DEVELOPMENT OF MESOSCALE MODELS SIMULATING POLYSACCHARIDE MOTION

模拟多糖运动的介观模型的开发

• 批准号: 7358170
• 负责人: ROBERT J WOODS
• 金额: $ 4.72万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-02-01 至 2007-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7358170
• 关键词: DEVELOPMENT; MESOSCALE; MODELS; SIMULATING; POLYSACCHARIDE

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. In order to extend molecular dynamics simulations to large polysaccharides as well as to study their motions on the micro- to millisecond timescale, we have begun to develop a low-resolution (molecular resolution rather than atomic) model for carbohydrate residues. This model uses a single spherical particle to model an individual glycosyl residue. The particles are hinged together through a vertex equivalent to the glycosidic oxygen atom. Electrostatic interactions are modeled as point centered multipole expansions, while steric and torsional terms are modeled as van der Waals surfaces and Fourier expansions respectively. Solvent effects will be incorporated using approaches based on the Poisson-Boltzmann approximation.

该子项目是利用NIH/NCRR资助的中心赠款提供的资源的许多研究子项目之一。子弹和调查员（PI）可能已经从其他NIH来源获得了主要资金，因此可以在其他清晰的条目中代表。列出的机构适用于该中心，这不一定是调查员的机构。为了将分子动力学模拟扩展到大型多糖，以及研究其在微量至毫秒的时间尺度上的运动，我们开始为碳水化合物残基开发低分辨率（分子分辨率而不是原子）模型。该模型使用单个球形粒子对单个糖基残基进行建模。这些颗粒通过等效于糖苷氧原子的顶点将其铰接在一起。 将静电相互作用建模为中心的多极膨胀，而空间和扭转项分别为范德华表面和傅立叶膨胀。将使用基于Poisson-Boltzmann近似的方法来合并溶剂效应。