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Computer Simulation of Amphiphilic Aggregates

两亲性聚集体的计算机模拟

基本信息

批准号：
7925093
负责人：
MICHAEL L. KLEIN
金额：
$ 13.8万
依托单位：
TEMPLE UNIV OF THE COMMONWEALTH
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-30 至 2011-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7925093
关键词：
Affect Amino Acids Area Award Benchmarking Binding Biological Cereals Chloride Channels Cholinergic Receptors Code Collaborations Complement Computer Simulation Cyclic Peptides Cytoplasm Dependence Development Event Goals Goat Grant Hydrophobic Interactions Ion Channel Length Letters Lipid Bilayers Lipids Liquid substance Mediating Membrane Membrane Fluidity Membrane Fusion Membrane Lipids Methodology Methods Micelles Modeling Nanotubes Nature Peptides Phase Physiological Polymers Principal Investigator Process Property Proteins Publications Publishing Reporting Research Research Personnel Role Sampling Scheme Sorting - Cell Movement Structure System Text Time Vesicle Water Work cost di-block copolymer graduate student insight interest membrane model models and simulation molecular dynamics novel programs protein aggregation research study self assembly simulation success

项目摘要

DESCRIPTION (provided by applicant): This competing renewal is requesting continuing support for the Klein group's computer simulation studies on membranes and membrane-bound species, with special emphasis on biophysical problems difficult to tackle with brute force application of standard codes. Specifically, the first aim is to extend our recently developed coarse grain (CG) simulation model for membranes to be able to explore the self-assembly of Ghadiri's membrane-active nanotubes composed of cyclic D, L-alpha-peptides. Of special interest, is the nature of the peptide - lipid membrane interactions, and the dependence on the choice of peptide amino acid residues and lipid composition. A key motif to be explored is the use of cyclic-peptide capping subunits to generate heteromeric assemblies with tailored properties. The second aim will use the CG model to study lipid sorting and membrane-mediated protein aggregation. The goal is to elucidate how proteins move lipids and lipids move proteins to alter the local bilayer membrane stability, thereby allowing for the curvatures required for vesicle budding and membrane fusion. The third aim is directed to understand how water soluble di-block copolymer micelles affect the translocation of synthetic hydrophobic molecules across biomembranes. The focus is on both the encapsulation by the polymer micelles and their interaction with lipid bilayers. In the fourth and final aim, new molecular dynamics simulation methodologies will be applied to gain insights into the mechanism of gating in ion channels. The first target will be the ClC chloride channel, whose structure was recently published by the MacKinnon group in both the closed and open states. These structures suggested a simple gating mechanism involving a conformational change of a single amino acid residue (Glu148) which, if correct, should be readily accessible to the new simulation methods. If the approach is indeed successful for this apparently simple example, it is proposed to tackle more difficult systems such as the acetylcholine receptor pore, for which Unwin has recently proposed a gating mechanism.

描述（由申请人提供）：这一竞争性更新要求继续支持Klein小组对膜和膜结合物种的计算机模拟研究，特别强调难以通过强力应用标准代码解决的生物物理问题。具体来说，第一个目标是扩展我们最近开发的膜粗粒（CG）模拟模型，以便能够探索由环D， l -肽组成的Ghadiri膜活性纳米管的自组装。特别感兴趣的是肽-脂质膜相互作用的性质，以及对肽氨基酸残基和脂质组成选择的依赖。要探索的一个关键基序是使用环肽盖住亚基来产生具有定制性质的异质组装。第二个目标将使用CG模型来研究脂质分选和膜介导的蛋白质聚集。目的是阐明蛋白质如何移动脂质和脂质如何移动蛋白质以改变局部双层膜稳定性，从而允许囊泡出芽和膜融合所需的曲率。第三个目标是直接了解水溶性二嵌段共聚物胶束如何影响合成疏水分子在生物膜上的易位。重点是聚合物胶束的包封及其与脂质双分子层的相互作用。在第四个也是最后一个目标中，新的分子动力学模拟方法将被应用于深入了解离子通道中的门控机制。第一个目标将是ClC氯离子通道，其结构最近由MacKinnon小组在封闭和开放状态下发表。这些结构表明了一个简单的门控机制，涉及单个氨基酸残基（Glu148）的构象变化，如果正确的话，应该很容易获得新的模拟方法。如果这种方法在这个看似简单的例子中确实是成功的，那么它将被提议用于解决更困难的系统，如乙酰胆碱受体孔，Unwin最近提出了一种门控机制。