Paper Citing NAMD - Abstract
Zomot, Elia; Bahar, Ivet
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state
MOLECULAR BIOSYSTEMS, 6:1040-1046, 2010
The recent elucidation of the sodium/galactose symporter structure from the Vibrio parahaemolyticus bacterium, vSGLT, has revealed a similarity in the core architecture with transporters from different gene families, including the leucine transporter (LeuT). Even though several transporters sharing this core have been structurally determined over the past few years, vSGLT is the only one crystallized in the substrate-bound inward-facing conformation so far. In this study, we report the first insight into the dynamics and coordination of the galactose (Gal) and proposed Na(+) ion in vSGLT using a series of molecular dynamics simulations with a total time of about 0.1 mu s. Our study reveals new residues, not observed in the crystal structure, which closely interact with the Na(+) ion or the substrate for extended times, and shows that in the crystallized conformation, a Na(+) ion placed at the site equivalent to Na2 in LeuT can escape into the intracellular (IC) space in the absence of external forces. We have identified the highly conserved Asp189 as a likely binding residue on the pathway of Na(+) into the IC cavity. The release of Gal, on the other hand, requires the rotation of the side chain of the inner hydrophobic gate, Tyr263, without a significant change in vSGLT backbone conformation. Our simulations further show that the crystal structure represents but one accessible binding pose of Gal and Na(+) among an ensemble of microstates, and that the Gal undergoes versatile alternate interactions at the binding pocket.
