10 ns Molecular Dynamics simulations of mAMCase at pH 2.0 and 6.5 in complex with GlcNAc6.

This directory contains all files required to analyze the 10 ns MD simulations of mouse AMCase at pH 2.0 and 6.5 presented in Figure 5 in the manuscript Díaz et al. (2023).

All simulations were performed using Molecular Operating Environment (Chemical Computing Group) and simulation data was analyzed using Graphpad Prism. Structure models were analyzed using PyMOL. Figures were compiled using Adobe Illustrator.

Files included in this directory:

Figures

- contains PDFs of Asp138 X1 angle distribution, Asp138 X1 angle timecourse, PNGs of representative structure models from pH 2.0 active conformation simulation and pH 6.5 inactive conformation simulation with and without distances labeled.

MOE

- README.txt defines what each variable in "Production_phX_Conformation.xlsx" represents

/MOE/pHX_Conformation

- contains the starting structure for each simulation, a video of the 10 ns simulation, different variables measured during the simulation as an Excel (.xlsx) and Moe databasse (.mdb) files.

PyMOL

- contains all structure models, 2mFo-DFc maps, mFo-DFc maps, PyMOL script, and PyMOL session used to generate Figure 5.

MD.pzfx

- contains raw data from 10 ns simulations at pH 2.0 and pH 6.5 with Asp138 starting conformation in the active or inactive conformation.

Contact:
Roberto Efraín Díaz, robertoefrain.diaz@ucsf.edu

James Fraser, jfraser@fraserlab.com