Probing protein conformation in cells by EPR distance measurements using Gd3+ spin labeling

J Am Chem Soc. 2014 Sep 24;136(38):13458-65. doi: 10.1021/ja5079392. Epub 2014 Sep 11.

Abstract

Protein structure investigations are usually carried out in vitro under conditions far from their native environment in the cell. Differences between in-cell and in vitro structures of proteins can be generated by crowding effects, local pH changes, specific and nonspecific protein and ligand binding events, and chemical modifications. Double electron-electron resonance (DEER), in conjunction with site-directed spin-labeling, has emerged in the past decade as a powerful technique for exploring protein conformations in frozen solutions. The major challenges facing the application of this methodology to in-cell measurements are the instabilities of the standard nitroxide spin labels in the cell environment and the limited sensitivity at conventional X-band frequencies. We present a new approach for in-cell DEER distance measurement in human cells, based on the use of: (i) reduction resistant Gd(3+) chelates as spin labels, (ii) high frequency (94.9 GHz) for sensitivity enhancement, and (iii) hypo-osmotic shock for efficient delivery of the labeled protein into the cell. The proof of concept is demonstrated on doubly labeled ubiquitin in HeLa cells.

MeSH terms

  • Electron Spin Resonance Spectroscopy / methods*
  • Gadolinium / chemistry*
  • HeLa Cells
  • Humans
  • Models, Molecular
  • Protein Conformation
  • Spin Labels*
  • Ubiquitin / chemistry*

Substances

  • Spin Labels
  • Ubiquitin
  • Gadolinium