Midwest Center for Structural Genomics

中西部结构基因组学中心

• 批准号: 8692857
• 负责人: ANDRZEJ JOACHIMIAK
• 金额: $ 624.44万
• 依托单位: UNIVERSITY OF CHICAGO
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-01 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8692857
• 关键词: Advanced Development; Area; Bioinformatics; Biology; Cloning; Collaborations; Collection; Communities; Crystallization; Data; Databases; Deposition; Development; Disease; Foundations; Generations; Genes; Genome; Genomics; Goals; Homology Modeling; Human; Human Microbiome; Informatics; Internet; Methods; Mission; Modeling; Peer Review; Performance; Production; Protein Family; Protein Structure Initiative; Proteins; Publications; Research; Roentgen Rays; Scientist; Signal Transduction; Solutions; Source; Structural Models; Structure; Synchrotrons; System; Technology; Time; Transcriptional Regulation; Validation; Virulence; Visit; X-Ray Crystallography; base; beamline; cost effective; data management; high throughput technology; improved; insight; interest; knowledge base; metagenome; microbial; pathogen; programs; protein complex; protein expression; protein folding; repository; research facility; structural biology; structural genomics; synchrotron radiation; tool

DESCRIPTION (provided by applicant): The primary objective of the Midwest Center for Structural Genomics (MCSG) will be to apply its structure determination pipeline to collaboratively determine the structures of targets nominated by the PSI:Biology Network and the broader biology community. The MCSG will devote a smaller fraction of its effort to contribute, together with its PSl colleagues, to a broader coverage of protein fold space by targeting proteins whose structures would provide the greatest insight into the relationships between sequence and structure. Finally, the MCSG will continue to drive three scientific programs: proteins associated with virulence in human pathogens, proteins overrepresented and associated with disease in human microbiomes and proteins involved in signaling and transcription regulation - an area we are already pursuing in collaboration with leaders in the scientific community. As part of its mandate, the MCSG will also continue to develop and improve technology, and to refine rapid, highly integrated, and cost-effective methods for de novo structure determination by X-ray crystallography using high-performance beamlines at third-generation synchrotron X- ray sources. Our ultimate goal is to build, together with our PSl colleagues, a foundation for 21st century structural biology where the structures of virtually any protein or protein complex will be available to the biology community through the Protein Data Bank. MCSG will achieve these goals by implementing and refining rapid, highly integrated and cost effective methods for structure determination by X-ray crystallography at 3rd generation synchrotrons. We will continue development of advanced data management systems and databases that are vital to the primary mission. The MCSG established a structure determination platform that include: (1) classifying all available genomic sequences to establish a prioritized target set, (2) cloning, and expressing genes and gene fragments of microbial and eukaryotic origin, (3) purifying and crystallizing native and derivatized protein for X-ray crystallography, (4) collecting data and determining structures, (5) analyzing structures for fold and function assignment, and homology modeling of related proteins. The platform provides for rapid model validation and deposition in PDB. In PSI:Biology, these steps will be further advanced and integrated using LIMs and databases into a system capable of determining 200+ structures per year.

描述(由申请人提供)：中西部结构基因组学中心(MCSG)的主要目标将是应用其结构确定管道来协作确定由PSI：生物网络和更广泛的生物界提名的目标的结构。MCSG将投入较小一部分的努力，与PSL的同事一起，通过瞄准结构将提供对序列和结构之间关系的最大洞察的蛋白质，为更广泛的蛋白质折叠空间做出贡献。最后，MCSG将继续推动三个科学项目：与人类病原体毒力相关的蛋白质，人类微生物中过度表达并与疾病相关的蛋白质，以及参与信号和转录调控的蛋白质--这是我们已经与科学界领袖合作追求的一个领域。作为其任务的一部分，MCSG还将继续开发和改进技术，并改进快速、高度集成和成本效益高的方法，通过使用第三代同步加速器X射线源的高性能光束线的X射线结晶学来确定从头结构。我们的最终目标是与PSL的同事一起为21世纪的结构生物学奠定基础，在那里，生物界将通过蛋白质数据库获得几乎任何蛋白质或蛋白质复合体的结构。MCSG将通过在第三代同步加速器上实施和改进快速、高度集成和成本效益高的X射线结晶学结构确定方法来实现这些目标。我们将继续开发对主要任务至关重要的先进数据管理系统和数据库。MCSG建立了一个结构测定平台，包括：(1)对所有可用的基因组序列进行分类，建立优先目标集；(2)克隆和表达微生物和真核来源的基因和基因片段；(3)纯化和结晶天然和衍生蛋白质，用于X射线结晶学；(4)收集数据和确定结构；(5)进行结构分析，进行折叠和功能分配，以及相关蛋白质的同源建模。该平台提供了快速模型验证和在PDB中的沉积。在PSI：生物学中，这些步骤将使用LIM和数据库进一步推进和整合到一个每年能够确定200多个结构的系统中。

项目成果

The CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis contains a [2Fe-2S] cluster: crystal structure and nuclease activity.

来自吡啶家的CRISPR相关的CAS4蛋白PCAL_0546包含[2FE-2S]簇：晶体结构和核酸酶活性。

• DOI: 10.1093/nar/gku797
• 发表时间: 2014
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Lemak S;Nocek B;Beloglazova N;Skarina T;Flick R;Brown G;Joachimiak A;Savchenko A;Yakunin AF
• 通讯作者: Yakunin AF

Structure of the ent-Copalyl Diphosphate Synthase PtmT2 from Streptomyces platensis CB00739, a Bacterial Type II Diterpene Synthase.

• DOI: 10.1021/jacs.6b04317
• 发表时间: 2016-08-31
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: Rudolf JD;Dong LB;Cao H;Hatzos-Skintges C;Osipiuk J;Endres M;Chang CY;Ma M;Babnigg G;Joachimiak A;Phillips GN Jr;Shen B
• 通讯作者: Shen B

A structural insight into the P1S1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidases.

对二氨基乙基膦酸和次膦酸（丙氨酸氨基肽酶的选择性抑制剂）的 P1S1 结合模式的结构深入了解。

• DOI: 10.1016/j.ejmech.2016.04.018
• 发表时间: 2016
• 期刊: European journal of medicinal chemistry
• 影响因子: 6.7
• 作者: Węglarz-Tomczak,Ewelina;Berlicki,Łukasz;Pawełczak,Małgorzata;Nocek,Bogusław;Joachimiak,Andrzej;Mucha,Artur
• 通讯作者: Mucha,Artur

New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium.

• DOI: 10.1007/s10969-013-9151-0
• 发表时间: 2013-03
• 期刊: Journal of structural and functional genomics
• 作者: Michalska, Karolina;Brown, Roslyn N;Li, Hui;Jedrzejczak, Robert;Niemann, George S;Heffron, Fred;Cort, John R;Adkins, Joshua N;Babnigg, Gyorgy;Joachimiak, Andrzej
• 通讯作者: Joachimiak, Andrzej

The kinase LYK5 is a major chitin receptor in Arabidopsis and forms a chitin-induced complex with related kinase CERK1.

激酶LYK5是拟南芥中的主要几丁质受体，并形成了与相关激酶CERK1的几丁质诱导的复合物。

• DOI: 10.7554/elife.03766
• 发表时间: 2014-10-23
• 期刊: eLife
• 影响因子: 7.7
• 作者: Cao Y;Liang Y;Tanaka K;Nguyen CT;Jedrzejczak RP;Joachimiak A;Stacey G
• 通讯作者: Stacey G