Liu Wei, Zhang Jingfeng, Fan Jing-Song, Tria Giancarlo, Grüber Gerhard, Yang Daiwen
Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
Nanyang Technological University, School of Biological Sciences, Singapore, Singapore.
Biophys J. 2016 May 10;110(9):1943-56. doi: 10.1016/j.bpj.2016.04.009.
Structure ensemble determination is the basis of understanding the structure-function relationship of a multidomain protein with weak domain-domain interactions. Paramagnetic relaxation enhancement has been proven a powerful tool in the study of structure ensembles, but there exist a number of challenges such as spin-label flexibility, domain dynamics, and overfitting. Here we propose a new (to our knowledge) method to describe structure ensembles using a minimal number of conformers. In this method, individual domains are considered rigid; the position of each spin-label conformer and the structure of each protein conformer are defined by three and six orthogonal parameters, respectively. First, the spin-label ensemble is determined by optimizing the positions and populations of spin-label conformers against intradomain paramagnetic relaxation enhancements with a genetic algorithm. Subsequently, the protein structure ensemble is optimized using a more efficient genetic algorithm-based approach and an overfitting indicator, both of which were established in this work. The method was validated using a reference ensemble with a set of conformers whose populations and structures are known. This method was also applied to study the structure ensemble of the tandem di-domain of a poly (U) binding protein. The determined ensemble was supported by small-angle x-ray scattering and nuclear magnetic resonance relaxation data. The ensemble obtained suggests an induced fit mechanism for recognition of target RNA by the protein.
结构集合的确定是理解具有弱结构域 - 结构域相互作用的多结构域蛋白质结构 - 功能关系的基础。顺磁弛豫增强已被证明是研究结构集合的有力工具，但仍存在许多挑战，如自旋标记的灵活性、结构域动力学和过拟合。在此，我们提出一种新的（据我们所知）方法，用最少数量的构象体来描述结构集合。在该方法中，各个结构域被视为刚性；每个自旋标记构象体的位置和每个蛋白质构象体的结构分别由三个和六个正交参数定义。首先，通过使用遗传算法针对结构域内顺磁弛豫增强优化自旋标记构象体的位置和丰度来确定自旋标记集合。随后，使用基于遗传算法的更高效方法和过拟合指标对蛋白质结构集合进行优化，这两者均在本研究中建立。该方法通过使用一组已知丰度和结构的构象体的参考集合进行了验证。此方法还应用于研究聚（U）结合蛋白串联双结构域的结构集合。所确定的集合得到了小角X射线散射和核磁共振弛豫数据的支持。所得集合表明该蛋白质识别靶RNA的诱导契合机制。
