Dongmei Ye

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

Léa El Khoury, David Mobley, Dongmei Ye, Susan Rempe, (2021). Enhancing paraoxon binding to organophosphorus hydrolase active site International Journal of Molecular Sciences https://doi.org/10.3390/ijms222312624 Publication ID: 77082

Brian Ehrhart, Gabriela Bran Anleu, Dongmei Ye, Ethan Hecht, (2020). Hydrogen Refueling Reference Station Lot Size Analysis for Urban Sites https://www.osti.gov/servlets/purl/1761025 Publication ID: 70693

Brian Ehrhart, Gabriela Bran Anleu, Dongmei Ye, Ethan Hecht, Alice Muna, Chris LaFleur, (2019). Hydrogen Stations for Urban Sites https://doi.org/10.2172/1570553 Publication ID: 65572

Brian Ehrhart, Gabriela Bran Anleu, Dongmei Ye, Ethan Hecht, (2019). Comparisons of Design Changes on Footprint of Hydrogen Refueling Stations for Urban Sites https://www.osti.gov/servlets/purl/1643003 Publication ID: 65934

Dongmei Ye, Dulce Hayes, Danae Maes, Casey Simoes, Leah Appelhans, Michael Kent, Jerilyn Timlin, (2019). Transport of lignin-beakdown products into bacteria and fungi https://www.osti.gov/servlets/purl/1639882 Publication ID: 68303

Brian Ehrhart, Gabriela Bran Anleu, Dongmei Ye, Ethan Hecht, Alice Muna, Ethan Sena, Chris LaFleur, Carl Rivkin, (2019). Hydrogen Stations for Urban Sites https://www.osti.gov/servlets/purl/1644467 Publication ID: 67335

Brian Ehrhart, Gabriela Bran Anleu, Dongmei Ye, Ethan Hecht, Alice Muna, Ethan Sena, Chris LaFleur, Carl Rivkin, (2019). Reference Design of Hydrogen Stations for Urban Sites https://www.osti.gov/servlets/purl/1644514 Publication ID: 67468

Lea Khoury, David Mobley, Susan Rempe, Dongmei Ye, (2019). Re-engineering of Substrate Binding Site in Organophosphorus Hydrolase (OPH) via Unnatural Amino Acids https://www.osti.gov/servlets/purl/1602927 Publication ID: 67192

Lea Khoury, David Mobley, Dongmei Ye, Susan Rempe, (2019). Identification of the binding mode of diethyl p-nitrophenyl phosphate to phosphotriesterase https://www.osti.gov/servlets/purl/1602940 Publication ID: 67204

Casey Karler, Kylea Parchert, James Ricken, Bryan Carson, Curtis Mowry, Hongyou Fan, Dongmei Ye, (2019). Identification of Porphyrin-Silica Composite Nanoparticles using Atmospheric Solids Analysis Probe Mass Spectrometry MRS Advances https://doi.org/10.1557/adv.2019.217 Publication ID: 68216

Kylea Parchert, Bryan Carson, Jaclyn Murton, James Ricken, James Hochrein, Dongmei Ye, (2018). Post-translational modifications of mammalian ribosomal proteins induced by virus infection https://www.osti.gov/servlets/purl/1576890 Publication ID: 60347

Hongyou Fan, Brian Billstrand, Kaifu Bian, Casey Karler, Dongmei Ye, Austin Hwang, (2018). Solution Based Synthesis of Cs₄PbBr₆ Perovskite Particles with High Luminescence and Stability MRS Advances https://doi.org/10.1557/adv.2018.308 Publication ID: 58955

Meghan Dailey, Dongmei Ye, Kenneth Sale, Danae Maes, Casey Simoes, Leah Appelhans, Dulce Hayes, Michael Kent, Jerilyn Timlin, (2018). Accumulation of lignin-breakdown products in several lignolytic and non-lignolytic bacteria and fungi https://www.osti.gov/servlets/purl/1495744 Publication ID: 60689

Kaifu Bian, Leanne Alarid, Casey Karler, Austin Hwang, Dongmei Ye, Hongyou Fan, (2018). Surfactant-Assisted Synthesis of Tetragonal Porphyrin Microparticles MRS Advances https://doi.org/10.1557/adv.2018.309 Publication ID: 58952

Anne Ruffing, Dongmei Ye, Thomas Reichardt, Randy Lacey, (2018). PHOTOSYNTHETIC BIOSENSORS: ENGINEERING SYNECHOCOCCUS SP. PCC 7002 FOR THE DETECTION OF HEAVY METALS https://www.osti.gov/servlets/purl/1512382 Publication ID: 58576

Meghan Dailey, Dongmei Ye, Danae Maes, Casey Simoes, Leah Appelhans, Dulce Hayes, Michael Kent, Jerilyn Timlin, (2017). Accumulation of lignin-breakdown products in several lignolytic and non-lignolytic bacteria and fungi https://www.osti.gov/servlets/purl/1483222 Publication ID: 54322

Kylea Parchert, Jaclyn Murton, Dongmei Ye, Bryan Carson, James Ricken, (2017). Viral Pathogen Identification Using Ribosomal Selection https://www.osti.gov/servlets/purl/1510602 Publication ID: 53466

Randy Lacey, Dongmei Ye, Anne Ruffing, (2017). Engineering Protein Based Whole Cell Biosensors for the Detection of Toxic Metals in the Environment https://www.osti.gov/servlets/purl/1474231 Publication ID: 53131

Meghan Dailey, Dulce Hayes, Dongmei Ye, Casey Simoes, Leah Appelhans, Danae Maes, Michael Kent, Jerilyn Timlin, (2017). Assimilation of lignin-breakdown products by lignolytic and non-lignolytic bacteria and fungi https://www.osti.gov/servlets/purl/1463441 Publication ID: 57769

Randy Lacey, Dongmei Ye, Anne Ruffing, (2017). Protein Engineering for the Detection of Toxic Metals in the Environment https://www.osti.gov/servlets/purl/1458186 Publication ID: 56705

Michael Kent, Meghan Dailey, Dongmei Ye, Casey Simoes, Leah Appelhans, Dulce Hayes, Michael Kent, Jerilyn Timlin, (2017). Characterizing transport of lignin breakdown products into P. chrysosporium E. lignolyticus S. cerevisiae and E. coli https://www.osti.gov/servlets/purl/1457997 Publication ID: 56304

Elisa La Bauve, Briana Vernon, Dongmei Ye, David Rogers, Cathryn Siegrist, Bryan Carson, Susan Rempe, Aihua Zheng, Margaret Kielian, Andrew Shreve, Michael Kent, (2016). Method for measuring the unbinding energy of strongly-bound membrane-associated proteins Biochimica et Biophysica Acta – Biomembranes https://doi.org/10.1016/j.bbamem.2016.07.004 Publication ID: 53923

Michael Kent, Elisa La Bauve, Briana Vernon, Dongmei Ye, David Rogers, Cathryn Mayes, Bryan Carson, Susan Rempe, Aihua Zheng, Margaret Kielian, Andrew Shreve, Michael Kent, (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 https://doi.org/10.1016/j.bpj.2015.11.3091 Publication ID: 49118

Anne Ruffing, Dongmei Ye, (2016). Engineering Two Component Signal Transduction in a Cyanobacterium https://www.osti.gov/servlets/purl/1339213 Publication ID: 46655

Reed Jacob, Feng Ding, Dongmei Ye, Eric Ackerman, Nikolay Dokholyan, (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/servlets/purl/1427256 Publication ID: 42994

Dongmei Ye, Jaclyn Murton, (2012). Enhanced Stabilities and Activities of OPH https://www.osti.gov/servlets/purl/1116246 Publication ID: 30904

Showing Results. Show More 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.