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 (≫k_BT), whereas the free energy change was negligible (<k_BT) 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）是穿过核膜的交通控制的唯一网关。虽然较小的货物（尺寸小于 5-9 nm）可以自由地通过 NPC 扩散，但较大的货物的通过仅限于那些伴随着核转运受体（NTR）的货物。NPC 的这种选择性屏障性质被认为与本质上无序的、含有核孔蛋白的苯丙氨酸-甘氨酸重复结构域（称为 FG-Nups）有关。然而，FG-Nups 如何以高吞吐量执行如此复杂的任务的精确机制仍然难以捉摸，并且是各种假设的主题。从热力学角度来看，自由能分析可以成为确定货物可运输性的一种方法，因为通过 NPC 的交通必须朝着减少自由能的方向。在本研究中，我们开发了一个计算模型来评估由 FG-Nups 构象熵组成的自由能以及与 FG-Nups 和 NTR 之间的结合相互作用相关的能量增益，并研究这些物理特征是否可以作为 NPC 选择性的基础。我们的结果表明，通过将货物插入 NPC 中，构象熵的减少使自由能的增加量大大大于热能 (≫ k _B T )，而自由能的变化可以忽略不计 (< k _B T )小货物（尺寸小于约 6 nm），表明熵效应产生了尺寸依赖性选择性。我们的模型表明，熵诱导的 NPC 选择性敏感地依赖于物理参数，例如 FG-Nups 的灵活性和长度。另一方面，通过结合相互作用获得的能量有效地抵消了熵的减少，将可运输货物的尺寸限制增加到核孔径。我们进一步研究了结合点空间分布的几何效应，发现与分散的分布相比，聚集的结合点分布更有效地降低了自由能。