Modeling Membrane Binding and Permeabilization by Antimicrobial Peptides

描述（由申请人提供）：抗菌肽（AMPs）是小的，通常是阳离子的，两性肽，通过渗透病原生物的膜为所有物种提供第一宿主防御机制。相对于哺乳动物膜的中性外叶，它们的正电荷被认为对带负电荷的细菌膜具有更高的亲和力。然而，它们的作用机制和活性的结构决定因素仍不清楚。在过去的两年中，我们的实验室开发了独特的建模工具，该工具隐含地考虑了膜环境，包括阴离子脂质和离子强度的影响，允许存在水孔，并纳入跨膜电压的影响。我们建议应用这些方法来深入了解amp的作用机制。具体目标是：1。表征AMPs的膜吸附并寻找其活性和选择性的相关性，即确定大量AMPs的膜结合构型和膜结合能作为膜电荷和离子强度的函数，并将其与观察到的肽的实验性质（如抗菌光谱）联系起来。这些研究将检验静电是目标选择性的主要决定因素的假设。2. 研究amp的膜渗透机制。我们将建立桶壁孔、环形孔和跨膜β桶的模型，并比较它们形成的自由能。我们提出了一个新的假设，即许多抗菌肽的不完美的两致病性使它们比平面膜表面更强烈地结合环状膜孔。3. 改进amp的模型测试和合理设计。在较低的浓度和较高的离子强度下，将提出对肽的序列修改，使其毒性更小，更有效，更有活性。与领先的实验小组合作将使我们能够将我们的设计付诸实践。意义：了解抗菌肽的作用机制有助于发现新的抗生素。

DESCRIPTION (provided by applicant): Antimicrobial peptides (AMPs) are small, usually cationic, amphipathic peptides that provide a first host defense mechanism for species in all kingdoms by permeabilizing the membrane of pathogenic organisms. Their positive charge is thought to afford them higher affinity for the negatively charged bacterial membranes relative to the neutral outer leaflet of mammalian membranes. However, their mechanism of action and structural determinants of activity are still unclear. Over the last two years our lab developed unique modeling tools that take into account the membrane environment implicitly, include the effect of anionic lipids and ionic strength, allow for the presence of an aqueous pore, and incorporate the effect of transmembrane voltage. We propose to apply these methods to gain insights into the mechanism of action of AMPs. The specific aims are: 1. Characterize membrane adsorption of AMPs and seek correlations with activity and selectivity, i.e. determine the membrane bound configuration and membrane binding energy of a large number of AMPs as a function of membrane charge and ionic strength and correlate these to the observed experimental properties of the peptides, such as antimicrobial spectrum. These studies will test the hypothesis that electrostatics is a major determinant of target selectivity. 2. Investigate mechanisms of membrane permeabilization by AMPs. We will build models of barrel-stave pores, toroidal pores, and transmembrane beta barrels and compare the free energy of their formation. We make the novel hypothesis that the imperfect amphipathicity of many antimicrobial peptides makes them bind toroidal membrane pores more strongly than flat membrane surfaces. 3. Testing of the models and rational design of improved AMPs. Sequence modifications will be proposed towards peptides that are less toxic, more potent, and more active at lower concentrations and higher ionic strength. Collaborations with leading experimental groups will allow us to put our designs to a practical test. Significance: Understanding the mechanism of action of AMPs could lead to the discovery of new antibiotics. Public Health Relevance: This project aims to understand the mechanism of action of antimicrobial peptides, small peptides that provide a first host defense mechanism for species in all kingdoms by permeabilizing the membrane of pathogenic organisms. This will be accomplished by computational studies of their binding to membranes and membrane pores. The results will be used to rationally design improved versions of these peptides that could be used as novel antibiotics.