Biological complexity: coiling DNA in chromosomes (Introduction)

by David Turell , Saturday, January 04, 2020, 00:13 (1786 days ago) @ David Turell

Protein snake-like cords seem to do the job:

https://phys.org/news/2020-01-snake-like-proteins-wrangle-dna.html

"Members of Rice's Center for Theoretical Biological Physics (CTBP) are taking a deep dive into the dynamics of essential proteins that help DNA fold into its compact, functional form in chromosomes. They found a key protein's "coiled coils" also braid around each other and writhe like snakes as they form bigger loops in the DNA.

"The loops, in turn, bring together sites on DNA that regulate the transcription of genetic messages. While the loops and their functions are becoming better understood, until now nobody has been able to take a close look at the condensin and cohesin proteins that wrangle the DNA into shape.

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"...structural maintenance of chromosomes (SMC) proteins may actively manage DNA through a novel mechanism.

"They found these proteins have ring-shaped lassos that consist of two 35-nanometer long protein coiled coils. These terminate on one end in a pair of "head unit" motors that bind to DNA coils, and on the other in "hinges" thought to open and close to entrap the strands.
The lab's simulations showed these coiled coils are anything but limp lariats.

"'We already knew the coiled coils have some sort of structural importance, but what we saw is that these long coils are quite active," Krepel said. "We're still investigating to what extent, but as we ran the simulations, we saw that the coils want to come together, kind of like headphones that get all twisted when you put them in your bag. We saw the twist right away."

"'Braiding is the word we use," Wolynes added. "People thought the coiled coils were simply hanging out, but they didn't think they'd coil again on top of each other in an organized fashion.

"'One of the key ideas of DNA physics is that DNA operates by changing its degree of coiling and its topology," he said. "Well, braiding is a topological feature. We think we see that the topology of the protein can interact with the topology of the DNA much as threads entwine with each other on a spinning wheel."

"Krepel noted the SMC proteins are positively charged, and DNA is negatively charged. "We're looking at how these positive and negative charges potentially play together," she said. "It seems clear the coils would almost certainly braid themselves around the DNA using these charge patterns," Wolynes said.

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"The models further suggested that the ATPase motors that bind DNA can twirl the braids.

"'We're still guessing at the details, but we think when the two motors are both twisting to extrude DNA into loops, one untwisting and the other uptwisting, the lassos could transfer twisting of the coils into twisting around the DNA," Wolynes said. "The coils aren't just passively hanging there. They're much more involved in the process than we thought.'"

Comment: Yet again we see protein molecules that act like they know what they are doing. They are controlled by the way they automatically fold and the way they are attracted by electrical charges, among other attributes. Protein molecules cannot think. And this is the key to understanding how cells work through automatically reacting molecules.