Glycoprotein Modeling System for Internal Coordinate Mechanics

内坐标力学糖蛋白建模系统

• 批准号: 7801569
• 负责人: Maxim Totrov
• 金额: $ 19.97万
• 依托单位: MOLSOFT, LLC
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-04-01 至 2012-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7801569
• 关键词: Acetylglucosamine; Amino Acids; Anticoagulation; Aphorisms; Benchmarking; Binding Proteins; Biological Models; Biological Process; Biopolymers; Blood; Carbohydrates; Cells; Charge; Code; Complex; Computer Simulation; Computer software; Data; Development; Disaccharides; Disease; Docking; Doctor of Philosophy; Fucose; Galactose; Generations; Glucose; Glucuronic Acids; Glycoconjugates; Glycoproteins; Glycosides; Heterogeneity; Hybrids; Imagery; Immune system; Libraries; Link; Mannose; Mechanics; Methods; Modeling; Molecular; Molecular Conformation; Molecular Models; Molecular Structure; Monosaccharides; Oligosaccharides; Performance; Phase; Physiological Processes; Play; Polysaccharides; Positioning Attribute; Probability; Procedures; Process; Proteins; Research; Residual state; Role; Sampling; Sialic Acids; Structural Biologist; Structure; Techniques; Testing; Torsion; Viral; Xylose; base; cancer cell; conformer; drug discovery; flexibility; glycosylation; graphical user interface; improved; molecular mechanics; molecular modeling; polypeptide; protein complex; protein structure; public health relevance; pyranose; quantum; simulation; small molecule; success; sugar; three dimensional structure; tool

DESCRIPTION (provided by applicant): We propose to develop several essential components that would allow comprehensive modeling of glycoproteins in ICM: a carbohydrate extension of the ECEPP05 force-field, a library of common glycosylating moieties, tools for glycan construction on protein structures, and simulations of their stochastic dynamics and docking to glycan-binding proteins. Together these components will comprise the Glycosylation Modeling System. Carbohydrate moieties on the proteins (glycans) play an essential role in a range of physiological processes, including viral evasion from the immune system, blood anticoagulation, the progression of cancer, cell-cell recognition, and the correct folding and processing of proteins. Understanding of their function on the level of three-dimensional structure has been lagging behind that of the regular polypeptides. Flexibility, disorder and heterogeneity of glycans make experimental structure determination difficult. Molecular mechanics techniques increasingly allow in-silico simulation of essential biological processes at the atomic level. Molsoft's ICM (Internal Coordinate Mechanics) software platform is a particularly efficient modeling tool because of its use of internal variables, rather than traditional Cartesian coordinates, in the description of the molecular structure. This proposed development will allow to apply this approach to modeling of carbohydrates. Equipping structural biologists with the Glycoprotein Modeling System in ICM will help bring molecular simulations and structure predictions for glycans to the next level of accuracy. Successful structure modeling will ultimately help improve our understanding of molecular mechanisms underlying disease and help to accelerate structure-based drug discovery efforts. PUBLIC HEALTH RELEVANCE: Carbohydrate moieties on the proteins (glycans) play an essential role in a range of physiological processes, including viral evasion from the immune system, blood anticoagulation, the progression of cancer, cell-cell recognition, and the correct folding and processing of proteins. Equipping structural biologists with the Glycoprotein Modeling System in ICM will help bring molecular simulations and structure predictions for glycans to the next level of accuracy. Successful structure modeling will ultimately help improve our understanding of molecular mechanisms underlying disease and help accelerate structure-based drug discovery efforts.

描述（由申请人提供）：我们建议开发几个基本组件，以实现ICM中糖蛋白的全面建模：ECEPP 05力场的碳水化合物扩展，常见糖基化部分的库，蛋白质结构上聚糖构建的工具，以及模拟其随机动力学和与聚糖结合蛋白的对接。这些组件将共同组成糖基化建模系统。蛋白质上的碳水化合物部分（聚糖）在一系列生理过程中发挥着重要作用，包括病毒逃避免疫系统、血液抗凝、癌症进展、细胞-细胞识别以及蛋白质的正确折叠和加工。对它们在三维结构水平上的功能的认识一直落后于常规多肽。聚糖的柔性、无序性和异质性使得实验结构确定变得困难。分子力学技术越来越多地允许在原子水平上对基本生物过程进行计算机模拟。Molsoft的ICM（内部坐标力学）软件平台是一种特别有效的建模工具，因为它在分子结构的描述中使用内部变量，而不是传统的笛卡尔坐标。这一拟议的发展将允许应用这种方法来建模的碳水化合物。为结构生物学家配备ICM中的糖蛋白建模系统将有助于将聚糖的分子模拟和结构预测提高到下一个准确水平。成功的结构建模最终将有助于提高我们对疾病分子机制的理解，并有助于加速基于结构的药物发现工作。 公共卫生相关性：蛋白质上的碳水化合物部分（聚糖）在一系列生理过程中发挥着重要作用，包括病毒逃避免疫系统、血液抗凝、癌症进展、细胞-细胞识别以及蛋白质的正确折叠和加工。为结构生物学家配备ICM中的糖蛋白建模系统将有助于将聚糖的分子模拟和结构预测提高到下一个准确水平。成功的结构建模最终将有助于提高我们对疾病分子机制的理解，并有助于加速基于结构的药物发现工作。