Molecular Dynamics Simulation of Bacterial [FeNi]-Hydrogenase Found in Desulfovibrio fructosovorans Solvated in a Water Sphere

IntroductionHydrogenase 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]

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.

AcknowledgementsEngineering 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.

MethodsMolecular 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).

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.

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.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.

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.

Jay Derick Department of Education, University of New Hampshire, Durham, NH

Results and DiscussionThe 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.

Future WorkFurther 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.

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.