Patel Sunita, Ramanujam Venkatraman, Srivastava Atul K, Chary Kandala V R
Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India.
Phys Chem Chem Phys. 2014 Jul 7;16(25):12703-18. doi: 10.1039/c3cp53558d.
The three-dimensional folded structure of a protein has been considered essential for its function. However, recently many proteins have been identified to function without having a definite structure and they have been classified as intrinsically disordered proteins (IDPs). Recently, we have identified a βγ-crystallin domain in the genome of a marine bacterium called Hahella chejuensis on the basis of known sequence signatures. This protein, called Hahellin, was characterized by NMR spectroscopy as an IDP, which upon Ca(2+)-binding was shown to undergo a large conformational transformation and acquires a typical βγ-crystallin fold. In this paper, we have characterized this IDP by a combined use of NMR and Replica Exchange Molecular Dynamics simulation and found it to be in a highly dynamic, inter-converting population having a molten globular state with the C-terminal Greek key motif relatively more flexible as compared to its N-terminal counterpart. Network analysis and clustering on the observed conformational ensemble showed a heterogeneous mixture of eleven distinct clusters, classified into near-native and far-native populations, which are not in equilibrium. Several conformational clusters display an increased propensity for helical conformation(s) and a decreased β-strand propensity, which is consistent with the NMR observations made on this protein. The negatively charged Ca(2+)-coordinating residues form parts of the highly flexible polypeptide stretches, and thus act as seeds for the origin of different conformational clusters observed. This study thus helps us to understand the relationship between the role of conformational dynamics and the structural propensities of the intrinsically disordered state of apo-Hahellin.
蛋白质的三维折叠结构一直被认为对其功能至关重要。然而，最近发现许多蛋白质在没有确定结构的情况下也能发挥功能，它们被归类为内在无序蛋白质（IDP）。最近，我们基于已知的序列特征，在一种名为济州海杆菌（Hahella chejuensis）的海洋细菌基因组中鉴定出一个βγ-晶状体蛋白结构域。这种名为海杆菌素（Hahellin）的蛋白质通过核磁共振光谱表征为一种IDP，在结合Ca(2+)后显示会发生大的构象转变并获得典型的βγ-晶状体蛋白折叠。在本文中，我们通过结合使用核磁共振和复制交换分子动力学模拟对这种IDP进行了表征，发现它处于高度动态的、相互转换的群体中，具有熔融球状状态，其C端希腊钥匙基序与其N端对应物相比相对更灵活。对观察到的构象集合进行网络分析和聚类显示出由11个不同簇组成的异质混合物，分为近天然态和远天然态群体，它们处于非平衡状态。几个构象簇显示出螺旋构象倾向增加而β链倾向降低，这与对该蛋白质的核磁共振观察结果一致。带负电荷的Ca(2+)配位残基形成高度灵活的多肽链段的一部分，因此充当了观察到的不同构象簇起源的种子。这项研究因此有助于我们理解构象动力学的作用与脱辅基海杆菌素内在无序状态的结构倾向之间的关系。
