Using EPR and Rosetta to study the LeuT-fold transporter family, which includes neurotransmitter-sodium symporters.
My goal within the Chemical and Physical Biology program (CPB) is to gather electron paramagnetic resonance (EPR) spectroscopy data, particularly double electron-electron resonance (DEER) data, in the Mchaourab laboratory and write scripts for the protein folding algorithm Rosetta in the Meiler lab capable of using this data to generate ensemble states for different functional conformations of membrane proteins, specifically transporters. I plan to simulate conformations of proteins that have already been crystallized in specific states. This work will focus on transporters, specifically the twelve-transmembrane helix LeuT-fold proteins, which are often crystallized in a single substrate-bound or antibody-stabilized state; because the substrate-free (apo) state is often more dynamic, comparable crystallographic data rarely exists (at this time, the proteins’ size puts them beyond the scope of structural examination by NMR and cryo-EM). Additionally, owing to the apo state’s flexibility, this work will focus on generating ensemble states, rather than single structures, in an attempt to reconcile RosettaEPR, which was written by another student at the interface, with the recent reevaluation of the importance of ensembles and protein dynamics in the field of structural biology.
Jens Meiler and Hassane Mchaourab
University of New Hampshire
- Crochiere ML, Baloglu E, Klebanov B, Donovan S, Del Alamo D, Lee M, Kauffman M, Shacham S, Landesman Y. A method for quantification of exportin-1 (XPO1) occupancy by Selective Inhibitor of Nuclear Export (SINE) compounds. Oncotarget. 2016 Jan 12;7(2). 1863-77. PMID: 26654943 [PubMed]. PMCID: PMC4811503.