Faculty Publications

Morris, H., Singh, P., Kohen, A.,* Tivanski, A.,* “Probing Single Molecule Enzyme-Drug Interaction with Molecular Recognition Force Spectroscopy”, Submitted to Chem. Commun., March 18, 2016.

Guo, Q., Gakhar., L., Wickersham., K., Francis, K., Vardi-Kilshtain., A., Major, T.D., Kohen, A.,* “Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii”, Submitted to Biochemistry, Feb 28, 2016.

Francis, K., Sapienza, P.J., Lee, A.L., Kohen, A.,* “The Effect of the Protein Mass Modulation on Human Dihydrofolate Reductase”, Biochemistry, 55, 1100–1106, 2016.

Mishanina, T.V., Yu, L., Karunaratne, K., Mondal, D., Corcoran, J.M., Choi, M.A., Kohen, A.,* “An unprecedented mechanism of nucleotide methylation in organisms containing thyX”, Science, 351, 507- 510, 2016.

Kohen, A.,* “Dihydrofolate Reductase as a Model for Studies of Enzyme Dynamics and Catalysis”, F1000Research 2015, 4 (F1000 Faculty Rev):1464. (Invited Review). Islam, Z., Strutzenberg, T.S., Ghosh, A.K., Kohen, A.,* “Activation of Two Sequential H-transfers in the Thymidylate Synthase Catalyzed Reaction”, ACS Cat., 2015, 5, 6061–6068.

Francis, K., Kohen, A.,* “Dihydrofolate Reductase as a Model for Enzyme Catalysis”, Current Biotech., 2015, 4, 1-10. (Invited review).

Singh, P., Francis, K., Kohen, A.,* “Network of remote and local protein dynamics in dihydrofolate reductase catalysis”, ACS Cat., 2015, 5, 3067–3073.

Guo, Q., Pagano, P., Li, Y., Kohen, A., Cheatum, C.M.,* “Line Shape Analysis of Two-dimensional Infrared Spectra”, J. Chem. Phys., 2015, 142, 212427.

Ghosh, A.K., Islam, Z., Krueger, J.D., Abeysinghe, D.T., Kohen, A.,* “The General Base in the Thymidylate Synthase Catalyzed Proton Abstraction”, Phys. Chem. Chem. Phys., 2015, 17, 30867-30875.

Świderek, K., Kohen, A., Moliner, V.,* “Influence of Active Site Conformations on the Hydride Transfer step of the Thymidylate Synthase Reaction Mechanism”, Phys. Chem. Chem. Phys., 2015, 17, 30793— 30804.

Abeysinghe, T., Kohen, A.,* “Role of Long-Range Protein Dynamics in Different Thymidylate Synthase Catalyzed Reactions”, Int. J. Mol. Sci., 2015, 16, 7304-7319,. Special Issue on Protein and ProteinLingand Interactions.

Nilaweera, T., Saeed, M. and Kohen, A.,* “Targeting the de novo Biosynthesis of Thymidylate for the Development of PET Probe for Pancreatic Cancer Imaging”, Biochemistry, 2015, 54, 1287–1293. Chosen to be highlighted on the journal’s home page: http://pubs.acs.org/journals/bichaw/index.html.

Singh, P., Abeysinghe, T., Kohen, A.,* “Linking Protein Motion to Enzyme Catalysis”, Molecules, 2015, 20, 1192-1209. (Invited review)

Doron, D., Stojković, V., Gakhar, L., Kohen, A., Major, D.,* “Free Energy Simulations of Active-Site Mutants of Dihydrofolate Reductase”, J. Phys. Chem. B., 2015, 119, 906–916.

Kohen, A.,* “Role of Dynamics in Enzyme Catalysis: Substantial vs. Semantic Controversies”, Acc. Chem. Res., 2015, 48, 466–473. (Special Issue on “Enzymes Dynamics and Catalysis”)

Singh, P., Morris, H., Tivanski, A.V., Kohen, A.,* “Determination of concentration and activity of immobilized enzymes”, Anal., Biochem., 2015, 484, 169–172.

Singh, P., Morris, H., Tivanski, A.V., Kohen, A.,* “A calibration curve for immobilized dihydrofolate reductase activity assay”, Data in Brief, 2015, 4, 19-21.

Mishanina, T., Kohen, A.,* “Synthesis and application of isotopically labeled flavin nucleotides”, J. Labeled Comp. Radiopharma., 2015, 58 370–375.

Khalid H. R. Algharrawi., Ryan M. Summers, Sridhar Gopishetty, and Mani Subramanian.  (2015) “Direct conversion of theophylline to 3-methylxanthine by metabolically engineered E. coli” Microbial Cell Factories. DOI:10.1186/s12934-015-0395-1 

Booth, K. T., Azaiez, H., Kahrizi, K., Simpson, A. C., Tollefson, W. T. A., Sloan, C. M., Meyer, N. C., Babanejad, M., Ardalani, F., Arzhangi, S., Schnieders, M. J., Najmabadi, H. and Smith, R. J. H. (2015). "PDZD7 and hearing loss: More than just a modifier." American Journal of Medical Genetics Part A:

 Britton, E. R., Ibberson, C. B., Horswill, A. R. and Cech, N. B. "A new mass spectrometry based bioassay for the direct assessment of hyaluronidase activity and inhibition." Journal of Microbiological Methods.

Cassandra L. Quave , J. T. L., Jeffery S. Kavanaugh, Kate Nelson, Corey P. Parlet, Heidi A. Crosby, Kristopher P. Heilmann, Alexander R. Horswill (2015). "Castanea sativa (European Chestnut) Leaf Extracts Rich in Ursene and Oleanene Derivatives Block Staphylococcus aureus Virulence and Pathogenesis without Detectable Resistance." PLoS ONE 10(8).

Cressiot, B., Braselmann, E., Oukhaled, A., Elcock, A. H., Pelta, J. and Clark, P. L. (2015). "Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore." ACS Nano 9(9): 9050-9061.

DeLuca, A. P., Whitmore, S. S., Barnes, J., Sharma, T. P., Westfall, T. A., Scott, C. A., Weed, M. C., Wiley, J. S., Wiley, L. A., Johnston, R. M., Schnieders, M. J., Lentz, S. R., Tucker, B. A., Mullins, R. F., Scheetz, T. E., Stone, E. M. and Slusarski, D. C. (2015). "Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis." Hum Mol Genet.

Dewan, N., Majestic, B. J., Ketterer, M. E., Miller-Schulze, J. P., Shafer, M. M., Schauer, J. J., Solomon, P. A., Artamonova, M., Chen, B. B., Imashev, S. A. and Carmichael, G. R. (2015). "Stable isotopes of lead and strontium as tracers of sources of airborne particulate matter in Kyrgyzstan." Atmospheric Environment 120: 438-446.

Elangovan, S., Khorsand, B., Do, A.-V., Hong, L., Dewerth, A., Kormann, M., Ross, R. D., Rick Sumner, D., Allamargot, C. and Salem, A. K. (2015). "Chemically modified RNA activated matrices enhance bone regeneration." Journal of Controlled Release 218: 22-28.

Geary, S. M., Hu, Q., Joshi, V. B., Bowden, N. B. and Salem, A. K. "Diaminosulfide based polymer microparticles as cancer vaccine delivery systems." Journal of Controlled Release.

Jorth, P., Staudinger, B. J., Wu, X., Hisert, K. B., Hayden, H., Garudathri, J., Harding, C. L., Radey, M. C., Rezayat, A., Bautista, G., Berrington, W. R., Goddard, A. F., Zheng, C., Angermeyer, A., Brittnacher, M. J., Kitzman, J., Shendure, J., Fligner, C. L., Mittler, J., Aitken, M. L., Manoil, C., Bruce, J. E., Yahr, T. L. and Singh, P. K. (2015). "Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs." Cell Host Microbe 18(3): 307-319.

Leelakanok, N., Fischer, C. L., Bates, A. M., Guthmiller, J. M., Johnson, G. K., Salem, A. K., Brogden, K. A. and Brogden, N. K. (2015). "Cytotoxicity of HBD3 for dendritic cells, normal human epidermal keratinocytes, hTERT keratinocytes, and primary oral gingival epithelial keratinocytes in cell culture conditions." Toxicology Letters 239(2): 90-96.

Long, T. R., Wongrakpanich, A., Do, A. V., Salem, A. K. and Bowden, N. B. (2015). "Long-term release of a thiobenzamide from a backbone functionalized poly(lactic acid)." Polymer Chemistry 6(40): 7188-7195.

Miller-Schulze, J. P., Shafer, M., Schauer, J. J., Heo, J., Solomon, P. A., Lantz, J., Artamonova, M., Chen, B., Imashev, S., Sverdlik, L., Carmichael, G. and DeMinter, J. (2015). "Seasonal contribution of mineral dust and other major components to particulate matter at two remote sites in Central Asia." Atmospheric Environment 119: 11-20.

Pujol, C., Daniels, K. J. and Soll, D. R. (2015). "A Comparison of Switching and Biofilm Formation Between MTL-homozygous Strains of Candida albicans and Candida dubliniensis." Eukaryot Cell.

Ross, K. A., Brenza, T. M., Binnebose, A. M., Phanse, Y., Kanthasamy, A. G., Gendelman, H. E., Salem, A. K., Bartholomay, L. C., Bellaire, B. H. and Narasimhan, B. (2015). "Nano-enabled delivery of diverse payloads across complex biological barriers." J Control Release.

Rupasinghe, T. P., Hutchins, K. M., Bandaranayake, B. S., Ghorai, S., Karunatilake, C., Bucar, D. K., Swenson, D. C., Arnold, M. A., MacGillivray, L. R. and Tivanski, A. V. (2015). "Mechanical Properties of a Series of Macro- and Nanodimensional Organic Cocrystals Correlate with Atomic Polarizability." J Am Chem Soc 137(40): 12768-12771.

Scherr, T. D., Hanke, M. L., Huang, O., James, D. B., Horswill, A. R., Bayles, K. W., Fey, P. D., Torres, V. J. and Kielian, T. (2015). "Staphylococcus aureus Biofilms Induce Macrophage Dysfunction Through Leukocidin AB and Alpha-Toxin." MBio 6(4).

Schwab, F., Zhai, G., Kern, M., Turner, A., Schnoor, J. L. and Wiesner, M. R. (2015). "Barriers, pathways and processes for uptake, translocation and accumulation of nanomaterials in plants - Critical review." Nanotoxicology: 1-22.

Smith, R. M. and Arnold, M. A. (2015). "Selectivity of Terahertz Gas-Phase Spectroscopy." Anal Chem 87(21): 10679-10683.

Wessels, D. J., Lusche, D. F., Kuhl, S., Scherer, A., Voss, E. and Soll, D. R. (2016). "Quantitative Motion Analysis in Two and Three Dimensions." Methods Mol Biol 1365: 265-292.

Worthington, K. S., Wiley, L. A., Mullins, R. F., Tucker, B. A. and Nuxoll, E. (2015). "Prevascularized silicon membranes for the enhancement of transport to implanted medical devices." Journal of Biomedical Materials Research Part B: Applied Biomaterials

Xin, X., Senthilkumar, P. K., Schnoor, J. L. and Ludewig, G. (2015). "Effects of PCB126 and PCB153 on telomerase activity and telomere length in undifferentiated and differentiated HL-60 cells." Environ Sci Pollut Res Int.    

Bircher, S., Card, M. L., Zhai, G., Chin, Y.-P. and Schnoor, J. L. (2015). "Sorption, uptake and biotransformation of 17β-estradiol, 17α-ethinylestradiol, zeranol and trenbolone acetate by hybrid poplar." Environmental Toxicology and Chemistry.

Ekuase, E. J., van ‘t Erve, T. J., Rahaman, A., Robertson, L. W., Duffel, M. W. and Luthe, G. (2015). "Mechanistic insights into the specificity of human cytosolic sulfotransferase 2A1 (hSULT2A1) for hydroxylated polychlorinated biphenyls through the use of fluoro-tagged probes." Environmental Science and Pollution Research: 1-9.

Mattes, T., Jin, Y., Livermore, J., Pearl, M. and Liu, X. (2015). "Abundance and activity of vinyl chloride (VC)-oxidizing bacteria in a dilute groundwater VC plume biostimulated with oxygen and ethene." Applied Microbiology and Biotechnology: 1-10.

Miller-Schulze, J. P., Shafer, M., Schauer, J. J., Heo, J., Solomon, P. A., Lantz, J., Artamonova, M., Chen, B., Imashev, S., Sverdlik, L., Carmichael, G. and DeMinter, J. (2015). "Seasonal contribution of mineral dust and other major components to particulate matter at two remote sites in Central Asia." Atmospheric Environment 119: 11-20.

Srivastava, J., Rajasekaran, D., Siddiq, A., Gredler, R., Robertson, C. L., Akiel, M. A., Shen, X.-N., Ebeid, K. A. N., Salem, A. K., Fisher, P. B. and Sarkar, D. (2015). "Abstract 5400: A novel combinatorial therapy for hepatocellular carcinoma (HCC)." Cancer Research 75(15 Supplement): 5400.
Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5400.

Stephen D. LuCore, J. M. L., Kyle T. Powers, Shibo Gao, Ava M. Lynn, William T.A. Tollefson, Timothy D. Fenn, M. Todd Washington, Michael J. Schnieders (2015). "Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures." Biophysical Journal 109(4): 816-826.

Wongrakpanich, A., Wu, M. and Salem, A. K. (2015). "Correlating intracellular non-viral polyplex localization with transfection efficiency using high-content screening." Biotechnology Progress.