SALT EFFECTS IN SOLUTIONS OF PEPTIDES AND NUCLEIC ACIDS

肽和核酸溶液中的盐效应

• 批准号: 7956070
• 负责人: Bernard MONTGOMERY PETTITT
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956070
• 关键词: Behavior; Biochemical; Biological Models; Biomedical Research; Biopolymers; Communities; Computer Retrieval of Information on Scientific Projects Database; Data; Dependence; Development; Electrostatics; Evaluation; Free Energy; Funding; Genetic Polymorphism; Grant; High Performance Computing; Institution; Manuscripts; Methods; Nucleic Acids; Peptide Nucleic Acids; Peptides; Probability; Property; Proteins; Radial; Research; Research Personnel; Resources; Saline; Simulate; Sodium Chloride; Solutions; Solvents; Source; Structure; Surface; Thermodynamics; United States National Institutes of Health; aqueous; base; density; molecular dynamics; programs; simulation

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. We will use molecular dynamics simulations and proximal Radial Distribution Functions to study the properties of proteins and nucleic acids in aqueous saline solution. The molecular dynamics simulations will be used to interpret structural and thermodynamic experimental data for the biopolymer projects. Using recent classical force field models these systems will be simulated with molecular dynamics using programs developed in this lab and those available to the community. Additionally, a recent project in development focuses on the calculation of the electrostatic solvation free energy as fast as continuum-based methods and as accurately as explicit simulation by treating the solvent, not as a structure-less dielectric continuum, but as structured. This method uses a special version of the probability distribution function called the proximal Radial Distribution Function (pRDF). The following scientific projects of biochemical/biotechnological significance related to this proposal are described: 1) Salt effect in peptide and protein solutions: non-ideal behavior, 2) DNA/RNA polymorphism and surface-proximity dependence, and 3) Evaluation of and free energies from probability densities. These are an ongoing set of funded projects. Considerable progress has been made with the last allocation. Several manuscripts have been and are being completed; these are listed in a separate section of this document.

该副本是利用众多研究子项目之一 由NIH/NCRR资助的中心赠款提供的资源。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。列出的机构是 对于中心，这不一定是调查员的机构。 我们将使用分子动力学模拟和近端径向分布函数来研究水溶液溶液中蛋白质和核酸的特性。分子动力学模拟将用于解释生物聚合物项目的结构和热力学实验数据。使用最新的经典力场模型，将使用本实验室中开发的程序以及社区可用的程序来模拟这些系统。此外，最新开发项目的重点是与基于连续的方法一样快地计算静电溶剂化的自由能，并且通过处理溶剂来准确地计算出明确的模拟，而不是作为无结构的介电连续性，而是结构结构。该方法使用称为近端径向分布函数（PRDF）的概率分布功能的特殊版本。描述了与该提案相关的生化/生物技术意义的以下科学项目：1）肽和蛋白质溶液中的盐效应：非理想行为，2）DNA/RNA多态性和表面差异性依赖性，以及3）对概率密度的评估和自由能量。这些是一组持续的资助项目。最后分配取得了很大的进步。几个手稿已经并且正在完成；这些在本文档的单独部分中列出。