Direct NMR Methods for Protein Structures and Assignment

描述（由申请人提供）：在蛋白质的核磁共振（NMR）研究中，将核自旋共振分配给单个原子是所有后续生物医学应用的先决条件，例如配体结合、蛋白质-DNA相互作用和动力学研究。共振分配是最耗时和劳动密集型的步骤之一，即使当蛋白质的3D X射线结构可用时。提出了一种新的策略，找到共振分配，使最佳利用的X射线结构，残余偶极耦合测量，和化学位移。通过这种方式，NMR、X射线晶体学和量子化学的互补优势得到了协同使用。与标准分配协议相比，不需要关于顺序连接性的NMR信息。分配问题在数学上用加权匹配问题来表示，该加权匹配问题可以使用计算高效的组合优化算法来解决。分配提供的化学位移信息可以直接用于各种NMR应用，包括配体结合研究，有助于表征结合位点，强度和特异性，这将有助于合理指导药物设计。拟议的工作将使大量的蛋白质，其结构存放在蛋白质数据库（PDB），适合详细的生物医学NMR调查。 结构基因组学的目的是从蛋白质的三维结构中推导出蛋白质的功能，这就需要快速的结构测定方法。对于蛋白质的结构不是由X射线晶体学确定的，提出了一种有效的方法，同时使用NMR残余偶极耦合信息，不完全顺序连接和建模技术的结构测定和共振分配。该方法通过直接构建与残余偶极偶联、氨基酸类型特异性化学位移和稀疏连续骨架连接性信息一致的3D蛋白质片段的文库来避免缓慢的分配步骤。单个片段具有良好的分辨率，并且它们不偏向于沉积在PDB中的已知结构。蛋白质片段，然后组装完成3D蛋白质结构的高性能计算方法，使用数据库衍生的惩罚函数。与标准NMR方法相比，该方法不依赖于NOESY导出的距离约束。该方法有望比标准NMR方法显著加快速度，将在模型蛋白质上进行测试和改进，然后应用于生物相关蛋白质。

DESCRIPTION (provided by applicant): In nuclear magnetic resonance (NMR) studies of proteins, the assignment of nuclear spin resonances to individual atoms is a prerequisite for all subsequent biomedical applications, such as studies of ligand binding, protein-DNA interactions, and dynamics. Resonance assignment is one of the most time consuming and labor intensive steps even when the 3D xray structure of the protein is available. A new strategy is proposed to find resonance assignments that makes optimal use of the x-ray structure, residual dipolar coupling measurements, and chemical shifts. In this way, the complementary strengths of NMR, x-ray crystallography, and quantum chemistry are synergetically used. In contrast to standard assignment protocols, no NMR information about sequential connectivities is required. The assignment problem is mathematically formulated in terms of a weighted matching problem that can be solved using a computationally efficient combinatorial optimization algorithm. The chemical shift information provided by the assignment can be directly used for a wide variety of NMR applications including ligand binding studies that help to characterize binding sites, strengths, and specificity that will help to rationally guide drug design. The proposed work will make a large number of proteins, whose structure is deposited in the protein database (PDB), amenable to detailed biomedical NMR investigations. Structural genomics, which aims at the derivation of protein function from its 3D structure, requires rapid structure determination methods. For proteins whose structure is not determined by x-ray crystallography, an efficient method is proposed for the simultaneous structure determination and resonance assignment using NMR residual dipolar coupling information, incomplete sequential connnectivities, and modeling techniques. The method avoids the slow assignment step by directly building a library of 3D protein fragments that are consistent with residual dipolar couplings, amino-acid type specific chemical shifts, and sparse sequential backbone connectivity information. The individual fragments have good resolution and they are not biased towards known structures deposited in the PDB. The protein fragments are then assembled to complete 3D protein structures by high-performance computional methods using database derived penalty functions. In contrast to standard NMR methods, this approach does not rely on NOESY-derived distance constraints. The method, which promises a significant speed-up over standard NMR methods, will be tested and refined on model proteins and then applied to biologically relevant proteins.