Science & Technology

Cellular environment shapes molecular structure

The model of the human nuclear pore complex represents the major proteins that make up the three rings of pores. From top to bottom: The cytoplasmic ring is blue and yellow. The inner ring is orange and pink. The nucleoplasmic ring is light blue and gold. Credit: Anthony Schuller

Researchers collect a more complete picture of the structure, called the nuclear pore complex, by studying it directly inside the cell.

Context is important. It applies to many aspects of life, including small molecular machines that perform important functions within our cells.

Scientists often purify cellular components, such as proteins and organelles, to individually examine them.However, a new study published in the journal on October 13, 2021 Nature This method indicates that the component in question can change significantly.

Researchers have devised a way to study large donut-shaped structures called nuclear pore complexes (NPCs) directly inside the cell. Their results reveal that the pores have larger dimensions than previously thought, emphasizing the importance of analyzing complex molecules in their natural environment.

“We have shown that the cellular environment has a significant impact on large structures like NPCs, which was unexpected when we started,” said Thomas Schwartz, a professor of biology at Boris Magasanik. I am. MIT And co-lead author of the study. “Scientists generally thought that large molecules were stable enough to maintain basic properties both inside and outside the cell, but our findings turned that assumption into their heads. I am. “

In eukaryotes like humans and animals, most cells DNA It is preserved in a rounded structure called a nucleus. This organelle is protected by the nuclear envelope. The nuclear envelope is a protective barrier that separates genetic material in the nucleus from the thick fluid that fills the rest of the cell. However, the molecule still needs a way to get in and out of the nucleus to facilitate important processes involving gene expression. That’s where NPCs come in. Hundreds, or even thousands, of these pores are embedded in the nuclear envelope, creating a gateway through which specific molecules can pass.

Former MIT postdoc Anthony Schuller, the lead author of this study, compares NPCs to sports stadium gates. “If you want to access the games inside, you have to show your ticket and go through one of these gates,” he explains.

Details of the nuclear pore complex

CR = cytoplasmic ring
IR = inner ring
NR = nucleoplasmic ring

NPCs may be small by human standards, but they are one of the largest structures in a cell. It is composed of about 500 proteins, which makes it difficult to analyze its structure. Traditionally, scientists have broken it down into individual components and studied them fragmentarily using a method called X-ray crystallography. According to Schwartz, the technology needed to analyze NPCs in a more natural environment has only recently become available.

Together with researchers at the University of Zurich, Schuller and Schwartz have taken two cutting-edge approaches to solving the structure of the pores. Cryo Focused Ion Beam (cryo-FIB) Milling and Cryo Electron Tomography (cryo-ET).

The entire cell is too thick to be seen under an electron microscope. However, researchers used cryo-FIB devices housed at MIT.nano’s Center for Cryogenic Electron Microscopy and the Peterson (1957) Nanotechnology Materials Core Facility at the Koch Institute for Integrative Cancer Research to extract frozen colon cells. Sliced ​​into thin layers. By doing so, the team captured a cross section of the cell containing the NPC, rather than simply looking at the NPC in isolation.

“The amazing thing about this approach is that we rarely manipulate cells,” says Schwartz. “We are not disrupting the internal structure of the cell. That is the revolution.”

What researchers saw when looking at microscopic images was quite different from the NPC’s existing description. They were surprised to discover that the innermost ring structure, which forms the central channel of the pores, is much wider than previously thought. When left in the natural environment, the pores open up to 57 nanometers. The result is a 75% increase in volume compared to previous estimates. The team was also able to explore in detail how the various components of the NPC work together to define the dimensions of the pores and the overall architecture.

“We’ve shown that the cellular environment affects NPC structure, but now we need to understand how and why,” says Schuller. Not all proteins can be purified, so the combination of cryo-ET and cryo-FIB is also useful for testing various other cellular components. “This dual approach unlocks everything.”

“This paper is a good example of how technological advances, in this case cryo-electron tomography of human cells ground with a cryo-focused ion beam, provide a fresh image of the cell structure,” said RWTH Aachen, Germany. Wolfram Antonin, a professor of biochemistry at the university, said. I was not involved in the study. The fact that the diameter of the central transport channel of NPCs is larger than previously thought suggests that the pores may have impressive structural flexibility. “This may be important for the cells to adapt to their increasing transport demand,” explains Antonin.

Next, Schuller and Schwartz want to understand how the size of the pores affects which molecules can pass through. For example, scientists have recently determined that there are pores large enough for an intact virus, such as HIV, to enter the nucleus. The same principle applies to treatment. Only drugs of the right size with specific properties can access the DNA of cells.

Schwartz is particularly interested in knowing if all NPCs are created the same, or if their structure depends on the species and cell type.

“We constantly manipulated cells and removed individual components from their original context,” he says. “Now we know that this method can have far greater consequences than we expected.”

Reference: “Cell environment forms the structure of nuclear pore complex” Anthony P. Schuller, Matthias Wojtynek, David Mankus, Meltem Tatli, Rafael Kronenberg-Tenga, Saroji G. Regmi, Phat V. Dip, Abigail KR Lytton-Jean, Edward J. Brignole, Mary Dasso, Karstenweiss, Ohad Medalia, Thomas U. Schwartz, October 13, 2021 Nature..
DOI: 10.1038 / s41586-021-03985-3

Cellular environment shapes molecular structure Cellular environment shapes molecular structure

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