PhD Candidate, University of California, Berkeley


Computational data-driven model of the biophysical properties of the nuclear pore complex

The nuclear pore complex (NPC) is the sole gateway between the cytoplasm and intra-nucleus space in eukaryotes. Thousands of NPCs sit on the nuclear envelope, directing the proteins and RNA family transport into and out of the nucleus in a process known as nucleocytoplasmic transport (NCT). The importance of the NPC function lies in the fact that the cellular genomes are encapsulated by the nuclear envelope, and so, it is extremely important to control the material transport into and out of the nucleus. If a harmful agent, a retrovirus like HIV for example, can bypass the NPC and enters the cell nucleus, it would endanger the cell viability and would lead to lethal consequences. Because of its importance in gating the heart of the life, the NPC has been subject to numerous research studies in the past four decades. However, the selective gating mechanism underlying NCT is still poorly understood and it is not known how the NPC regulates transport with such a high efficiency and specificity.This uncertainty originates from 1) a lack of high spatiotemporal information of what is happening inside the NPC channel and 2) the limited knowledge of the biophysical aspects of the selective gating mechanism. Moreover, in recent years it has been hypothesized that the NPC might also play a role in keeping the mechanical integrity of the cell nucleus by physically connecting the inner- and outer nuclear membranes. To address these uncertainties, I have developed a computational data-driven model with a high spatiotemporal resolution of the nuclear pore complex. The model mimics the physiological conditions and provides an unprecedented micro-dynamical insight into the NCT process. It also enables us to look into the mechanical properties of the NPC structure with a high spatiotemporal resolution. The model has been established and the related results and model predictions have been published in several peer-reviewed journals, including, Nature Scientific Reports, Biophysical Journal, PLoS Computational, PLoS ONE, and Biomat. Science & Engineering.


Brownian dynamics simulation of nucleocytoplasmic transport: a coarse-grained model for the functional state of the nuclear pore complex.

Abstract: The nuclear pore complex (NPC) regulates molecular traffic across the nuclear envelope (NE). Selective transport happens on the order of milliseconds and the length scale of tens of nanometers; however, the transport mechanism remains elusive. Central to the transport process is the hydrophobic interactions between karyopherins (kaps) and Phe-Gly (FG) repeat domains. Taking into account the polymeric nature of FG-repeats grafted on the elastic structure of the NPC, and the kap-FG hydrophobic affinity, we have established a coarse-grained model of the NPC structure that mimics nucleocytoplasmic transport. To establish a foundation for future works, the methodology and biophysical rationale behind the model is explained in details. The model predicts that the first-passage time of a 15 nm cargo-complex is about 2.6±0.13 ms with an inverse Gaussian distribution for statistically adequate number of independent Brownian dynamics simulations. Moreover, the cargo-complex is primarily attached to the channel wall where it interacts with the FG-layer as it passes through the central channel. The kap-FG hydrophobic interaction is highly dynamic and fast, which ensures an efficient translocation through the NPC. Further, almost all eight hydrophobic binding spots on kap-β are occupied simultaneously during transport. Finally, as opposed to intact NPCs, cytoplasmic filaments-deficient NPCs show a high degree of permeability to inert cargos, implying the defining role of cytoplasmic filaments in the selectivity barrier.

Pub.: 16 Jun '11, Pinned: 29 Jun '17

Biophysical coarse-grained modeling provides insights into transport through the nuclear pore complex.

Abstract: The nuclear pore complex (NPC) is the gatekeeper of the nucleus, capable of actively discriminating between the active and inert cargo while accommodating a high rate of translocations. The biophysical mechanisms underlying transport, however, remain unclear due to the lack of information about biophysical factors playing role in transport. Based on published experimental data, we have established a coarse-grained model of an intact NPC structure to examine nucleocytoplasmic transport with refined spatial and temporal resolutions. Using our model, we estimate the transport time versus cargo sizes. Our findings suggest that the mean transport time of cargos smaller than 15 nm is independent of size, while beyond this size, there is a sharp increase in the mean transport time. The model confirms that kap-FG hydrophobicity is sufficient for active cargo transport. Moreover, our model predicts that during translocation, small and large cargo-complexes are hydrophobically attached to FG-repeat domains for 86 and 96% of their transport time, respectively. Inside the central channel FG-repeats form a thick layer on the wall leaving an open tube. The cargo-complex is almost always attached to this layer and diffuses back and forth, regardless of the cargo size. Finally, we propose a plausible model for transport in which the NPC can be viewed as a lubricated gate. This model incorporates basic assumptions underlying virtual-gate and reduction-of-dimensionality models with the addition of the FG-layer inside the central channel acting as a lubricant.

Pub.: 16 Mar '11, Pinned: 29 Jun '17

Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex.

Abstract: Conformational behavior of intrinsically disordered proteins, such as Phe-Gly repeat domains, alters drastically when they are confined in, and tethered to, nan channels. This has challenged our understanding of how they serve to selectively facilitate translocation of nuclear transport receptor (NTR)-bearing macromolecules. Heterogeneous FG-repeats, tethered to the NPC interior, nonuniformly fill the channel in a diameter-dependent manner and adopt a rapid Brownian motion, thereby forming a porous and highly dynamic polymeric meshwork that percolates in radial and axial directions and features two distinguishable zones: a dense hydrophobic rod-like zone located in the center, and a peripheral low-density shell-like zone. The FG-meshwork is locally disrupted upon interacting with NTR-bearing macromolecules, but immediately reconstructs itself between 0.44 μs and 7.0 μs, depending on cargo size and shape. This confers a perpetually-sealed state to the NPC, and is solely due to rapid Brownian motion of FG-repeats, not FG-repeat hydrophobic bonds. Elongated-shaped macromolecules, both in the presence and absence of NTRs, penetrate more readily into the FG-meshwork compared to their globular counterparts of identical volume and surface chemistry, highlighting the importance of the shape effects in nucleocytoplasmic transport. These results can help our understanding of geometrical effects in, and the design of, intelligent and responsive biopolymer-based materials in nanofiltration and artificial nanopores.

Pub.: 30 Jul '16, Pinned: 29 Jun '17