C. Denise Okafor - Penn State Cancer Institute
Researcher Profile
C. Denise Okafor
Assistant Professor, Biochemistry & Molecular Biology
Scientific Program:Mechanisms of Carcinogenesis
Recent Publications
2026
Khan, SH, Yennawar, N & Okafor, DD 2026, 'DNA induces non-canonical dimerization of the farnesoid X receptor', Nucleic acids research, vol. 54, no. 4, gkag087. https://doi.org/10.1093/nar/gkag087
Yamamoto, N, Sudhakar, N, Khan, SH, Biswas, A, Mooney, EJ, Hoshino, Y, Gaucher, EA & Okafor, CD 2026, 'Evolutionary remodeling of the FXR binding pocket drove functional divergence and ligand discrimination', Molecular biology and evolution, vol. 43, no. 2, msag031. https://doi.org/10.1093/molbev/msag031
2025
Pavelich, IJ, Schureck, MA, Srinivas, P, Blackburn, TM, Wang, D, Hoffer, ED, Boamah, M, Zaldana, K, Onuoha, N, Miles, SJ, Grabowicz, M, Okafor, CD & Dunham, CM 2025, 'Antitoxin control of optimal transcriptional repression in the atypical HigB-HigA toxin-antitoxin system from Proteus vulgaris', Nucleic acids research, vol. 53, no. 13, gkaf610. https://doi.org/10.1093/nar/gkaf610
Yu, T, Villalona, P, Khan, SH, Mikeasky, N, Meinert, E, Magafas, J, Pulahinge, T, Bader, A & Okafor, CD 2025, 'Enhanced dynamic coupling in a nuclear receptor underlies ligand activity', Journal of Biological Chemistry, vol. 301, no. 2, 108081. https://doi.org/10.1016/j.jbc.2024.108081
Eisert-Sasse, RK, Biswas, A & Okafor, CD 2025, 'Impact of Bile Acid Amidation on In Silico Farnesoid X Receptor Dynamics', Journal of Physical Chemistry B, vol. 129, no. 41, pp. 10621-10630. https://doi.org/10.1021/acs.jpcb.5c02361
2024
Glasser, NR, Cui, D, Risser, DD, Okafor, CD & Balskus, EP 2024, 'Accelerating the discovery of alkyl halide-derived natural products using halide depletion', Nature Chemistry, vol. 16, no. 2, pp. 173-182. https://doi.org/10.1038/s41557-023-01390-z
Khan, SH, Dube, N, Sudhakar, N, Fraser, O, Villalona, P, Braet, SM, Leedom, S, Reilly, ER, Sivak, J, Crittenden, K & Okafor, CD 2024, 'Ancient and modern mechanisms compete in progesterone receptor activation', RSC Chemical Biology, vol. 5, no. 6, pp. 518-529. https://doi.org/10.1039/d4cb00002a
Hazarika, S, Fehrle, M & Okafor, CD 2024, 'How nuclear receptors transition between active and inactive forms: An energetic perspective', Journal of Chemical Physics, vol. 160, no. 11, 115102. https://doi.org/10.1063/5.0189234
Yu, T, Sudhakar, N & Okafor, CD 2024, 'Illuminating ligand-induced dynamics in nuclear receptors through MD simulations', Biochimica et Biophysica Acta - Gene Regulatory Mechanisms, vol. 1867, no. 2, 195025. https://doi.org/10.1016/j.bbagrm.2024.195025
Biswas, A, Eisert-Sasse, RK & Okafor, CD 2025, 'Impact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain', ChemPhysChem, vol. 26, no. 3, e202400783. https://doi.org/10.1002/cphc.202400783
Hazarika, S, Yu, T, Biswas, A, Dube, N, Villalona, P & Okafor, CD 2024, 'Nuclear Receptor Interdomain Communication is Mediated by the Hinge with Ligand Specificity', Journal of Molecular Biology, vol. 436, no. 22, 168805. https://doi.org/10.1016/j.jmb.2024.168805
Yu, T, Biswas, A, Dube, N & Okafor, CD 2025, 'Simulations Reveal Unique Roles for the FXR Hinge in the FXR-RXR Nuclear Receptor Heterodimer', ACS Bio and Med Chem Au, vol. 5, no. 1, pp. 194-203. https://doi.org/10.1021/acsbiomedchemau.4c00105
2023
Dube, N, Khan, SH, Sasse, R & Okafor, CD 2023, 'Identification of an Evolutionarily Conserved Allosteric Network in Steroid Receptors', Journal of Chemical Information and Modeling, vol. 63, no. 2, pp. 571-582. https://doi.org/10.1021/acs.jcim.2c01096
Mays, SG, Hercules, D, Ortlund, EA & Okafor, CD 2023, 'The nuclear receptor LRH-1 discriminates between ligands using distinct allosteric signaling circuits', Protein Science, vol. 32, no. 10, e4754. https://doi.org/10.1002/pro.4754
Surrett, ED, Guckes, KR, Cousins, S, Ruskoski, TB, Cecere, AG, Ludvik, DA, Okafor, CD, Mandel, MJ & Miyashiro, TI 2023, 'Two enhancer binding proteins activate σ54-dependent transcription of a quorum regulatory RNA in a bacterial symbiont', eLife, vol. 12. https://doi.org/10.7554/eLife.78544
2022
Mays, SG, D'Agostino, EH, Flynn, AR, Huang, X, Wang, G, Liu, X, Millings, EJ, Okafor, CD, Patel, A, Cato, ML, Cornelison, JL, Melchers, D, Houtman, R, Moore, DD, Calvert, JW, Jui, NT & Ortlund, EA 2022, 'A phospholipid mimetic targeting LRH-1 ameliorates colitis', Cell Chemical Biology, vol. 29, no. 7, pp. 1174-1186.e7. https://doi.org/10.1016/j.chembiol.2022.03.001
Collins, SL, Stine, JG, Bisanz, JE, Okafor, CD & Patterson, AD 2023, 'Bile acids and the gut microbiota: metabolic interactions and impacts on disease', Nature Reviews Microbiology, vol. 21, no. 4, pp. 236-247. https://doi.org/10.1038/s41579-022-00805-x
Cato, ML, Cornelison, JL, Spurlin, RM, Courouble, VV, Patel, AB, Flynn, AR, Johnson, AM, Okafor, CD, Frank, F, D'Agostino, EH, Griffin, PR, Jui, NT & Ortlund, EA 2022, 'Differential Modulation of Nuclear Receptor LRH-1 through Targeting Buried and Surface Regions of the Binding Pocket', Journal of Medicinal Chemistry, vol. 65, no. 9, pp. 6888-6902. https://doi.org/10.1021/acs.jmedchem.2c00235
Russell, TJ, De Silva, EK, Crowley, VM, Shaw-Saliba, K, Dube, N, Josling, G, Pasaje, CFA, Kouskoumvekaki, I, Panagiotou, G, Niles, JC, Jacobs-Lorena, M, Okafor, CD, Gamo, FJ & Llinás, M 2022, 'Inhibitors of ApiAP2 protein DNA binding exhibit multistage activity against Plasmodium parasites', PLoS pathogens, vol. 18, no. 10, e1010887. https://doi.org/10.1371/journal.ppat.1010887
Khan, SH & Okafor, CD 2022, 'Interactions governing transcriptional activity of nuclear receptors', Biochemical Society transactions, vol. 50, no. 6, pp. 1941-1952. https://doi.org/10.1042/BST20220338
Khan, SH, Braet, SM, Koehler, SJ, Elacqua, E, Anand, GS & Okafor, CD 2022, 'Ligand-induced shifts in conformational ensembles that describe transcriptional activation', eLife, vol. 11, e80140. https://doi.org/10.7554/eLife.80140
Braffman, NR, Ruskoski, TB, Davis, KM, Glasser, NR, Johnson, C, Okafor, CD, Boal, AK & Balskus, EP 2022, 'Structural Basis for an Unprecedented Enzymatic Alkylation in Cylindrocyclophane Biosynthesis', eLife, vol. 11, e75761. https://doi.org/10.7554/ELIFE.75761