Atomistic simulations of the nitrogen fixation by Mo-dependent nitrogenase
EMSL Project ID
49374
Abstract
We propose to use EMSL supercomputing resources to gain a molecular level understanding of how substrate binding, electron, and proton delivery are controlled by the nitrogenase metalloenzyme to synthesize ammonia (NH3) from dinitrogen (N2). This research is a key component of the DOE Basic Energy Sciences Physical Biosciences proposal at PNNL, aimed at characterizing key biochemical and biophysical features of enzymatic processes and translate catalytic principles from enzymes' activity to synthetic robust catalytic platforms. Specifically we will (1) test reaction pathways, calculate structures and energy profiles for N2 reduction intermediates, and (2) characterize large-amplitude protein fluctuations gating the electron transport steps. Characterization of structural, dynamic and thermodynamic aspects of ammonia synthesis by nitrogenase is expected to yield insights that will inform the development of functional biomimetic catalysts, which are more efficient and environmentally friendly than industrial processes currently in use.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2016-10-01
End Date
2018-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Keable S.M., O. Zadvornyy, L.E. Johnson, B. Ginovska, A.J. Rasmussen, K. Danyal, and S. Raugei, et al. 2018. "Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase." Journal of Biological Chemistry 293, no. 25:9629-9635. PNNL-SA-132325. doi:10.1074/jbc.RA118.002435
Lukoyanov D, N Khadka, DR Dean, S Raugei, LC Seefeldt, and B Hoffman. 2017. "Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H2 Intermediate." Inorganic Chemistry 56(4):2233-2240. doi:10.1021/acs.inorgchem.6b02899