PARAMETRIZATION, MD SIMULATION, CALCULATION OF POLYALANINE ALPHA-HELIX SPECTRA

参数化、分子动力学模拟、聚丙氨酸α螺旋谱的计算

• 批准号: 7956695
• 负责人: DENIZ SEZER
• 金额: $ 0.36万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2010-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956695
• 关键词: Affect; Alanine; Computer Retrieval of Information on Scientific Projects Database; Diffusion; Electron Spin Resonance Spectroscopy; Funding; Grant; Hydrophobic Interactions; Institution; Muramidase; Proteins; Research; Research Personnel; Resources; Side; Simulate; Site; Solutions; Solvents; Source; Spin Labels; Technology; Time; United States National Institutes of Health; alpha helix; methyl methanethiosulfonate; molecular dynamics; polyalanine

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. The nitroxide spin label 1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl-methanethiosulfonate (MTSSL), commonly used in site-directed spin labeling of proteins, was studied with molecular dynamics (MD) simulations. After developing force field parameters for the nitroxide moiety and the spin label linker, we simulated MTSSL attached to a polyalanine R-helix in explicit solvent to elucidate the factors affecting its conformational dynamics. Electron spin resonance spectra at 9 and 250 GHz were simulated in the time domain using the MD trajectories and including global rotational diffusion appropriate for the tumbling of T4 Lysozyme in solution. Analysis of the MD simulations reveals the presence of significant hydrophobic interactions of the spin label with the alanine side chains

这个子项目是许多研究子项目中的一个 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来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 采用分子动力学模拟方法对蛋白质定点自旋标记中常用的氮氧自由基自旋标记物1-氧-2，2，5，5-四甲基吡咯啉-3-甲基硫代磺酸盐（MTSSL）进行了研究。开发力场参数的氮氧自由基部分和自旋标记连接器后，我们模拟MTSSL连接到一个聚丙氨酸R-螺旋在明确的溶剂，以阐明其构象动力学的影响因素。在9和250 GHz的电子自旋共振光谱进行了模拟，在时域中使用MD轨迹，包括全球旋转扩散适当的T4溶菌酶在溶液中翻滚。分子动力学模拟的分析揭示了自旋标记物与丙氨酸侧链之间存在显著的疏水相互作用