Publications

2023

77. Sementilli, A., Rengifo, R., Twahir, U., Kim, Y., Yue, J., Li, W., Stewart, A., Mehta, A., Stewart, K., Shearer, J., Warncke, K., and Lynn, D. G. (2023). Engineering synthetic electron transfer chains from metallopeptide membranes, (submitted).
76. Scasny, A., Alibayov, B., Khan, F., Rao, S. J., Murin, L., Vidal, A. G. J., Smith, P., Li, W., Edwards, K., Warncke, K., and Vidal, J. E. (2023). Streptococcus pneumoniae collapses the cell cytoskeleton and disrupts mitochondrial respiration leading to cytotoxicity of human lung cells, (submitted).
75. Whitcomb, K. L., and Warncke, K. (2023). Oligomeric and fibrillar alpha-synuclein display persistent dynamics and compressibility under controlled confinement, ACS Chem. Neurosci. (under revision).
74. Li, W., and Warncke, K. (2023). Native and non-native reactions in ethanolamine ammonia-lyase are actuated by different dynamics, Biophys. J. (accepted).
73. Li, W., Kohne, M., and Warncke, K. (2023). Reactivity tracking of an enzyme progress coordinate, J. Phys. Chem. Lett. 14, 7157-7164.

2022

72. Li, W., Whitcomb, K. L., and Warncke, K. (2022). Confinement Dependence of Protein-Associated Solvent Dynamics around Different Classes of Proteins, from the EPR Spin Probe Perspective, Phys. Chem. Chem. Phys., 24(38), 23919-23928.
71. Kohne, M., Li, W., Ionescu, A., Zhu, C., and Warncke, K. (2022). Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase, Methods Enzymol. 668, 229-259.
70. Li, W., Nforneh, B., Whitcomb, K. L., and Warncke, K. (2022). Resolution and characterization of confinement- and temperature-dependent dynamics in solvent phases that surround proteins in frozen aqueous solution by using spin-probe EPR spectroscopy, Methods Enzymol. 666, 25-57.

2021

69. Ionescu, A., Li, W., Nforneh, B., and Warncke, K. (2021). Coupling of ethanolamine ammonia-lyase protein and solvent dynamics characterized by the temperature-dependence of EPR spin probe mobility and dielectric permittivity, J. Chem. Phys., 154(17), 175101.

2020

68. Li, Z., Greenhalgh, E. D., Twahir, U. T., Kallon, A., Ruetz, M., Warncke, K. Brunold, T. C. and Banerjee, R. (2020). Chlorocob(II)alamin Formation Which Enhances the Thiol Oxidase Activity of the B12-Trafficking Protein CblC, Inorganic Chemistry, 59(21), 16065-16072.
67. Li, Z., Mascarenhas, R., Twahir, U.T., Kallon, A., Deb, A., Yaw, M., Penner-Hahn, J.E., Koutmos, M., Warncke, K. and Banerjee, R. (2020). An interprotein Co-S coordination complex in the B12-trafficking pathway, J. Am. Chem. Soc. 142, 16334–16345.

2019

66. Ruetz, M., Campanello, G. C., Purchal, M., Shen, H., McDevitt, L., Gouda, H., Wakabayashi, S., Zhu, J., Rubin, E., Warncke, K., Mootha, V., Koutmos, V. and Banerjee, R. (2019). Itaconyl-CoA forms a stable biradical in methylmalonyl-CoA mutase and derails its activity and repair, Science, 366(6465), 589–593.
65. Wu, X., Gordon, O., Jiang, W., Antezana, B.S., Angulo-Zamudio, U., del Rio, C., Moller, A., Brissac, T., Tierney, A.R., Warncke, K. and Orihuela, C.J. (2019). Interaction between Streptococcus pneumoniae and Staphylococcus aureus generates •OH radicals that rapidly kills Staphylococcus aureus strains, Journal of Bacteriology, JB-00474.
64. Kohne, M., Li, W., Zhu, C., and Warncke, K. (2019). Radical Reaction Pathway Redundancy Revealed by Blocking Catalysis-Coupled Protein Reconfiguration in B12-Dependent Ethanolamine Ammonia-Lyase, Biochemistry, 58(35), 3683-3690.
63. Chen, G., Luo, Y., Warncke, K., Sun, Y., David, S. Y., Fu, H., ... & Lammers, M. (2019). Acetylation regulates ribonucleotide reductase activity and cancer cell growth, Nature Communications, 10(1), 3213.
62. Nforneh, B., and Warncke, K. (2019). Control of solvent dynamics around the B12-dependent ethanolamine ammonia-lyase enzyme in frozen aqueous solution by using dimethyl sulfoxide modulation of mesodomain volume, The Journal of Physical Chemistry B, 123(26), 5395-5404.

2018

61. Huang, Y., Xu, Z., Jin, S., Li, C., Warncke, K., Evangelista, F., Lian, T., and Egap, E. (2018) Conjugatd oligomers with stable radical substituents: Synthesis, single crystal structures, electronic structure, and excited state dynamics, Chem. Mater., 30(21), 7840-7851.
60. Campanello, G. O., Ruetz, M., Dodge, G. J., Gouda, H., Gupta, A., Twahir, U. T., Killian, M. M., Watkins, D., Rosenblatt, D. S., Brunold, T. C., Warncke, K., Smith, J. L., and Banerjee, R. (2018) Sacrificial cobalt-carbon bond homolysis in coenzyme B12 as a cofactor conservation strategy, J. Am. Chem. Soc. 140, 13205-13208.
59. Ucuncuoglu, N., and Warncke, K.(2018) Protein configurational states guide radical rearrangement catalysis in ethanolamine ammonia-lyase, Biophys. J. 114, 2775-2786.

2017

58. Nforneh, B., & Warncke, K. (2017). Mesodomain and Protein-Associated Solvent Phases with Temperature-Tunable (200–265 K) Dynamics Surround Ethanolamine Ammonia-Lyase in Globally Polycrystalline Aqueous Solution Containing Dimethyl Sulfoxide. The Journal of Physical Chemistry B, 121(49), 11109-11118.
57. Nforneh, B., Bovell, A. M., & Warncke, K. (2018) Electron spin-labelling of the EutC subunit in B12-dependent ethanolamine ammonia-lyase reveals dynamics and a two-state conformational equilibrium in the N-terminal, signal-sequence-associated domain. Free radical research, 52(3), 307-318.
56. Kohne, M., Zhu, C., & Warncke, K. (2017) Two dynamical regimes of the substrate radical rearrangement reaction in B12-dependent ethanolamine ammonia-lyase resolve contributions of native protein configurations and collective configurational fluctuations to catalysis. Biochemistry, 56(25), 3257-3264.
55. Li, Z., Kitanishi, K., Twahir, U. T., Cracan, V., Chapman, D., Warncke, K., and Banerjee, R. (2017) Cofactor editing by the G-protein metallochaperone domain regulates the radical B12 enzyme IcmF, J. Biol. Chem. 292, 3977-3987.

2016 and Before

54. Wang, M., Zhu, C., Kohne, M., and Warncke, K. (2015) Resolution and characterization of chemical steps in enzyme catalytic sequences by using low-temperature and time-resolved, full-spectrum EPR spectroscopy in fluid cryosolvent and frozen solution systems, Methods Enzymol. 563, 59-94.
53. Wang, M., and Warncke, K. (2013) Entropic origin of cobalt-carbon bond cleavage catalysis in adenosylcobalamin-dependent ethanolamine ammonia-lyase, J. Am. Chem. Soc. 135, 15077-15084.
52. Hernandez-Guzman, J., Sun, L., Mehta, A. K., Dong, J., Lynn, D. G., and Warncke, K. (2013) Copper(II)-bis-histidine coordination structure in a fibrillar amyloid-b peptide fragment and model complexes revealed by using electron spin echo envelope modulation spectroscopy, ChemBioChem 14, 1762-1771.
51. Sun, L., Savory, J. J., and Warncke, K. (2013) Design and implementation of an FPGA-based timing pulse programmer for pulsed-electron paramagnetic resonance applications, Concept Magnetic Res. B: Magn. Reson. Engineering 43, 100-109.
50. Robertson, W. D., Bovell, A. M., and Warncke, K. (2013) Development of a protein-integrated, cobalt-corrin catalyst for hydrogen production under green conditions, J. Biol. Inorg. Chem. 18, 701-713.
49. Chen, H., Sun, L., and Warncke, K. (2013) Heterogeneous ordered-disordered structure of the mesodomain in frozen sucrose-water solutions revealed by multiple electron paramagnetic resonance spectroscopies, Langmuir Article ASAP.
48. Bovell, A. M., and Warncke, K. (2013) Structure model of Salmonella typhimurium ethanolamine ammonia-lyase directs a rational approach to the assembly of the functional [(EutB-EutC)2]3 oligomer from isolated subunits, Biochemistry 52, 1419-1428.
47. Gunderson, W. A., Hernandez-Guzman, J., Karr, J. W., Sun, L., Szalai, V. A., and Warncke, K. (2012) Local structure and global patterning of Cu2+ binding in fibrillar amyloid-b protein, J. Am. Chem. Soc. 134, 18330-18337.
46. Robertson, W. D., Wang, M., and Warncke, K. (2011) Characterization of Protein Contributions to Cobalt-Carbon Bond Cleavage Catalysis in Adenosylcobalamin-Dependent Ethanolamine Ammonia-Lyase by using Photolysis in the Ternary Complex, J. Am. Chem. Soc. 133, 6968-6977.
45. Zhu, C., and Warncke, K. (2010) Kinetic Isolation and Characterization of the Radical Rearrangement Step in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase, J. Am. Chem. Soc. 132, 9610-9615.
44. Sun, L., Hernandez-Guzman, J., and Warncke, K. (2009) OPTESIM, a versatile toolbox for numerical simulation of electron spin echo envelope modulation (ESEEM) that features hybrid optimization and statistical assessment of parameters, J. Magn. Reson.200, 21-28. (Cover Article)
43. Robertson, W. D., and Warncke, K. (2009) Photolysis of Adenosylcobalamin and Radical Pair Recombination in Ethanolamine Ammonia-Lyase Probed on the Micro- to Millisecond Time Scale by using Time-Resolved Optical Absorption Spectroscopy, Biochemistry 48, 140-147.
42. Zhu, C., and Warncke, K. (2008) Reaction of the CoII-Substrate Radical Pair Catalytic Intermediate in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase in Frozen Aqueous Solution from 190 to 217 Kelvin, Biophys. J. 95, 5890-5900.
41. Wang, M., and Warncke, K. (2008) Kinetic and Thermodynamic Characterization of CoII-Substrate Radical Pair Formation in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase in a Cryosolvent System by using Time-Resolved, Full-Spectrum Continuous-Wave Electron Paramagnetic Resonance Spectroscopy, J. Am. Chem. Soc. 130, 4846-4858.
40. Sun, L., Groover, O. A., Canfield, J. M., and Warncke, K. (2008) Critical role of arginine 160 of the EutB protein subunit for active site structure and radical catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase, Biochemistry 47, 5523-5535.
39. Dong, J., Canfield, J. M., Mehta, A. K., Shokes, J. E., Tian, B., Childers, W. S., Simmons, J. A., Mao, Z., Scott, R. A., Warncke, K., and Lynn, D. G. (2007) Engineering metal ion coordination to regulate amyloid fibril assembly and toxicity, Proc. Natl. Acad. Sci. 104, 13313-13381.
38. Sun, L., and Warncke, K. (2006) Comparative model of EutB from coenzyme B12-dependent ethanolamine ammonia-lyase reveals a b8a8, TIM-barrel fold and radical catalytic site structural features, Proteins 64, 308-319.
37. Warncke, K. (2005) Characterization of the Product Radical Structure in the CoII-Product Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase by using Three-Pulse 2H ESEEM Spectroscopy, Biochemistry 44, 3184-3193.
36. Canfield, J. M., and Warncke, K. (2005) Active Site Reactant Center Geometry in the CoII-Product Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase Determined by Using Orientation-Selection-ESEEM Spectroscopy, J. Phys. Chem. B 109, 3053-3064.
35. Warncke, K., and Canfield, J. M. (2004) Direct Determination of Product Radical Structure Reveals the Radical Rearrangement Pathway in a Coenzyme B12-Dependent Enzyme, J. Am. Chem. Soc. 126, 5930-5931.
34. Khoroshun, D. V., Warncke, K., Ke, S.-C., Musaev, D. G., and Morokuma, K. (2003) Internal Degrees of Freedom, Structural Motifs and Conformational Energetics of 5'-Deoxyadenosyl Radical: Implications for Function in Adenosylcobalamin-Dependent Enzymes.? A Computational Study, J. Am. Chem. Soc. 125, 570-579.
33. Canfield, J. M., and Warncke, K. (2002) Geometry of Reactant Centers in the CoII-Substrate Radical Pair State of Coenzyme B12-Dependent Ethanolamine Deaminase Determined by using Orientation-Selection-ESEEM Spectroscopy, J. Phys. Chem. B 106, 8831-8841.
32. Warncke, K., and Utada, A. S. (2001) Interaction of the Substrate Radical and the 5'-Deoxyadenosine-5'-Methyl Group in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase, J. Am. Chem. Soc. 123, 8564-8572.
31. Warncke, K., and Perry, M. S. (2001) Redox State Dependence of Rotamer Distributions in Tyrosine and Neutral Tyrosyl Radical, Biochim. Biophys. Acta 1545, 1-5.
30. Trommel, J. S., Warncke, K., and Marzilli, L. G. (2001) Assessment of the Existence of Hyper-Long Axial Co(II)-N Bonds in Cobinamide B12 Models by Using Electron Paramagnetic Resonance Spectroscopy, J. Am. Chem. Soc. 123.
29. Warncke, K., Schmidt, J. C., and Ke, S.-C. (1999) Identification of a Rearranged-Substrate, Product Radical Intermediate and the Contribution of a Product Radical Trap in Vitamin B12 Coenzyme-Dependent Ethanolamine Deaminase Catalysis, J. Am. Chem. Soc. 121, 10522-10528.
28. Torrent, M., Musaev, D. G., Morokuma, K., Ke, S.-C., and Warncke, K. (1999) Calculation of Nuclear Quadrupole Parameters in Imidazole Derivatives and Extrapolation to Coenzyme B12. A Theoretical Study, J. Phys. Chem. B 103, 8618-8627.
27. Ke, S. C., and Warncke, K. (1999) Interactions of substrate and product radicals with CoII in cobalamin and with the active site in ethanolamine deaminase, characterized by ESE-EPR and 14N ESEEM spectroscopies, J. Am. Chem. Soc. 121.
26. Ke, S. C., Torrent, M., Museav, D. G., Morokuma, K., and Warncke, K. (1999) Identification of Dimethylbenzimidazole Axial Coordination and Characterization of 14N Superhyperfine and Nuclear Quadrupole Coupling in Cob(II)alamin Bound to Ethanolamine Deaminase in a Catalytically-Engaged Substrate Radical-Cobalt(II) Biradical State, Biochemistry 38, 12681-12689.
25. Babcock, G. T., Espe, M., Hoganson, C., Lydakis-Simantiris, N., McCracken, J., Shi, W., Styring, S., Tommos, C., and Warncke, K. (1997) Tyrosyl radicals in enzyme catalysis: some properties and a focus on photosynthetic water oxidation, Acta Chemica Scandinavica 51, 533-540.
24. Warncke, K., Babcock, G. T., and McCracken, J. (1996) Static Conformational Distributions in the Solid State: Analysis and Application to Angular Dispersion in Side Chain Orientations in Model Tyrosine in Aqueous Glass, J. PHys. Chem. 100, 4654-4661.
23. Warncke, K., Tang, X.-S., Tommos, C., Babcock, G. T., Diner, B. A., and McCracken, J. (1995) Static side chain conformational distribution in the YZ tyrosine radical in manganese-depleted, YD- photosystem II, Photosynthesis: From Light to Biosphere, Proceedings of the International Photosynthesis Congress, 10th, Montpellier, Fr., Aug. 20-25, 1995 1, 711-714.
22. Warncke, K., and McCracken, J. (1995) Analysis of static distributions in hydrogen hyperfine interactions in randomly oriented radicals in the solid state by using 2H electron spin echo envelope modulation spectroscopy: conformational dispersion of b-2H coupling in the model tyrosyl radical, J. Chem. Phys. 103, 6829-6840.
21. Warncke, K., Brooks, H. B., Lee, H.-i., McCracken, J., Davidson, V. L., and Babcock, G. T. (1995) Structure of the Dithionite-Generated Tryptophan Tryptophyloquinone Cofactor Radical in Methylamine Dehydrogenase Revealed by ENDOR and ESEEM Spectroscopies, J. Am. Chem. Soc. 117, 10063-10075.
20. Tommos, C., Tang, X.-S., Warncke, K., Hoganson, C. W., Styring, S., McCracken, J., Diner, B. A., and Babcock, G. T. (1995) Spin-Density Distribution, Conformation, and Hydrogen Bonding of the Redox-Active Tyrosine YZ in Photosystem II from Multiple-Electron Magnetic-Resonance Spectroscopies: Implications for Photosynthetic Oxygen Evolution, J. Am. Chem. Soc. 117, 10325-10335.
19. Hoganson, C. W., Lydakis-Simantiris, N., Tang, X.-S., Tommos, C., Warncke, K., Babcock, G. T., Diner, B. A., McCracken, J., and Styring, S. (1995) A hydrogen-atom abstraction model for the function of Yz in photosynthetic oxygen evolution, Photosyn. Res. 46, 177-184.
18. Warncke, K., McCracken, J., and Babcock, G. T. (1994) Structure of the YD Tyrosine Radical in Photosystem II as Revealed by 2H Electron Spin Echo Envelope Modulation (ESEEM) Spectroscopic Analysis of Hydrogen Hyperfine Interactions, J. Am. Chem. Soc. 116, 7332-7340.
17. Warncke, K., and McCracken, J. (1994) 2H electron spin echo envelope modulation spectroscopy of strong, a-hydrogen hyperfine coupling in randomly oriented paramagnetic systems, J. Chem. Phys. 101, 1832-1841.
16. Warncke, K., Gunner, M. R., Braun, B. S., Gu, L., Yu, C.-A., Bruce, J. M., and Dutton, P. L. (1994) Influence of Hydrocarbon Tail Structure on Quinone Binding and Electron-Transfer Performance at the QA and QB Sites of the Photosynthetic Reaction Center Protein, Biochemistry 33, 7830-7841.
15. Warncke, K., Babcock, G. T., Dooley, D. M., McGuirl, M. A., and McCracken, J. (1994) Structure of the Topa-semiquinone Catalytic Intermediate of Amine Oxidase as Revealed by Magnetic Interactions with Exchangeable 2H and 1H Nuclei, J. Am. Chem. Soc. 116, 4028-4037.
14. Warncke, K., and Dutton, P. L. (1993) Influence of QA site redox cofactor structure on equilibrium binding, in situ electrochemistry, and electron-transfer performance in the photosynthetic reaction center protein Biochemistry 32, 4769-4779.
13. Warncke, K., and Dutton, P. L. (1993) Experimental resolution of the free energies of aqueous solvation contributions to ligand-protein binding: Quinone-QA site interactions in the photosynthetic reaction center protein, Proc. Natl. Acad. Sci. 90, 2920-2924.
12. Warncke, K., Brooks, H. B., Babcock, G. T., Davidson, V. L., and McCracken, J. (1993) The nitrogen atom of substrate methylamine is incorporated into the tryptophan tryptophyl-semiquinone catalytic intermediate in methylamine dehydrogenase, J. Am. Chem. Soc. 115, 6464-6465.
11. Moser, C. C., Keske, J. M., Warncke, K., Farid, R. S., and Dutton, P. L. (1993) Electron-transfer mechanisms in reaction centers: engineering guidelines, in The Bacterial Photosynthetic Reaction Center: Structure, Spectroscopy and Dynamics (Norris, J. R., and Deisenhofer, J., Eds.), pp 1-22, Academic Press, New York.
10. Moser, C. C., Keske, J. M., Warncke, K., Farid, R. S., and Dutton, P. L. (1992) Nature of biological electron transfer, Nature 355, 796-802.
9. Moser, C. C., Keske, J. M., Warncke, K., and Dutton, P. L. (1992) Electron transfer in photosynthetic reaction centers, Stud. Phys. Theor. Chem. 78, 111-125.
8. Warncke, K., Gunner, M. R., Giangiacomo, K. M., Keske, J. H., Bruce, J. M., and Dutton, P. L. (1990) Elements of quinone-mediated redox catalysis in the photosynthetic reaction center protein, in The Molecular Basis of Metabolism (Hauska, G., and Thauer, R., Eds.), pp 84-93, Springer-Verlag, Berlin.
7. Warncke, K., and Dutton, P. L. (1990) Effect of cofactor structure on control of electron transfer rates at the QA site of the reaction center protein, in Structure and Function of Bacterial Reaction Centers (Michel-Beyerle, M. E., Ed.), Springer-Verlag, Berlin.
6. Warncke, K., and Dutton, P. L. (1990) Resolution of in situ interaction energies between molecules and the reaction center QA site: implications for electron transfer function, Curr. Res. Photosynth. 1, 157-160.
5. Moser, C. C., Keske, J. H., Warncke, K., and Dutton, P. L. (1990) Electron Transfer in Photosynthetic Reaction Centers, in Electron and Proton Transfer in Chemistry and Biology (Diemann, E., Junge, W., Mueller, A., and Ratajczak, Eds.), pp 198-207, Springer-Verlag, Berlin.
4. Warncke, K., Gunner, M. R., Braun, B. S., Yu, C.-A., and Dutton, P. L. (1987) Hydrocarbon tail structure and its effect on the affinity and kinetic performance of quinones at the QA site in reaction centers of Rhodobactor sphaeroides R26, Prog. Photosynth. Res. 1, 225-227.
3. McCarty, R. E., Davenport, J. W., Ketcham, S. R., Moroney, J. V., Nalin, C. M., Patrie, W. J., and Warncke, K. (1984) Protons, thiols and coupling factor 1 in relation to photophosphorylation, Adv. Photosynth. Res. 2, 371-378.
2. Ketcham, S. R., Davenport, J. W., Warncke, K., and McCarty, R. E. (1984) Role of the gamma subunit of chloroplast coupling factor 1 in the light-dependent activation of photophosphorylation and ATPase activity by dithiothreitol, J. Biol. Chem. 259, 7286-7293.
1. Moroney, J. V., Warncke, K., and McCarty, R. E. (1982) The distance between thiol groups in the gamma subunit of coupling factor 1 influences the proton permeability of thylakoid membranes, J. Bioenerg. Biomembr. 14, 347-359.