Computational protocol: Electric fields control the orientation of peptides irreversibly immobilized on radical-functionalized surfaces

Similar protocols

Protocol publication

[…] Two molecular dynamics equilibrium simulations were run to assess the secondary-structural behaviour of the FLAG peptide, each using different starting structures. The peptide starting coordinates were generated using Avogadro software as either fully linear or alpha-helix. These structures were solvated with TIP3P water using the VMD Solvate plugin, with box sizes 14 Angstrom larger than the peptide’s longest axis in the x, y and z directions using periodic boundary conditions. This ensured the peptides did not interact with their periodic images in an adjacent box. Each system had 150 mM NaCl added. The systems were minimized for 4000 steps and the water equilibrated for 1 ns by restraining the alpha-carbon atoms.The alpha helical peptide equilibrium simulation was run for 300 ns. The alpha helix conformation was unstable and by this point had unfolded. This simulation was stopped since the peptide was longer and could interact with periodic copies of itself. The linear peptide simulation was run for 800 ns. Both simulations used a constant pressure of 1 atm and temperature of 298 K maintained using a Langevin Piston and Langevin thermostat respectively. The CHARMM27 force field was used for the protein parameters, and the simulations, using a 2 fs timestep, were run using NAMD2.91. […]

Pipeline specifications

Software tools Avogadro, VMD
Applications Drug design, Protein structure analysis