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The simulations show how the hexagonal helicase protein separates double strands into single strands along the DNA strand during replication
Just knowing the structure of a complex biological system is not enough to understand how it works
"These are dynamic processes that cannot be captured well by experimental methods alone," said Gao, an assistant professor of biological sciences and a CPRIT Cancer Research Scholar
Hexameric helicases have six ends and self-assemble from polypeptides into a washer-like loop that separates the parental DNA duplex into daughter single strands
The simulation results support the idea that the DNA-binding loops within the six subunits of the helicase form a sort of staircase that travels down the DNA backbone under the action of ATP hydrolysis, in which Stored chemical energy is released
ATP is known to be attracted to each subunit of the NTPase protein to drive the stepping motion
Because the helicase-DNA complex is so large, there have been only a few attempts to mimic the helicase going from one end of the chain to the other, the researchers noted
The simulations revealed several previously unknown intermediate states and identified interactions involved in the long-distance movement of the helicase
To search for this mechanism, the team focused on the T7 phage, a virus that infects bacteria and is often used as a model system
Both force fields are machine-learning-based coarse-grained molecular models that use only a fraction of the atoms in the system but still provide accurate results while greatly reducing computational time
It helps that T7 is only half the size of a human cellular helicase
Wolynes, associate director of the Centre for Theoretical Biophysics, said: "Because our new form of open3SPN2 deals with single-stranded DNA, it allows us to analyze the process by which normally double-stranded DNA opens in the presence of a helicase
"The cryo-EM structures we provide for these essential complexes are physiologically accurate, but these systems are dynamic," Gao said.
Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA
