FACTOR ANALYTICAL DECONVOLUTION OF MULTICOMPONENT HEME/LIGAND UV/VIS SPECTRA

双酯的最新皮秒和纳秒动力学研究 光解离的CO重组为肌红蛋白，以及肌红蛋白突变体， 已经提出了关于不同的影响的根本问题 影响与血球蛋白特异性结合的配基过程的因素，以及 对金属蛋白的影响。我们建议使用计算方法 如密度泛函理论、分子力学、分子 动力学和自由能微扰计算要学习，以及 表征，控制配体结合过程的因素 肌红蛋白(Mb)及其简单模型。我们选择了这一组 系统，因为存在大量的结构信息 它们是使用所提议的计算技术的必要条件。 具体地说，我们将重点模拟三个因素 影响上述过程：1)远端空间效应，2) 局部极性的影响，以及3)溶剂的影响。我们会 通过使用琥珀软件包来描述这些因素 模拟血红素的平衡和动力学性质，以及 肌红蛋白。简而言之，建议的方法概述于 以下步骤：1)将当前的血红素力场扩展到 无血红素和异氰化物-血红素体系的模拟。2)再现趋势 在配体与血红素、Mb和Mb突变体的结合亲和力中 自由能微扰，并将它们分解成立体和 静电元件。3)描述相关对象的运动 通过分子动力学研究结合部位附近的氨基酸。最初 这些计算将在真空中运行，然后在溶剂中运行，以及 最后是溶剂中的肌红蛋白，由于它们的大小，它将是 以有限的方式完成。基于简单的血红素配体的初步工作 系统中，我们预计血球蛋白的主要影响因素 控制配基结合的过程都是静电的，用范德 瓦尔斯相互作用的贡献较小。相对人是如何 这两个因素的重要性，也许还有其他因素，都因约束而不同- 网站结构，是一个需要解决的重要问题。我们的 研究将大大有助于量化这种结构-功能 两性关系。我们提出的问题的答案的主要应用 在合成血液，一氧化氮激活血红素蛋白， 和镰状细胞性贫血。 使用最先进的分子建模软件和 对于当今的科学家来说，图形工作站正变得不可或缺 这对下一代科学家来说肯定是必要的。 将对学生进行规划、使用和解释 这里描述的计算，因此将更好地为使用 这些工具在未来。

Recent picosecond and nanosecond kinetic studies on the geminate recombination of photodissociated CO to Myoglobin, and Myoglobin mutants, has raised fundamental questions concerning the influence of different factors on the ligand binding processes to hemoproteins specifically, and to metalloproteins in general. We propose to use computational methods such as Density Functional theory, Molecular Mechanics, Molecular Dynamics, and Free Energy Perturbation calculations to study, and characterize, the factors which control ligand binding processes to Myoglobin (Mb) and the simple models thereof. We choose this group of systems because there exist a great deal of structural information on them; a requisite for using the proposed computational techniques. Specifically, we shall focus on the simulation of three factors as they affect the processes described above: 1) The Distal Steric effect, 2) The effect of local polarity, and 3) the effect of solvent. We will characterize these factors by using the AMBER software package to simulate both the equilibrium and kinetic properties of hemes, and Myoglobin. Briefly, the proposed methodology is summarized in the following steps: 1) Extend the current heme force field to the simulation of NO-heme and isocyanide-heme systems. 2) Reproduce trends in the binding affinities of ligands to hemes, Mb and Mb mutants via free-energy perturbation, and decompose these down into steric and electrostatic components. 3) Characterize the motion of the pertinent amino acids near the binding site via molecular dynamics. Initially these calculations will be run in vacuo, then the hemes in solvent, and finally the Myoglobin in solvent, which because of their size, will be done in a limited way. Based on preliminary work with simple heme-ligand systems, we anticipate that the major factors by which hemoproteins control the process of ligand binding are electrostatic, with Van der Waals interactions making a smaller contribution. How the relative importance of these two factors, and perhaps others, vary with binding- site structure, is an important question that needs to be addressed. Our studies will go a long way toward quantifying this structure-function relationship. Major applications of the answers to the questions we pose are in the fields of synthetic blood, activation of hemeproteins by NO, and sickle cell anemia. Training in the use of state-of-the-art molecular modeling software and graphics workstations is becoming essential for scientists today and certainly will be necessary for the next generation of scientists. Students will be trained in the planning, use, and interpretation of the calculations described herein and so will better prepare them for using these tools in the future.