Computational protocol: Organic bioelectronics probing conformational changes in surface confined proteins

Similar protocols

Protocol publication

[…] The initial structure of the AV-Biotin complex was obtained from the Protein Data Bank (PDB), entry 2AVI. To increase the structure confidence level (to correct missing hydrogen atoms, incomplete side chains and loops, ambiguous protonation states and flipped residues) the 2AVI crystal was first pre-treated using the Schrödinger’s Protein Preparation Wizard (Version 9.5). The optimal protonation state for Histidine residues was determined according to the pH experimental value of 7.5. The simulation system was built using Visual Molecular Dynamics (VMD). Cl− ions were added to neutralize the system using the VMD’s autoionize plugin. In the case of AV-Biotin complex system 4 extra Na+ ions were added to counterbalance the net negative charge carried by the four bounded biotins. The initial positions of the ions were taken from a previous all-atoms MD simulation performed in explicit solvent at 150 mM NaCl concentration. All modeled systems (AV, AV-biotin complex and AV-B5F complex) were simulated in vacuum in a cubic periodic box of 100 Å side generating a final system of 7524 atoms (number computed for the tetramer of the AV-biotin complex). The simulations were performed with an implicit solvent model assuming a relative permittivity εr = 3, typical for a protein system. All MD simulations were performed using NAMD 2.9 and the CHARMM36 force-field. Atomic charges of biotin and B5F were determined by the Restrained Electrostatic Potential (RESP) method using Hartree-Fock theory and the 6-31G**basis set. The full systems were minimized to remove steric clashes in the initial geometry and gradually heated up to 297 K within 500 ps of MD. The SHAKE algorithm was employed to constrain all R–H bonds. Periodic boundary conditions were applied in all directions. A non-bonded cut-off of 12 Å was used, whereas the Particle-Mesh-Ewald (PME) was employed to include the contributions of long-range interactions. All simulations were performed in an isothermal-isobaric ensemble (1 atm, 297 K) with a Nosè–Hoover Langevin barostat (oscillation period 200 fs, decay coefficient 100 fs) and a Langevin thermostat (damping coefficient 1 ps−1). The time step was set to 2 fs, and coordinates were saved every 5000 steps (10 ps). For all the considered systems, a MD trajectory of 50 ns was obtained and since the equilibration of the structure required less than 5 ns, the first 5 ns were removed from the analysis.The electric dipole moment was calculated for each monomer (including the ligand when present) as the modulus of: where i runs over the atoms of the monomer (monomer-ligand complex), qi is the partial charge of the i-th atom and ri is the position vector of the i-th atom respect to the center of mass of the monomer (monomer-ligand complex). Root Mean Square Deviations (RMSDs) and Root Mean Square Fluctuations (RMSFs) were obtained after alignment of the trajectory to all the C-alpha atoms belonging to the monomer under investigation […]

Pipeline specifications

Software tools VMD, NAMD
Application Protein structure analysis
Chemicals Biotin