Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models.
The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.
Euston
Stephen R
SR
School of Life Sciences and International Centre for Brewing and Distilling, Heriot-Watt University, Riccarton, Edinburgh, United Kingdom. s.r.euston@hw.ac.uk
D000327:Adsorption; D000473:Alkanes / Q000737:chemistry*; D052179:Antigens, Plant / Q000737:chemistry*; D002352:Carrier Proteins / Q000737:chemistry*; D001467:Hordeum / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D010940:Plant Proteins / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics; D014618:Vacuum; D014867:Water / Q000737:chemistry*
D000473:Alkanes; D052179:Antigens, Plant; D002352:Carrier Proteins; D010940:Plant Proteins; C511920:lipid transfer proteins, plant; D014867:Water; C012867:decane