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Site-Specific Incorporation of a Cu²⁺ Spin Label into Proteins for Measuring Distances by Pulsed Dipolar Electron Spin Resonance Spectroscopy B

Merz, Gregory E., Borbat, Peter P., Muok, Alise R., Srivastava, Madhur, Bunck, David N., Freed, Jack H., Crane, Brian R.
The Journal of physical chemistry 2018 v.122 no.41 pp. 9443-9451
amino acids, copper, electron paramagnetic resonance spectroscopy, fluorescent proteins, histidine kinase, metal ions, metalloproteins, physical chemistry, solvents
Pulsed dipolar electron spin resonance spectroscopy (PDS) is a powerful tool for measuring distances in solution-state macromolecules. Paramagnetic metal ions, such as Cu²⁺, are used as spin probes because they can report on metalloprotein features and can be spectroscopically distinguished from traditional nitroxide (NO)-based labels. Here, we demonstrate site-specific incorporation of Cu²⁺ into non-metalloproteins through the use of a genetically encodable non-natural amino acid, 3-pyrazolyltyrosine (PyTyr). We first incorporate PyTyr in cyan fluorescent protein to measure Cu²⁺-to-NO distances and examine the effects of solvent conditions on Cu²⁺ binding and protein aggregation. We then apply the method to characterize the complex formed by the histidine kinase CheA and its target response regulator CheY. The X-ray structure of CheY–PyTyr confirms Cu labeling at PyTyr but also reveals a secondary Cu site. Cu²⁺-to-NO and Cu²⁺-to-Cu²⁺ PDS measurements of CheY–PyTyr with nitroxide-labeled CheA provide new insights into the conformational landscape of the phosphotransfer complex and have implications for kinase regulation.