Computer simulations of lipids

脂质的计算机模拟

• 批准号: RGPIN-2015-05305
• 负责人: Tieleman, Peter
• 金额: $ 6.48万
• 依托单位: University of Calgary
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2018
• 资助国家: 加拿大
• 起止时间: 2018-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=666839
• 关键词: Computer; simulations; lipids

Biomolecules, such as proteins, DNA, lipids, and carbohydrates, exist in a microscopic universe with time and length scales 6-12 orders of magnitude smaller than the meters and seconds in which we measure length and time. They move rapidly on a time scale of nanoseconds and interact with individual water molecules the size of a few tenths of a nanometer. Most biomolecules are very small compared to the wavelength of visible light. This means they cannot be seen with ordinary microscopes, although there are many sophisticated experimental methods to measure aspects of the behaviour, shape, and interactions of biomolecules. Computer modeling is a complimentary approach to such experiments, both by themselves and in direct combination with experiments that otherwise could not be interpreted at a molecular level.***Using powerful computers and a description of how atoms interact with each other, it is possible to calculate in atomic detail how biomolecules move and interact in time. In recent years, this molecular dynamics simulation method has become an essential method to solve problems involving molecules of all types, in my research group primarily lipids. ***Lipids are the major building block of cell membranes that define the boundary between a cell and its surroundings. Cell membranes have remarkable mechanical and electrical properties, a complex chemical composition, and a surprisingly complex physical behaviour. These properties are primarily derived from the molecular structure of lipids, which have a water-loving head and a water-avoiding tail. This structure leads to self-aggregation in water into fascinating structures. These include cell membranes based on biological lipids, but also a wide variety of other structures by synthetic lipids and lipid mixtures, which are both of fundamental interest and of interest in technical and scientific applications. ***This research project is aimed at developing and applying computational models of molecules to better understand the properties of lipids and surfactant molecules. We will use and improve both detailed atomistic models and a somewhat coarser model in which a few atoms are grouped into a single 'bead'. Although we lose detail in this case, it is computational cheaper by several orders of magnitude to explore such models. Our main interests are the properties of domains in membranes, which are thought to underly many biologically important processes, the properties of mixtures of surfactants and lipids that form micelles, bicelles, and nanodiscs, and an improved link with experimental methods that give insight in lipid structure, including x-ray and neutron diffraction as well as spectroscopic methods. **

生物分子，例如蛋白质，DNA，脂质和碳氢化物，存在于微观宇宙中，其时间和长度尺度比我们测量长度和时间的仪表和秒数小6-12个数量级。它们以纳秒秒的时间尺度迅速移动，并与单个水分子相互作用，大小为十分之一的纳米分子。与可见光的波长相比，大多数生物分子非常小。这意味着它们无法通过普通显微镜看到它们，尽管有许多复杂的实验方法来测量生物分子的行为，形状和相互作用的各个方面。计算机建模是这种实验的一种免费方法，无论是自己还是直接与无法在分子级别无法解释的实验结合使用。近年来，在我的研究组主要脂质中，这种分子动力学模拟方法已成为解决涉及各种类型分子的问题的必要方法。 ***脂质是定义细胞及其周围环境之间边界的细胞膜的主要组成部分。细胞膜具有显着的机械和电性能，复杂的化学成分以及令人惊讶的复杂物理行为。这些特性主要源自脂质的分子结构，这些脂质具有热爱水的头部和避开水的尾巴。这种结构导致水中的自我聚集成迷人的结构。这些包括基于生物脂质的细胞膜，以及合成脂质和脂质混合物的多种其他结构，这些结构既具有基本兴趣，又是技术和科学应用的兴趣。 ***该研究项目旨在开发和应用分子计算模型，以更好地了解脂质和潜在分子的特性。我们将使用并改善详细的原子模型，以及一些更粗的模型，其中一些原子分为单个“珠”。尽管在这种情况下我们会丢失细节，但探索此类模型的计算更便宜。我们的主要兴趣是膜中域的特性，膜上被认为是许多重要的生物学重要过程，生存主义者和脂质的混合的特性，这些过程形成了胶束，双皮细胞和纳米散发，以及与X-ray和Netrone drefraction spempers spempers spempercip sepsept的实验方法的改进联系，并具有改进的链接。