Liu Xu, Speckhard David C, Shepherd Tyson R, Sun Young Joo, Hengel Sarah R, Yu Liping, Fowler C Andrew, Gakhar Lokesh, Fuentes Ernesto J
Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
Department of Chemistry, Loras College, Dubuque, IA 52004-0178, USA.
Structure. 2016 Dec 6;24(12):2053-2066. doi: 10.1016/j.str.2016.08.019. Epub 2016 Oct 27.
Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.
构象动力学在酶催化中已确立其作用，但其对配体结合和特异性的贡献在很大程度上尚未得到探索。在这里，我们使用Tiam1 PDZ结构域和具有拓宽特异性的工程变体（QM PDZ）来研究结构和构象动力学在分子识别中的作用。QM PDZ结构域游离态和与配体结合态的晶体结构显示了结合（焓）的核心结构特征，而基于核磁共振的甲基弛豫实验和等温滴定量热法表明构象熵有助于亲和力。除了与热力学相关的运动外，在QM PDZ配体结合位点中普遍存在较慢的微秒到毫秒级切换，这与配体特异性的作用一致。我们的数据表明，构象动力学在调节分子相互作用的亲和力（构象熵）和特异性（激发态构象）方面发挥着独特而基本的作用。更广泛地说，我们的结果对蛋白质-配体相互作用的进化、调控和设计具有重要意义。
