Transcription factor IIH, or TFIIH, pronounced «TF two H,» is a real feature among the protein complexes that control human cell activity. It plays an important role in both transcription—the highly regulated synthesis of RNA from a DNA template—and in the repair of damaged DNA. But how can one set of proteins be involved in two such wildly different and critically important genomic tasks?
A team of researchers led by Georgia State University chemistry professor Ivaylo Ivanov used the Summit supercomputer at the Department of Energy’s Oak Ridge National Laboratory to help answer that question. By conducting multiple molecular dynamics simulations of TFIIH in states capable of DNA transcription and repair, and then contrasting the structural mechanisms at work, Ivanov and his team made a discovery. Interesting discovery: TFIIH is a morphing tool that reconfigures itself to meet the requirements of each mission.
Elucidating the inner workings of TFIIH at the DNA repair and transcription interface is key to understanding the origins of mutation-induced genetic disorders—genetic diseases such as xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome. The GSU team published its results in the journal natural communication.
«This project illustrates how versatile protein combinations can be, given their participation in very different cellular processes,» said Ivanov. «Understanding how genetic mutations impair TFIIH function is the first step. in the design of therapeutic strategies such as gene editing».
The project’s findings are just the latest in Ivanov’s ongoing research into the molecular mechanisms of gene expression using supercomputers at the Oak Ridge Leadership Computing Facility, the user base of the Office of Science. DOE at ORNL.
Initiation of transcription versus DNA repair
The structure of TFIIH was mapped via cold electron microscopy, but to understand its functional dynamics during transcription initiation and DNA repair, the GSU team needed dynamic modeling. large scale system of nearly 2 million atoms—with multiple copies running concurrently.
«We often rely on copy-chain simulations to characterize large-scale conformational changes in biomolecular complexes,» says Ivanov. «To do these types of simulations, you must be able to run multiple copies of the emulation system at the same time. This is only possible if you have a large number of GPU nodes available, such as on Summit. In one case, we used about 70 replicas, so the computational cost to characterize any of these mechanisms adds up very quickly.»
TFIIH is an integral component of the pre-transcriptional initiation complex, or PIC, a set of proteins important for gene expression that Ivanov and his team also previously modeled on Summit. As the name implies, PIC helps trigger the transcription process in which the DNA sequence of a gene is copied into messenger RNA. The mRNA then transfers that genetic information into the cytoplasm of the cell, where it is translated into a protein, thereby allowing it to begin performing a coding function, such as preventing disease or providing energy.
«TFIIH is part of a molecular motor assembly that uncoils duplex DNA at a specific location in the genome and pushes it towards the active site of RNA polymerase. Without this initial DNA uncoils to expose the template sequence, the transcription will actually ‘inactive’,» says Ivanov.
Transcription factor IIH is also a key component of the protein machinery that performs nucleotide excision repair—a flexible DNA repair pathway that eliminates a wide range of genomic damage caused by things like ultraviolet light, methods chemotherapy treatment and exposure to environmental carcinogens.
The team focused on how two subunits of TFIIH, XPB and XPD, work differently to reshape DNA. XPB and XPD sit at the edges of TFIIH’s horseshoe complex. At the start of transcription, the horseshoe has an open conformation with XPB serving as the active component of DNA disassembly. Meanwhile, XPD fulfills a purely structural role—DNA is directed away from it and its DNA binding groove is blocked.
«XPD is regulated in a way that prevents it from processing DNA,» said Ivanov. its».
However, when scanning for lesions during DNA repair—nucleotide excision repair or transcription-coupled NER—TFIIH adopts a closed conformation and the roles of XPB and XPD are reversed.
“Previously, we dynamically modeled TFIIH in the PIC, which allowed us to partition the assembly into functional modules,” says Ivanov. «Interestingly, we found that the interfaces between functional modules contain most of the disease-associated TFIIH mutations. However, at the time, we did not have simulations of the state. modality is capable of nucleotide excision repair—and that provides an incomplete picture of what TFIIH does in DNA repair.»
The new, detailed picture of the mechanistic dynamics of TFIIH provides insights into the key movements that allow TFIIH to upregulate DNA during transcription initiation versus nucleotide excision repair. This can be useful information in finding treatment for genetic disorders.
«Innovative computational methods, such as those described in this report, come to life,» said Manju Hingorani, program director at the National Science Foundation’s Director of Biological Sciences. static images of biological machines and enriching dynamic views of how they work». «In this case, the new knowledge of how protein complexes reconfigure and self-regulate to enable repair of damaged DNA and restore cellular function may explain defects in this process. how to cause disease.»
Dynamic structural analysis
The GSU team used a graph algorithm to partition the TFIIH’s protein network into tightly connected components, thereby allowing them to identify dynamic modules—parts that move together. In turn, these models show how modules move with respect to other parts of the structure.
«We can now compare and contrast the functional dynamics of TFIIH when it is active during transcription versus when it is active during nucleotide excision repair,» said Ivanov. «Suddenly, you see communities that were previously locked together begin to open up and engage in movements that you couldn’t have foreseen from just looking at the copy-authority state.»
Researchers can also map different types of information onto the protein network model, such as dynamic correlations or exposure probabilities. This allows them to focus on the critical interfaces that are changing during the respective structural transformation and analyze them in detail. It is then possible to classify mutants of different disease phenotypes based on their position in the structure of TFIIH and their dynamic role.
“Having these different dynamic populations in the case of transcription versus the authoritative state of NER, you can do a very detailed analysis of how the patient mutations for the Various genetic disorders are localized to the dynamic communities we have identified.” «Essentially, it is possible—by understanding the transcriptional and NER mechanisms in TFIIH—to direct its function toward one pathway or another.»
More information:
Jina Yu et al, Dynamic conformational switching underlies TFIIH function in DNA transcription and repair and impact on genetic diseases, natural communication (2023). DOI: 10.1038/s41467-023-38416-6
Journal information:
natural communication
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