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

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 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. 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. 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