SALT EFFECTS IN SOLUTIONS OF PEPTIDES AND NUCLEIC ACIDS

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 我们将使用分子动力学模拟和近径向分布函数来研究蛋白质和核酸在盐水溶液中的性质。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。使用最近的经典力场模型，这些系统将使用本实验室开发的程序和社区可用的程序，用分子动力学进行模拟。此外，最近一个正在开发的项目专注于计算静电溶剂化自由能，其速度与基于连续介质的方法一样快，并与显式模拟一样准确，方法是将溶剂处理为无结构的介电连续介质，而不是结构化的介电介质。这种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)。描述了与这一提议有关的下列具有生物化学/生物技术意义的科学项目：1)多肽和蛋白质溶液中的盐效应：非理想行为；2)DNA/RNA多态和表面亲和性依赖；3)从概率密度计算和自由能。这些是一套正在进行的资助项目。上一次拨款取得了相当大的进展。几份手稿已经完成并正在完成；这些手稿列在本文件的单独一节中。

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.