Mechanism of membrane pore formation by antimicrobial peptides

抗菌肽膜孔形成机制

基本信息

批准号：
9009511
负责人：
THEMIS LAZARIDIS
金额：
$ 31.52万
依托单位：
CITY COLLEGE OF NEW YORK
依托单位国家：
美国
项目类别：
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

项目摘要

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.

抗菌肽提供针对微生物感染的天然防御，因此有望作为基础大量证据表明，它们通过形成细菌膜来靶向细菌膜。然而，对这一过程的理解达到了预测行为的水平。在过去的几年中，PI 团队使用了新型隐式膜模型，以及详细的全原子模拟，以获得对这些肽的功能的重要见解。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，开发预测结构的系统方法肽稳定的膜孔与实验实验室的密切相互作用将有助于验证预测。这项工作有三个目标，第一个目标是β-发夹抗菌肽protegrin。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、染料渗漏和抗菌活性测量将用于验证理论其他两个目标提供了肽诱导膜综合理论的关键要素。孔的形成：肽-肽相互作用和膜变形的自由能。孔形成过程中肽之间的相互作用是 PI 团队尚未解决的一个关键问题。首先通过与实验和显式模拟潜力进行比较来验证隐式溶剂化模型平均力，然后继续表征蜂毒肽和马加宁在膜上的聚集程度 Magainin 与 PGLa 的混合物也将被考虑解决观察到的问题。这两种肽之间的协同作用是将膜的自由能纳入理论。肽稳定孔的自由能包含肽-孔相互作用的贡献，肽-肽相互作用和膜变形具有四个特性：全原子模拟中的尺寸、形状、头基分布和电荷分布。用于获取将参数化这四个属性的分析函数的数据。通过隐式溶剂模拟，将用于确定作为半径和的函数的自由能分布最低自由能肽孔结构将通过全原子模拟进行测试。中性和带电膜中不同肽的孔结构应该提供明确的答案蜂毒肽和马加宁之间选择性差异的起源以及设计的坚实基础高效低毒的肽或肽模拟物。