Biology Department Biology Department  


Deborah Stoner-Ma

Brookhaven National Laboratory
Bldg. 463 - P.O. Box 5000
Upton, NY 11973-5000

Phone: (631) 344-6388
Lab Phone: (631) 344-5726
Fax: (631) 344-2741

Deborah Stoner-Ma is a spectroscopist in the Macromolecular Crystallography Research Resource (PXRR) which provides facilities and support at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR is supported by the NIH's National Center for Research Resources and the DOE Office of Biological and Environmental Research in its mission to create optimal facilities and environments for macromolecular structure determination by synchrotron X-ray diffraction. With a staff of about 24, the PXRR innovates new access modes such as mail-in crystallography, builds new facilities including the Beamline MicroSpectrophotometer at X26-C, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports visiting investigators with 7day, 20 hours staff coverage.


Research Interests

Spectroscopy, protein-ligand/chromophore interactions, structural basis for enzyme catalysis

      An interdisciplinary approach to research has become vital in order to achieve a greater understanding of protein structure and function. The combination of information from spectroscopic studies and X-ray crystallography represents one such approach, one which is now available at beamline X26-C at the NSLS. Electronic absorption, Raman scattering and x-ray diffraction data can be collected from the same crystal, under constant conditions (fluorescence will be available in the near future). This approach can provide insight into diffraction artifacts and the nature of X-ray damage, as well as information on non-covalent interactions between proteins and ligands (substrate or transition state analogs, lead drug compounds, cofactors or chromophores), oxidation states of metal cofactors, and possible intermediates of catalysis, information beyond the reach of X-ray diffraction alone. My aims are to fully exploit the capabilities of the Beamline MicroSpectrophotometer at X26-C and to develop enhancements that will allow for 1) a fuller understanding of the role of structure in catalysis, 2) mechanistic determinations, and 3) identification of critical interactions in protein-ligand pairs. Systems of particular interest include members of the green fluorescent protein family and photoactive flavoproteins.


Selected Publications

  • Orville A., Buono R., Cowan M., Heroux A., Shea-McCarthy G., Schneider D., Skinner J., Skinner M., Stoner-Ma D., and Sweet R.
    Correlated Single-Crystal Electronic Absorption Spectroscopy and X-ray Crystallography at NSLS Beamline X26-C.
    J. Synch. Radiat. (2011, accepted).
  • Stoner-Ma D., Skinner J.M., Schneider D.K., Cowan M., Sweet R.M., and Orville A.M.
    Single-crystal Raman spectroscopy and x-ray crystallography at beamline X26-C of the NSLS.
    J. Synch. Rad. 18(1):37-40 (2011).  PubMed
  • Berman L.E., Allaire M., Chance M.R., Hendrickson W.A., Héroux A., Jakoncic J., Liu Q., Orville A.M., Robinson H.H., Schneider D.K., Shi W., Soares A.S., Stojanoff V., Stoner-Ma D., and Sweet R.M.
    Optics Concept for a Pair of Undulator Beamlines for MX. Nuclear Instrum. Meth.
    Physics Res. A (NIM-A) (2010, in press, available online 24 December 2010).
  • Kondo M., Heisler I.A., Stoner-Ma D., Tonge P.J. and Meech S.R.
    Ultrafast dynamics of protein proton transfer on the short hydrogen bond potential energy surface of S65T/H148D GFP
    J. Am. Chem. Soc. 132: 1452-1453 (2010).
    Cover: We have measured time-resolved proton transfer dynamics on a short hydrogen bond within a protein. Proton transfer reactions, which are common in proteins, can occur on a sub-100 fs time scale in response to changes to the local environment, such as pKa or hydrogen bond strength. The present data can test simulations and calculations of such protein proton transfer reactions. PubMed
  • Stoner-Ma D., Jaye A.A., Ronayne K.L., Nappa J., Meech S.R., and Tonge P.J.
    Ultrafast Electronic and Vibrational Dynamics of Stabilized A State Mutants of the Green Fluorescent Protein (GFP): Snipping the Proton Wire.
    Chemical Physics, 350(1-3):193-200 (2008).  PubMed
  • Stoner-Ma D., Tonge P.J., Ronayne K.L., Nappa J. and Meech S.R.
    An Alternate Proton Acceptor for Excited State Protein Transfer in Green Fluorescent Protein: Rewiring GFP.
    J. Am. Chem. Soc., 130(4):1227-1235 (2008).  PubMed
  • Stoner-Ma D., Melief E.H., Nappa J., Towrie M., Ronayne K.L., Tonge P.J., and Meech S.R.
    Proton Relay Reaction in Green Fluorescent Protein (GFP): Polarization Resolved Ultrafast Vibrational Spectroscopy of Isotopically Edited GFP.
    J. Phys. Chem B, 110(43):22009-22018 (2006).  PubMed
  • Jaye A.A., Stoner-Ma D., Matousek P., Towrie M., Tonge P.J., and Meech S.R.
    Time resolved emission spectra of the green fluorescent protein (GFP).
    Photochem. Photobio., 82:373-379 (2006).  PubMed
  • Stoner-Ma D., Jaye A.A., Matousek P., Towrie M., Tonge P.J. and Meech S.R.
    Ultrafast Dynamics in the Green Fluorescent Protein (GFP): Proton Transfer and Time Resolved Fluorescence Spectroscopy.
    Twelfth International Conference on Time-Resolved Vibrational Spectroscopy, 107-109 (2005). 
  • Stoner-Ma D., Jaye A.A., Matousek P., Towrie M., Meech S.R., and Tonge P.J.
    Observation of excited-state proton transfer in green fluorescent protein using ultrafast vibrational spectroscopy.
    J. Am. Chem. Soc., 127(9):2864-2865 (2005).  PubMed
  • Bell A.F., Stoner-Ma D., Wachter R.M., and Tonge P.J.
    Light-driven decarboxylation of wild-type green fluorescent protein.
    J. Am. Chem. Soc., 125(23):6919-6926 (2003).  PubMed


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Last Modified: February 11, 2011
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