Computational materials for "Negative Membrane potential accelerates sugar uptake by stabilizing the outward-facing conformation of the Na+/glucose symporter vSGLT"

Materials used for running of MD simulations and computational model calculations described in the article:

Farha Khan, Matthias Elgeti, Samuel Grandfield, Aviv Paz, Fiona B. Naughton, Frank V. Marcoline, Thorsten Althoff, Natalia Ermolova, Ernest M. Wright, Wayne L. Hubbell, Michael Grabe, Jeff Abramson "Negative Membrane potential accelerates sugar uptake by stabilizing the outward-facing conformation of the Na+/glucose symporter vSGLT". 2023.

• init_vSGLT[+/-]na.gro: Initial coordinate files for production molecular dynamics simulation runs of vSGLT with (+na) and without (-na) sodium bound
• md_vSGLT[+/-]na_[01/02/03].tpr: Simulation input files in Gromacs 2020.6 format for production MD runs of vSGLT starting with (+na) or without (-na) sodium in the binding site; three repeats (01,02,03) with different initial velocities
• md_vSGLT[+/-]na_[01/02/03].gro: Final snapshots at 100ns for each MD run above
• KhanMathModel08.20.2023.mmd: Berkeley Madonna (Version 10) code for 5 state model of transport; will reproduce Figure 6 panels b, c and d.
• vSGLT_gatingcharge.solv.in: code for calculating gating charges
• vSGLT_[inward/outward]-facing3.orient1.pqr: structures used in gating charge calculation

Associated experimental data can be found at 10.5281/zenodo.8431613.