Molecular dynamics simulations of hyaluronan octamer–tetrapeptide mixtures

<p><strong>To cite:</strong> Riopedre-Fernandez, M.; Biriukov, D.; Drač&iacute;nsk&yacute;, M.; Martinez-Seara, H. Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity. Carbohydr. Polym. 2024, 325, 121568. DOI: <a href="https://doi.org/10.1016/j.carbpol.2023.121568">10.1016/j.carbpol.2023.121568</a></p> <p>MD simulations of hyaluronan octamer (HA8) with tetrapeptides. Simulation files and molecular topologies are provided.</p> <p>Tetrapeptides simulated: tetraarginine (R4), tetralysine (K4), tetraalanine (A4), tetraproline (P4), tetraglycine (G4), arginine-lysine-arginine-lysine (RKRK), and tetraglutamic acid (E4).</p> <p>Two force fields were compared: CHARMM (version charmm36-jul2020.ff.tgz from <a href="http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs">http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs</a>) and prosECCo75 (<a href="https://gitlab.com/sparkly/prosecco/prosECCo75">https://gitlab.com/sparkly/prosecco/prosECCo75</a>).</p> <p>Each simulation contained one hyaluronan polymer, one tetrapeptide, CHARMM-specific TIP3P water, and potassium counterions (standard "K" model in CHARMM and "K_s" model in prosECCo75) when necessary.</p> <p>We also additionally performed: (i) reference simulations with only hyaluronan octamer and potassium counterions; (ii) reference simulations with only R4 or K4 peptide and chloride counterions; (iii) simulations with two peptides (R4, K4, or G4) and two hyaluronan octamers.</p> <p>Simulations were done in Gromacs.</p> <p>Length - at least 1 &micro;s, prolonged till 2 &micro;s for prosECCo75 systems with R4, K4, or G4 peptides.</p> <p>Temperature - 300 K.</p> <p>For peer-reviewing process, extracted PDB configurations (a configuration every 10 ns of 2 &mu;s simulations excluding the first 100 ns of equilibration) from selected systems were separately uploaded to <a href="http://doi.org/10.5281/zenodo.8423276">http://doi.org/10.5281/zenodo.8423276</a></p>