Data for 'Dynamical origins of heat capacity changes in enzyme catalysed reactions'

Dynamical origins of heat capacity changes in enzyme catalysed reactions

Marc W van der Kamp, Erica J. Prentice, Kirsty L. Kraakmann, Michael Connolly, Adrian J. Mulholland & Vickery L. Arcus

School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, UK.

Centre of Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol, BS8 1TS, UK.

School of Science, University of Waikato, Hamilton, New Zealand.

The data files contained in this repository are as follows:

1a. Input coordinates (starting structures) in PDB format are named as enzyme_state.pdb.

1b. Input coordinates are named as enzyme_state.inpcrd and are in the standard Amber format (generated with Amber12).

2. Topology and parameter files are named as enzyme_state.prmtop and are also in standard Amber format (generated with Amber12).

3. Input files for the MD simulations are in the subdirectories KSI_md_input_files and MalL_md_input files. Input files are included for the equilibration, heating and production runs of molecular dynamics, which were performed in this order:

a. minsolv.i

b. mdsolv.i

c. min.i

d. heat.i

e. npt_release1.i

f. npt_release2.i

g. npt_release3.i

h. npt_release4.i

i. eq_npt.i

j. md10.i

For KSI, a restraint was used in both RS and IS states, which is included in the file r7.RST.

A restraint was also used in the MalL states (RS and TSA), which is included in the file d_com.rst. All input files are in the standard Amber format (see e.g. Amber16.pdf manual).