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

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 对蛋白质定点自旋标记中常用的氮氧化物自旋标记1-oxyl-2，2，5，5-tetramethylpyrroline-3-methyl-methanethiosulfonate进行了分子动力学模拟研究。在建立了氮氧基和自旋标记连接基的力场参数后，我们模拟了在显性溶剂中连接在聚丙氨酸R-螺旋上的MTSSL，以阐明影响其构象动力学的因素。利用分子动力学轨迹在时间域中模拟了9 GHz和250 GHz的电子自旋共振谱，并考虑了适合T4溶菌酶在溶液中翻滚的全局旋转扩散。分子动力学模拟的分析表明，自旋标记与丙氨酸侧链存在显著的疏水相互作用

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