Pseudomonas aeruginosa Outer Membrane Protein Modeling

铜绿假单胞菌外膜蛋白模型

基本信息

批准号：
7189888
负责人：
T P STRAATSMA
金额：
$ 34.52万
依托单位：
BATTELLE PACIFIC NORTHWEST LABORATORIES
依托单位国家：
美国
项目类别：
财政年份：
2005
资助国家：
美国
起止时间：
2005-03-01 至 2010-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7189888
关键词：
Address Antibiotics Behavior Binding Charge Computer Simulation Computer software Computing Methodologies Development Disruption Divalent Cations Electronics Electrostatics Elements Environment Escherichia Exhibits Free Energy Gentamicins Goals Gram-Negative Bacteria Human Infection Integral Membrane Protein Ion Channel Protein Ions Laboratories Lipid Bilayers Lipopolysaccharides Location Membrane Membrane Proteins Methods Microbe Modeling Molecular Molecular Models Oligosaccharides OmpA protein Permeability Phosphorylation Procedures Proteins Pseudomonas aeruginosa Research Personnel Resistance Role Salmonella typhimurium Shewanella Structure Suggestion Thermodynamics Vibrio cholerae Work aquatic organism base carboxylate computational chemistry design inorganic phosphate interest membrane model microbial model design models and simulation molecular dynamics molecular modeling pathogen porin programs simulation small molecule tool

项目摘要

DESCRIPTION (provided by applicant): This proposal outlines the development and application of new modeling and simulation capabilities for the study of the outer membrane proteins of Pseudomonas aeruginosa and Escherichia coil in realistic, atomicdetail models of the lipopolysaccharide (LPS) membrane. Simulations of lipid bilayers membranes have contributed significantly to our understanding of their energetics and dynamics, as well as the function and dynamics of embedded proteins. However, because of the complexity of LPS membranes, this is not the case for the outer membranes and outer membrane proteins of Gram-negative bacteria. The goal of this work is to develop the computational capabilities to construct realistic models for LPS membranes with embedded outer membrane proteins for use in molecular dynamics simulations. Our focus will be on the outer membrane of P. aeruginosa, one of the most important opportunistic human pathogens, in comparison with the outer membrane of E. coil to determine the role of elements that are specifically found in the LPS structure of the outer membrane of P. aeruginosa. However, the tools and procedures that will be developed as part of the proposed work will be applicable to the study of outer "membranes of any Gram-negative microbe. The goals of this proposal will be achieved through extension and implementation of new capabilities of NWChem, our massively parallel computational chemistry software suite for electronic structure calculations and classical molecular dynamics simulations.

描述（由申请人提供）：该建议概述了新建模和模拟能力的开发和应用，用于研究铜绿假单胞菌的外膜蛋白和脂多糖（LPS）膜的脂多糖模型（LIPOPOLYSDAIL模型）。脂质双层膜的模拟为我们对它们的能量和动力学以及嵌入式蛋白质的功能和动力学做出了重大贡献。但是，由于LPS膜的复杂性，革兰氏阴性细菌的外膜和外膜蛋白不是这种情况。这项工作的目的是开发计算能力，以构建具有嵌入式外膜蛋白的LPS膜的现实模型，用于分子动力学模拟。与E. coil的外膜相比，我们的重点将放在铜绿假单胞菌的外膜，铜绿假单胞菌是最重要的机会性人体病原体之一，以确定铜绿假单胞菌外膜的LPS结构中特异性元素的作用。但是，将作为拟议工作的一部分开发的工具和程序适用于研究任何革兰氏阴性微生物的外部膜。该提案的目标将通过扩展和实施NWCHEM的新功能来实现，NWCHEM是我们用于电子结构计算和经典分子动力学模拟的大量平行计算化学软件套件。