Simulation vs. Reality: A Comparison of In Silico Distance Predictions with DEER and FRET Measurements

Site specific incorporation of molecular probes such as fluorescent- and nitroxide spin-labels into biomolecules, and subsequent analysis by Förster resonance energy transfer (FRET) and double electron-electron resonance (DEER) can elucidate the distance and distance-changes between the probes. However, the probes have an intrinsic conformational flexibility due to the linker by which they are conjugated to the biomolecule. This property minimizes the influence of the label side chain on the structure of the target molecule, but complicates the direct correlation of the experimental inter-label distances with the macromolecular structure or changes thereof. Simulation methods that account for the conformational flexibility and orientation of the probe(s) can be helpful in overcoming this problem. We performed distance measurements using FRET and DEER and explored different simulation techniques to predict inter-label distances using the Rpo4/7 stalk module of the M. jannaschii RNA polymerase. This is a suitable model system because it is rigid and a high-resolution X-ray structure is available. The conformations of the fluorescent labels and nitroxide spin labels on Rpo4/7 were modeled using in vacuo molecular dynamics simulations (MD) and a stochastic Monte Carlo sampling approach. For the nitroxide probes we also performed MD simulations with explicit water and carried out a rotamer library analysis. Our results show that the Monte Carlo simulations are in better agreement with experiments than the MD simulations and the rotamer library approach results in plausible distance predictions. Because the latter is the least computationally demanding of the methods we have explored, and is readily available to many researchers, it prevails as the method of choice for the interpretation of DEER distance distributions

Variation in Methane Emission Rates from Well Pads in Four Oil and Gas Basins with Contrasting Production Volumes and Compositions

Atmospheric methane emissions from active natural gas production sites in normal operation were quantified using an inverse Gaussian method (EPA’s OTM 33a) in four major U.S. basins/plays: Upper Green River (UGR, Wyoming), Denver-Julesburg (DJ, Colorado), Uintah (Utah), and Fayetteville (FV, Arkansas). In DJ, Uintah, and FV, 72–83% of total measured emissions were from 20% of the well pads, while in UGR the highest 20% of emitting well pads only contributed 54% of total emissions. The total mass of methane emitted as a percent of gross methane produced, termed throughput-normalized methane average (TNMA) and determined by bootstrapping measurements from each basin, varied widely between basins and was (95% CI): 0.09% (0.05–0.15%) in FV, 0.18% (0.12–0.29%) in UGR, 2.1% (1.1–3.9%) in DJ, and 2.8% (1.0–8.6%) in Uintah. Overall, wet-gas basins (UGR, DJ, Uintah) had higher TNMA emissions than the dry-gas FV at all ranges of production per well pad. Among wet basins, TNMA emissions had a strong negative correlation with average gas production per well pad, suggesting that consolidation of operations onto single pads may reduce normalized emissions (average number of wells per pad is 5.3 in UGR versus 1.3 in Uintah and 2.8 in DJ)