Researchers at the Beckman Institute for AdvancedScience and Technology at the University of Illinois atUrbana-Champaign have opened a window by way of computer simulationthat lets them see how and where hydrogen and oxygen travel to reachand exit an enzyme’s catalyst site – the H cluster – where the hydrogenis converted into energy.
The Illinois scientists and threecolleagues from the National Renewable Energy Laboratory in Golden,Colo., detailed their findings in the September issue of the journalStructure. What they found could help solve a long-standing economicsproblem. Because oxygen permanently binds to hydrogen in the H cluster,the production of hydrogen gas is halted. As a result, the supply isshort-lived.
Numerous microorganisms have enzymes known as hydrogenases that simply use sunlight and water to generate hydrogen-based energy.
“Understandinghow oxygen reaches the active site will provide insight into howhydrogenase’s oxygen tolerance can be increased through proteinengineering, and, in turn, make hydrogenase an economical source ofhydrogen fuel,” said Klaus Schulten, Swanlund Professor of Physics atIllinois and leader of the Beckman’s Theoretical Biophysics Group.
Usingcomputer modeling developed in Schulten’s lab – Nanoscale MolecularDynamics (NAMD) and Visual Molecular Dynamics (VMD) – physics doctoralstudent Jordi Cohen created an all-atom simulation model based on thecrystal structure of hydrogenase CpI from Clostridium pasteurianum.
Thismodel allowed Cohen to visualize and track how oxygen and hydrogentravel to the hydrogenase’s catalytic site, where the gases bind, andwhat routes the molecules take as they exit. Using a new computingconcept, he was able to describe gas diffusion through the protein andpredict accurately the diffusion paths typically taken.
“What wediscovered was surprising,” Schulten said. “Both hydrogen and oxygendiffuse through the protein rather quickly, yet, there are cleardifferences.”
Oxygen requires a bit more space compared with thelighter and smaller hydrogen, staying close to few well localizedfluctuating channels. The hydrogen gas traveled more freely. Becausethe protein is more porous to hydrogen than to oxygen, the hydrogendiffused through the oxygen pathways but also through entirely newpathways closed to oxygen, the researchers discovered.
Theresearchers concluded that it could be possible to close the oxygenpathways of hydrogenase through genetic modification of the proteinand, thereby, increase the tolerance of hydrogenases to oxygen withoutdisrupting the release of hydrogen gas.
Co-authors with Schultenand Cohen were Kwiseon Kim, Paul King and Michael Seibert, all of theNational Renewable Energy Laboratory. The National Institutes ofHealth, National Science Foundation and the U.S. Department of Energyfunded the research.
NAMD is a parallel molecular dynamics codedesigned for high-performance simulation of large biomolecular systems.VMD is a molecular visualization program for displaying, animating andanalyzing large biomolecular systems using 3-D graphics.
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