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Stefan Stoll

Stefan Stoll

Associate Professor of Chemistry

Adjunct Associate Professor of Physiology & Biophysics
Ph.D. ETH Zürich, 2003

(Physical Chemistry, Spectroscopy, Biophysics)

(206) 543-2906


Stoll group website



Research Interests

The Stoll lab focuses on determining the structure and function of proteins and enzymes in their diverse roles in both natural and human-designed molecular systems, using advanced electron paramagnetic resonance (EPR) spectroscopy as a central tool.




Quantifying protein conformational landscapes
Proteins need to be flexible in order to perform their function, such as catalysis, transport, or signaling. We study the conformational flexibility of proteins and how they move, with the goal of increasing the knowledge base about these fundamental processes. We use double electron-electron resonance (DEER) spectroscopy, an advanced EPR technique, to quantify the structural, energetic and dynamic aspects of conformational flexibility and change. DEER measures absolute distances and distance distributions between labels attached to specific sites in proteins, with a range of 15-80 Å and a precision of < 1 Å.






Radical and metalloenzymes

Many difficult and complex chemical transformations are catalyzed by enzymes with transition metal ions, metal ion clusters, and very reactive organic radicals in their catalytic centers. These reactions are essential to life, and some of them are pathologically relevant. We study the structural and dynamic details of these reactions to understand how nature generates, harnesses and controls reactive paramagnetic intermediates in these enzymes.








EPR spectroscopy

Our core technology is EPR spectroscopy in all its basic and advanced variants. EPR reveals the structure and dynamics of the nanoenvironment around unpaired electrons. We develop improved theory, software, and hardware to gain faster, more detailed and more robust results through increased sensitivity and resolution of measurements and increased reliability and reproducibility of data analysis and interpretation. Our Matlab-based software EasySpin for the simulation and analysis of EPR spectra is widely used.





Other interests
The Stoll lab revolves around unpaired electrons. Our interests thus extend to other topics involving electron spins, such as energy conversion materials, molecular magnetism, and quantum computing.


Representative Publications

Evans, E. G. B.; Morgan, J. L. W.; DiMaio, F.; Zagotta, W. N.; Stoll, S.
Allosteric coupling mechanism of a cyclic nucleotide-gated ion channel revealed by DEER spectroscopy.
Proc. Natl. Acad. Sci. USA 2020, 117, 10839–10847

Canarie, E. R.; Jahn, S.; Stoll, S.
Quantitative Structure-Based Prediction of Electron Spin Decoherence in Organic Radicals.

J. Phys. Chem. Lett. 2020, 11, 3396–3400

Martin, P. D.; Svensson, B.; Thomas, D. D.; Stoll, S.

Trajectory-Based Simulation of EPR Spectra: Models of Rotational Motion for Spin Labels on Proteins.

J. Phys. Chem. B 2019, 123, 10131–10141

Mannikko, D.; Stoll, S.
Vanadyl Porphyrin Speciation Based on Submegahertz Ligand Proton Hyperfine Couplings.

Energy & Fuels 2019, 33, 4237–4243


Collauto, A.; DeBerg, H. A.; Kaufmann, R.; Zagotta, W. N.; Stoll, S.; Goldfarb, D.

Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

Phys. Chem. Chem. Phys. 2017, 19, 15324–15334.


Tait, C. E.; Stoll, S.

ENDOR with band-selective shaped inversion pulses.

J. Magn. Reson. 2017, 277, 36–44.


Hayes, E. C.; Jian, Y.; Li, L.; Stoll, S.

EPR study of UV-irradiated thymidine microcrystals supports radical mechanism in spore photoproduct formation.

J. Phys. Chem. B 2016, 120, 10923–10931.


Edwards, T. H.; Stoll, S.

A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy.

J. Magn. Reson. 2016, 270, 87–97.


Tait, C. E.; Stoll, S.

Coherent pump pulses in Double Electron Electron Resonance spectroscopy.

Phys. Chem. Chem. Phys. 2016, 18, 18470–18485.


Hayes, E. C.; Porter, T. R.; Barrows, C. J.; Kaminsky, W.; Mayer, J. M.; Stoll, S.

Electronic structure of a CuII-alkoxide complex modeling intermediates in copper-catalyzed alcohol oxidations.

J. Am. Chem. Soc. 2016, 138, 4132–4145.


DeBerg, H. A.; Brzovic, P. S.; Flynn, G. E.; Zagotta, W. N.; Stoll, S.

Structure and energetics of allosteric regulation of HCN2 ion channels by cyclic nucleotides.

J. Biol. Chem. 2016, 291, 371–381.


DeBerg, H. A.; Bankston, J. R.; Rosenbaum, J. C.; Brzovic, P. S.; Zagotta, W. N.; Stoll, S.

Structural mechanism for the regulation of HCN ion channels by the accessory protein TRIP8b.

Structure 2015, 23, 734–744.


Nehrkorn, J.; Schnegg, A.; Holldack, K.; Stoll, S.

General magnetic transition dipole moments for Electron Paramagnetic Resonance.

Phys. Rev. Lett. 2015, 114, 010801.


Puljung, M. C.; DeBerg, H. A.; Zagotta, W. N.; Stoll, S.

Double electron-electron resonance reveals cAMP-induced conformational change in HCN channels.

Proc. Natl. Acad. Sci. USA 2014, 111, 9816–9821.


S. Stoll, Y.-T. Lee, M. Zhang, R. F. Wilson, R. D. Britt, D. B. Goodin

Double electron-electron resonance shows cytochrome P450cam undergoes a conformational change in solution upoin binding substrate

Proc. Natl. Acad. Sci. 2012, 109, 12888-12893.


S. Stoll, H. S. Shafaat, J. Krzystek, A. Ozarowski, M. J. Tauber, J. E. Kim, R. D. Britt

Hydrogen bonding of tryptophan radicals revealed by EPR at 700 GHz

J. Am. Chem. Soc. 2011, 133, 18098-18101.


S. Stoll, R. D. Britt

General and efficient simulation of pulse EPR spectra

Phys. Chem. Chem. Phys. 2009, 11, 6614-6625.


Awards & Activities

  • Research Corporation Cottrell Scholar Award (2015)
  • National Science Foundation CAREER Award (2015)
  • University of Washington Distinguished Teaching Award for Innovations in Technology (2015)

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