Researchers at the Beckman Institute for Advanced Science and Technology
at the University of Illinois at Urbana-Champaign have opened a window by
way of computer simulation that lets them see how and where hydrogen and
oxygen travel to reach and exit an enzyme's catalyst site -- the H cluster
-- where the hydrogen is converted into energy.
The Illinois scientists and three colleagues from the National Renewable
Energy Laboratory in Golden, Colo., detailed their findings in the
September issue of the journal Structure. What they found could
help solve a long-standing economics problem. Because oxygen permanently
binds to hydrogen in the H cluster, the production of hydrogen gas is
halted. As a result, the supply is short-lived.
Numerous microorganisms have enzymes known as hydrogenases that simply use
sunlight and water to generate hydrogen-based energy.
"Understanding how oxygen reaches the active site will provide insight
into how hydrogenase's oxygen tolerance can be increased through protein
engineering, and, in turn, make hydrogenase an economical source of
hydrogen fuel," said Klaus Schulten, Swanlund Professor of Physics at
Illinois and leader of the Beckman's Theoretical and Computational
Biophysics Group.
Using computer modeling developed in Schulten's lab -- NAMD, a scalable
molecular dynamics program, and Visual Molecular Dynamics (VMD) -- physics
doctoral student Jordi Cohen created an all-atom simulation model based on
the crystal structure of hydrogenase CpI from Clostridium pasteurianum.
This model allowed Cohen to visualize and track how oxygen and hydrogen
travel to the hydrogenase's catalytic site, where the gases bind, and what
routes the molecules take as they exit. Using a new computing concept, he
was able to describe gas diffusion through the protein and predict
accurately the diffusion paths typically taken.
"What we discovered was surprising," Schulten said. "Both hydrogen and
oxygen diffuse through the protein rather quickly, yet there are clear
differences."
Oxygen requires a bit more space compared with the lighter and smaller
hydrogen, staying close to few well localized fluctuating channels. The
hydrogen gas traveled more freely. Because the protein is more porous to
hydrogen than to oxygen, the hydrogen diffused through the oxygen pathways
but also through entirely new pathways closed to oxygen, the researchers
discovered.
The researchers concluded that it could be possible to close the oxygen
pathways of hydrogenase through genetic modification of the protein and
thereby increase the tolerance of hydrogenases to oxygen without
disrupting the release of hydrogen gas.
Co-authors with Schulten and Cohen were Kwiseon Kim, Paul King and Michael
Seibert, all of the National Renewable Energy Laboratory. The National
Institutes of Health, National Science Foundation and the U.S. Department
of Energy funded the research.
NAMD is a parallel molecular dynamics code designed for high-performance
simulation of large biomolecular systems. VMD is a molecular visualization
program for displaying, animating and analyzing large biomolecular systems
using 3D graphics.