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.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目及 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 我们将使用分子动力学模拟和近端径向分布函数来研究盐水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，这些系统将使用本实验室开发的程序和社区可用的程序通过分子动力学进行模拟。此外，最近正在开发的一个项目重点关注静电溶剂化自由能的计算，其速度与基于连续体的方法一样快，并且通过将溶剂处理为结构化的溶剂，而不是无结构的介电连续体，与显式模拟一样准确。该方法使用一种特殊版本的概率分布函数，称为近端径向分布函数 (pRDF)。描述了与本提案相关的以下具有生化/生物技术意义的科学项目：1) 肽和蛋白质溶液中的盐效应：非理想行为，2) DNA/RNA 多态性和表面邻近依赖性，以及 3) 评估和自由来自概率密度的能量。这些是一组正在进行的资助项目。上次分配已取得相当大的进展。几份手稿已经或正在完成；这些内容列在本文档的单独部分中。