Druggable Mechanisms

药物机制

• 批准号: 8380641
• 负责人: YOSHIHIRO NAKATANI
• 金额: $ 40.23万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-07-01 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8380641
• 关键词: Binding; Bioinformatics; Biological; Biological Models; Buffers; Chromatin; Complex; Computer software; Cysteine; DNA; DNA Sequence; DNA-Protein Interaction; Data; Data Analyses; Data Quality; Development; Dimensions; Employee Strikes; Ensure; Feedback; Fractionation; Gene Targeting; Generations; Genetic; Genetic Transcription; Genome; Genomics; Goals; Housing; Human Resources; Individual; Instruction; Libraries; Mass Spectrum Analysis; Methodology; Methods; Molecular; Nature; Neurons; Online Systems; Pathway interactions; Peptides; Performance; Phase; Plant Resins; Play; Post-Translational Protein Processing; Process; Proteins; Proteomics; Protocols documentation; RNA Sequences; Reading; Research; Research Personnel; Resources; Role; Sampling; Services; Solid; Stable Isotope Labeling; Standardization; Sulfhydryl Compounds; System; Techniques; Technology; Therapeutic; Training; Validation; base; computing resources; data acquisition; drug discovery; experience; flexibility; improved; innovation; instrument; nerve stem cell; neuropathology; novel; protein complex; research study; stoichiometry; therapeutic target; tool; transcription factor

The overriding objective of the Druggable Mechanisms Core (DMC) is to provide state-of-the-art technologies in high-throughput chromafin-immunoprecipitafion sequencing (ChlP-seq), RNA sequencing (RNA-seq), and mass spectrometry-based proteomics to each Project for in-depth characterization of transcription factor protein complexes and their respective genetic targets. Data from the DMC will reveal interacting protein partners for Oligl (Project 1), Runxl (Project 2), and NPAS4 (Project 3), characterize associated post-translational modifications, identify downstream genetic targets, and finally quantify the coordinate action of these protein-protein and protein-DNA interactions with respect to transcription of respective target genes. The comprehensive view of molecular interactions provided by the DMC will encompass both direct and surrogate therapeutic entry points for neuropathologies associated with Oligl, Runxl, and NPAS4. Over fime the synergy established between the DMC and Projects 1-3 may provide an experimental paradigm for transcription factor-directed drug discovery. The specific aims of the DMC are: 1.) Implement innovative mass spectrometry-based proteomics techniques for analysis of protein complexes. We will implement novel proteomics methods to improve dynamic range of protein and pepfide identificafion in conjuncfion with tandem immunoaffinity purificafion of protein complexes. These will include solid-phase capture of cysteine-containing peptides combined with stable isotope labeling for quantitative proteomics, and a multidimension separation strategy based on a combination of reversed phase resins (RP/RP). 2.) Develop ChlP-seq and RNA-seq libraries and optimize sequencing on an Applied Biosystems SOLID genome analyzer. The goal of this aim will be to develop reliable ChlP-seq and RNA-seq library construcfion protocols. Each project will require short read sequencing, which we will perform on our SOLiD genome analyzer. Continuous development of in-house protocols in consultafion with AppliedBiosystems will ensure efficient and rapid sequencing on our SOLiD instrument. 3.) Deploy web-based, bioinformatic tools for integrated analysis of ChIP- an RNA-seq data and for comprehensive, user-driven analysis of proteomics data. The goal of this aim is to deploy a web-based system that will provide personnel in Projects 1-3 with an interactive, comprehensive, and dynamic computational platform for interrogation of their genomic and proteomic data, and extension of their observations to the level of pathways and networks.

可药用机制核心（DMC）的首要目标是提供最先进的 高通量染色质免疫沉淀测序（ChIP-seq）、RNA测序 （RNA-seq）和基于质谱的蛋白质组学，以深入表征每个项目 转录因子蛋白复合物及其各自的遗传靶点。DMC的数据将揭示 Oligl（项目1）、Runxl（项目2）和NPAS4（项目3）的相互作用蛋白伴侣，表征 相关的翻译后修饰，鉴定下游遗传靶点，并最终定量 这些蛋白质-蛋白质和蛋白质-DNA相互作用对于转录的协调作用， 各自的靶基因。DMC提供的分子相互作用的全面视图将 包括与Oligl相关的神经病理学的直接和替代治疗切入点， Runxl和NPAS4。在一段时间内，DMC和项目1 - 3之间建立的协同作用可能会提供一个 转录因子导向的药物发现的实验范例。DMC的具体目标是： 1.）的人。实施创新的基于质谱的蛋白质组学技术，用于分析蛋白质 配合物我们将实施新的蛋白质组学方法，以提高蛋白质和肽的动态范围 结合蛋白质复合物的串联免疫亲和纯化进行鉴定。这些将包括 固相捕获含半胱氨酸的肽并结合稳定同位素标记用于定量 蛋白质组学和基于反相树脂组合的多维分离策略 (RP/RP）。 2.）的情况。在Applied Biosystems上开发ChIP-seq和RNA-seq文库并优化测序 SOLID基因组分析仪。该目标的目标将是开发可靠的ChIP-seq和RNA-seq文库 构建协议。每个项目都需要短读段测序，我们将在SOLiD上进行 基因组分析仪持续开发内部方案，与生物系统公司协商 将确保在我们的SOLiD仪器上进行高效快速的测序。 3.）第三章部署基于网络的生物信息学工具，用于ChIP-RNA测序数据的综合分析， 对蛋白质组学数据进行全面、用户驱动的分析。这一目标的目标是部署一个基于Web的 系统将为项目1 - 3的人员提供一个互动的，全面的，动态的 用于询问其基因组和蛋白质组数据的计算平台， 观察路径和网络的水平。