AB INITIO CALCULATIONS OF THE RAMAN VIBRATIONAL MODES OF CYSTEINE AND ITS DERIV

半胱氨酸及其衍生物拉曼振动模式的从头计算

• 批准号: 8364290
• 负责人: Jayanti Pande
• 金额: $ 0.11万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-15 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8364290
• 关键词: Biomedical Research; Cataract; Cattle; Chemicals; Computer software; Crystallins; Cysteine; Environment; Frequencies; Funding; Glutathione; Goals; Grant; High Performance Computing; Human; Methods; Modeling; National Center for Research Resources; Principal Investigator; Proteins; Research; Research Infrastructure; Resolution; Resources; Rest; Source; Sulfhydryl Compounds; United States National Institutes of Health; cost; disulfide bond; lens; mutant; protein aggregation; protein structure; vibration

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Mutants of human gamma-D (HGD) crystallin are implicated in cataract formation. We have shown that R14C, a mutant form of HGD readily aggregates forming reducible intermolecular disulfide bonds. Cys14 introduced in the mutant in place of Arg, is the likely cause of such dramatic protein aggregation. The Cys-SH bond vibration is unequivocally determined in the Raman spectrum of proteins, and we have experimentally determined the SH contribution of Cys 14 in the Raman spectrum of the R14C mutant. Now, we would like to use ab-initio and DFT methods in order to model the Raman spectrum of Cys 14 to understand the chemical environment of the SH group, which not only determines its Raman frequency and intensity but may also influence its reactivity. Towards this goal, we would like to use software products such as Gaussian and Gamess available in the SGI machine POPEL. In a related project, we have identified the Raman SH bands of all the seven Cys residues individually in bovine gamma-B crystallin. Some of these Cys residues are known to react with glutathione, forming disulfide bonds and giving rise to the glutathiolated protein derivatives found normally in the lens. Here again, we would like to use ab-initio and DFT methods to calculate the Raman vibrational frequencies and intensities of protein-thiol -SH bonds. To facilitate the use of these theoretical methods, we already have available high-resolution x-ray crystal structures of these proteins. We propose using QM/MM methods whereby we would select a small region around the -SH group for the application of high-level theoretical methods and for the rest of the protein we would use MM methods using the AMBER forcefield.

该子项目是利用资源的许多研究子项目之一 由NIH/NCRR资助的中心赠款提供。次级项目的主要支助 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 为子项目列出的总成本可能 代表子项目使用的中心基础设施的估计数量， NCRR赠款不直接向子项目或子项目工作人员提供资金。 人γ-D（HGD）晶状体蛋白突变体与白内障形成有关。我们已经表明，R14 C，突变形式的HGD容易聚集形成可还原的分子间二硫键。在突变体中引入Cys 14代替Arg，可能是这种戏剧性蛋白质聚集的原因。Cys-SH键振动在蛋白质的拉曼光谱中是明确确定的，并且我们已经通过实验确定了Cys 14在R14 C突变体的拉曼光谱中的SH贡献。现在，我们想使用从头算和DFT方法来模拟Cys 14的拉曼光谱，以了解SH基团的化学环境，这不仅决定了其拉曼频率和强度，而且还可能影响其反应性。为了实现这一目标，我们希望使用SGI机器POPEL中可用的Gaussian和Gamess等软件产品。在一个相关的项目中，我们已经确定了所有七个半胱氨酸残基的拉曼SH带单独在牛γ-B晶体蛋白。已知这些Cys残基中的一些与谷胱甘肽反应，形成二硫键并产生通常在透镜中发现的谷胱甘肽化蛋白衍生物。在这里，我们想再次使用从头算和DFT方法来计算蛋白质-巯基-SH键的拉曼振动频率和强度。为了便于使用这些理论方法，我们已经有了这些蛋白质的高分辨率X射线晶体结构。我们建议使用QM/MM方法，我们将选择一个小区域周围的-SH组的应用程序的高层次的理论方法和其余的蛋白质，我们将使用MM方法使用琥珀力场。