Abstract
With the sensitivity enhancements conferred by dynamic nuclear polarization (DNP), magic angle spinning (MAS) solid state NMR spectroscopy experiments can attain the necessary sensitivity to detect very low concentrations of proteins. This potentially enables structural investigations of proteins at their endogenous levels in their biological contexts where their native stoichiometries with potential interactors is maintained. Yet, even with DNP, experiments are still sensitivity limited. Moreover, when an isotopically-enriched target protein is present at physiological levels, which typically range from low micromolar to nanomolar concentrations, the isotope content from the natural abundance isotopes in the cellular milieu can outnumber the isotope content of the target protein. Using isotopically enriched yeast prion protein, Sup35NM, diluted into natural abundance yeast lysates, we optimized sample composition. We found that modest cryoprotectant concentrations and fully protonated environments support efficient DNP. We experimentally validated theoretical calculations of the limit of specificity for an isotopically enriched protein in natural abundance cellular milieu. We establish that, using pulse sequences that are selective for adjacent NMR-active nuclei, proteins can be specifically detected in cellular milieu at concentrations in the hundreds of nanomolar. Finally, we find that maintaining native stoichiometries of the protein of interest to the components of the cellular environment may be important for proteins that make specific interactions with cellular constituents.
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Funding
W.N.C. was supported by a graduate research fellowship from the NSF and NIH MB T32 GM008297. This work was supported by grants from the National Science Foundation [1751174]; the Welch Foundation [1-1923-20200401]; NIH R01NS134921; the Lupe Murchison Foundation, and the Kinship Foundation (Searle Scholars Program) to K.K.F. The National High Magnetic Field Laboratory (NHMFL) is supported by the NSF Division of Materials Research (DMR1644779 and DMR-2128556) and by the State of Florida. The 14.1T DNP system at NHMFL is supported by the National Institutes of Health Grant NIH P41 GM122698 and RM1 GM148766.
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KKF and WNC wrote the main manuscript text. WNC prepared figures 1, 2, 4 & 5. YX prepared figure 3. FM-V and JK performed experiments. All authors reviewed the manuscript.
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Costello, W.N., Xiao, Y., Mentink-Vigier, F. et al. DNP-assisted solid-state NMR enables detection of proteins at nanomolar concentrations in fully protonated cellular milieu. J Biomol NMR (2024). https://doi.org/10.1007/s10858-024-00436-9
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DOI: https://doi.org/10.1007/s10858-024-00436-9