Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins

Achieving facile specific recognition is essential for intrinsically disordered proteins (IDPs) that are involved in cellular signaling and regulation. Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein folding for specific IDP recognition could lead to kinetic bottlenecks. How IDPs overcome such potential kinetic bottlenecks to viably function in signaling and regulation in general is poorly understood. Our recent computational and experimental study of cell-cycle regulator p27 (Ganguly et al., J. Mol. Biol. (2012)) demonstrated that long-range electrostatic forces exerted on enriched charges of IDPs could accelerate protein-protein encounter via “electrostatic steering” and at the same time promote “folding-competent” encounter topologies to enhance the efficiency of IDP folding upon encounter. Here, we further investigated the coupled binding and folding mechanisms and the roles of electrostatic forces in the formation of three IDP complexes with more complex folded topologies. The surface electrostatic potentials of these complexes lack prominent features like those observed for the p27/Cdk2/cyclin A complex to directly suggest the ability of electrostatic forces to facilitate folding upon encounter. Nonetheless, similar electrostatically accelerated encounter and folding mechanisms were consistently predicted for all three complexes using topology-based coarse-grained simulations. Together with our previous analysis of charge distributions in known IDP complexes, our results support a prevalent role of electrostatic interactions in promoting efficient coupled binding and folding for facile specific recognition. These results also suggest that there is likely a co-evolution of IDP folded topology, charge characteristics, and coupled binding and folding mechanisms, driven at least partially by the need to achieve fast association kinetics for cellular signaling and regulation.

实现便捷的特异性识别对于参与细胞信号转导与调控的固有无序蛋白（intrinsically disordered proteins, IDPs）而言至关重要。结合蛋白质折叠的物理时间尺度与扩散限制的蛋白质-蛋白质相遇过程开展分析后可发现，若要实现对IDPs的特异性识别往往需要蛋白质先完成折叠，这一过程可能会引发动力学瓶颈。目前学界对IDPs究竟如何克服这类潜在的动力学瓶颈，从而在信号转导与调控中正常发挥功能的机制仍知之甚少。我们此前针对细胞周期调控蛋白p27开展的计算与实验研究（Ganguly等，J. Mol. Biol., 2012）表明，IDPs表面富集电荷所受的长程静电力，可通过“静电导向”作用加速蛋白质-蛋白质的相遇过程，同时还能促进形成“具备折叠能力”的相遇构象，从而提升相遇后IDPs的折叠效率。本研究进一步针对3种具有更为复杂折叠拓扑结构的IDP复合物，探究了其结合与折叠耦联的机制，以及静电力在复合物形成过程中所发挥的作用。这些复合物的表面静电势并未呈现出类似p27/Cdk2/细胞周期蛋白A复合物中可直接体现静电力促进相遇后折叠能力的显著特征。尽管如此，通过基于拓扑的粗粒度模拟，我们仍一致预测这3种复合物均采用了静电力加速的相遇与折叠机制。结合我们此前对已知IDP复合物中电荷分布的分析，本研究结果证实，静电相互作用在促进高效的结合与折叠耦联、实现便捷的特异性识别过程中发挥着普遍的关键作用。本研究结果还表明，IDPs的折叠拓扑结构、电荷特征以及结合与折叠耦联机制可能存在共同进化，这一过程至少部分源于细胞信号转导与调控对快速结合动力学的需求。