Computer simulations of lipids

脂质的计算机模拟

• 批准号: RGPIN-2020-04209
• 负责人: Tieleman, Peter
• 金额: $ 7.65万
• 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: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=744841
• 关键词: Computer; simulations; lipids

My long-term aim is the development of accurate computational models to describe the molecular interactions between membrane components and the use of these models to solve fundamental problems in the area of the biophysics and biochemistry of lipid bilayers and monolayers. Computer simulations of lipids and more generally membrane models have grown significantly in the past five years and are now a widely used technique to study the physical chemistry and biophysics of lipids, both by themselves and in combination with experiment. My group has contributed to this area since its inception in the 1990s, when computer power was ca. 5 orders of magnitude less than today and the models much less sophisticated. In the past five years we have made significant progress in improving lipid models, increasing the complexity of our models, and moving closer towards the complexity of biological systems while continuing our work on well-controlled model systems including simple lipid mixtures, micelles and bicelles. We use primarily molecular dynamics simulations and free energy calculations, based on atomistic and coarse-grained descriptions of lipids and other molecules, supplemented by other methods such as electronic structure calculations and continuum electrostatics calculations where required. We co-develop Martini, currently the most popular coarse-grained model for molecular simulation. We will pursue two major directions in our research program. The first is aimed at expanding our computational toolkit to model complex membranes and includes the further development of Martini, computational methods to more efficiently sample mixing of lipid mixtures using a combined molecular dynamics/Monte Carlo method, and the use of virtual reality software in visualization and analysis of membrane simulations. The second direction is driven by fundamental questions about membrane structure and the role of the many components of biological membranes. We will investigate the complex properties of lipid mixtures as a function of composition, including model membranes that, like biological membranes, have a different composition in each of the two leaflets that form their basic bilayer structure. Related to this problem is how cholesterol, a major component of most cell membranes, redistributes within the membrane and interacts with other components, and how lipid distributions and protein conformation are coupled to each other through membrane curvature. These two directions are interrelated as improved computational tools are essential to answer the fundamental questions and to more closely link experiment and simulations. The systems used to study fundamental questions typically are also useful to develop, test, and validate models and new methods. The program will result in improved computational tools that can be used in a broad range of future studies, as well as insight in the fundamental building blocks of biological membranes.

我的长期目的是开发准确的计算模型，以描述膜成分之间的分子相互作用，并使用这些模型来解决生物物理学和脂质双层和单层生物化学领域的基本问题。在过去的五年中，脂质和更普遍的膜模型的计算机模拟已经显着增长，现在是一种广泛使用的技术，用于研究脂质的物理化学和生物物理学，无论是自己还是与实验结合使用。自1990年代的计算机电源大约成立以来，我的小组就为该领域做出了贡献。 5个数量级比今天少，模型的复杂程度要少得多。在过去的五年中，我们在改善脂质模型，提高模型的复杂性方面取得了重大进展，并越来越靠近生物系统的复杂性，同时继续我们在控制良好的模型系统上的工作，包括简单的脂质混合物，胶束和bicelles。我们基于脂质和其他分子的原子和粗粒描述，使用一级分子动力学模拟和自由能计算，并补充了其他方法，例如电子结构计算以及在需要的情况下继续进行静电计算。我们共同开发马提尼酒，目前是分子模拟的最流行的粗粒细胞模型。我们将在我们的研究计划中追求两个主要方向。第一个旨在扩展我们的计算工具包，以建模复杂的膜，包括马提尼酒的进一步开发，即使用组合的分子动力学/Monte Carlo方法更有效地对脂质混合物进行采样，以及使用虚拟现实软件在可视化和分析膜模拟中使用虚拟现实软件。第二个方向是由有关膜结构以及生物膜许多组成部分的作用的基本问题驱动的。我们将研究脂质混合物的复杂特性，这是组成的函数，包括模型膜，这些模型膜像生物膜一样，在形成其基本双层结构的两个小叶中具有不同的组成。与此问题相关的是，胆固醇是大多数细胞膜的主要组成部分，膜中的重新分布以及与其他成分相互作用，以及脂质分布和蛋白质构象如何通过膜曲率相互耦合。这两个方向相互关联，因为改进的计算工具对于回答基本问题以及更紧密地链接实验和模拟至关重要。用于研究基本问题的系统通常也可用于开发，测试和验证模型和新方法。该计划将导致改进的计算工具，这些工具可用于广泛的未来研究，以及对生物机制的基本构建基础的见解。