Supercomputer Draws Molecular Blueprint For Repairing Damaged DNA

Using the Summit supercomputer at the Department of Energy's Oak Ridge National Laboratory, researchers have modeled a key component of nucleotide excision repair (NER) called the pre-incision complex (PInC), which plays a crucial role in DNA damage repair. Their study, published in Nature Communications, provides new insights into how the PInC machinery orchestrates precise DNA excision, potentially leading to advancements in treating genetic disorders, preventing premature aging, and understanding conditions like xeroderma pigmentosum and Cockayne syndrome. Phys.Org reports: "Computationally, once you assemble the PInC, molecular dynamics simulations of the complex become relatively straightforward, especially on large supercomputers like Summit," [said lead investigator Ivaylo Ivanov, a chemistry professor at Georgia State University]. Nanoscale Molecular Dynamics, or NAMD, is a molecular dynamics code specifically designed for supercomputers and is used to simulate the movements and interactions of large biomolecular systems that contain millions of atoms. Using NAMD, the research team ran extensive simulations. The number-crunching power of the 200-petaflop Summit supercomputer -- capable of performing 200,000 trillion calculations per second -- was essential in unraveling the functional dynamics of the PInC complex on a timescale of microseconds. "The simulations showed us a lot about the complex nature of the PInC machinery. It showed us how these different components move together as modules and the subdivision of this complex into dynamic communities, which form the moving parts of this machine," Ivanov said.

The findings are significant in that mutations in XPF and XPG can lead to severe human genetic disorders. They include xeroderma pigmentosum, which is a condition that makes people more susceptible to skin cancer, and Cockayne syndrome, which can affect human growth and development, lead to impaired hearing and vision, and speed up the aging process. "Simulations allow us to zero in on these important regions because mutations that interfere with the function of the NER complex often occur at community interfaces, which are the most dynamic regions of the machine," Ivanov said. "Now we have a much better understanding of how and from where these disorders manifest."

I would not mind living forever.

[ndsurvivor]

"They" say it is boring, but I would like to have the opportunity.

Re: I would not mind living forever.

[PsychoSlashDot]

See, I've always looked at it as not being all-or-nothing. I'd like to live... until I don't want to anymore.

Re:

[evil_aaronm]

"Into Thy Hands" is an early sci-fi story where one of the SA-10 robots realizes that he's done his job restoring the humans after the inevitable nuclear war, and shuts himself off. I've always found that poignant.

Re:

[PsychoSlashDot]

"The Last Command" is a short-story by Keith Laumer in his Bolo setting. Basically massive sentient main battle tanks. In this story, one wakes up, realizes it's buried and badly damaged, virtually every resource depleted or destroyed. It forces its way to the surface, gets no answer on brigade frequencies, decides it's been subject to a sneak-attack, and starts heading for a city it sees in the distance. It's more than a little radioactive. An extremely elderly war vet sees news footage of this thing

Re:

[nightflameauto]

"They" say it is boring, but I would like to have the opportunity.

As interested as I would be in where we're headed in the distant future, I'm not real sure I want to live through the bullshit era we're currently embroiled in to get there. Living forever sounds like it'd be fun on the surface, but only if you have some form of hope that there's going to be something to do other than continue to be a slave to a system that doesn't give a fuck about the individual cogs making up the machine. If I get the forever cure and just have to stay chained to a desk for 10 hours a da

Can't wait to see Bryan Johnson

[fishfrys]

get his hands on a crispr and a supercomputer. Clearly he risks getting drawn into the rabbit hole of endless nocturnal erections, but there's a lot of potential here.

A major win for longevity research

[LondoMollari]

This is a big win for IBM, who designed and built the Summit supercomputer, especially if this turns out to be a keystone longevity discovery.

Wow! What nonsense!

[methano]

Somebody does a molecular dynamics simulation on a supercomputer, probably using a force field model, and they're predicting "advancements in treating genetic disorders, preventing premature aging, and understanding conditions like xeroderma pigmentosum and Cockayne syndrome." That's about as big a bullshit reach as I've ever seen.

I think maybe someone has "Crockayne syndrome".

Re: Wow! What nonsense!

[PsychoSlashDot]

With research, there's always the "what's it good for" crew. At most stages application is either impossible or unclear yet, but there's always a general aim. Including that in a press release is important.