PROTEIN DYNAMICS FROM NMR WITH RHOMBIC LOCAL POTENTIALS

这个子项目是利用由NIH/NCRR资助的中心拨款提供的资源的许多研究子项目之一。子项目和调查员(PI)可能从另一个NIH来源获得了主要资金，因此可能会出现在其他CRISE条目中。列出的机构是针对中心的，而不一定是针对调查员的机构。5N-1H自旋驰豫是研究蛋白质骨架动力学的有效方法。为了从实验数据中获得尽可能多的信息，需要一种与现有数据的完整性相匹配的理论方法。我们已经证明，慢弛豫局部结构(SRLS)方法能够实现这一点。主要现象，如探针的局部运动(例如，N-H键)和蛋白质的全局翻滚之间的动力学耦合，以及局部几何的一般特征，都明确地包括在SRLS中。在最近的工作中，我们集中在几何方面，特别是模耦合势的对称性，它反映了关于15N位的局域几何。势的对称性取决于下图所示的局域扩散/局域有序标架M和局域指向标架C的对称性。我们发现M骨架的特殊的菱形对称性是“近平面的ym-ym”型，这与多肽平面和N-H位的立体化学相一致。(曲轴波动和肽主轴上相邻碳键的肽平面重定向)是功能上重要的内部运动，必然涉及菱形空间限制，可以用SRLS处理，而无模型方法不能显式地允许它们。我们发现，需要一个合适的SRLS理论来识别这种功能上的重要运动。我们用腺苷酸激酶、钙调素、结合酶和核糖核酸酶H的核磁共振弛豫数据的例子证明了这一点。在模式耦合和局部几何结构正确考虑的情况下，SRLS似乎与目前蛋白质中15N弛豫数据的质量相匹配。因此，SRLS提供了关于主干动态的有洞察力的信息，这些信息可以直接与功能相关。

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. 5N-1H spin relaxation is a powerful method for elucidating protein backbone dynamics. In order to derive as much information as possible from the experimental data a theoretical approach is needed which matches the integrity of currently available data. We have shown that the slowly relaxing local structure (SRLS) approach is capable of accomplishing this. Dominant phenomena such as dynamical coupling between the local motion of the probe (e.g., N-H bond) and the global tumbling of the protein, and general features of local geometry, are explicitly included in SRLS. In recent work we have focused on the geometric aspects, in particular the symmetry of the mode-coupling potential, which reflects the local geometry about the 15N site. The symmetry of the potential depends on the symmetry of the local diffusion/local ordering frame, M, and the symmetry of the local director frame, C, which are illustrated below top. We found that the particular rhombic symmetry of the M frame is of the "nearly planar Ym-Ym" type, in agreement with the stereo-chemistry of the peptide plane and the N-H site. (crankshaft fluctuations and peptide-plane reorientation of adjacent carbon bonds in peptide backbone axis) are functionally important internal motions, which necessarily involve rhombic spatial restrictions, can be treated satisfactorily with SRLS whereas the model free approach is not able to explicitly allow for them. We found that a proper SRLS theory is required to discern such functionally important motions. We demonstrated this with examples of NMR relaxation data from adenylate kinase, calmodulin, binase and ribonuclease H. With mode-coupling and the local geometry properly accounted for, SRLS appears to match the quality of current 15N relaxation data in proteins. Thus SRLS provides insightful information on backbone dynamics which can be related directly to function.