Computational Assembly of Beta Barrel Membrane Protein

β 桶膜蛋白的计算组装

基本信息

批准号：
8506731
负责人：
Jie Liang
金额：
$ 28.83万
依托单位：
UNIVERSITY OF ILLINOIS AT CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2007
资助国家：
美国
起止时间：
2007-03-01 至 2017-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8506731
关键词：
Accounting Acid Fast Bacillae Staining Method Antibiotic Resistance Antibiotics Antigens Antineoplastic Agents Apoptosis Apoptosis Regulator Archaea Architecture Bacillus anthracis Biological Biological Process Cells Cereals Chloroplasts Communicable Diseases Complex Computer Simulation Cytosol DNA Sequence Detection Drug Delivery Systems Encapsulated Energy Metabolism Engineering Environment Escherichia coli Exotoxins Family Genus Mycobacterium Germany Goals Gram-Negative Bacteria Gram-Positive Bacteria Hemolysin Homeostasis Homo Homologous Gene Immunologic Surveillance Induction of Apoptosis Integral Membrane Protein Ion Transport Israel Knowledge Learning Letters Life Lipids Membrane Membrane Proteins Metabolism Methods Mitochondria Modeling Molecular Conformation Mycobacterium tuberculosis Neisseria gonorrhoeae Oligonucleotides Outer Mitochondrial Membrane Pharmaceutical Preparations Principal Investigator Property Protein translocation Proteins Research Resistance Site Space Models Staphylococcus aureus Structure Techniques Technology Testing Vaccines Validation Virulence Voltage-Dependent Anion Channel Work base beta barrel computer studies computerized tools cost design insight mutant nanodevice nanopore novel porin programs protein protein interaction protein structure public health relevance research study therapeutic target tool

项目摘要

DESCRIPTION (provided by applicant): Barrels are found in the outer membrane of gram-negative bacteria, acid-fast gram-positive bacteria, eukaryotic mitochondria, chloroplasts (e.g., in E. coli, N. meningitidis, N. gonorrheae, and mycobacteria such as M. tuberculosis). Many pore-forming exotoxins from gram-positive bacteria are also -barrel membrane proteins (e.g., ?-hemolysin of S. aureus and protective antigen of B. anthracis). ?-barrel membrane proteins are important for many fundamental biological processes. They control the ex- change and transport of ions and organic molecules across the bacterial and mitochondrial outer membranes. They are essential for protein translocation in all domains of life, except archaea. They regulate metabolism and apoptosis. They are also important for immune surveillance, in providing resistance to antibiotics, and are key determinants of bacterial virulence. As a result, ?-barrel membrane proteins are important therapeutic targets for developing drugs and vaccines against infectious diseases. They are also the focus of significant engineering efforts in developing biological nanopores for high-throughput DNA sequencing, as well as nano-devices for targeted cancer drug delivery. Although much has been learned through experimental and computational studies, current knowledge of ?-barrel membrane proteins is incomplete Only a small number of structures are known, and there is a lack of understanding of the general organizing principles of ?-barrel membrane proteins. The long term goal of the proposed research is to gain fundamental understanding and mechanistic insight into the structures, interactions, and functions of ?-barrel membrane proteins, and to develop enabling technology for design of ?-barrel membrane proteins with enhanced biophysical properties. The specific aims are to: 1) Develop computational models of physical principles governing the assembly of ?-barrel membrane proteins. Coarse-grained models will be developed to account for key determinants of structural stability and protein-protein interactions (PPIs) of ?-barrel membrane proteins. This will enable quantitative assessment of protein stability through computation. 2) Predict structures, oligomerization state, and protein-protein interfaces of ?-barrel membrane proteins. The focus will be on the challenging tasks of predicting structures of novel architecture or structures with no known templates. In addition, methods will be developed to predict protein oligomerization states and to identify protein-protein interaction sites. Structures with known templates will also be predicted through detection of remote homologs using newly developed technique of evolutionary analysis. 3) Develop engineering principles for designing ?-barrel porins with desirable stability, oligomerization state, and pore geometry. Design strategies for ?-barrel membrane porins with altered oligomerization states and altered stability will be developed. Proteins with enhanced as well as weakened stability, for both monomeric and oligomeric proteins will be designed. In addition, porins with complex pore geometry using naturally occurring building blocks will also be designed. 4) Experimental validation of computational prediction and design. Computational predictions will be verified by experimental studies. Extensive mutant studies will be carried out to test whether designed ?-barrel membrane proteins have the intended changes in stability, in oligomerization state, as well as in geometry.

描述（由申请人提供）：枪管在革兰氏阴性细菌的外膜，酸性革兰氏阳性细菌，真核生物线粒体，叶绿体（例如，在大肠杆菌中，N。Meningitidis，N。Meningitidis，N。gonorrheae和Mycobacteria等大肠杆菌）。革兰氏阳性细菌的许多形成孔的外毒素也是-Barrel膜蛋白（例如金黄色葡萄球菌的 - 蛋白蛋白和炭疽芽孢杆菌的保护性抗原）。？ - 桶膜蛋白对于许多基本生物学过程很重要。它们控制了离子和有机分子在细菌和线粒体外膜上的发生变化和转运。除古细菌外，它们对于生命的所有领域中的蛋白质易位至关重要。它们调节新陈代谢和凋亡。它们对于免疫监测，提供对抗生素的耐药性也很重要，并且是细菌毒力的关键决定因素。结果，？ - 桶膜蛋白是针对传染病开发药物和疫苗的重要治疗靶标。它们也是为开发用于高通量DNA测序的生物纳米孔以及用于靶向癌症药物递送的纳米驱动器的重要工程努力的重点。尽管通过实验和计算研究已经学到了很多东西，但是当前对“桶膜蛋白的知识”是不完整的，只有少数结构是已知的，并且缺乏对桶膜蛋白的一般组织原理的了解。拟议的研究的长期目标是获得对？ - 桶膜蛋白的结构，相互作用和功能的基本理解和机械洞察力，并开发具有增强生物物理特性的设计技术来设计？ - 桶膜蛋白。具体目的是：1）开发管理组装的物理原理的计算模型。将开发粗粒模型，以说明？ - 桶膜蛋白的结构稳定性和蛋白质 - 蛋白质相互作用（PPI）的关键决定因素。这将通过计算对蛋白质稳定性进行定量评估。 2）预测？ - 桶膜蛋白的结构，低聚状态和蛋白质蛋白界面。重点将放在预测新型建筑结构的挑战性任务上或没有已知模板的结构。此外，将开发方法来预测蛋白质寡聚态并鉴定蛋白质 - 蛋白质相互作用位点。具有已知模板的结构也将通过使用新开发的进化分析技术检测到远程同源物来预测。 3）开发设计用于设计的工程原理？ - 具有理想稳定性，低聚状态和孔几何形状的式孔托林。将开发针对具有改变寡聚状态和稳定性改变的桶膜孔的设计策略。将设计具有增强和稳定性的蛋白质，对于单体和寡聚蛋白，都将设计。此外，还将设计具有自然存在的构件的复杂孔几何形状的孔。 4）计算预测和设计的实验验证。计算预测将通过实验研究验证。将进行广泛的突变研究以测试是否设计？ - 桶膜蛋白具有稳定性的预期变化，在低聚状态和几何形状中。