SuperComputer draws molecular blueprints to repair damaged DNA

Sunburn and aging skin are the obvious effects of exposure to harmful UV rays, tobacco smoke and other carcinogens. However, the effect is not just on the skin. In the body, DNA is literally torn apart.

Understanding how the body heals, protects and protects against DNA damage is essential for treating life-threatening diseases such as cancer. However, despite many research and medical advances, much of the molecular mechanisms of DNA repair remains a mystery.

Over the past few years, researchers at Georgia State University have tapped onto the Summit Supercomputer at the Department of Energy’s Oak Ridge National Laboratory to study an elaborate molecular pathway called nucleotide excision repair (NER). NER relies on an array of highly dynamic protein complexes to cleave damaged DNA with surgical accuracy.

In the latest research published in Nature Communications, the team built a computer model of a critical NER component called the Pre-Incision Complex or PINC. PINC plays an important role in regulating the DNA repair process during the late stages of the NER pathway. Deciphering the role of PINC in a sophisticated set of events and pathways in NER can provide important insights into the development of new treatments and preventing conditions leading to premature aging and certain types of cancer.

Prime Minister Ivaylo Ivanov, professor of chemistry at Georgia State University, said: “NER is a versatile pathway that uses a three-step process that relies on delicately balanced molecular machines to repair all sorts of different DNA damage. Unfortunately, harmful mutations can interfere with this machine and cause severe human disease.”

“However, the effects of genetic mutations can vary significantly depending on their location within the repair complex. In some cases, mutations are predisposed to UV light sensitivity and extreme cancer. In other cases, they cause abnormal development and premature aging.” “Why this happens is not fully understood at the molecular level. That’s the mystery our computer modeling efforts aim to unravel.”

Three actions of repair

NER unfolds in three different stages: recognition, verification and repair. Each stage requires different protein groups to perform certain functions, such as the trauma team has the various specialists needed to treat injured patients in the emergency room. In this way, the NER machine can adapt and change its shape according to the task at hand.

In the first stage, the NER protein XPC (XeRoderma pigtmentosum Group C) acts like a first responder identifying the site of the damaged DNA or lesion, twisting the DNA helix to allow access to the damage. XPC calls other repair proteins to help in the initiation of a second stage called damage verification or lesion scan.

Here, the NER protein machinery shifts to the following shape: When XPC recedes, a protein complex called transcription factor IIH or TFIIH (pronounced TF-2-H) moves to position. TFIIH further releases sections of DNA and scans newly exposed strands for lesions.

Then it is in the hands of the surgeon at the third and final stages of repair.

Once the “patient” is steady and prepared for surgery, surgery can be started to remove damaged DNA strands. Two enzymes, XPF and XPG (XeRoderma pigtmentosum groups F and G), place precisely on either side of the lesion and act as molecular scissors to cut out damaged segments of DNA.

Once the lesion is removed, new DNA is synthesized to fill the remaining gaps. Finally, the DNA backbone is sealed and damaged DNA is returned to health.

“What we want to know is how PINCs are formed after the lesion scanning stage,” Ivanov said. “How do you control the position of the two enzyme subunits that perform double incisions of damaged DNA strands? And importantly, is there crosstalk between the two enzymes? Do they feel each other?”

“It’s important that once a damaged DNA strand is cut, the repair process is completed by filling that gap,” he added. “If not, it leads to cell death or the introduction of double-stranded rests. These are extremely harmful to the cells.”

To answer these questions, researchers had to resolve the structure of PINC. In biology, understanding protein structure is essential for understanding the behavior or function of protein assemblies. The shape, size, and interaction of proteins determine how they fit to form large biomolecular assemblies.

“We integrated the structural model of PINC using a variety of biophysical methods, particularly data from ultra-low electron microscopy,” Ivanov said. “But in the end, calculations are what brings it all together.”

Just like the jigsaw puzzle fragments, the PINC model had to be assembled from known structures of constituent proteins, and all individual pieces had to be combined into 3D. However, many of the PINC components had no known experimental structures.

To overcome this challenge, researchers used a neural network-based model called Alphafold2 to predict unknown structures and interfaces between proteins that group PINCs together.

The final simulation of the summit

“Computationally, assembling PINCs makes molecular dynamics simulations of complexes relatively easy, especially on large-scale supercomputers like Summit,” Ivanov said.

Nanoscale Molecular Dynamics (NAMD) is a molecular dynamics code specifically designed for supercomputers and is used to simulate the movement and interaction of large biomolecular systems containing millions of atoms. Using NAMD, the research team performed a large-scale simulation. The numerical power of the 200 Petaflop Summit supercomputer can perform 200,000 trillion calculations per second, but was essential to elucidating the functional dynamics of pink complexes on a microsecond timescale.

“The simulations showed a lot about the complex nature of the pink machine. They show how these different components move as modules and sub-sections of this complex, forming the moving parts of this machine,” Ivanov said.

The findings are important in that XPF and XPG mutations can lead to severe human genetic disorders. They include xeroderma pigmentosa, a condition that makes them susceptible to skin cancer, and Cocaine syndrome, which can affect human growth and development, lead to hearing and vision loss, and speed up the aging process.

“Simulations allow zeros to be placed in these critical regions, because mutations that hinder the function of the ner complex often occur in the community interface, the most dynamic region of the machine,” Ivanov said. “Now we have a better understanding of how and where these obstacles emerge.”

Most of the molecular dynamics simulations were performed at the summit. However, after six years of production, the Summit retired at the end of 2024.

Ibanov and his team will use Frontier, the successor to the summit.

Their research at the frontier includes examining transcriptional conjugated NERs. This is a DNA repair process that corrects damage to actively transcribed genes, allowing essential proteins to continue to be produced.

In addition to Ivanov, the research team includes Zina Yu, Chunli Yang, Tanmoy Paul and Lucas Brewer of Georgia State University. Susan E. Tsutakawa and John A. Tenner of Lawrence Berkeley National Laboratory. Cheerinzeye from the University of Texas MD Anderson Cancer Center. Samir M. Hamdan of King Abdullah University of Science and Technology.