SALT EFFECTS IN SOLUTIONS OF PEPTIDES AND NUCLEIC ACIDS

该子项目是利用 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH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 中心，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进行分子动力学模拟。此外，最近的一个开发项目的重点是计算的静电溶剂化自由能一样快，连续为基础的方法和准确的显式模拟处理溶剂，而不是作为一个无结构的介电连续体，但结构。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）。描述了与该提案相关的以下具有生物化学/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）从概率密度评估和自由能。这是一系列正在进行的资助项目。在最后一次拨款方面取得了相当大的进展。已经完成和正在完成若干手稿;这些手稿列于本文件的单独一节。

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.