Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation

Gemma Fisher, Marina Corbella, Magnus S. Alphey, John Nicholson, Benjamin J. Read, Shina C. L. Kamerlin, and Rafael G. da Silva

School of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.

Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, S-751 23 Uppsala, Sweden. 


** DESCRIPTION **

Topologies and molecular dynamics files to run simulations of the nonactivated and activated ATP phosphoribosyltransferases.

Topologies (Amber topology and coordinates files for MD simulations):
PaHisGs_WT.top
PaHisGs_WT.crd

PaHisGs_R56A.crd
PaHisGs_R56A.top

PaATPPRT_WT.crd
PaATPPRT_WT.top

PaATPPRT_R56A.crd
PaATPPRT_R56A.top

Libraries (Libraries for non-standard residues):
ATP.prep --> Amber parameters file for ATP.
PRP.off --> Amber library file for PRP.
Mg.lib --> Amber library for the Magnesium dummy model.
Mg_midC4.frcmod --> Amber modified parameters file for the Magnesium dummy model.

Inputs (Input files for MD simulations):
min1.in
min2.in
eq_nvt_1.in
eq_nvt_2.in
eq_nvt_3.in
eq_nvt_4.in
eq_nvt_5.in
eq_npt_6.in
eq_npt_7.in
md.in (for 100 ns)

Simulation_snapshots (Structures of the most populated cluster):
PaHisGs_WT.c0.pdb
PaHisGs_R56A.c0.pdb
PaATPPRT_WT.c0.pdb
PaATPPRT_R56A.c0.pdb

Correlation_matrices (Correlation matrices used to build the DCCM plots)
corr_R56A_activated.dat
corr_R56A_nonactivated.dat
corr_WT_activated.dat
corr_WT_nonactivated.dat

*******
