Nature Subjournal: Size-specific barriers to passive transport of proteins through the nuclear pore complex

In middle school biology class, we learn about the nucleus, the inner sanctuary of biological cells, where the genome and the cell's blueprint for making proteins exist together, which are the building blocks of
life.

The pores, known as nuclear pore complexes (NPCs), penetrate the membrane and act as cross-guards
for macromolecules moving in and out of the nucleus.
If the cross-guard fails, it can lead to human diseases such as cancer, viral infections and neurodegenerative diseases
.

The nuclear pore complex mechanism was discovered

Now researchers have identified for the first time a new mechanism
for the passive transport of biomolecules in nuclear pore complexes.
The work was published in
the journal Nature Communications.

The team developed their NPC model through supercomputer simulations on the Frontera and Stampede2 systems at the Texas Advanced Computing Center (TACC), and hopes their work will help guide the development of
future therapies.

David Winogradoff, co-author of the study, said: "Our main finding is that the reticular interior of the nuclear pore exhibits a conversion behavior based on protein size, shifting from a soft barrier for small proteins to a hard barrier that exceeds a certain threshold, essentially making it difficult for proteins to pass through
.
"

Winogradoff completed the research as a postdoctoral research assistant in collaboration with Professor
Aleksei Aksimentiev of the Department of Physics at the University of Illinois at Urbana-Champaign.
He is now a computational polymer chemist
at the U.
S.
Food and Drug Administration.

Develop the model

Winogradoff's team used brute force simulations to study the transport dynamics of nuclear pores on timescales of tens of milliseconds, a remarkable achievement
for a system nominally 200 million atoms.

To do this, they combined several existing models, in particular the coarse-grained model
developed by the Onck group at the University of Groningen.
In contrast to all-atom simulations, coarse-grained simulations address the disordered dynamics of only groups of atoms, while all-atom simulations address the interaction
of each atom.

The nuclear envelope model was also obtained
by cryo-electron microscopy data from two different scaffold structures (the composite structure of Lynn2016 and the yeast structure of Kim2018).

"In a way, the model itself is an independent achievement," Aksimentiev said
.

"In the coarse-grained model, we see proteins being transported
spontaneously through this fluctuating filamentous grid that extends to the cytoplasm.
It's very, very difficult to probe with all-atomical methods," Aksimentiev added
.

From these unbiased simulations, the team observed rare fast crossover events
.

"We observed a shift in the size of the protein, from always having a continuous path to a continuous path connecting the top and bottom of the nuclear pore through a central channel is very rare
," Winogradoff said.

Supercomputer resources

The graphics processing unit (GPU) node on TACC's Frontera supercomputer runs software
called Atomic Resolution Brownian Dynamics (ARBD) developed by Aksimentiev Labs.

In addition, the scientists used TACC's Stampede2 and the University of Illinois at Urbana-Champaign's Blue Water System, both of which were granted by the National Science Foundation (NSF)-funded Advanced Network Infrastructure Coordinated Ecosystem: Services and Support (ACCESS), formerly known as the Extreme Science and Engineering Discovery Environment (XSEDE).

"What really helped us access the resources of Frontera and Stampede2 was that we were able to model a wide range of protein sizes
," Winogradoff said.
"It speeds up the process and it only takes a few days instead of months from local resources
.
" Being able to run multiple copies in different conditions made our results more robust
.
He added
.

The simulations were conducted during TACC's "Texascale Day," in which selected teams were granted full access
to the Frontera system.
The Frontera system is a flagship computer funded by the National Science Foundation and is currently the top academic supercomputer in any university in the United States

Winogradoff's team extended their NAMAD simulation of an all-atom nuclear pore system to about half of Frontera's nodes, totaling about 250,000 processors
.

Potential drug treatments and next steps

"In many ways, I think this study can provide some guidelines for future treatment development," Winogradoff said
.

The goal of cutting-edge emerging technologies is to deliver drug treatments directly into the nucleus, which is difficult to reliably cross.

"This study can provide information about drug cargo size thresholds and whether transportation involving other proteins needs to be facilitated if the cargo is too large
," Winogradoff said.

According to Aksimentiev, this work is a first step
toward the long-term goal of studying how the nucleus works.
His lab is conducting all-atom simulations, which include a variety of proteins, mimicking the real, high-density protein environment
inside living cells.

Aksimentiev concludes: "A supercomputer is a unique tool that allows you to see what individual atoms are doing
.
From this, you can see how the behavior of individual atoms is projected onto the properties of
larger molecular machines.
This is something
that we can only do with supercomputers at the moment.
”