They mimic the behavior of a living small cell in 3D – Science – Life

A scientific team led by Dr University of Illinois Urbana-Champaign (USA) has built a file live small cell With a genome reduced to the most important, a computer model of the cell reflects its behaviour.

The authors of this work, published this week in the journal Cell, note that they are developing a system for predicting how changes in genomes, living conditions or physical properties of living cells alter their functions.

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Its minimum cells genome “Reduced cells that carry the genes needed to replicate their DNA, grow, divide, and perform most of the other functions that define life,” says Zane (Zann) Luthy Schulten, a professor of chemistry at American University, who led the work. With graduate student Zane Thornberg.

“What is new is that we have developed 3D Kinetic Model and quite dynamic for a small living cell that mimics what happens in a real cell,” adds Luthey-Schulten.

The developed simulations map the exact location and chemical properties of thousands of cellular components in 3D at the atomic scale. You can see how long it takes for these molecules to travel through the cell and find each other, what kind of chemical reactions take place when they happen, and how much energy is needed for each step, the university explained in a statement.

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To build the miniature cell, researchers at the J. Craig Venter Institute (JCVI) in La Jolla, California, turned to the simplest of living cells: Mycoplasma, a genus of bacteria that parasitizes other organisms.

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In previous studies, JCVI scientists created an artificial genome that was missing as many nonessential genes as possible and grew the cell in an environment rich in all the nutrients and factors needed to maintain it.

In the new work, the team added some genes again to improve cell viability. This is simpler than any normal cell, so it is easier to design it on a computer.

Data from decades of research

According to Luthey-Schulten, “Simulation of something as complex as a living cell relies on data from decades of research. To build the computer model, she and her colleagues took into account the physical and chemical properties of the cell’s DNA, lipids, amino acids, and the machinery of gene transcription, translation, and protein construction.” “.

To build the computational model, she and her colleagues needed to consider the physical and chemical properties of a cell’s DNA, lipids, amino acids, gene transcription, translation, and protein building mechanisms.

They also had to model how each component propagated through the cell, keeping track of the energy needed for each step of the cell’s life cycle. NVIDIA GPUs were used to run the simulations.

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“We built a computer model based on what we know about the small cell, then ran simulations, and also checked whether our simulated cell behaves like the real thing,” explains Thornburg.

The simulations allowed the researchers to understand how “a real cell balances the demands of metabolism, genetic processes, and growth,” says Lothi Schulten.

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Why do cells use most of their energy?

For example, the model revealed that the cell used most of its energy to import ions and essential molecules through the cell membrane. “This makes sense because mycoplasma gets most of what it needs to survive from other organisms,” says the researcher.

The simulations also allowed Thornburg to calculate the normal lifespan of messenger RNA, the genetic blueprints for building proteins. They also revealed a relationship between the rate of membrane lipidation and protein synthesis and changes in membrane surface area and cell volume.

“We simulate all of the chemical reactions inside a small cell, from its birth until the moment it divides two hours later,” Thornberg details, and from there, we get a model that tells us how it works and how we can make it more complex to change their behaviour.

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Luthey-Schulten insists that his team has developed “a fully dynamic 3D kinematic model of a small living cell, which opens a window into the inner workings of the cell, and shows us how all the components interact and change in response to internal and external signals.”

The researcher concludes that “this model – and others that are more complex – will help us better understand the basic principles of life.”

Sync Agency

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