|Guo, W., Granger, J., Sigman, D. M. , Nitrate isotope fractionation during biological nitrate reduction: Insights from first principles theoretical modeling, Eos Trans. AGU, Fall Meet. Suppl. Abstract PP34A-08, 2010|
Coupled fractionations of N and O isotopes during biological nitrate reduction provide important constraints on the marine nitrogen cycle at present and in the geologic past. Recent laboratory experiments with mono-cultures of nitrate-assimilative algae and plankton, and denitrifying bacteria demonstrate that N and O isotopic compositions of the residual nitrate co-vary linearly with a constant ratio (i.e., Δδ18O: Δδ15N) of ~1 or ~0.6 . These systematic variations have been inferred to derive from the kinetic isotope fractionations associated with nitrate reductases. The isotope fractionation mechanisms at the enzymatic level, however, remain elusive. Here we present models of isotope fractionations accompanying the nitrate reduction (NO3-→NO2-) by three functional types of nitrate reductases, using techniques from ab initio, transition state and statistical thermodynamic theory.
We consider three types of nitrate reductases: eukNR (eukaryotic assimilatory nitrate reductase), NAR (prokaryotic respiratory nitrate reductase) and Nap (prokaryotic periplasmic nitrate reductase). All are penta- or hexa-coordinated molybdo-enzymes, but bear considerable differences in protein geometry among functional types. Our models, based on the simplified structures of their active sites, predict N and O isotope effects (15ɛ and 18ɛ) ranging from 32.7 to 36.6‰ and from 33.5 to 34.8‰, respectively, at 300K with 18ɛ:15ɛ ratios of 0.9-1.1. The predicted amplitudes of N and O isotope fractionations are in the range measured for eukNR in vitro (~27‰, Karsh et al. in prep), and also correspond to the upper amplitudes observed for denitrifiers in vivo (~25‰, ). Moreover, the computed 18ɛ:15ɛ ratios corroborate the consistent relationships of ~1 observed experimentally for eukNR and the respiratory NAR. These findings indicate the enzymatic reduction is likely the rate-limiting step in most biological nitrate reductions. In addition, the predicted similarity of 18ɛ:15ɛ ratios among different nitrate reductases suggests that the nitrate isotope fractionations by nitrate reductases are governed by the kinetics of the O-N bond cleavage, which incurs negligible differences from variations in surrounding moieties at the active sites. However, our model similarly predicts a 15ɛ of 36.6‰ and 18ɛ:15ɛ of 0.9 for the auxiliary Nap, although it exhibits a 15ɛ of ~15‰ and 18ɛ:15ɛ of ~0.6 in vivo . This discrepancy is suspected to arise from slower binding and release of NO3- from Nap, which could be partially rate-determining in this enzymatic catalysis, or from the assumptions of our modeled enzyme structures.
By extending our above models to include the multiply-substituted (clumped) isotopologues, we predict that isotope fractionations during biological nitrate reduction decrease the proportion of 15N-18O bonds in the residual nitrate relative to their expected equilibrium abundances (~0.02‰ decrease for every 1‰ kinetic enrichment in nitrate δ15N). Future quantification of 15N-18O clumped isotope anomalies in natural nitrate may provide additional constraints on the nitrogen cycle in the ocean.