Computational protocol: Ultra-thin enzymatic liquid membrane for CO2 separation and capture

Similar protocols

Protocol publication

[…] The simulations were performed with the GROMACS software package. The CHARMM36 force field, was used to model the bovine CA enzyme (Protein Data Bank accession number 1V9E) under different conditions relevant to CO2 separation, including interaction with silica nanopores. The silica nanopore atoms were modeled with the CHARMM36-compatible INTERFACE force field,. Protonation states of amino acids of the CA enzyme were selected according to the results of PROPKA analysis at pH 7. A rectangular silica nanopore was built based on the structure of the alpha-cristobalite unit cell. The pore’s outer dimensions are 11 × 12 × 10 nm and its internal dimensions are 8 × 8 × 10 nm. The average surface silanol density of the pore is 5.9 Si–OH nm–2, which provides a reasonable model of the amorphous silica surface used in the experimental membranes,. A percentage (16.5%) of the surface silanols were ionized to match the pH 7 conditions. Sodium (Na+) ions were added to counter the negative charge of the ionized silanol groups. No additional salt molecules, either Na+ or Cl−, were added to the simulation, except to produce an overall neutral charge simulation system. A vertical water-filled space exists between periodic images of the simulation cell of height 6 nm, giving the CA enzyme the ability to exit the nanopore. Three CA-nanopore systems were simulated with one, two, and four enzymes within the pore to observe possible crowding effects. A free CA enzyme in solution was also simulated for reference. All systems were simulated at room temperature (298 K) for 300 ns using a Nose–Hoover thermostat. The simulation volume for pore systems was adjusted during the early stages of the simulation to obtain an average pressure of 1 atm, and subsequently simulated at constant volume. The free CA enzyme was simulated at constant 1 atm pressure using a Parrinello–Rahman barostat. […]

Pipeline specifications

Software tools GROMACS, IFF, PROPKA
Application Protein structure analysis
Chemicals Carbon Dioxide, Carbonic Acid