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Research team models moving ‘rings’ that help DNA replicate

A helicase protein model created at Rice University shows a before-and-after of how the six-sided ring moves along DNA to cleave double strands into single strands in response to ATP hydrolysis during replication. Credit: Shikai Jin

Knowing the structure of a complex biological system is not nearly enough to understand how it works. It helps to know how the system moves.

In that light, researchers at Rice University have modeled a key mechanism by which DNA replicates.

By combining structural experiments and computer simulations, bioscientist Yang Gao, theoretical physicist Peter Wolynes, graduate student Shikai Jin and their colleagues have uncovered details about how helicases, a family of ring-like motor proteins, wrangle DNA during replication. Their work could reveal new targets for disease-fighting drugs.

The synergy between the experiments and large-scale simulations they describe in the Proceedings of the National Academy of Sciences could become a paradigm for modeling the mechanisms of many complex biological systems.

“These are dynamic processes that cannot be captured well with experimental methods alone,” said Gao, an assistant professor of biosciences and a CPRIT scientist in cancer research. “But it’s important to show the mechanisms of these helicases because they are essential for DNA replication and also for potential drug targets.”

Hexameric helicases have six sides that self-assemble from peptides into a ring-like ring that separates the parental DNA double strands into single daughter strands. So far, researchers have been unable to determine how the helicase will last as it unzips the double strand.

The Rice simulations support the idea that DNA-binding loops within the six subunits of the helicase form a sort of staircase that moves down the DNA backbone, driven by ATP hydrolysis, the process of releasing stored chemical energy in ATP molecules. .

It was known that ATP is attracted to NTPase proteins in each subunit to drive the step movement. But researchers hadn’t exactly understood that ATP hydrolysis is key. The Rice team found that ATP binds the helicase subunits tightly, but that hydrolysis significantly lowers the energy barrier to subunit disassociation, allowing the protein to step forward.

A simulation shows how a six-sided helicase protein moves along a DNA strand as it separates double strands into single strands during replication. Rice University theorists found that ATP hydrolysis is key to the stair-step movement of the proteins. A full step can be seen here. Credit: Yang Gao and Shikai Jin

The researchers noted that because the helicase-DNA complex is so large, there have been only a few attempts to simulate translocation of the helicase from one end of the strand to the other. The Rice hybrid of two coarse-grained simulation techniques provided the opportunity to study the process from start to finish.

The simulations revealed several previously unknown intermediate states and pinpointed the interactions involved in the long-range motion of the helicase. They showed that each step of translocation can travel more than 12 nucleotides along the backbone.

To look for the mechanism, the team focused on the T7 bacteriophage, a virus that infects bacteria often used as a model system. To simulate its helicase, known as gp4, the researchers combined two force fields: AWSEM, originally developed by Wolynes and his colleagues to predict how proteins fold, and open3SPN2, a DNA simulator developed by molecular engineer Juan de Pablo at the University. from Chicago. Force fields describe the forces that determine how atoms and molecules move when in contact. (The new combination of force fields was the subject of a Rice-led 2021 paper in PLOS Computational Biology.)

Both force fields are coarse-grained molecular machine learning models that use only a subset of the atoms in a system, yet provide accurate results while significantly reducing computation time.

“Combining the models enabled GPU acceleration, so we could run our molecular dynamic simulations very quickly,” Jin said. “The combined software is now 30 times faster than versions we used for other studies.”

It helps that T7 is half the size of helicases in human cells. “In human systems, there are six different polypeptide chains in the helicase, but in T7 it’s the same one that makes six copies,” he said.

“Because our new form of open3SPN2 deals with a single strand of DNA, we can analyze processes where the normal double-stranded DNA opens up as in the presence of the helicase,” said Wolynes, co-director of Rice’s Center for Theoretical Biological Physics. “The single-stranded DNA force field itself is new, but this was just background in this project, where it allows us to look at the process in detail.”

“The cryo-EM structures we have for these essential complexes are physiologically accurate, but these systems are dynamic,” Gao said. “They have to move to do their job, and there’s still a lot we want to know about how they do it.

“That’s where these computational models can make a big contribution and they will certainly be adapted to other large systems to explore quite important questions,” he said.


Researchers identify how the bacterial replicative helicase opens to start the DNA replication process


More information:
Shikai Jin et al, Computational study on the mechanism of bacteriophage T7 gp4 helicase moving along ssDNA, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2202239119

Provided by Rice University

Quote: Models of research teams moving ‘washers’ that help DNA replicate (2022, August 9,), retrieved August 9, 2022 from https://phys.org/news/2022-08-team-washers-dna-replicate.html

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