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

Input and output data for MD of mouse/human LYVE-1 and mouse CD44, both, as apo proteins (PDB codes 8ORX, 8OS2, 2JCP, respectively) and in complex with hyaluronan hexasaccharide (HA6; PDB codes 8OX3, 8OXD, 2JCR, respectively).  AMBER parm7 topology (.top), restart (.rst), minimisation and MD inputs (.tin, .in), binary NETCDF trajectories (.netcdf) and volumetric maps (.dx) are shared.

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. Bridging water molecule occupancies were calculated by summing up binary, ternary and quaternary interactions (the cutoff for each was set to a minimum of 10 %).