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Sodium coupled cotransporters of the five-helix inverted repeat (5HIR) superfamily use an alternating access mechanism to transport a myriad of small molecules across the cell membrane. One of the primary steps in this mechanism is the conformational transition from a state poised to bind extracellular substrates to a state that is competent to deliver… (More)
We have explored the impact of a number of basic simulation parameters on the results of a recently developed hybrid molecular dynamics-quantum mechanics (MD-QM) method (Mercer et al., J Phys Chem B 1999, 103, 7720). The method utilizes MD simulations to explore the ground-state configuration space of the system and QM evaluation of those structures to… (More)
To my father, my first and foremost scientific and personal mentor. data from the McCoy group enabled the rotational analysis of Section 3.1, and geometries and MULTIMODE vibrational frequencies from the Bowman group enabled the discussion of Section 3.2.