Computational Assembly of Beta Barrel Membrane Protein

β 桶膜蛋白的计算组装

基本信息

批准号：
8728892
负责人：
Jie Liang
金额：
$ 29.96万
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/8728892
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 Geometry Germany Goals Gram-Negative Bacteria Gram-Positive Bacteria Hemolysin High-Throughput DNA Sequencing 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 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 biophysical properties 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）：桶存在于革兰氏阴性菌、抗酸革兰氏阳性菌、真核线粒体、叶绿体（例如大肠杆菌、脑膜炎奈瑟菌、淋病奈瑟菌和分枝杆菌）的外膜中。例如结核分枝杆菌）。许多来自革兰氏阳性菌的成孔外毒素也是β-桶膜蛋白（例如，金黄色葡萄球菌的β-溶血素和炭疽芽孢杆菌的保护性抗原）。 β-桶膜蛋白对于许多基本生物过程很重要。它们控制离子和有机分子穿过细菌和线粒体外膜的交换和运输。它们对于除古细菌之外的所有生命领域的蛋白质易位都是必不可少的。它们调节新陈代谢和细胞凋亡。它们对于免疫监视、提供抗生素耐药性也很重要，并且是细菌毒力的关键决定因素。因此，β-桶膜蛋白是开发抗传染病药物和疫苗的重要治疗靶点。它们也是开发用于高通量 DNA 测序的生物纳米孔以及用于靶向癌症药物输送的纳米设备的重大工程工作的重点。尽管通过实验和计算研究已经了解了很多，但目前对β-桶膜蛋白的了解并不完整。仅已知少量结构，并且缺乏对β-桶膜蛋白的一般组织原理的理解。拟议研究的长期目标是获得对β-桶膜蛋白的结构、相互作用和功能的基本了解和机制洞察，并开发用于设计具有增强生物物理特性的β-桶膜蛋白的使能技术。具体目标是： 1) 开发控制 β-桶膜蛋白组装的物理原理的计算模型。将开发粗粒度模型来解释β-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。这将能够通过计算定量评估蛋白质稳定性。 2) 预测β-桶膜蛋白的结构、寡聚状态和蛋白质-蛋白质界面。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，还将开发预测蛋白质寡聚状态并识别蛋白质-蛋白质相互作用位点的方法。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远程同源物来预测。 3) 开发设计具有理想稳定性、寡聚状态和孔几何形状的β-桶孔蛋白的工程原理。将开发具有改变的寡聚状态和改变的稳定性的β-桶膜孔蛋白的设计策略。对于单体和寡聚蛋白质，将设计具有增强和减弱稳定性的蛋白质。此外，还将使用天然存在的结构单元设计具有复杂孔几何形状的孔蛋白。 4）计算预测和设计的实验验证。计算预测将通过实验研究得到验证。将进行广泛的突变研究，以测试设计的β-桶膜蛋白是否在稳定性、寡聚状态以及几何形状方面具有预期的变化。