Kuszewski J, Gronenborn A M, Clore G M
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
Protein Sci. 1996 Jun;5(6):1067-80. doi: 10.1002/pro.5560050609.
A new conformational database potential involving dihedral angle relationships in databases of high-resolution highly refined protein crystal structures is presented as a method for improving the quality of structures generated from NMR data. The rationale for this procedure is based on the observation that uncertainties in the description of the nonbonded contacts present a key limiting factor in the attainable accuracy of protein NMR structures and that the nonbonded interaction terms presently used have poor discriminatory power between high- and low-probability local conformations. The idea behind the conformational database potential is to restrict sampling during simulated annealing refinement to conformations that are likely to be energetically possible by effectively limiting the choices of dihedral angles to those that are known to be physically realizable. In this manner, the variability in the structures produced by this method is primarily a function of the experimental restraints, rather than an artifact of a poor nonbonded interaction model. We tested this approach with the experimental NMR data (comprising an average of about 30 restraints per residue and consisting of interproton distances, torsion angles, 3JHN alpha coupling constants, and 13C chemical shifts) used previously to calculate the solution structure of reduced human thioredoxin (Qin J, Clore GM, Gronenborn AM, 1994, Structure 2:503-522). Incorporation of the conformational database potential into the target function used for refinement (which also includes terms for the experimental restraints, covalent geometry, and nonbonded interactions in the form of either a repulsive, repulsive-attractive, or 6-12 Lennard-Jones potential) results in a significant improvement in various quantitative measures of quality (Ramachandran plot, side-chain torsion angles, overall packing). This is achieved without compromising the agreement with the experimental restraints and the deviations from idealized covalent geometry that remain within experimental error, and the agreement between calculated and observed 1H chemical shifts that provides an independent NMR parameter of accuracy. The method is equally applicable to crystallographic refinement, and should be particular useful during the early stages of either an NMR or crystallographic structure determination and in cases where relatively few experimental restraints can be derived from the measured data (due, for example, to broad lines in the NMR spectra or to poorly diffracting crystals).
本文提出了一种新的构象数据库势，该势涉及高分辨率高度精制蛋白质晶体结构数据库中的二面角关系，作为一种提高由核磁共振（NMR）数据生成的结构质量的方法。此过程的基本原理基于以下观察结果：非键接触描述中的不确定性是蛋白质NMR结构可达到的精度的关键限制因素，并且目前使用的非键相互作用项在高概率和低概率局部构象之间的区分能力较差。构象数据库势背后的想法是，在模拟退火精修过程中，通过有效地将二面角的选择限制在已知可物理实现的角度，将采样限制在能量上可能的构象。通过这种方式，该方法产生的结构变化主要是实验约束的函数，而不是不良非键相互作用模型的伪影。我们用先前用于计算还原型人硫氧还蛋白溶液结构的实验NMR数据（每个残基平均约30个约束，包括质子间距离、扭转角、3JHNα耦合常数和13C化学位移）测试了这种方法（Qin J，Clore GM，Gronenborn AM，1994，Structure 2:503 - 522）。将构象数据库势纳入用于精修的目标函数（该目标函数还包括实验约束、共价几何形状以及以排斥、排斥 - 吸引或6 - 12 Lennard - Jones势形式的非键相互作用项）会导致各种质量定量指标（拉氏构象图、侧链扭转角、整体堆积）有显著改善。这是在不影响与实验约束的一致性以及与理想化共价几何形状的偏差（该偏差仍在实验误差范围内）的情况下实现的，并且计算和观察到的1H化学位移之间的一致性提供了一个独立的NMR精度参数。该方法同样适用于晶体学精修，并且在NMR或晶体学结构测定的早期阶段以及从测量数据中可获得相对较少实验约束的情况下（例如，由于NMR谱线宽或晶体衍射差）应该特别有用。
