Data from simulations of mutations of tryptophan synthase

Data from the article "A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the Dynamic
Behavior of the Catalytic Site of the Tryptophan Synthase", A. Roy and M. Karttunen
 

• J. Chem. Inf. Model. (in press (2024)
• Web: https://doi.org/10.1021/acs.jcim.3c01966
• Preprint: https://doi.org/10.26434/chemrxiv-2023-4bhpv

Four systems of TS (Tryptophan Synthase):

   System = Denoted by

1.  E(PLP)  = e-plp
2.  E(AEX1) = e-aex1
3.  E(AA)   = e-aa
4.  E(c3)   = e-c3

Each system has 3 versions:

1.  wt     = WildType
2.  ala114 = mutated version (Gln114 mutated to Ala114)
3.  asn114 = mutated version (Gln114 mutated to Asn114)

Folder names:

     1_E(PLP) System Folders

1.  1_wt-e-plp
2.  2_ala114-e-plp
3.  3_asn114-e-plp

    2_E(AEX1) System Folders

1.  4_wt-e-aex1
2.  5_ala114-e-aex1
3.  6_asn114-e-aex1

    3_E(AA) System Folders

1.  7_wt-e-aa
2.  8_ala114-e-aa
3.  9_asn114-e-aa

    4_E(c3) System Folders

1.  10_wt-e-c3
2.  11_ala114-e-c3
3.  12_asn114-e-c3

File names:

Each folder contains AMBER readable topology, restart, input files, and also last frame pdb file:

• initial system topology     = system.parm7
• initial restart file               = system.rst7
• minimization 1 input file   = min.in
• minimization 1 restart file = min.rst7
• minimization 2 input file    = min-all.in
• minimization 2 restart file  = min-all.rst7
• heating input file               = heat.in
• heating restart file            = heat.rst7
• equilibration input file       = equil.in
• equilibration restart file     = equil.rst7
• production 1 input file       = md.in
• production 1 restart file     = md.rst7
• production 2 input file       = md2.in
• production 2 restart file     = md2.rst7
• last frame of production    = frame40000_800ns.pdb