Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California.
Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California.
Biophys J. 2021 Sep 7;120(17):3628-3640. doi: 10.1016/j.bpj.2021.07.025. Epub 2021 Jul 31.
The nuclear pore complex (NPC) is the exclusive gateway for traffic control across the nuclear envelope. Although smaller cargoes (less than 5-9 nm in size) can freely diffuse through the NPC, the passage of larger cargoes is restricted to those accompanied by nuclear transport receptors (NTRs). This selective barrier nature of the NPC is putatively associated with the intrinsically disordered, phenylalanine-glycine repeat-domains containing nucleoporins, termed FG-Nups. The precise mechanism underlying how FG-Nups carry out such an exquisite task at high throughputs has, however, remained elusive and the subject of various hypotheses. From the thermodynamics perspective, free energy analysis can be a way to determine cargo's transportability because the traffic through the NPC must be in the direction of reducing the free energy. In this study, we developed a computational model to evaluate the free energy composed of the conformational entropy of FG-Nups and the energetic gain associated with binding interactions between FG-Nups and NTRs and investigated whether these physical features can be the basis of NPC's selectivity. Our results showed that the reduction in conformational entropy by inserting a cargo into the NPC increased the free energy by an amount substantially greater than the thermal energy (≫kT), whereas the free energy change was negligible (<kT) for small cargoes (less than ~6 nm in size), indicating the size-dependent selectivity emerges from the entropic effect. Our models suggested that the entropy-induced selectivity of the NPC depends sensitively upon the physical parameters such as the flexibility and the length of FG-Nups. On the other hand, the energetic gain via binding interactions effectively counteracted the entropic reduction, increasing the size limit of transportable cargoes up to the nuclear pore size. We further investigated the geometric effect of the binding spot spatial distribution and found that the clustered binding spot distribution decreased the free energy more efficiently as compared to the scattered distribution.
核孔复合体（NPC）是核膜上物质运输的唯一通道。尽管较小的货物（小于 5-9nm）可以自由扩散通过 NPC，但较大货物的通过则受到核转运受体（NTR）的限制。NPC 的这种选择性屏障特性与内在无序的、富含苯丙氨酸-甘氨酸重复序列的核孔蛋白（FG-Nups）有关。然而，FG-Nups 如何以高吞吐量执行如此精细任务的精确机制仍然难以捉摸，这也是各种假说的主题。从热力学的角度来看，自由能分析可以用来确定货物的可运输性，因为货物通过 NPC 的运输必须是降低自由能的方向。在这项研究中，我们开发了一种计算模型来评估由 FG-Nups 的构象熵和 FG-Nups 与 NTR 之间结合相互作用所产生的能量增益组成的自由能，并研究了这些物理特性是否可以成为 NPC 选择性的基础。我们的结果表明，将货物插入 NPC 会导致构象熵减小，从而使自由能增加，增加量大大超过热能（≫kT），而对于较小的货物（小于~6nm），自由能变化可以忽略不计（<kT），这表明尺寸依赖性的选择性来自于熵效应。我们的模型表明，NPC 的熵诱导选择性对 FG-Nups 的物理参数（如灵活性和长度）非常敏感。另一方面，通过结合相互作用获得的能量增益有效地抵消了熵的减少，从而将可运输货物的尺寸限制提高到核孔的尺寸。我们进一步研究了结合点空间分布的几何效应，发现与分散分布相比，聚集的结合点分布更有效地降低了自由能。
