Mechanism of membrane pore formation by antimicrobial peptides

抗菌肽膜孔形成机制

• 批准号: 9197316
• 负责人: THEMIS LAZARIDIS
• 金额: $ 30.14万
• 依托单位: CITY COLLEGE OF NEW YORK
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9197316
• 关键词: Alamethicin; Anti-Bacterial Agents; Antibiotics; Behavior; Benchmarking; Binding; Biohazardous Substance; Biological; Biology; Budgets; Collaborations; Consensus; Data; Dimerization; Dyes; Electrophysiology (science); Elements; Environment; Extravasation; Fluorescence; Fluorescence Resonance Energy Transfer; Free Energy; Geometry; Growth; Human; Infection; Ions; Kansas; Kinetics; Letters; Lipid Bilayers; Lipids; Mammalian Cell; Measurement; Membrane; Methodology; Methods; Modeling; Molecular; Organism; Peptides; Process; Property; Radial; Resistance; Resource Sharing; Scheme; Shapes; Solvents; Structure; Surface; Testing; Thermodynamics; Toxic effect; Universities; Vertebrates; Work; analog; antimicrobial; antimicrobial peptide; base; computer studies; computing resources; design; dimer; experimental study; human subject; human subject protection; improved; insight; magainin; membrane model; microbial; molecular dynamics; novel; peptide structure; peptidomimetics; protegrins; protein aminoacid sequence; simulation; success; synergism; theories

Antimicrobial peptides provide natural defense against microbial infection and thus hold promise as the basis of new antibiotics. Substantial evidence suggests that they target the bacterial membranes, by either forming pores or disintegrating them. However, an understanding of this process to the level of predicting the behavior of specific peptides is lacking. Over the last few years the PI’s group used novel implicit membrane modeling, as well as detailed all-atom simulations, to obtain significant insights into the function of these peptides. The PI now aims to use a multipronged approach that encompasses all-atom simulations, implicit-solvent simulations, and molecular thermodynamic modeling, to develop a systematic approach that predicts the structure of peptide-stabilized membrane pores. Close interaction with experimental labs will help validate the predicted models. This work has three aims. The first focuses on the β-hairpin antimicrobial peptide protegrin, and aims to elucidate whether it forms complete β-barrels, incomplete barrels (arcs), or classical toroidal pores. Electrophysiology, dye leakage, and antimicrobial activity measurements will be used to validate the theoretical results. The other two aims provide key elements in a comprehensive theory of peptide-induced membrane pore formation: peptide-peptide interactions and the free energy of membrane deformation. The extent of interactions between peptides in the process of pore formation is a crucial unsolved problem. The PI’s group will first validate the implicit solvation models by comparison to experiments and explicit simulation potentials of mean force and then proceed to characterize the extent of aggregation of melittin and magainin on membrane surfaces and in pores. Mixtures of magainin with PGLa will also be considered to address the observed synergy between these two peptides. The third aim is to include in the theory the free energy of membrane deformation. The free energy of a peptide-stabilized pore contains contributions from peptide-pore interactions, peptide-peptide interactions and membrane deformation. Pore structure is characterized by four properties: size, shape, headgroup distribution, and charge distribution in mixed membranes. All-atom simulations will be used to obtain data that will parameterize an analytical function of these four properties. This function, together with implicit-solvent simulations, will be used to determine profiles of free energy as a function of radius and lowest free energy peptide-pore structures. The resulting structures will be tested by all-atom simulations. The pore structure of different peptides in neutral and charged membranes should provide a definitive answer to the origin of the difference in selectivity between melittin and magainin and a firm basis for the design of peptides or peptidomimetics with high potency and low toxicity.

抗微生物肽提供了对微生物感染的天然防御，因此有望作为基础 新的抗生素。大量证据表明，它们通过形成细菌膜， 毛孔或分解它们。然而，对这一过程的理解，以预测的行为水平， 缺乏特定的肽。在过去的几年里，PI的团队使用了新颖的隐式膜模型， 以及详细的全原子模拟，以获得这些肽的功能的重要见解。的PI 现在的目标是使用多管齐下的方法，包括全原子模拟，隐式溶剂模拟， 和分子热力学建模，以开发一种系统的方法，预测结构， 肽稳定的膜孔。与实验室的密切互动将有助于验证预测 模型这项工作有三个目标。第一部分主要研究β-发夹抗菌肽Protegrin， 以阐明它是否形成完整的β-桶、不完整的桶（弧）或经典的环形孔。 电生理学、染料渗漏和抗微生物活性测量将用于验证理论 结果其他两个目标提供了肽诱导膜的综合理论的关键要素 孔形成：肽-肽相互作用和膜变形的自由能。的程度 在孔形成过程中肽之间的相互作用是一个关键的未解决的问题。PI小组 将首先通过与实验和显式模拟潜力的比较来验证隐式溶剂化模型， 然后进一步表征蜂毒肽和爪蟾抗菌肽在膜上的聚集程度 表面和孔隙中。还将考虑爪蟾抗菌肽与PGLa的混合物，以解决观察到的 这两种肽之间的协同作用。第三个目标是在理论中包括膜的自由能 变形肽稳定的孔的自由能包含来自肽-孔相互作用的贡献， 肽-肽相互作用和膜变形。孔隙结构的特征在于四种性质： 尺寸、形状、头基分布和混合膜中的电荷分布。全原子模拟将是 用于获得将参数化这四个属性的分析函数的数据。这个功能，一起 与隐式溶剂模拟，将用于确定作为半径的函数的自由能的分布， 最低自由能的肽孔结构。由此产生的结构将通过全原子模拟进行测试。的 中性和带电膜中不同肽的孔结构应该提供一个明确的答案， 蜂毒肽和爪蟾抗菌肽选择性差异的起源和设计的坚实基础 具有高效力和低毒性的肽或肽模拟物。