Department of Chemistry



Sunil Saxena




Chevron Science Center, 219 Parkman Avenue

Pittsburgh, PA 15260

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Research Overview

Analytical, Biophysical, and Physical Chemistry

We develop pulsed electron spin resonance methods and their application to otherwise inaccessible problems in biophysics and materials sciences. The coupling of electron spin angular momentum to its environment—as revealed by the ESR spectrum—provides rich information about the electronic, structural and dynamical properties of the molecule. We create methods that measure the precise distance between two units in a protein, in order to determine their folding patterns and conformational dynamics. These ESR Spectroscopic Rulers— based on multiple quantum coherences and double resonance experiments—are unique in that they resolve distances in the 1 - 7 nm lengthscale even on bulk amorphous materials. Much of this work is based on the use of first-principles theory to develop new experimental protocols and to analyze experimental results.

Our group continues to develop applications of these spectroscopic rulers that range from capturing the essence of structural changes - such as misfolding - in proteins, to measuring the atomic-level details of ion-permeation in a ligand gated ion-channel. We invite you to visit our group website and to contact us to explore the diversity of research projects currently underway in our group.

Projects include:

  • Pulsed ESR methods to measure distance constraints in systems containing paramagnetic metals
  • Measurement of structural and dynamical determinants of the protein-DNA interactions and functional dynamics in pentameric ligand gated ion-channels.
  • Application of the spectroscopic ruler to measure and predict global structures of nanostructured materials.
  • Role of metals in aggregation of Amyloid-b peptide.


  • Crano Memorial Lecture, ACS-Akron Section, 2014
  • Arts and Sciences Tina and David Bellet Teaching Excellence Award, 2012
  • NSF CAREER Award, 2004-2009



“A simple double quantum coherence ESR sequence that minimizes nuclear modulations in Cu(II)-ion based distance measurements,” S. Ruthstein, M. Ji, B.-k. Shin, and S. Saxena, J.Magn. Reson., Vol. 257, 2015, Pages 45
“Conformational changes underlying pore opening and desensitization in the pentameric ligand gated ion channel ELIC,” M.N. Kinde, Q. Chen, M.J. Lawless, E. Seyoum, D.D. Mowrey, J. Xu, V. Bandarenko, T.S. Tillman, S. Saxena, Y. Xu, P. Tang, Structure, Vol. 23, 2015, Pages 995
“The double histidine Cu2+-binding motif: A highly rigid, site-specific spin probe for electron spin resonance distance measurements,” T.F. Cunningham, M.R. Putterman, A. Desai, W.S. Horne, S. Saxena , Angew. Chem. Int. Ed., 2015, Pages 6330-6334
“Origins of structural flexibilities in protein-based supramolecular polymers probed by DEER spectroscopy,” N. A. Tavenor, K. I. Silva, S. Saxena, W. S. Horne, J. Phys. Chem. B., Vol. 118, 2014, Pages 9881
“Insight into the Cu2+ binding site in a protein-DNA complex,” M. Ji, L. Tan, L. Jen-Jacobson, S. Saxena, Mol. Phys., 2014, Pages in press
“Paramagnetic metal ions in pulsed ESR distance distribution measurements,” M. Ji, S. Ruthstein, and S. Saxena, Acc. of Chem. Res., Vol. 47, 2014, Pages 688
“Zn(II)-ions substantially perturb Cu(II)-ion coordination in Amyloid-ß at physiological pH,” K. I. Silva, S. Saxena, J. Phys. Chem. B, Vol. 117, 2013, Pages 9386
“Sensitive Cu(II)-Cu(II) distance measurements in a protein-DNA complex by DQC-ESR,” S. Ruthstein, M. Ji, P. Mehta, L. Jen-Jacobson, and S. Saxena, J. Phys. Chem. B, Vol. 117, 2013, Pages 6227
“Measuring Cu(II)-nitroxide distances using double electron-electron resonance and saturation recovery,” J. Sarver, K. I. Silva, and S. Saxena, Appl. Magn. Reson., Vol. 44, 2013, Pages 583
“High-resolution structure of a protein spin-label in a solvent-exposed beta-sheet and comparison with DEER spectroscopy,” T. F. Cunningham, M. S. McGoff, I. Sengupta, C. P. Jaroniec, W. Seth Horne and S. Saxena, Biochem, Vol. 51, 2012, Pages 6350
“ESR spectroscopy identifies inhibitory Cu(II) sites in a DNA modifying enzyme to reveal determinants of catalytic specificity,” Z. Yang, M. Kurpiewski, M. Ji, J. E. Townsend, P. Mehta, L. Jen-Jacobson, and S. Saxena, Proc Natl. Acad. Sci., Vol. 109, 2012, Pages 6366
“Simulating the dynamics and orientations of spin labeled side chains in a protein-DNA complex,” J. L. Sarver, J.E. Townsend, G. Rajapakse, L. Jen-Jacobson, and S. Saxena, J. Phys. Chem. B, 2012,