In Torabifard group, we are interested in applying computational methods to understand different biological and chemical phenomena.
Membrane transport proteins
The membrane transport proteins are the molecular gatekeepers of the cell, which import vital nutrients and export dangerous toxins within the cell. We model various system including, but not limited to excitatory amino acid transporters 3 (EAAT3), metal transporters, CLC Cl–/H+ antiporters, CLCF-type F–/H+ antiporters and the “Fluc-type” F– ion. For example, we investigate Fluoride exporters to shed light on how microbes evolved resistance mechanism to Fluoride ion toxicity and to aid in identifying their vulnerabilities that could pave the way for therapeutic drug discovery for harmful bacterial diseases. We use computational methods including MD, QM/MM, structure/sequence alignments and structural predictions to study the biological function and structure of these proteins.
Histone tails dynamics and post-translational modification
Histone tail post-translational modifications (PTMs) and PTMs enzymes are proposed to be used as novel cancer therapies and biomarkers. However, their specific mechanisms of histone tail PTMs in many of cancers are not completely understood. We use MD simulations to understand the molecular basis that underlies the histone tail PTMs and their cross-talk in different cancers.
Force field development and computational design of bio-based ionic liquids
We study bio-based ionic liquids, which has been recently introduced to overcome the drawbacks of currently employed ILs such as toxicity and low biodegradability. Some ILs have already been synthesized from renewable, nontoxic bio sources such as amino acids and fatty acids, etc. However, the wide variety of cation-anion combinations makes the synthesis and experimental determination of bio-based ILs properties an expensive and time-consuming process. Moreover, predicting which ILs are well suited for a given application remains an important pre-synthesis pursuit. To this end, we apply computational methods (from force field development to MD simulations) to design bio-based ILs and predict their properties to aid in the discovery process.