Dongmei Ye

Member of the Technical Staff

Author profile picture

Member of the Technical Staff

dye@sandia.gov

(505) 844-2912

Sandia National Laboratories, New Mexico
 P.O. Box 5800
 Albuquerque, NM 87185-0829

Education

Bachelor’s Degree: Chemistry, Jilin University (1987-1991)

Master’s Degree: Chemistry, Jilin University (1991-1994)

Doctoral Degree: Chemistry and Chemical Biology, University of New Mexico (1997-2001)

Postdoctoral Fellowships: Chemistry and Chemical Biology, University of New Mexico (2001-2003)

Ye’s Ph.D. work was focused on protein engineering and enzyme kinetics. She developed a fluorescence reporting system to monitor the structural changes coupled with chemical events of pyruvate phosphate dikinase (PPDK) catalyzed reaction, elucidated the compositions of PPDK active site in catalysis and substrate binding to assist rational design of chemical inhibitors of PPDK, and identified crucial molecular structure at the domain interfaces of PPDK.

Research Interests

Protein Engineering and Kinetics

Ye established the roles of chemical interactions in domain communication and catalysis of PPDK by employing steady state and transient state kinetic analysis. She facilitated the crystal structure analysis of conformational change of PPDK under different catalytic stages by altering the molecular structure of the enzyme, chemical interactions at domain interface, and domain linker structure. Additionally, Ye investigated the role of the domain linkers in separate site catalysis and examined the structure, stability, and catalytic potential in the Engineered Phosphoryl Carrier Domain of PPDK.

Cell Signaling Pathway Regulations

Ye examined the regulatory mechanisms of signaling pathways in cytokine induced intestinal epithelial tight junction malfunction and investigated the role of myosin light chain kinase in tight junction barrier modulation.

Nerve Agent Countermeasure Development

Ye assisted in the cell-free protein synthesis of rationally-designed unnatural amino acid to re-engineer a nerve agent degrading enzyme.

Biomarker Identification using Mass-Spectrometry

Ye developed NanoFlow-MS, UPLC-MS and ASAP-MS methods for biomarker identification.

Relevant Prior Positions

Research Assistant Professor, Department of Internal Medicine, University of New Mexico School of Medicine (2006–2012)

Research Associate Scientist II, Department of Internal Medicine, University of New Mexico School of Medicine (2003–2006)

Awards, Honors, and Memberships

2018 R&D 100 Award: Detergent-Assisted Fabrication (DAF) of Multifunctional Nanomaterials

Publications

  • Rempe, S.B., Ye, D., el Khoury, L., Mobley, D.L., & Mobley, D.L. (2021). Enhancing paraoxon binding to organophosphorus hydrolase active site. International Journal of Molecular Sciences, 22(23). https://doi.org/10.3390/ijms222312624 Publication ID: 77082
  • Ehrhart, B.D., Bran-Anleu, G., Sena, E., Muna, A., Ye, D., Hecht, E.S., Rivkin, C., & Rivkin, C. (2020). Hydrogen Refueling Reference Station Lot Size Analysis for Urban Sites. https://doi.org/10.2172/1604872 Publication ID: 105604
  • Ehrhart, B.D., Bran-Anleu, G., Ye, D., Hecht, E.S., & Hecht, E.S. (2020). Hydrogen Refueling Reference Station Lot Size Analysis for Urban Sites [Presentation]. https://www.osti.gov/biblio/1762823 Publication ID: 70841
  • Ehrhart, B.D., Bran-Anleu, G., Ye, D., Hecht, E.S., & Hecht, E.S. (2020). Hydrogen Refueling Reference Station Lot Size Analysis for Urban Sites [Presentation]. https://www.osti.gov/biblio/1761025 Publication ID: 70693
  • Ehrhart, B.D., Bran-Anleu, G., Ye, D., Hecht, E.S., & Hecht, E.S. (2019). Comparisons of Design Changes on Footprint of Hydrogen Refueling Stations for Urban Sites [Conference Poster]. https://www.osti.gov/biblio/1643003 Publication ID: 65934
  • Ehrhart, B.D., Bran-Anleu, G., Ye, D., Hecht, E.S., Muna, A., Lafleur, A., & Lafleur, A. (2019). Hydrogen Stations for Urban Sites. https://doi.org/10.2172/1570553 Publication ID: 65572
  • Hecht, E.S., Panda, P., Roy Chowdhury, B., Ye, D., & Ye, D. (2019). Characteristics of Cryogenic Hydrogen Releases Under Unignited and Ignited Conditions. https://doi.org/10.2172/1763216 Publication ID: 102784
  • Ye, D., Hayes, D.C., Maes, D., Simoes, C.T., Appelhans, L., Kent, M.S., Timlin, J.A., & Timlin, J.A. (2019). Transport of lignin-beakdown products into bacteria and fungi [Conference Poster]. https://www.osti.gov/biblio/1639882 Publication ID: 68303
  • Ehrhart, B.D., Bran-Anleu, G., Ye, D., Hecht, E.S., Muna, A., Sena, E., Lafleur, A., Rivkin, C., & Rivkin, C. (2019). Reference Design of Hydrogen Stations for Urban Sites [Presentation]. https://www.osti.gov/biblio/1644514 Publication ID: 67468
  • Ehrhart, B.D., Bran-Anleu, G., Ye, D., Hecht, E.S., Muna, A., Sena, E., Lafleur, A., Rivkin, C., & Rivkin, C. (2019). Hydrogen Stations for Urban Sites [Presentation]. https://www.osti.gov/biblio/1644467 Publication ID: 67335
  • Khoury, L., Mobley, D., Ye, D., Rempe, S.B., & Rempe, S.B. (2019). Identification of the binding mode of diethyl p-nitrophenyl phosphate to phosphotriesterase [Conference Poster]. https://www.osti.gov/biblio/1602940 Publication ID: 67204
  • Khoury, L., Mobley, D., Rempe, S.B., Ye, D., & Ye, D. (2019). Re-engineering of Substrate Binding Site in Organophosphorus Hydrolase (OPH) via Unnatural Amino Acids [Conference Poster]. https://www.osti.gov/biblio/1602927 Publication ID: 67192
  • Karler, C., Parchert, K.J., Ricken, B., Carson, B., Mowry, C.D., Fan, H., Ye, D., & Ye, D. (2019). Identification of Porphyrin-Silica Composite Nanoparticles using Atmospheric Solids Analysis Probe Mass Spectrometry. MRS Advances, 4(38-39), pp. 2079-2086. https://doi.org/10.1557/adv.2019.217 Publication ID: 68216
  • Fan, H., Bonal, D.A., Bian, K., Schunk, H., Ye, D., Hwang, A., Luk, T.S., Li, R., Wang, Z., & Wang, Z. (2018). Formation of self-assembled gold nanoparticle supercrystals with facet-dependent surface plasmonic coupling. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-04801-9 Publication ID: 98420
  • Parchert, K.J., Carson, B., Murton, J.K., Ricken, B., Hochrein, J.M., Ye, D., & Ye, D. (2018). Post-translational modifications of mammalian ribosomal proteins induced by virus infection [Conference Poster]. https://www.osti.gov/biblio/1576890 Publication ID: 60347
  • Dailey, M., Ye, D., Sale, K.L., Maes, D., Simoes, C.T., Appelhans, L., Hayes, D.C., Kent, M.S., Timlin, J.A., & Timlin, J.A. (2018). Accumulation of lignin-breakdown products in several lignolytic and non-lignolytic bacteria and fungi [Conference Poster]. https://www.osti.gov/biblio/1495744 Publication ID: 60689
  • Fan, H., Billstrand, B., Bian, K., Karler, C., Ye, D., Hwang, A., & Hwang, A. (2018). Solution Based Synthesis of Cs4PbBr6 Perovskite Particles with High Luminescence and Stability. MRS Advances, 3(45-46), pp. 2825-2831. https://doi.org/10.1557/adv.2018.308 Publication ID: 58955
  • Fan, H., Bian, K., Alarid, L., Karler, C., Hwang, A., Ye, D., & Ye, D. (2018). Surfactant-Assisted Synthesis of Tetragonal Porphyrin Microparticles. MRS Advances, 3(45-46), pp. 2757-2762. https://doi.org/10.1557/adv.2018.309 Publication ID: 58952
  • Ruffing, A.M., Ye, D., Reichardt, T.A., Lacey, R., & Lacey, R. (2018). PHOTOSYNTHETIC BIOSENSORS: ENGINEERING SYNECHOCOCCUS SP. PCC 7002 FOR THE DETECTION OF HEAVY METALS [Conference Poster]. https://www.osti.gov/biblio/1512382 Publication ID: 58576
  • Ye, D., Kumar, S.K., Grest, G.S., Mahynski, N.A., Panagiotopoulos, A.Z., & Panagiotopoulos, A.Z. (2017). Reentrant equilibrium disordering in nanoparticle-polymer mixtures. npj Computational Materials, 3(1), pp. 1-21. https://doi.org/10.1038/s41524-016-0005-8 Publication ID: 52749
  • Dailey, M., Ye, D., Maes, D., Simoes, C.T., Appelhans, L., Hayes, D.C., Kent, M.S., Timlin, J.A., & Timlin, J.A. (2017). Accumulation of lignin-breakdown products in several lignolytic and non-lignolytic bacteria and fungi [Conference Poster]. https://www.osti.gov/biblio/1483222 Publication ID: 54322
  • Parchert, K.J., Murton, J.K., Ye, D., Carson, B., Ricken, B., & Ricken, B. (2017). Viral Pathogen Identification Using Ribosomal Selection [Presentation]. https://www.osti.gov/biblio/1510602 Publication ID: 53466
  • Lacey, R., Ye, D., Ruffing, A.M., & Ruffing, A.M. (2017). Engineering Protein Based Whole Cell Biosensors for the Detection of Toxic Metals in the Environment [Conference Poster]. https://www.osti.gov/biblio/1474231 Publication ID: 53131
  • Dailey, M., Hayes, D.C., Ye, D., Simoes, C.T., Appelhans, L., Maes, D., Kent, M.S., Timlin, J.A., & Timlin, J.A. (2017). Assimilation of lignin-breakdown products by lignolytic and non-lignolytic bacteria and fungi [Conference Poster]. https://www.osti.gov/biblio/1463441 Publication ID: 57769
  • Lacey, R., Ye, D., Ruffing, A.M., & Ruffing, A.M. (2017). Protein Engineering for the Detection of Toxic Metals in the Environment [Conference Poster]. https://www.osti.gov/biblio/1458186 Publication ID: 56705
  • Kent, M.S., Dailey, M., Ye, D., Simoes, C.T., Appelhans, L., Hayes, D.C., Timlin, J.A., & Timlin, J.A. (2017). Characterizing transport of lignin breakdown products into P. chrysosporium E. lignolyticus S. cerevisiae and E. coli [Conference Poster]. https://www.osti.gov/biblio/1457997 Publication ID: 56304
  • Kent, M.S., la Bauve, E., Vernon, B.C., Ye, D., Rogers, D.M., Mayes, C., Carson, B., Rempe, S.B., Zheng, A., Kielian, M., Shreve, A.P., & Shreve, A.P. (2016). Method for measuring the unbinding energy of strongly-bound membrane-associated proteins. Biochimica et Biophysica Acta – Biomembranes, 1858(11), pp. 2753-2762. https://doi.org/10.1016/j.bbamem.2016.07.004 Publication ID: 53923
  • Kent, M.S., la Bauve, E., Vernon, B.C., Ye, D., Rogers, D.M., Mayes, C., Carson, B., Rempe, S.B., Zheng, A., Kielian, M., Schreve, A.P., & Schreve, A.P. (2016). New Method for Measuring the Anchoring Energy of Strongly-Bound Membrane-Associated Proteins [Method for measuring the anchoring energy of strongly-bound membrane-associated proteins]. Biophysical Journal, 110(S1). https://doi.org/10.1016/j.bpj.2015.11.3091 Publication ID: 49118
  • Ruffing, A.M., Ye, D., & Ye, D. (2016). Engineering Two Component Signal Transduction in a Cyanobacterium [Conference Poster]. https://www.osti.gov/biblio/1339213 Publication ID: 46655
  • Jacob, R.B., Ding, F., Ye, D., Ackerman, E., Dokholyan, N.V., & Dokholyan, N.V. (2015). Computational redesign reveals allosteric mutation hotspots of organophosphate hydrolase that enhance organophosphate hydrolysis. Sandia journal manuscript; Not yet accepted for publication. https://www.osti.gov/biblio/1427256 Publication ID: 42994
  • Ye, D., Murton, J.K., & Murton, J.K. (2012). Enhanced Stabilities and Activities of OPH [Conference]. https://www.osti.gov/biblio/1116246 Publication ID: 30904
Showing 10 of 31 publications.

Selected Publications

  • Elisa La Bauve, Briana C. Vernon, Dongmei Ye, David M. Rogers, Cathryn M. Siegrist, Bryan Carson, Susan L. Rempe, Aihua Zheng, Margaret Kielian, Andrew P. Schreve, Michael S. Kent, “New method for measuring the unbinding energy of strongly-bound membrane-associated proteins”, Biochim Biophhys Acta, 2016, 1858(11): 2753.
  • Dongmei Ye, Rana Al-Sadi, Michel Boivin, Shuhong Guo, Thomas Ma, “Interleukin-6 modulation of intestinal epithelial tight junction permeability is mediated by JNK pathway activation of claudin-2 gene”, PLos One, 2014, 9(3): e85345.
  • Dongmei Ye, Shuhong Guo, Rana Al-Sadi, Thomas Ma, “MicroRNA regulation of intestinal epithelial tight junction permeability”, Gastroenterology, 2011, 141(4): 1323-33.
  • Dongmei Ye, Thomas Y Ma, “Cellular and Molecular Mechanisms that Mediate the Basal and Tumor Necrosis Factor-a Induced Regulation of Myosin Light Chain Kinase Gene Activity”, J Cell and Mol Med., 2008, 12(4):1331-46.
  • Dongmei Ye, Iris Ma, Thomas Y Ma, “Molecular mechanism of tumor necrosis factor-{alpha} modulation of intestinal epithelial tight junction barrier”, Am J Physiol Gastrointest Liver Physiol., 2006, 290(3), G496-504.
  • Dongmei Ye, Min Wei, Marielena McGuire, Kui Huang, Geeta Kapadia, Osnat Herzberg, Brain Martin and Debra Dunaway-mariano, “Investigation of the catalytic site within the ATP-grasp domain of clostridium symbiosum pyruvate phosphate dikinase”, Journal of Biological Chemistry, 2001, 276, 37630.