cells, and defects in scaffolding have been associated with diverse disease processes, including cancer, chronic inflammaton, and developmental abnormalities. By showing how scaffolding proteins can alsoactively shape signaling events through dynamical conformational change, this work should help extend our understanding of the normal and pathological states of cellular signlaing systems.

细胞通过复杂的蛋白质网络收集和处理外部世界的信息 和我们称之为信号转导机制的小分子。的功能 转导机制通常是巨大的;微弱的输入信号可以被选择性地放大和过滤， 生理刺激的最佳感测，以及反馈控制层提供了复杂的调节功能。 特性和输出饱和保护。例如，眼睛的感觉神经元可以 在暗适应条件下对单光子的吸收产生可靠的电响应，但 还可以调整增益，以继续在明亮的日光条件下工作，而不会出现响应饱和。的 我们研究计划的总体目标是了解信号系统如何提供这种功能 特征，以及疾病过程如何从潜在机制的缺陷中产生。 在这个应用中，我们建议从机械上理解一种特定的大分子复合物， 是果蝇视觉功能所必需的。该复合物是由一个多PDZ结构域蛋白组装而成的， InaD，我们最近的工作表明，这种蛋白质不是被动的支架，而是动态的 在视觉信号的时间尺度上经历光依赖性构象变化的机器。在 在这里提出的实验过程中，我们将（1）了解确切的生理过程 由InaD动力学控制，（2）定义光信号如何耦合到构象转换， InaD，（3）定义构象变化如何调节视觉输出，以及（4）进行研究，看看是否 InaD组织信号分子的空间梯度。InaD已经作为一个经典的模型系统 来理解信号系统的大分子结构。我们希望这项工作能揭露 InaD功能的新机制，并将有助于解决目前的脚手架模型一般。 支架被认为可以增强许多细胞中信号传导事件的效率和特异性， 支架的缺陷与多种疾病过程有关，包括癌症、慢性 炎症和发育异常通过展示支架蛋白是如何 通过动态构象变化来塑造信号事件，这项工作应该有助于扩展我们的 了解细胞信号系统的正常和病理状态。

项目成果

Protein sectors: evolutionary units of three-dimensional structure.

• DOI: 10.1016/j.cell.2009.07.038
• 发表时间: 2009-08-21
• 期刊: Cell
• 影响因子: 64.5
• 作者: Halabi N;Rivoire O;Leibler S;Ranganathan R
• 通讯作者: Ranganathan R

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing.

利用高通量测序对全蛋白饱和诱变文库进行功能评估的方案。

• DOI: 10.3791/54119
• 发表时间: 2016
• 期刊: Journal of visualized experiments : JoVE
• 作者: Stiffler,MichaelA;Subramanian,SubuK;Salinas,VictorH;Ranganathan,Rama
• 通讯作者: Ranganathan,Rama

Surface sites for engineering allosteric control in proteins.

• DOI: 10.1126/science.1159052
• 发表时间: 2008-10-17
• 期刊: Science (New York, N.Y.)
• 作者: Lee J;Natarajan M;Nashine VC;Socolich M;Vo T;Russ WP;Benkovic SJ;Ranganathan R
• 通讯作者: Ranganathan R

Evolution-based design of proteins.

基于进化的蛋白质设计。

• DOI: 10.1016/b978-0-12-394292-0.00010-2
• 发表时间: 2013
• 期刊: Methods in enzymology
• 作者: Reynolds,KimberlyA;Russ,WilliamP;Socolich,Michael;Ranganathan,Rama
• 通讯作者: Ranganathan,Rama

Hot spots for allosteric regulation on protein surfaces.

• DOI: 10.1016/j.cell.2011.10.049
• 发表时间: 2011-12-23
• 期刊: Cell
• 影响因子: 64.5
• 作者: Reynolds KA;McLaughlin RN;Ranganathan R
• 通讯作者: Ranganathan R