New Methods and Applications for the Dynamic Characterization of Proteins by the Combination of NMR Spectroscopy and Computer Simulations

本研究的目的是通过核磁共振（NMR）和计算方法研究蛋白质动力学。NMR弛豫参数现在常规测量的蛋白质骨架，但较少这样的蛋白质侧链。虽然侧链弛豫研究主要集中在甲基基团弛豫，但大多数侧链碳原子属于亚甲基部分。如果不是部分氘化的，偶极-偶极互相关通常使它们的弛豫行为和它们的解释变得困难。新的弛豫实验开发，有效地抑制偶极偶极交叉相关弛豫完全碳标记的蛋白质。弛豫数据将被解释的重取向本征模动力学（RED）分析，将NMR弛豫数据与分子动力学模拟研究的运动相关效应在ns和亚ns的时间尺度范围内。直到最近，蛋白质在数百ns到ms范围内的较慢的时间尺度动力学一直很难评估没有显示交换增宽的自旋。剩余偶极耦合的出现现在为全面的实验研究打开了这个时间窗口。通过应用和改进最近推出的无模型方法，该方法使用偶极耦合数据在各种对齐介质与不同的对齐张量，这些较慢的时间尺度上的蛋白质动力学将研究蛋白质骨架以及侧链。动力学信息将以平均球谐函数的形式检索，球谐函数定义了序参数以及运动的各向异性。现实的分析运动模型将开发本地蛋白质片段的运动，以及涉及氨基酸基团和整个二级结构元素的集体运动的特点。蛋白质的结构动力学在生物化学过程中起着重要的作用。在原子水平上的蛋白质动力学的详细信息是理解它们的功能的根本重要性。本研究的总体目标是探索和发展新的实验和计算方法，用于在广泛不同的时间尺度上全面描述复杂蛋白质动力学，并证明其对生物相关系统的适用性。

The objective of this research is to study protein dynamics by nuclear magnetic resonance (NMR) and computational approaches. NMR relaxation parameters are now routinely measured for the protein backbone, but less so for protein side chains. While side-chain relaxation studies have mainly focused on methyl group relaxation, the majority of side-chain carbon atoms belong to methylene moieties. If not partially deuterated, dipole-dipole cross correlations generally make their relaxation behavior and their interpretation difficult. New relaxation experiments are developed that efficiently suppress dipole-dipole cross-correlated relaxation in fully carbon-labeled proteins. The relaxation data will be interpreted in terms of reorientational eigenmode dynamics (RED) analysis that integrates NMR relaxation data with molecular dynamics simulations for studying motional correlation effects in the ns and sub-ns time scale range. Until recently, slower time-scale dynamics of proteins in the hundreds of ns to ms range have been very hard to assess for spins that do not show exchange broadening. The advent of residual dipolar couplings is now opening up this time window for comprehensive experimental investigations. By applying and improving the recently introduced model-free approach that uses dipolar coupling data in a variety of alignment media with different alignment tensors, protein dynamics on these slower time scales will be investigated for the protein backbone as well as for the side chains. The dynamics information will be retrieved in the form of averaged spherical harmonics that define an order parameter as well as the anisotropy of motion. Realistic analytical motional models will be developed to characterize motions of local protein fragments as well as collective motions involving amino-acid groups and whole secondary structural elements. Structural dynamics of proteins play an important role in biochemical processes. Detailed information on protein dynamics at an atomic level is of fundamental importance for understanding their function. The overall goal of this research is the exploration and development of new experimental and computational methods for a comprehensive description of complex protein dynamics on widely different time scales and to demonstrate their applicability to biologically relevant systems.