Du Qi-Shi, Chen Dong, Xie Neng-Zhong, Huang Ri-Bo, Chou Kuo-Chen
a State Key Laboratory of Non-food Biomass and Enzyme Technology , National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences , 98 Daling Road, Nanning , Guangxi 530007 , China.
J Biomol Struct Dyn. 2015 Sep;33(9):1957-72. doi: 10.1080/07391102.2014.984333. Epub 2014 Dec 22.
Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding.
尽管环段不像α螺旋和β链那样被归类为最基本的蛋白质结构元件，但它可能在蛋白质稳定性、柔韧性和动态活性方面发挥重要作用。同时，蛋白质环段也相当难以捉摸；也就是说，它与蛋白质其他部分的相互作用以及其自身的形状维持力仍然是一个谜，或者至少还不太清楚。在这里，我们报道了一种分子力，即所谓的极性氢-π相互作用（Hp-π），它可能在支撑蛋白质环段的主链方面发挥重要作用。通过在肽键单元的准π平面上进行势能面扫描计算，我们观察到以下有趣的现象：（1）当一个肽单元的极性氢原子垂直指向其他肽键单元的π平面时，会发生显著的Hp-π相互作用；（2）这种相互作用依赖于距离和取向，在广阔的空间中起作用，属于“点对面”相互作用。这里报道的分子力可能提供有用的相互作用概念，并有助于更好地理解环段独特的稳定性和柔韧性特征，以及蛋白质整体折叠的驱动力。
