Molecular Dynamics Of DHHC20 Acyltransferase Suggests Principles of Lipid and Protein Substrate Selectivity
Creators
- 1. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- 2. Institute of Virology, Department of Veterinary Medicine, Free University Berlin, Germany
- 3. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
Description
Data for Publication "Molecular Dynamics With DHHC20 Acyltransferase Suggests Principles of Lipid and Protein Substrate Selectivity"
Free hDHHC20 enzyme and two of its mutants (S29F and Y181A) describe the protein in the unbound state, prior to the auto- and transacylation reactions. (2)
Starting structures of the hDHHC20 and two mutants DHHC20S29F and DHHC20Y181A in .gro format (without water molecules) in pure POPC bilayer and mixed bilayer, respectively, along with trajectories (dt=1000 ps) in .xtc format:
| System | Starting structure | Trajectory | Topology |
| DHHC20 in POPC bilayer | DHHC20_PC.gro | DHHC20_PC.xtc | DHHC20.itp |
| DHHC20 in mixed bilayer | DHHC20_PIPEPG.gro | DHHC20_PIPEPG.xtc | DHHC20.itp |
| DHHC20S29F in POPC bilayer | DHHC20S29F_PC.gro | DHHC20S29F_PC.xtc | DHHC20S29F.itp |
| DHHC20S29F in mixed bilayer | DHHC20S29F_PIPEPG.gro | DHHC20S29F_PIPEPG.xtc | DHHC20S29F.itp |
| DHHC20Y181A in POPC bilayer | DHHC20Y181A_PC.gro | DHHC20Y181A_PC.xtc | DHHC20Y181A.itp |
| DHHC20Y181A in mixed bilayer | DHHC20Y181A_PIPEPG.gro | DHHC20Y181A_PIPEPG.xtc | DHHC20Y181A.itp |
The pre-acylation step, when the substrate analogue has already entered hDHHC’s cavity, but has not yet reacted. DHHC20 accommodates acyl-β-mercapto-ethylamine (MEA), an acyl-CoA analogue lacking a large 3’-phosphorylated ADP, within its inner cavity without a chemical bond formation. (3)
Starting structures of the hDHHC20 with substrate in .gro format (without water molecules) in mixed bilayer, along with trajectories (dt=1000 ps) in .xtc format:
| System | Starting structure | Trajectory | Topology |
| DHHC20 with C12-MEA | DHHC20_meaC12.gro | DHHC20_meaC12.xtc | DHHC20.itp, meaC12.itp |
| DHHC20 with C14-MEA | DHHC20_meaC14.gro | DHHC20_meaC14.xtc | DHHC20.itp, meaC14.itp |
| DHHC20 with C16-MEA | DHHC20_meaC16.gro | DHHC20_meaC16.xtc | DHHC20.itp, meaC16.itp |
| DHHC20 with C18-MEA | DHHC20_meaC18.gro | DHHC20_meaC18.xtc | DHHC20.itp, meaC18.itp |
| DHHC20 with C20-MEA | DHHC20_meaC20.gro | DHHC20_meaC20.xtc | DHHC20.itp, meaC20.itp |
The post-autoacylation step. hDHHC20 topology was modified to form a chemical bond between the cysteine’s sulfur atom and the fatty acid’s Cɑ-atom, which restricts the movement of the fatty acid residue. (4)
Starting structures of the acylated hDHHC20 .gro format (without water molecules) in mixed bilayer, along with trajectories (dt=1000 ps) in .xtc format:
| System | Starting structure | Trajectory | Topology |
| DHHC20-C12 | DHHC20_C12.gro | DHHC20_C12.xtc | DHHC20_C12.itp |
| DHHC20-C14 | DHHC20_C14.gro | DHHC20_C14.xtc | DHHC20_C14.itp |
| DHHC20-C16 | DHHC20_C16.gro | DHHC20_C16.xtc | DHHC20_C16.itp |
| DHHC20-C18 | DHHC20_C18.gro | DHHC20_C18.xtc | DHHC20_C18.itp |
| DHHC20-C20 | DHHC20_C20.gro | DHHC20_C20.xtc | DHHC20_C20.itp |
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