Publications

  1. Shah T., Stefan M. C., and Torabifard, H.* “Dynamics of amphiphilic poly(ε-caprolactone) micelles with doxorubicin and transition temperature predictions using all-atom molecular dynamics simulation”. ChemRxiv 2024.
  1. Heidari, S. and Torabifard, H.* “Investigating the Properties of Fatty Acid-based Ionic Liquids: Advancement in AMOEBA Force Field”. ChemRxiv 2024.
  1. Goldman, A.R., Shah, T. and Torabifard, H.* “Histone H3 Orchestrates the Ubiquitination of Nucleosomal H2A by BRCA1/BARD1-UbcH5c Complex”. bioRxiv 2024.04.09.588726.
  1. Mills, K.R., Misra, J. and Torabifard, H.* “Allosteric Modulation of the YAP/TAZ-TEAD Interaction by Palmitoylation and Small-Molecule Inhibitors”. J. Phys. Chem. B 2024, 128, 16, 3795–3806.
  1. Mills, K.R. and Torabifard, H.* “Computational approaches to investigate fluoride binding, selectivity and transport across the membrane”. Methods in Enzymology. 2024, 696, 109-154.
  1. Mills, K.R. and Torabifard, H.* “Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter”. J. Chem. Inf. Model., 63, 8, 2445-2455, 2023.
Umbrella sampling revealed the proton transfer and release steps in the transport of the CLCF F-/H+ antiporter protein
  1. Ranathunga, D.T.S and Torabifard, H.* “Histone tail electrostatics modulate E2–E3 enzyme dynamics: a gateway to regulate ubiquitination machinery”. Phys. Chem. Chem. Phys, 25, 3361-3374, 2023.
Histone tail electrostatics affect conformational transitions of
BRCA1/BARD1-UbcH5c (E3-E2) enzymes on the nucleosome surface that regulate H2A C-tail dynamics and ubiquitination.
  1. Yeaton, A., Cayanan, G., Loghavi, S., Dolgalev, I., Leddin, E.M., Loo, C.E., Torabifard, H., Nicolet, D., Wang, J., Corrigan, K., Paraskevopoulou, V., Starczynowski, D.T., Wang, E., Abdel-Wahab, O., Viny, A.D., Stone, R.M., Byrd, J.C., Guryanova, O.A., Kohli, R.M., Cisneros, G.A., Tsirigos, A., Eisfeld, A., Aifantis, I., Guillamot, M., “The impact of inflammation-induced tumor plasticity during myeloid transformation”. Cancer Discovery, 12 (10), 2392-2413, 2022.
  1. Ji, K., Baek, K., Alberto, K.A., Peng, W., Torabifard, H., Nielsen, S.O., Dodani, S. “Biophysical and in silico characterization of NrtA: A protein-based host for aqueous nitrate and nitrite recognition”. Chem. Comm. 58, 965-968, 2021.

Prior to UTD:

  1. Torabifard, H., Panahi, A., Brooks III, C.L. “M2 amphipathic helices drive pH-dependent conformational transition in influenza A virus”. PNAS. 117(7): 3583-3591, 2020.
  1. Torabifard, H., Cisneros, G.A. “Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using ab initio  QM/MM calculations” Chem. Sci. 9 (4):8433-8445, 2018.

The calculated NEB path for 5hmC/5fC oxidation of WT TET2

  1. Lagardere, L., Jolly, L.H., Lipparini, F., Aviat, F., Stamm, B., Jing, Z.F., Harger, M., Torabifard, H., Cisneros, G.A., Schnieders, M.J., Gresh, N., Maday, Y., Ren, P., Ponder, J.W., Piquemel, J.P. “TINKER-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields” Chem. Sci. 9, 956:972, 2018.
  1. Torabifard, H., Reed, L., Berry, M., Hein, J., Menke, Erik., Cisneros, G.A. “Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications” J. Chem. Phys., 147, 16:161731, 2017″.
  1. Torabifard, H., Cisneros, G.A. “Computational investigation of O2  diffusion through an intra{molecular tunnel in AlkB; influence of polarization on O2  transport” Chem. Sci., 8, 9:6230, 2017.
Two main tunnels for O2 diffusion into the AlkB active site.
  1. Liu, M.Y.,Torabifard, H., Crawford, D.J., DeNizio, J.E., Cao, X., Garcia, B.A., Cisneros, G.A., Kohli, R.M. “Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine” Nat. Chem. Biol., 13, 181, 2017.
MD modeling reveals a critical Thr1372–Tyr1902 scaffold that is disrupted in the low-efficiency and hmC-dominant mutants.
  1. Cisneros, G.A., Wikfeldt, K.Y., Ojamae, L., Lu, j., Xu, J.,Torabifard, H., Bartok, A.P., Csanyi, G.,Molinero, V., Paesani, F. “Modeling molecular interactions in water: from pairwise to many-body potential energy functions” Chem. Rev., 116, 13:7501, 2016.
  1. Torabifard, H., Starovoytov, O.N., Ren, P., Cisneros, G.A. “Development of an AMOEBA water model using GEM distributed multipoles” Theor. Chem. Acc., 134, 101:1, 2015.
  1. Starovoytov, O.N.,Torabifard, H., Cisneros, G.A. “Development of AMOEBA force eld for 1,3-dimethylimidazolium based ionic liquids” J. Phys. Chem. B, 118, 7156, 2014.
Snapshot from MD simulation for liquid structure of [dmim+][BF4-] at T=475 K.
  1. Torabifard, H., Fattahi, A. “DFT study on Thiotepa and Tepa interactions with their DNA receptor” Struct. Chem., 24, 1, 2013.
  1. Torabifard, H., Fattahi, A. “Mechanism and kinetic of Thiotepa and Tepa hydrolysis: DFT study” J. Mol. Model., 18, 3563, 2012.
  1. Tehrani, Z.A.,Torabifard, H., Fattahi, A. “Thermochemical Properties of Some Vinyl Chloride-Induced DNA Lesions: Detailed View from NBO and AIM Analysis” Struct. Chem., 23, 1987, 2012.