Project 2/Dev't and evaluation of computational tools for structural studies by E

项目 2/Devt 和 E 的结构研究计算工具评估

• 批准号: 8064809
• 负责人: ERIC J HUSTEDT
• 金额: $ 63.6万
• 依托单位: VANDERBILT UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8064809
• 关键词: Affect; Anion Exchangers (Proteins); Applications Grants; Arginine; Binding Proteins; Biological Process; Collaborations; Computational algorithm; Computing Methodologies; Cytoplasmic Tail; Data; Electron Spin Resonance Spectroscopy; Electrons; Elements; Environment; Erythrocytes; Evaluation; Frequencies; Goals; Hereditary Spherocytosis; Individual; Label; Laboratories; Macromolecular Complexes; Measurement; Measures; Methods; Modeling; Molecular Models; Molecular Structure; Muramidase; Mutation; Proline; Protein Dynamics; Proteins; Refractory; Resolution; Roentgen Rays; Site; Spectrum Analysis; Spin Labels; Structural Models; Structure; Surface; Techniques; Testing; Time; X-Ray Crystallography; band 3 protein Tuscaloosa; computerized tools; flexibility; improved; macromolecular assembly; methanethiosulfonate; molecular dynamics; molecular modeling; novel; protein function; protein protein interaction; research study; tool

The objectives of this project are to develop and evaluate novel molecular modeling and computational approaches to extract accurate structural information from site-directed spin-labeling (SDSL) studies. The combination of SDSL and electron paramagnetic resonance spectroscopy (EPR) has made remarkable advances in the past 15 years (for reviews see (Hubbell and Altenbach, 1994; Hustedt and Beth, 1999; Hubbell et al., 2000; Mchaourab and Perozo, 2000; Columbus and Hubbell, 2002; Klug and Feix, 2005) and it is now widely employed to study the structures and structural transitions of proteins and large macromolecular assemblies, many of which have been refractory to structural characterization by techniques such as X-ray crystallography and NMR. Even in those cases where atomic resolution structures can be obtained, SDSL is being increasingly employed in complementary studies to elucidate the dynamics of structural transitions that determine biological function (e.g. (Dong et al., 2005). In addition, SDSL has been employed to study the assembly of macromolecular complexes composed of elements whose individual structures have been determined by NMR or X-ray crystallographic methods (e.g. (Park et al., 2006)). We propose to combine the full power of modern molecular dynamics and computational approaches in the Lybrand laboratory with advanced EPR methods in the Hustedt laboratory to develop tools that will dramatically improve the quality of the structural models that are obtained from SDSL data. Molecular dynamics (MD) and Monte Carlo (MC) modeling strategies will be developed to treat the structure and dynamics of the methanethiosulfonate spin label (MTSSL). These strategies will be used to predict both the continuous wave EPR (CW-EPR) lineshapes of singly labeled proteins and the distance distributions measured by both CWEPR and double electron-electron resonance (DEER) experiments on doubly labeled proteins. These new computational algorithms will be tested on the well-studied protein T4 lysozyme (T4L) and then used to investigate the effect of a proline to arginine mutation on the structure and dynamics of the cytoplasmic domain of the erythrocyte anion exchange protein, band 3 (CDB3) in an ongoing collaboration with Project 2 of this grant proposal.. The overall goal of the following Specific Aims is to enable the maximum structural and dynamic information to be derived from a given set of EPR data.

这个项目的目标是开发和评估新的分子建模和计算方法 从定点自旋标记（SDSL）研究中提取准确的结构信息。相结合 SDSL和电子顺磁共振谱（EPR）的研究取得了显著进展， 过去15年（综述参见（Hubbell和Altenbach，1994;胡斯特和Beth，1999; Hubbell等，二○年; Mchaourab和Perozo，2000年;哥伦布和Hubbell，2002年; Klug和Feix，2005年），现在已被广泛采用 研究蛋白质和大分子组装体的结构和结构转变， 其中许多已经难以通过诸如X射线晶体学的技术进行结构表征 和NMR。即使在那些可以获得原子分辨率结构的情况下，SDSL也越来越多地被应用于 用于补充研究，以阐明决定生物学特性的结构转变的动力学 函数（例如（Dong等人，2005年）。此外，SDSL还被用于研究大分子的组装 由通过NMR或X射线确定其单个结构的元素组成的络合物 晶体学方法（例如（Park等，2006））。 我们建议将现代分子动力学和计算方法的全部力量联合收割机结合起来， 莱布兰德实验室与先进的EPR方法在胡斯特实验室开发的工具，将显着 提高从SDSL数据获得的结构模型的质量。分子动力学（MD） 和蒙特卡罗（MC）建模策略将被开发来处理的结构和动力学的 甲硫基磺酸盐自旋标记物（MTSSL）。这些策略将用于预测连续波 单标记蛋白质的EPR（CW-EPR）线形和CWEPR测量的距离分布 和双电子-电子共振（DEER）实验。这些新 计算算法将在充分研究的蛋白质T4溶菌酶（T4 L）上进行测试，然后用于研究 脯氨酸到精氨酸突变对细胞质结构域的结构和动力学的影响， 红细胞阴离子交换蛋白，带3（CDB 3），与本赠款项目2正在进行的合作 建议..以下具体目标的总体目标是实现最大的结构和动态信息 从一组给定的EPR数据中导出。