Free energy calculations shed light on the nuclear pore complex’s selective barrier nature

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(B)T), whereas the free energy change was negligible (<k(B)T) 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.