Improving yields of deuterated, methyl labeled protein by growing in H₂O

Solution NMR continues to make strides in addressing protein systems of significant size and complexity. A fundamental requirement to fully exploit the ¹⁵N-¹H TROSY and ¹³C-¹H₃ methyl TROSY effects is highly deuterated protein. Unfortunately, traditional overexpression in Escherichia coli (E. coli) during growth on media prepared in D₂O leads to many difficulties and limitations, such as cell toxicity, decreased yield, and the need to unfold or destabilize proteins for back exchange of amide protons. These issues are exacerbated for non-ideal systems such as membrane proteins. Expression of protein during growth in H₂O, with the addition of ²H-labeled amino acids derived from algal extract, can potentially avoid these issues. We demonstrate a novel fermentation methodology for high-density bacterial growth in H₂O M9 medium that allows for appropriate isotopic labeling and deuteration. Yields are significantly higher than those achieved in D₂O M9 for a variety of protein targets while still achieving 75-80% deuteration. Because the procedure does not require bulk D₂O or deuterated glucose, the cost per liter of growth medium is significantly decreased; taking into account improvements in yield, these savings can be quite dramatic. Triple-labeled protein is also efficiently produced including specific ¹³CH₃ labeling of isoleucine, leucine, and valine using the traditional ILV precursors in combination with an ILV-depleted mix of ²H/¹⁵N amino acids. These results are demonstrated for the membrane protein sensory rhodopsin II and the soluble proteins human aldoketoreductase AKR1c3, human ubiquitin, and bacterial flavodoxin. Limitations of the approach in the context of very large molecular weight proteins are illustrated using the bacterial Lac repressor transcription factor.