Molecular dynamics of LYVE-1 and CD44 in complex with hyaluronan

Description

Input and output data for MD of mouse/human LYVE-1 and mouse CD44, both, as apo proteins (PDB code 2JCP for mCD44) and in complex with hyaluronan hexasaccharide (HA6; PDB: 2JCR for mCD44). AMBER parm7 topology (.top), restart (.rst), minimisation and MD inputs (.tin, .in), binary NETCDF trajectories (.netcdf) and volumetric maps (.dx) are shared.

Steps to reproduce

LYVE-1/CD44 input structures in their apo forms or with HA6 bound were immersed in an octahedral box of TIP3P water molecules and 150 mM NaCl was added. Hydrogen mass repartitioning to 3Da enabled us to use a time step of 4 fs. A stepwise relaxation protocol using sander.MPI of AMBER20 was followed by 1 µs MD production run using pmemd.cuda of AMBER20. Trajectories were first analysed for structural stability using RMSD metrics by use of cpptraj of AMBER20. Due to the high flexibility of the systems, we analysed only portions of 500 ns length of residues 29 to 138, 24 to 133 and 25 to 134 for mLYVE-1/hLYVE-1/CD44, respectively. The following hydrogen-bonding criteria were used: 3.6 Å cutoff for acceptor‧‧‧donor distance and 120-180º range for acceptor‧‧‧H-donor angle. Water molecule occupancies were calculated from a 10 ns MD simulation with the protein-HA6 complexes fixed using the GIST procedure by summing up binary, ternary and quaternary interactions. To avoid double-counting, the ternary and quaternary interactions were added to the respective less populated interaction.

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