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Molecular Dynamics Simulation of Bacterial [FeNi]-Hydrogenase Found in
Desulfovibrio fructosovorans Solvated in a Water Sphere
Jay Derick
Department of Education, University of New Hampshire, Durham, NH
Results and Discussion
Hydrogenase is an enzyme commonly utilized in microbial energy
metabolism and is used to naturally catalyze H2 (H2  2H+ + 2e).[1] It is
found in bacteria and fungi inhabiting extreme environments such as
underwater thermal vents, anaerobic environments, and within digestive
tracks of larger organisms.[2] While hydrogenase effectively catalyzes H2,
their receptor sites are greatly sensitive to oxygen and carbon monoxide gas.
If the receptor site is exposed to either gas the enzyme will become inert
and unable to catalyze H2. [3] There are two types of hydrogenase classified
by metals at their activation site. Both [FeNi]-hydrogenase (Figure 1) and
[FeFe]-hydrogenase are naturally occurring and are studied for their
potential in green energy generation.
Natural catalyzation of H2 through hydrogenase production has the
potential of lowering the expense of more traditional manufacturing
methods. Currently the catalyzation of H2 on industrial scales requires
platinum, an expensive and rare metal. While the use of platinum is
effective it is an environmentally unsustainable process for long term green
production. [3]
The protein was successfully solvated in water and allowed to equilibrate. The RMSD (root mean squared
deviation) was monitored and found to have an average of 0.86 Å over 40 picoseconds (Figure 3).
A trajectory graphic of the equilibrium (Figure 4) was also captured that shows the flex and shifting movement
that took place within individual portions of the protein strand from the original crystalized form over 4
picoseconds.
RMSD for the [FeNi]-hydrogenase in a water sphere
1.2
1
RMSD (Å)
Figure 1: [FeNi]-hydrogenase
(PDB: 1YQW). The red sphere is
the iron (Fe) atom surrounded by a
histidine and charged amino acids.
The green sphere is the nickel (Ni)
atom surrounded by sulfur (yellow)
atoms at the activation site.
Introduction
0.8
0.6
0.4
0.2
0
0
5
10
15
20
25
30
35
40
Time (picoseconds)
Figure 3: The equilibration of [FeNi]-hydrogenase over 40
picoseconds while solvated in a water sphere. The RMSD measures
the difference in distance among atoms in the protein.
Figure 4: [FeNi]-hydrogenase after 4 picoseonds
of equilibration. The blue protein indicates the
starting position at 0 ps and the violet at 40 ps.
Future Work
Figure 2: One copy (chain A and chain Q as shown in blue) of the [FeNi]-hydrogenase was taken from the raw protein 1YQW
from the Protein Data bank. After seperation, clean coordinate and structure files were generated and then solvated in water.
Methods
Molecular Dynamics (MD) simulations allow researchers to gain a greater understanding of molecules in a
variety of different experimental conditions such as pressure and temperature. The software program Visual
Molecular Dynamics (VMD) was utilized to visualize and solvate [FeNi]-hydrogenase. The protein was
solvated in water (Figure 2) and allowed to equilibrate for 40 picoseconds at 310K using the program NAMD
(NAnoscale Molecular Dynamics).
Further investigation of [FeNi]-Hydrogenase and its potential use in environmentally friendly hydrogen
catalyzation will be of great value as an alternative form of energy. Future simulations of its behavior in a
variety of environments will give researchers a better understanding of its function.
References
[1] Baltazar, Vixeira, and Soares. "Structural Features Of [Nifese] And [Nife] Hydrogenases Determining Their
Different Properties: A Computational Approach." Journal Of Biological Inorganic Chemistry 17.4 (2012):
543-555. Academic Search Alumni Edition. Web.
[2] Ghirardi, Zhang, Lee, Flynn, Seibert, Greenbaum, and Melis. "Microalgae: A Green Source of Renewable
H(2)." Trends Biotechnol 18.12 (2000): 506-11. Pubmed. Web
[3] Wang, Best, and Blumberger. "A Microscopic Model For Gas Diffusion Dynamics In A [Nife]Hydrogenase."Physical Chemistry Chemical Physics (PCCP) 13.17 (2011): 7708. Publisher Provided Full
Text Searching File. Web.
Acknowledgements
Engineering Grant (ENG-1132468). Funding and support from the Joan and James Leitzel Center for Mathematics, Science, and Engineering
Education is gratefully acknowledged, as is support from Dr. Harish Vashisth and the UNH Department of Chemical Engineering.