MULTIFREQUENCY ESR SPECTRA OF SPIN-LABELED PROTEIN FROM MD SIMULATIONS

MD 模拟中自旋标记蛋白的多频 ESR 谱

• 批准号: 7724004
• 负责人: DENIZ SEZER
• 金额: $ 0.1万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7724004
• 关键词: Agreement; Computer Retrieval of Information on Scientific Projects Database; Data; Electron Spin Resonance Spectroscopy; Environment; Funding; Grant; Helix (Snails); Institution; Label; Molecular; Molecular Conformation; Motion; Muramidase; Numbers; Positioning Attribute; Proteins; Research; Research Personnel; Resources; Side; Site; Solvents; Source; Spin Labels; Surface; Time; United States National Institutes of Health; alpha helix; ear helix; insight; magnetic field; markov model; molecular dynamics; research study; simulation

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. Multifrequency electron spin resonance (ESR) spectra provides a wealth of structural and dynamics information about the local environment of the spin label, and indirectly about the proteins to which they are attached. Unambiguously relating the features of the observed spectra to the underlying molecular motions and interactions is, however, challenging. To progress toward a rigorous interpretation of ESR spectra, we performed extensive molecular dynamics (MD) simulations of fully solvated T4 Lysozyme, labeled with spin labeled at positions 72 and 131. These two sites have been the object of numerous experimental studies, and have established themselves as prototypical solvent-exposed sites on the surface of alpha-helices. To extend the time window afforded by the simulations, stochastic Markov models, reflecting the dynamics of spin label side chains in terms of their rotameric states, are constructed from the trajectories. Without adjustable parameters, the multifrequency ESR spectra calculated at three different magnetic field strengths for positions 72 and 131 were found to be in quantitative agreement with experiment. During dynamics the spin label has access to a fairly large number of conformations and displays a significant propensity to form interactions with protein residues other than the nearest neighbors along the helix. The detailed picture of the spin label emerging from the MD simulations unifies the diverse spectroscopic and crystallographic data and provides unprecedented insight into their molecular origins.

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。 多频电子自旋共振(ESR)谱提供了关于自旋标记的局部环境的丰富的结构和动力学信息，并间接地提供了关于它们所连接的蛋白质的信息。然而，明确地将观察到的光谱特征与潜在的分子运动和相互作用联系起来是具有挑战性的。为了对ESR谱进行严格的解释，我们对完全溶剂化的T4溶菌酶进行了广泛的分子动力学(MD)模拟，并在第72和131位标记了自旋标记。这两个位置已经成为许多实验研究的对象，并且已经确立了它们自己是α-螺旋表面典型的暴露于溶剂的位置。为了延长模拟所提供的时间窗口，根据轨迹构造了反映自旋标签侧链的旋转态动力学的随机马尔可夫模型。在没有可调参数的情况下，在三个不同磁场强度下计算的第72和131位的多频ESR谱与实验定量一致。在动力学过程中，自旋标记可以接触到相当多的构象，并显示出与螺旋上最近邻以外的蛋白质残基形成相互作用的显著倾向。从分子动力学模拟中出现的自旋标记的详细图像统一了不同的光谱和结晶学数据，并提供了对它们的分子起源的前所未有的洞察。