STRUCTURAL AND FUNCTIONAL GENOMICS OF PROTEIN FAMILIES

蛋白质家族的结构和功能基因组学

• 批准号: 7726209
• 负责人: MIREK CYGLER
• 金额: $ 2.38万
• 依托单位: BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-18 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7726209
• 关键词: Acids; Bacterial Proteins; Bacteroides thetaiotaomicron; Binding; Biochemical; Biological Process; Campylobacter jejuni; Cancer cell line; Carbohydrates; Cell Line; Complement; Complex; Computer Retrieval of Information on Scientific Projects Database; Data; Data Collection; Enzymes; Escherichia coli; Escherichia coli Proteins; Flavobacteria; Flavobacterium genus; Funding; Genes; Glycosaminoglycans; Goals; Grant; Helicobacter pylori; Institution; Lyase; Metabolism; Modeling; Neoplasm Metastasis; Organelles; Protein Family; Proteins; Proteomics; Publishing; Range; Research; Research Personnel; Resources; Scaffolding Protein; Signal Pathway; Site-Directed Mutagenesis; Source; Structure; Therapeutic Intervention; United States National Institutes of Health; base; cofactor; comparative; functional/structural genomics; genome sequencing; glycosylation; inhibitor/antagonist; interest; pathogenic Escherichia coli; pathogenic bacteria

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. The data collection activities carried out within the PXRR in this project are focused on medium-throughput structure determination and characterization, primarily of enzymatic mechanisms of proteins from prokaryotic and eukaryotic sources that are involved in a variety of biological processes. The specific goals of these projects are to (a) determine the structure of the apo-protein (b) determine the co-crystal structure with a variety of possible substrate/product/inhibitor or cofactor molecules to clarify the enzymatic mechanism and (c) perform additional biophysical and biochemical characterization and site-directed mutagenesis of these proteins in order to better understand their function and to complement the crystal structure. Bacterial proteins of both known and unknown function are predominantly selected from the three sequenced genomes of Escherichia coli. Some of the proteins are unique to both E. coli pathogenic strains, as well as to other pathogenic bacteria, and may represent potential targets for therapeutic intervention. Over 30 crystal structures of E. coli proteins have arisen from this these studies, and represent a broad range of metabolic processes. In addition to E. coli proteins, we are interested in bacterial enzymes from Helicobacter pylori and Campylobacter jejuni involved in pseudaminic acid other carbohydrates synthesis and the general N-glycosylation machinery. Finally, we have a long standing interest in glycosaminoglycan lyases from Flavobacterium heparinum, Bacteroides thetaiotaomicron and other species Most of our published results are based on structure of a native enzyme together with several complexes. Eukaryotic proteins are selected based on proteomics analysis of cellular organelles carried within the Montreal Proteomics Network (e.g. CREG, ENTH domain of enthoprotin) and based on comparative microarray data for normal and cancer cell lines carried within a large-scale NRCC project. Targets of interest were selected following TGF-b treatment of a cell line used as a model for metastasis. Genes that are signifcantly up- or down-regulated were selected for structural studies. In addition, we are interested in scaffolding proteins in signaling pathways and their complexes with binding partners (e.g. MP1-p14 complex).

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 在该项目中，PXRR内进行的数据收集活动侧重于中等通量结构测定和表征，主要是涉及各种生物过程的原核和真核来源的蛋白质的酶促机制。 这些项目的具体目标是：（a）确定脱辅基蛋白的结构（B）确定与各种可能的底物/产物/抑制剂或辅因子分子的共晶体结构，以阐明酶促机制;（c）对这些蛋白进行额外的生物物理和生物化学表征以及定点诱变，以更好地了解其功能并补充晶体结构。 已知和未知功能的细菌蛋白质主要选自大肠杆菌的三个测序基因组。有些蛋白质是两种大肠杆菌所特有的。大肠杆菌致病菌株，以及其他致病细菌，并可能代表潜在的治疗干预的目标。 E.大肠杆菌蛋白质是从这些研究中产生的，代表了广泛的代谢过程。除E.大肠杆菌蛋白质，我们感兴趣的细菌酶幽门螺杆菌和空肠弯曲菌参与假氨基酸其他碳水化合物的合成和一般的N-糖基化机制。最后，我们对肝素黄杆菌、多形拟杆菌和其他物种的糖胺聚糖裂解酶有着长期的兴趣。我们发表的大多数结果都是基于天然酶与几种复合物的结构。 真核蛋白质的选择是基于蒙特利尔蛋白质组学网络（例如CREG，enthoprotin的ENTH结构域）内携带的细胞器的蛋白质组学分析，并基于大规模NRCC项目内携带的正常和癌细胞系的比较微阵列数据。在TGF-β处理用作转移模型的细胞系后选择感兴趣的靶标。选择显著上调或下调的基因进行结构研究。此外，我们对信号通路中的支架蛋白及其与结合伴侣的复合物（例如MP 1-p14复合物）感兴趣。