Science Success Story

Supercomputers Unlock Reproductive Mysteries of Viruses and Life

XSEDE's Stampede2, Comet supercomputers complete simulations pertinent to coronavirus, DNA replication

By Jorge Salazar, Texas Advanced Computing Center

Supercomputer simulations led scientists to a mechanism for the budding off of viruses such as the coronavirus. A related study also used simulations to find a mechanism for how the DNA of all life adds a base to its growing strand during replication. This fundamental research could help lead to new strategies and better technology that combats infectious and genetic diseases. [Credit: Mandal et al.]

 

Fundamental research could help lead to new strategies and better technology that combats infectious and genetic diseases.

Viruses such as the novel coronavirus rely on the host cell membrane to drastically bend and eventually let loose the replicated viruses trapped inside the cell. Scientists have used supercomputer simulations to help propose a mechanism for this budding off of viruses. A related study also used simulations to find a mechanism for how the DNA of all life adds a base to its growing strand during replication.

Researchers used supercomputer time awarded through XSEDE funded by the National Science Foundation for this research on both the Stampede2 supercomputer at TACC, and the Comet supercomputer at SDSC.

Atomistic simulation of membrane deformation with two Vps32 trimers separated by (a) ~25 nm and (b) ~50 nm on a membrane ribbon. (c and d) Results of continuum mechanics analysis that illustrate the effect of two filaments separated by different distances on the shape of the membrane are shown; the spontaneous curvature is zero outside of the region of the filament, shown here in red. [Credit: Mandal et al.]
Structure of DNA polymerase, highlighting the active site groups that were treated at the quantum mechanical level during simulations. Reactant state shown here. Credit: Roston et al.

The study on cell membrane remodeling, important for viral reproduction, cell growth and communication, and other biological processes was published online in the Biophysical Journal in February 2020. The study co-author, Qiang Cui, also was part of a study on DNA base addition published in the Proceedings of the National Academy of Sciences, December 2019. Cui is a professor in the Departments of Chemistry, Physics, and Biomedical Engineering, Boston University.

"Supercomputers with massive parallelization are very much required to push the boundary of biomolecular simulations," Cui said.

Cui's science team developed supercomputer simulations of the cell membrane, in particular filaments of the Vps32 protein, a major component of the endosomal sorting required for transport complex (ESCRT-III), which was the prime suspect for the driving force that causes the cell membrane to form buds in a process called membrane invagination. ESCRT proteins function in the cytosol, the liquid inside cells surrounding organelles, the cell subunits. They perform various jobs such as making organelles; sorting recyclable material in the cell and ejecting waste, and more.

Left: Qiang Cui, Professor in the Departments of Chemistry, Physics, and Biomedical Engineering, Boston University. Right: Daniel Roston, Assistant Project Scientist, Department of Chemistry and Biochemistry at UC San Diego.

"The most interesting observation is that the ESCRT-III polymer that we studied features a clear intrinsic twist," Cui said. "This suggests that twisting stress that accumulates as the polymer grows on the surface might play a major role in creating the three-dimensional buckling of the membrane. People focused more on the bending of the filament in the past."

The proposed mechanism supported by simulations basically involves initially dimpling and then pushing out of the membrane as the corkscrew Vps32 protein filament grows, eventually causing the neck of the membrane invagination.

Simulations of systems containing up to two million atoms posed a large hurdle for Cui and colleagues. "Stampede2 has been crucial for us to set up these relatively large-scale membrane simulations," Cui said.

While this study is pure research, the knowledge gained could help benefit society.

"Membrane remodeling is an important process that underlies many crucial cellular functions and events, such as synaptic transmission and virus infection. Understanding the mechanism of membrane remodeling will ultimately help propose new strategies for battling human diseases due to impaired membrane fusion activities — or preventing viral infection — a timely topic these days given the quick spread of the new coronavirus," Cui said.

Cui also co-authored a computational study that used supercomputer simulations to determine a chemical mechanism for the reaction of nucleotide addition, used in the cell to add nucleotide bases to a growing strand of DNA.

Diagram of plausible mechanism of membrane curvature development catalyzed by Vps32 filaments. (a) Initial adsorption of Vps32 induces local positive curvature because of insertion of the N-terminal helix; (b) adsorption of a ring of Vps32 polymers induces a negative curvature at the center of the circular ring; (c) as the Vsp32 filament continues to elongate, bending and twisting deformations of the filament lead to the formation of a three-dimensional (3D) helical spiral that creates the neck of the membrane invagination. [Credit: Mandal et al.]

"By doing that, computationally, we are also able to determine the role of a catalytic metal ion of magnesium that's in the active site of the enzyme DNA polymerase," said study co-author Daniel Roston, assistant project scientist in the Department of Chemistry and Biochemistry at UC San Diego. "This metal has been a bit controversial in the literature. Nobody was really sure exactly what it was doing there. We think it's playing an important catalytic role."

DNA polymerase adds the nucleotides guanine, adenine, thymine, cytosine (G-A-T-C) to DNA by removing a proton from the end of the growing strand through reaction with a water molecule.

"When we say in the study that a water molecule serves as the base, it serves as a base to remove a proton, an acid base chemistry. What's left there after you remove the proton is much more chemically active to react with a new nucleotide that needs to be added to the DNA," Roston said.

The chemistry needs multiple proton transfers in a complex active site. Experimental probes using X-ray crystallography have been unable to distinguish among the many possible reaction pathways.

"Simulations offer a complement to crystallography because you can model in all the hydrogens and run molecular dynamics simulations, where you allow all the atoms to move around in the simulation and see where they want to go, and what interactions are helping them get where they need to go," Roston said.

"Our role was to do these molecular dynamics simulations and test different models for how the atoms are moving around during the reaction and test different interactions that are helping that along."

Mechanism (A), transition state structure (B), and free-energy surfaces for a mechanism with a Mg2+-coordinated hydroxide as the base under 4 different conditions (C–F). The 4 conditions are: 2 Mg2+ and deprotonated leaving group (C), 3 Mg2+ and deprotonated leaving group (D), 2 Mg2+ and protonated leaving group (E), 3 Mg2+ and protonated leaving group (F). The proposed mechanism achieves all the characteristics of the mechanism suggested by experiments, including rate acceleration by a third Mg2+ and by protonation of the leaving group. The structure in the Upper Right is representative of the transition state region for that reaction with the breaking and forming bonds shown as transparent. The proton shown in red is only present in the Bottom simulations. The dotted lines guide the eye along the minimum free-energy path from reactant to product; the transition state corresponds to the location of the maximum free energy along this minimum path. Roston et al

The number of energy calculations needed to complete the molecular dynamics simulations was huge, on the order of 10e8 to 10e9 for the system with thousands of atoms and many complex interactions. That's because timesteps at the right resolution are on the order of femtoseconds, 10e-15 seconds.

"Chemical reactions, life, doesn't happen that quickly," Roston said. "It happens on a timescale of people talking to each other. Bridging this gap in timescale of many, many orders of magnitude requires many steps in your simulations. It very quickly becomes computationally intractable."

"One of the great things about XSEDE is that we can take advantage of a ton of computational power," Roston added. Through XSEDE, Roston and colleagues used about 500,000 CPU hours on Comet system at SDSC. Comet allowed them to simultaneously run many different simulations that all feed off one another.

Said Roston: "DNA replication is what life is about. We're getting at the heart of how that happens, the really fundamental process to life as we know it on Earth. This is so important, we should really understand how it works at a deep level. But then, there are also important aspects of technology such as CRISPR that take advantage of this kind of work to develop systems to manipulate DNA. Understanding the details of how life has evolved to manipulate DNA will surely play a role in feeding our understanding and our ability to harness technologies in the future."

‘Molecular simulation of mechanical properties and membrane activities of the ESCRT-III complexes' was published online February 2020 in the journal Biophysical Journal. The study co-authors are Taraknath Mandal and Qiang Cui of Boston University; Wilson Lough, Saverio E. Spagnolie, and Anjon Audhya of the University of Wisconsin-Madison. Study funding came from the National Science Foundation. Computations are also supported in part by the Shared Computing Cluster, which is administered by Boston University's Research Computing Services.

‘Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase' was published December 2019 in the Proceedings of the National Academy of Sciences. The study co-authors are Daniel Roston of the University of California San Diego; Darren Demapan of the University of Wisconsin-Madison; and Qiang Cui of Boston University. Study funding came from the National Institutes of Health.

The Stampede2 supercomputer at the Texas Advanced Computing Center (left) and the Comet supercomputer at the San Diego Supercomputer Center (right) are allocated resources of the Extreme Science and Engineering Discovery Environment (XSEDE) funded by the National Science Foundation (NSF). Credit: TACC, SDSC.

 

At a Glance:

  •  XSEDE supercomputer simulations support a new mechanism for the budding off of viruses.
  • The ESCRTIII polymer features a clear intrinsic twist in molecular dynamics simulations, and might play a major role in creating the 3D buckling of the cell membrane. A related study used simulations to find the mechanism for DNA base addition during replication.
  • The computational study determined the role of catalytic magnesium ion in the active site of DNA polymerase.
  • The XSEDE-allocated supercomputers Stampede2 of TACC and Comet of SDSC supported the studies.
  • This fundamental research could help lead to new strategies and better technology that combats infectious and genetic diseases.