Abstract
Atomistic molecular dynamics (MD) simulations are a much-used tool for investigating the structure and dynamics in biomembranes with atomic resolution. The validity of the representations obtained is determined by the accuracy and realism of the MD model (force field). Here, we evaluated the proprietary OPLS4 force field of Schrödinger, Inc. against atomic-resolution experimental data and compared its performance to CHARMM36, one of the best-performing openly available force fields. As benchmark, we used high-resolution Nuclear Magnetic Resonance (NMR) order parameters for C–H bonds—directly and reliably calculable from MD simulations—measured in phosphatidylcholine (PC) lipid bilayers under varying hydra- tion conditions. Comparisons were made with two dehydration datasets: for saturated (1,2- dimyristoylphosphatidylcholine DMPC) lipid bilayers from the literature, and for unsaturated (1-palmitoyl-2-oleoylphosphatidylcholine POPC) lipid bilayers measured here. Our findings indicate that OPLS4 reproduces the structure and dehydration-response of PC-lipid bilayers fairly well, even slightly outperforming CHARMM36. Both models’ main inaccuracies appear in (1) the order parameter magnitudes in the glycerol backbone and unsaturated carbon segments, and (2) the qualitatively differing structural response of the PC-headgroup to dehydration compared to experiments. In summary, the presented work underscores the importance of independent validation for (proprietary) force fields and highlights the strik- ing similarities and nuanced differences between OPLS4 and CHARMM36 in describing biomembranes.
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Title
Solid-state NMR data
Description
The dataset contains solid-state Nuclear Magnetic Resonance (NMR) recordings at 500 MHz from ~25 mg samples of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) in lamellar phase prepared at different hydration states (from 10 mass % to 50 mass %).
For every sample we put R-type proton-detected local field (R-PDLF) recoupling experiments recorded with magic angle spinning (MAS) at 5 kHz. This type of experiment allows us to extract the absolute values of order parameters of every C-H bond. We also put 31P spectrum at both 0Hz and 5kHz spinning to verify the lipid phase state. Most of samples contains also recordings of 13C spectra recorded with high repetition number.
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