Rebekka Wachter

Rebekka Wachter

Emeritus Professor,
School of Molecular Sciences
Other ASU affiliations
Faculty Member, Biodesign Center for Applied Structural Discovery
  • rebekka.wachter@asu.edu
  • Phone: 480-965-8188
  • ‌
  • BD-C563 Biodesign C TEMPE, AZ 85287
  • ‌
  • ‌
Biography Research Teaching
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Long Bio

Dr. Wachter is currently Emerita Professor of Chemistry and Biochemistry in the School of Molecular Sciences at Arizona State University. She is member of the Biodesign Center for Structural Discovery and the Center for Bioenergy and Photosynthesis at ASU. Dr. Wachter received her PhD in Chemistry from the University of Oregon (Eugene, OR) in 1996, then carried out postdoctoral work at the Institute of Molecular Biology at the University of Oregon. She obtained a position as Assistant Professor at ASU in 2001, was promoted to Associate Professor in 2007, and to Full Professor in 2016.  Her research interests concern the structure, function and dynamics of enzymes and large protein assemblies, with particular focus on the maturation of fluorescent proteins and the regulation of biological carbon fixation.

 

 

 

Education

Ph.D. University of Oregon 1996

Google Scholar URL
https://scholar.google.com/citations?hl=en&user=Ysc9UoIAAAAJ&view_op=list_works…
Research Interests

The Wachter laboratory is interested in understanding how a protein’s three-dimensional structure, dynamic motions and self-assembly guide its biological function.  Research efforts are primarily focused on chemo-mechanical motor proteins and chromophore-bearing proteins.  The experimental approach comprises a variety of biophysical methods, with some emphasis on macromolecular X-ray crystallography, protein engineering, mechanistic enzymology, spectroscopic methods and computer modeling.

  • Re-engineering Photosynthesis: The regulation of biological carbon fixation.  We are interested in understanding the conformational transitions, subunit assembly and catalytic mechanism of Rubisco activase (Rca).  This ATP-driven molecular motor protein regulates carbon assimilation by releasing inhibitors from the enzyme Rubisco, the primary carbon-fixing enzyme in nature. In the chloroplast of higher plants, Rca modulates the level of CO2 fixation as a function of stromal energy charge and temperature. Therefore, the “fitness” of the Rubisco-Rca system has broad implications with respect to global carbon cycles, opening the door to co-engineering efforts for improved performance in a changing climate.
  • Protein self-modification reactions: Light capture and energy conversion in GFP-like proteins. In this project area, we are interested in fluorescent protein maturation, a process that involves the spontaneous biogenesis of an intrinsic chromophore and leads to the acquisition of a variety of colors.  The buried fluorophore is optically tuned by specific interactions with the surrounding protein matrix.  Our work on the mechanism of green-to-red photoconversion in Kaede-type GFPs has opened the door to a new research area in dynamics-driven protein evolution.

 

Publications

  • Breen, B., Whitlegge, J. P., Wachter, R. M. Kinetic isotope effect reveals rate-limiting step in green-to-red photoconvertible fluorescent proteins. Protein Science 33, e5069. doi: https://doi.org/10.1002/pro.5069

  • Krueger, T. D., Tang, L, Chen, C.,  Zhu, L., Breen, I. B., Wachter, R. W.,  Fang, C. (2023) To twist or not to twist: From chromophore structure to dynamics inside engineered photoconvertible and photoswitchable fluorescent proteins. Protein Science 32, e4517. doi:  https://doi.org/10.1002/pro.4517.

  • Krueger, T.D.; Tang, L.; Zhu, L.; Breen, I.L.; Wachter, R.M.; Fang, C. (2020) Dual Illumination Enhances Transformation of an Engineered Green-to-Red Photoconvertible Fluorescent Protein.  Angewandte Chemie-International Edition.  59, (4) 1644-1652, https://pubmed.ncbi.nlm.nih.gov/31692171/

  • Serban, A.J.; Breen, I.L.; Bui, H.Q.; Levitus, M.; Wachter, R.M. (2018) Assembly-disassembly is coupled to the ATPase cycle of tobacco Rubisco activase.  Journal of Biological Chemistry.  293, 50, 19451-19465, https://www.jbc.org/content/293/50/19451.short

  • Fristedt, R.; Hu, C.; Wheatley, N.; Roy, L.M.; Wachter, R.M.; Savage, L.; Harbinson, J.; Kramer, D.M.; Merchant, S.S.; Yeates, T.; Croce, R. (2018) RAF2 is a RuBisCO assembly factor in Arabidopsis thaliana.  Plant Journal.  94, 1, 146-156, https://onlinelibrary-wiley-com.ezproxy1.lib.asu.edu/doi/full/10.1111/t…

  • Wang, Quan; Serban, Andrew J.; Wachter, Rebekka M.; Moerner, W. E. (2018) Single-molecule diffusometry reveals the nucleotide-dependent oligomerization pathways of Nicotiana tabacum Rubisco activase.  Journal of Chemical Physics.  148, 12, https://doi-org.ezproxy1.lib.asu.edu/10.1063/1.5005930

  • Wachter, R.M. (2017) Photoconvertible Fluorescent Proteins and the Role of Dynamics in Protein Evolution.  Perspective. Int. J. Mol. Sci. 18, 1792, doi:10.3390/ijms18081792.

  • Peterson-Forbrook, D., Hilton, M.T., Henderson, J.N., Tichacek, L., Bui, H.B., Wachter, R.M. (2017) Nucleotide Dependence of Subunit Rearrangements in Short-form Rubisco Activase from Spinach Biochemistry 56, 4906-4921 (doi: 10.1021/acs.biochem.7b00574)

  • Wachter, R.M. (2017) A Peptide Adhesive Molded by Magnesium Glues Rubisco’s Subunits Together. J. Biol. Chem. 292, 6851-6852. doi:10.1074/jbc.H116.767145.

  • Doerner, K., Martin-Garcia, J.M., Kupitz, C., Gong, Z., Mallet, T.C., Chen, L., Wachter, R.M., Fromme, P.  (2016) Characterization of Protein Nanocrystals Based on the Reversibility of Crystallization. Cryst. Growth Des. 16, 3838-3845. 

  • Abdallah, B. G., Zatsepin, N. A., Roy-Chowdhury, S., Coe, J., Conrad, C. E., Dörner, K., Sierra, R. G., Stevenson, H. P., Camacho-Alanis, F., Grant, T. D., Nelson, G., James, D. R., Calero, G., Wachter, R. M., Spence, J. C. H., Weierstall, U., Fromme, P., Ros, A. (2015).  XFEL Diffraction from Protein Nanocrystals Isolated Using a Microfluidic Sorter.  Structural Dynamics 2, Article No. 041719.
  • Hazra, S., Henderson, J. N., Liles, K., Hilton, M., Wachter, R. M. (2015) Regulation of Rubisco Activase: Product Inhibition, Cooperativity, and Magnesium Activation. J. Biol. Chem. 290, 24222-24236.
  • Zook, J., Mo, G., Sisco, N., Craciunescu, F., Hansen, D., Baravati, B., Cherry, B., Wachter, R. M., Van Horn, W., Fromme, P. (2015).  NMR Structure of F. tularensis Virulence Determinant Reveals Structural Homology to Bet v1 Allergen Proteins. Structure 23, 1116-1122.
  • Wachter, R. M. and Henderson, J. N. (2015) Rubisco Rescue.  News & Views, Nature Plants 1, Article No. 14010 (epub January 8, 2015).
  • Kim, H., Zou, T., Modi, C., Doerner, K., Grunkemeyer, T. J., Chen, L., Fromme, R., Matz, M. V., Ozkan, B., Wachter, R. M. (2015).  A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins.  Structure 23, 34-43 (epub 12/31/2014).  International Press Release.
  • Kuriata, A. M., Chakraborty, M., Henderson, J. N., Hazra, S., Serban, A. J., Pham, T. V. T., Levitus, M., Wachter, R. M. (2014). ATP and Magnesium Promote Rubisco Activase Hexamer Formation at Low Micromolar Concentrations.  Biochemistry 53, 7232–7246 (epub 10/30/2014). 
  • Martin-Garcia, J., Hansen, D., Zook, J., Loskutov, A., Robida, M., Craciunescu, F, Sykes, K., Wachter, R. M., Fromme, P., Allen, J. P. (2014). Purification and Biophysical Characterization of the CapA Membrane Protein FTT0807 from Francisella tularensis. Biochemistry 53, 1958-1970. 
  • Kim, H., Grunkemeyer, T. J., Modi, C., Chen, L., Fromme, R., Matz, M. V., Wachter, R. M. (2013), Acid-Base Catalysis and Crystal Structures of a Least-Evolved Ancestral GFP-like Protein Undergoing Green-to-Red Photoconversion. Biochemistry 52, 8048-8059.  Highlighted on the Journal’s Home Page.  
  • Wachter, R. M., Salvucci, M. E., Carmo-Silva, A. E., Barta, C., Genkhov, T., Spreitzer, R. J. (2013), Activation of Interspecies-hybrid Rubisco Enzymes to Assess Different Models for the Rubisco – Rubisco Activase interaction.  Photosynth. Res. 117, 557-566. 
  • Kennis, J. T. M., van Stokkum, I. H. M., Peterson, D. S., Pandit, A., Wachter, R. M. (2013), Ultrafast Proton Shuttling in Psammocora Cyan Fluorescent Protein. J. Phys. Chem. B117, 11134-11143. 
  • Watkins, J. L., Kim, H., Markwardt, M. L., Chen, L., Fromme, R., Rizzo, M. A., Wachter, R. M. (2013) The 1.6 Å structure of a FRET-optimized Cerulean Fluorescent Protein.  Acta Crystallogr. D69, 767-773.  
  • Henderson, J. N., Hazra, S., Dunkle, A. M., Salvucci, M. E., Wachter, R. M. (2013) Biophysical Characterization of Higher Plant Rubisco Activase. Biophys. Biochim. Acta 1834, 87-97. 
  • Chakraborty, M., Kuriata, A. M., Henderson, J. N., Salvucci, M. E., Wachter, R. M., Levitus, M. (2012) Protein Oligomerization Monitored by Fluorescence Fluctuation Spectroscopy: Self-Assembly of Rubisco Activase.  Biophys. J. 103, 949-958.  
  • Henderson, J. N., Kuriata, A. M., Fromme, R., Salvucci, M. E., Wachter, R. M. (2011) Atomic Resolution X-ray Structure of the Substrate Recognition Domain of Higher Plant Rubisco Activase.  J. Biol. Chem. 286, 35683-35688.  
  • Markwardt, M. L., Kremers, G.-J., Kraft, C. A., Ray, K., Cranfill, P. J. C., Wilson, K. A., Day, R. N., Wachter, R. M., Davidson, M. W., Rizzo, M. A. (2011) An Improved Cerulean Flourescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching.  PlosOne 6, e17896. 
  • Wachter, R. M., Watkins, J. L., Kim, H. (2010) Mechanistic Diversity of Red Fluorescence Acquisition by GFP-like Proteins. Biochemistry 49, 7417-7427.  Current Topics Invited Review. Highlighted on the Journal’s Home Page. 
  • Barta, C., Dunkle, A. M., Wachter, R. M., Salvucci, M. E. (2010) Structural Changes Associated with the Acute Thermal Instability of Rubisco Activase. Arch. Biochem. Biophys. 499, 17-25. 
  • Pouwels, L. J., Zhang, L., Chan, N. H., Dorrestein, P. C., Wachter, R. M.  (2008) Kinetic Isotope Effect Studies on the de novo Rate of Chromophore Formation in Fast- and Slow-maturing GFP Variants.  Biochemistry 47, 10111-10122.
  • Malo, G. D., Wang, M., Wu, D., Stellin, A., Tonge, P. J., Wachter, R. M.  (2008) Crystal Structure and Raman Studies of dsFP483, a Cyan Fluorescent Protein from Discosoma striata.  J. Mol. Biol. 378, 869-884.
  • Malo, G. D., Pouwels, L. J., Wang, M., Weichsel, A., Montfort, W. R., Rizzo, M. A., Piston, D. W., Wachter, R. M. (2007). X-ray Structure of Cerulean GFP: A Tryptophan-Based Chromophore Useful for Fluorescence Lifetime Imaging.  Biochemistry 46, 9865-9873.  Accelerated Publication. Featured as “Hot Article”, Featured on the Journal’s Most Accessed Articles Website. 
  • Wachter, R. M. (2007).   Chromogenic Cross-link Formation in Green Fluorescent Protein.  Acc. Chem. Res. 40, 120-127.  Invited Review. 
  • Zhang, L., Patel, H. N., Lappe, J. W., Wachter, R. M. (2006).  Reaction Progress of Chromophore Biogenesis in Green Fluorescent Protein.  J. Am. Chem. Soc. 128, 4766-4772. 
  • Wachter, R. M. (2006).  The family of GFP-like proteins: Structure, Function, Photophysics and Biosensor Applications.  Introduction and Perspective, Symposium-in-print, Photochem. Photobiol. 82, 339-344.  Invited Review.  
  • Wachter, R. M. (2006).  Mechanistic Aspects of GFP Chromophore Biogenesis.  Progress in Biomedical Optics and Imaging 7. Proc. of SPIE Vol. 6098, 609803-1 – 609803-8.  Keynote Paper.
  • Wang, M., Patel, H. N., Wachter, R. M. (2005).  X-ray Diffraction Analysis and Molecular Replacement Solution of the Cyan Fluorescent Protein dsFP483.  Acta Crystallogr. F61, 922-924. 
  • Sniegowski, J. A., Phail, M. E., Wachter, R. M. (2005).  Maturation Efficiency, Trypsin Sensitivity and Optical Properties of Arg96, Glu222 and Gly67 Variants of Green Fluorescent Protein.  Biochem. Biophys. Res. Comm. 332, 657-663. 
  • Scruggs, A. W., Flores, C. L., Wachter, R. M., Woodbury, N. W. (2005).  Development and Characterization of Green Fluorescent Protein Mutants with Altered Lifetimes.  Biochemistry 44, 13377- 13384. 
  • Rosenow, M. A., Patel, H. N, Wachter, R. M. (2005).  Oxidative Chemistry in the GFP Active Site Leads to Covalent Cross-Linking of a Modified Leucine Side Chain with a Histidine Imidazole:  Implications for the Mechanism of Chromophore Formation.  Biochemistry 44, 8303-8311. 
  • Sniegowski, J. A., Lappe, J. W., Patel, H. N., Huffman, H. A., Wachter, R. M. (2005).  Base-catalysis of Chromophore Fromation in Arg96 and Glu222 variants of Green Fluorescent Protein.  J. Biol. Chem. 280, 26248-26255. 
  • Remington, S. J., Wachter, R. M., Yarbrough, D. K., Branchaud, B. P., Anderson, D. C., Kallio, K., Lukyanov, K. A. (2005).  zFP538, a Yellow Fluorescent Protein from Zoanthus, Contains a Novel Three-Ring Chromophore.  Biochemistry 44, 202-212.  “Top ten most cited”, Year 2005.
  • Rosenow, M. A., Huffman, H. A., Phail, M. E., Wachter, R. M. (2004).  The Crystal Structure of the Y66L Variant of Green Fluorescent Protein Supports a Cyclization-Oxidation-Dehydration Mechanism for Chromophore Maturation.  Biochemistry 43, 4464-4472. 
  • Wachter, R. M. (2004).  Focus Note: The Art of Disentangling Difference Electron Density Maps:  Snapshots of Early States in the Photoactive Yellow Protein Photocycle?  Photochem. Photobiol. 80, No.1, ix-x.  Invited Editorial.
  • Bell, A. F., Stoner-Ma, D., Wachter, R. M., Tonge, P. J. (2003).  Light Driven Decarboxylation of Wild-Type Green Fluorescent Protein.  J. Am. Chem. Soc. 125, 6919-6926. 
  • Yarbrough, D., Wachter, R. M., Kallio, K., Matz, M. V., Remington, S. J. (2001).  Refined Crystal Structure of DsRed, a Red Fluorescent Protein from Coral, at 2.0 Å Resolution.  Proc. Natl. Acad. Sci. USA 98, 462-467. 
  • Wachter, R. M., Yarbrough, D., Kallio, K., Remington, S. J. (2000).  Crystallographic and Energetic Analysis of Binding of Selected Anions to the Yellow Variants of Green Fluorescent Protein.  J. Mol. Biol. 301, 159-173. 
  • Bell, A. F., He, X., Wachter, R. M., Tonge, P. J. (2000).  Probing the Ground State Structure of the Green Fluorescent Protein Chromophore Using Raman Spectroscopy.  Biochemistry 39, 4423-4431. 
  • Jayaraman, S.,  Haggie, P.,  Wachter, R. M.,  Remington, S. J.,  Verkman, A. S. (2000).  Mechanism and Cellular Applications of a Green Fluorescent Protein-based Halide Sensor.  J. Biol. Chem. 275, 6047-6050. 
  • Wachter, R. M., Remington, S. J. (1999).  Sensitivity of the YFP Form of Green Fluorescent Protein to Halides and Nitrate.  Curr. Biol. 9, R628-R629. 
  • Elsliger, M.-A.,  Wachter, R. M.,  Kallio, K.,  Hanson, G. T.,  Remington, S. J. (1999).  Structural and Spectral Response of Green Fluorescent Protein Variants to Changes in pH.  Biochemistry  38, 5296-5301. 
  • Wachter, R. M., Elsliger, M.-A.,  Kallio, K.,  Hanson, G. T.,  Remington, S. J. (1998).  Structural Basis of Spectral Shifts in the Yellow-emission Variants (YFPs) of Green Fluorescent Protein.  Structure 6, 1267-1277. 
  • Wachter, R. M., Branchaud, B. P. (1998).  Construction and Analysis of a Semi-quantitative Energy Profile for the Reaction Catalyzed by the Radical Enzyme Galactose Oxidase.  Biochim. Biophys. Acta  1384, 43-54. 
  • Wachter, R. M., King, B. A.,  Heim, R.,  Kallio, K.,  Tsien, R. Y.,  Boxer, S. G.,  Remington, S. J. (1997).  Crystal Structure and Photodynamic Behavior of the Blue-emission Variant Y66H/Y145F of Green Fluorescent Protein.  Biochemistry 36, 9759-9765. 
  • Wachter, R. M., Montague-Smith, M. P.,  Branchaud, B. P. (1997).  Beta-Haloethanol Substrates as Probes for Radical Mechanisms for Galactose Oxidase.  J. Am. Chem. Soc. 119, 7743-7749. 
  • Wachter, R. M.,  Branchaud, B. P. (1996).  Thiols as Mechanistic Probes for Catalysis by the Free Radical Enzyme Galactose Oxidase.  Biochemistry 35, 14425-14435. 
  • Wachter, R. M., Branchaud, B. P (1996). Molecular Modeling Studies on Oxidation of Hexopyranoses by Galactose Oxidase.  An Active Site Topology Apparently Designed to Catalyze Radical Reactions, Either Concerted or Stepwise.  J. Am. Chem. Soc. 118, 2782-2789. 
  • Montague-Smith, M. P., Wachter, R. M., Branchaud, B. P. (1992).  Preparation of Fully Oxidized Active and Reduced Inactive Forms of Galactose Oxidase from Dactylium dendroides Using Ferricyanide-containing Oxidizing and Ferrocyanide-containing Reducing Forms of Ion Exchange Resins.  Anal. Biochem. 207, 353-355.
  • Serban, A. J., Hilton, M. T., Bui, H. B., Henderson, J. N., Levitus, M., Wachter, R. M. (2018)  Assembly-disassembly is coupled to the ATPase cycle of tobacco Rubisco activase.  J. Biol. Chem. 293, 19451-19465.
Research Activity
  • Re-engineering Photosynthesis: The regulation of biological carbon fixation.  We are interested in understanding the conformational transitions, subunit assembly and catalytic mechanism of Rubisco activase (Rca).  This ATP-driven molecular motor protein regulates carbon assimilation by releasing inhibitors from the enzyme Rubisco, the primary carbon-fixing enzyme in nature. In the chloroplast of higher plants, Rca modulates the level of CO2 fixation as a function of stromal energy charge and temperature. Therefore, the “fitness” of the Rubisco-Rca system has broad implications with respect to global carbon cycles, opening the door to co-engineering efforts for improved performance in a changing climate.
  • Protein self-modification reactions: Light capture and energy conversion in GFP-like proteins. In this project area, we are interested in fluorescent protein maturation, a process that involves the spontaneous biogenesis of an intrinsic chromophore and leads to the acquisition of a variety of colors.  The buried fluorophore is optically tuned by specific interactions with the surrounding protein matrix.  Our work on the mechanism of green-to-red photoconversion in Kaede-type GFPs has opened the door to a new research area in dynamics-driven protein evolution.
Courses
2024 Summer
Course Number Course Title
BDE 792 Research
2024 Spring
Course Number Course Title
BDE 799 Dissertation
BDE 792 Research
BDE 795 Continuing Registration
BDE 799 Dissertation
2023 Summer
Course Number Course Title
BDE 792 Research
2023 Spring
Course Number Course Title
BDE 799 Dissertation
BDE 792 Research
BDE 795 Continuing Registration
BDE 799 Dissertation
2022 Summer
Course Number Course Title
BDE 792 Research
2022 Spring
Course Number Course Title
BDE 799 Dissertation
BDE 792 Research
BDE 792 Research
BDE 795 Continuing Registration
BDE 799 Dissertation
2021 Summer
Course Number Course Title
BDE 792 Research
2021 Spring
Course Number Course Title
BDE 799 Dissertation
BDE 792 Research
2020 Summer
Course Number Course Title
BDE 792 Research
2020 Spring
Course Number Course Title
BDE 799 Dissertation
BDE 792 Research
Expertise Areas
Biochemistry
Organic Chemistry
Physical Chemistry
Proteins
X-ray Crystallography
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