Researchers create the most complete model of complex protein machinery

Environmental conditions, lifestyle choices, exposure to chemicals, and foodborne and atmospheric pathogens are among the external factors that can cause disease. In contrast, internal genetic factors may be responsible for the onset and progression of diseases ranging from degenerative neurological disorders to certain cancers.

A team led by Ivaylo Ivanov of Georgia State University used the IBM AC922 Summit system at 200 petaflops, the world's smartest and most powerful supercomputer, to develop an integrative model of the transcriptional preinitiation complex (PIC), a complex of proteins essential for gene expression. . The results of this work are published in Nature Structural and Molecular Biology.

Gene expression involves the conversion of genetic information derived from DNA to produce functional molecules such as proteins, constituent elements of all living organisms, through steps known as transcription and translation. Since gene mutations can interfere with gene expression and cause disease, biomedical scientists are particularly interested in understanding the connection between the patient's unique genetic makeup, or genotype, and the external manifestation of the disease. a disease, or phenotype.

A better understanding of the complex relationship between a genotype and a phenotype could reveal how mutations cause genetic diseases and thus inform the development of more effective treatments. Researchers still do not fully understand how inherited mutations affect the function of proteins.

"Like a broken gear in a machine, mutational changes destroy the function of the defective protein, a process that involves changes in structure and dynamics," Ivanov said. "This confluence of factors presents a challenge for conventional methods of structural biology."

Throughout the complex and highly regulated process of gene transcription, enzymes called Pol I, Pol II and Pol III, collectively called RNA polymerases, play an important role. Pol II helps the mediation of protein synthesis, process of transformation of genetic information into proteins.

During the initiation – the first stage of transcription – Pol II and a host of general transcription factors (GTFs) assemble in a region of the DNA called promoter to form the PIC. The opening of the promoter depends on the human transcription factor II (TFIIH), a GTF consisting of several protein chains, which has the ability to unwind the double helix strands of the DNA to initiate transcription. TFIIH also contributes to the repair of DNA.

Since the biochemical pathways responsible for gene expression and repair are inseparable, it is essential to understand the molecular mechanism behind this process to advance biomedical applications. For example, the presence of mutations in three TFIIH subunits leads directly to serious genetic diseases, including autoimmune and neurological disorders.

Previous attempts to characterize the ICP have been limited by incomplete models. The most comprehensive model of the PIC so far, the new version of the team provides superior information on the structural organizations of these proteins, which transcribe genes and repair DNA.

To develop their PIC model, the researchers combined data from cryo-electron microscopy (CryoEM) – a structural biology method that uses an electron beam to study cryogenically frozen protein samples – and simulations. Large scale molecular dynamics using molecular dynamics at the nanoscale (NAMD) code. Summit is located at the Oak Ridge Leadership Computing Facility (OLCF), a user facility of the US Department of Energy's (DOE) Office of Science located at the Oak Ridge National Laboratory (ORNL).

"The new model gives us the most complete view of TFIIH structure, which helps us to understand the dynamics of these proteins and allows us to map the origins of mutations derived from patients, potentially enabling future biochemical experiments focused on the understanding of the structural mechanisms of TFIIH. "said Ivanov.

The simulations revealed the hierarchical organization of the PIC and explained the functioning of its many structural components to modify the DNA. By mapping 36 different mutations derived from the patient in the PIC model, the team determined that mutations tend to cluster in crucial areas of TFIIH, including a subunit called XPD, which prevents the GTF from functioning. and leads to the disease.

"The calculation is absolutely decisive for establishing a link between the structure, which comes from the CryoEM data, and the phenotype of the disease, a high-level concept difficult to explain with answers based solely on traditional biochemistry and structural biology", Ivanov said.

Based on these findings, the team obtained detailed information on three distinct genetic disorders associated with cancer, aging, and developmental abnormalities by unveiling their distinctive molecular mechanisms.

"If you know which regions of a protein are affected, you can potentially develop therapies for genetic diseases, but without a basic understanding of the underlying mechanism, all the bets are in vain," Ivanov said.

This accomplishment lays the groundwork for future experimental and computer-based efforts to accurately locate the mutations that cause genetic disorders, to explain the distinct contributions of TFIIH to the transcription and repair of DNA and DNA. To deepen the mechanisms of gene expression.

Although this research would have been feasible on other high-performance computing platforms, access to Summit has dramatically accelerated the team's simulations.

"Running on Summit speeds up our research," Ivanov said. "Instead of spending several months running on another system, we were able to finish our calculations in a few days, saving us a lot of time and effort."

This year, the team will perform Summit-related calculations as part of the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program in 2019. Researchers have primarily studied Pol II, but are considering expanding their project. to investigate the functional dynamics of Pol I and Pol III, which could lead to more revolutionary information.

"We are looking forward to going beyond simply describing the mechanisms of transcription to elucidate their link to genetic diseases," Ivanov said.