Science Success Story

Supercomputers Help Reveal Dynamic Plastic-Eating Duo

NREL scientists discover synergy in PET plastic-degrading enzymes using XSEDE resources

Jorge Salazar, Texas Advanced Computing Center (TACC) 

 

The dynamic enzyme duo of PETase and MHETase work well together break down PET plastic, commonly found in disposable bottles. Supercomputer simulations have revealed greater understanding of the reaction mechanism of this recently discovered two-enzyme system. Scientists hope this research can inform future cocktail-based strategies for plastic upcycling. Credit: Knott et al., DOI: 10.1073/pnas.2006753117

Plastic waste is a big problem for the environment. About 300 million tons are produced every year, according to the United Nations. Much of that is polyethylene terephthalate (PET) used to make single-use plastic bottles, carpets, and clamshell packaging. In the U.S., the Environmental Protection Agency estimates annually only about 29% of PET bottles are recycled.  

In 2016, Japanese scientists discovered the bacteria Ideonella sakaiensis had evolved digestive enzymes called PETase that break down PET. And in 2020, XSEDE-allocated supercomputers helped reveal more about a sidekick enzyme that helps PETase break down PET plastic.  

While dealing with plastic pollution at scale remains daunting, in the words of Jeff Goldblum's character in Jurassic Park, "Life finds a way." 

 

Why It's Important 

In a nutshell, supercomputer simulations revealed how the two enzymes work better when they cooperate in breaking down PET plastic, a six-fold improvement versus PETase alone. Scientists at the National Renewable Energy Laboratory (NREL) hope this research can inform future strategies for plastic upcycling, which takes plastic waste and breaks it down into commercially valuable components that can make new products. 

"This most recent study focuses on the partner enzyme of PETase, which is called Metasets. It works on mono (2-hydroxyethyl) terephthalate (MHET), one of the plastic breakdown molecules PETase produces," said Brandon Knott, a staff engineer at NREL in Golden, Colorado. 

National Renewable Energy Laboratory scientists who co-authored the MHETase PNAS study: Erika Erickson, Postdoctoral Researcher – Bioengineering (left); Brandon Knott, Group Research Manager II - Chemical Engineering. Credit: NREL.

Knott co-authored the study on MHETase published in the Proceedings of the National Academy of Sciences in October 2020.  

"There are some aspects in which the enzymes are quite similar, including their catalytic residues," Knott explained. "But there are other aspects where they're quite different, which leads to them having different substrates specificities." These differences help explain why they work well together, where MHETase cleans up what PETase can't. 

Co-author Erika Erickson, a postdoctoral researcher at NREL, led the wet lab investigation of MHETase, expressing and purifying it to characterize what substrates it is able to break down, how quickly, and what the limitations of that reaction are. She also explored different MHETase mutations to see if they improved or abolished activity. 

"There's a synergistic behavior between PETase and MHETase," Erickson explained. "While PETase is very exciting on its own, when friends are involved it's a much more efficient process." 

Knott added that pivotal to the paper was quantifying how much MHETase helps PETase in terms of how much PET plastic is broken down.  

"By adding MHETase into the mix with PETase, PET is broken down twice as well," he said. "Add the chimera enzyme where they're covalently bonded together, and you get another factor of three improvements in the PET depolymerization. Altogether going from PETase alone to the chimera enzyme, you have a six-fold improvement in terms of PET depolymerization." 

 

How XSEDE Helped 

The research team was awarded supercomputer allocations to run molecular dynamics simulations of MHETase and PETase in their plastic degradation research on XSEDE-allocated supercomputers. Stampede2 at the Texas Advanced Computing Center; Comet at the San Diego Supercomputer Center; and the NREL Eagle supercomputer supported by the DOE Office of Energy Efficiency and Renewable Energy were relied upon for this study.  

"Our group has been convinced for a very long time that coupling computer simulations with wet-lab experiments, with crystal structures, and with various other techniques is really powerful," Knott said.  

The simulations allowed the team to add a dynamic complement to the static crystal structures that otherwise would not have been feasible in their investigation of the reaction mechanisms. 

Supercomputers searching for solutions to plastic waste. Stampede2 at the Texas Advanced Computing Center (top), Eagle at the National Renewable Energy Laboratory (left), Comet at the San Diego Supercomputer Center.

Corresponding author Gregg Beckham has employed XSEDE resources continuously since 2009 in the context of investigating biological systems to degrade recalcitrant natural polymers such as cellulose, and now with PET plastic. In 2018, Beckham's group used XSEDE to solve the structure of PETase

In this latest study, the researchers used simulation to find the rate-limiting step of reaction, whether the ethylene glycol released by the PETase hangs around the active site of MHETase and helps in the reaction. The simulations showed ethylene glycol leaves the active site between step one and step two after it's cleaved off.  

"We can get at these kinds of questions in detail with exquisite time and space resolution with the molecular simulations," Knott said. "They would be very difficult or impossible to answer with experiment, given the space and time resolution that we have available to us in molecular simulation."  

The supercomputing resources were critical in helping the researchers overcome challenges and to facilitate the work. 

"Having these reliable resources from XSEDE with such a high capacity, in terms of the number of high-performance nodes, professionally administrative, and the high level of support is essential to the science that we've been able to accomplish on this front," Knott added. 

The MHETase catalytic mechanism: (A) reactant, (B) transition state, and (C) product of acylation in which His528 transfers a proton from Ser225 to the ethylene glycol (EG) leaving group. (G) The free-energy surface for acylation computed along a reaction coordinate described by the breaking and forming C-O bonds. Minimum free energy path (MFEP) is shown in black dashes. (H) Following acylation, EG leaves the active site within 1 ns of a classic MD simulation. (I) The free-energy surface for deacylation, exhibiting a predicted higher barrier than acylation. The MFEP is shown in black dashes. Credit: Knott et al., DOI: 10.1073/pnas.2006753117

While still far from a solution that deals with the scale of the global plastic waste problem, the scientists see reason for hope.  

"Some companies have started to truly make progress in this direction, that there could be some enzymatic or biological processes for degrading certain types of plastic waste. But there's still a lot of work to do here in optimization and achieving a scale that will make a real difference, and not just be a demonstration," Erickson said. 

"One of the advantages of doing this biologically is that the breakdown to monomers gives you a lot of flexibility, not only to recycle plastic and displace that petroleum usage and divert waste from landfills or the environment, but also the flexibility to produce virgin quality PET again," Knott added. 

It's remarkable that nature rapidly identified a possible strategy to help with humanity's plastic waste problem.  

"This isn't a magic bullet that fixes our situation and saves us from ourselves," Erickson said. "This may be one of many solutions — the impact of this type of research is to remind the public that this is an issue." 

The study, "Characterization and engineering of a two-enzyme system for plastics depolymerization," was published October 2020 in the Proceedings of the National Academy of Sciences. Funding was provided by the DOE, Office of Energy Efficiency and Renewable Energy, Advanced Manufacturing Office and Bioenergy Technologies Office. Computer time was provided by Extreme Science and Engineering Discovery Environment allocation MCB-090159 at the San Diego Supercomputing Center and the Texas Advanced Computing Center, and by the National Renewable Energy Laboratory Computational Sciences Center supported by the DOE Office of Energy Efficiency and Renewable Energy under Contract DE-AC36-08GO28308. 

 

At a Glance:

  • MHETase structure solved to 1.6 angstrom resolution, showing similarities and differences to PETase enzyme that degrades polyethylene terephthalate (PET) plastic.
  • Interdisciplinary research involving computer simulation, wet lab experiments, and structural analysis reveal synergy of MHETase-PETase two-enzyme system in plastic degradation.
  • XSEDE-allocated Stampede2 of TACC and Comet of SDSC provided molecular dynamics simulations of enzymes and find rate limiting step in reaction mechanism.
  • Research can inform future cocktail-based strategies for plastic upcycling.