Methods, systems, and computer program products for simulating biomembrances using coarse grain models
View Patent ↗A coarse grain model that mimics a lipid molecule, such as dimyristoylphosphatidylcholine (DMPC), is used to simulate self-assembly of a lamellar bilayer starting from a disordered configuration. The coarse grain model is orders of magnitude less demanding of CPU time compared to all-atom models. An initial bilayer-like structure is generated from a disordered configuration of the coarse grain models using a Monte Carlo simulation. The initial bilayer-like structure is refined using a molecular dynamics simulation. For relatively small systems, the molecular dynamics simulation can be performed under constant volume or constant pressure conditions. For larger systems, the molecular dynamics simulation is preferably performed under constant pressure conditions.
1. A method for simulating assembly of a membrane lipid bilayer with a coarse grain model of the membrane lipid, comprising:
(1) representing the membrane lipid, with a coarse grain model;
(2) generating an initial bilayer-like structure from a group of the coarse grain models using a Monte Carlo simulation procedure;
(3) refining the initial bilayer-like structure using a molecular dynamics simulation to produce a substantially defect-free refined bilayer-like structure; and
(4) outputting a representation of the refined substantially defect-free bilayer-like structure to a computer system,
wherein each of (1)-(4) is performed on a suitably programmed computer,
wherein the refined bilayer-like structure in (4) is substantially defect-free within 500 psec of simulation time when the method is performed on a model consisting of 548 W sites and 64 dimyristoyl-sn-glycero-phosphatidylcholine molecules run at 303.15 K in a constant temperature and volume ensemble, wherein each W site represents a triplet of water molecules,
and wherein the coarse grain model results in an effective time scale of at least 100 ns.
2. The method according to claim 1 , wherein (3) comprises performing the molecular dynamics simulation under constant pressure conditions.
3. The method according to claim 1 , wherein (1) comprises representing a dimyristoyl-sn-glycero-phosphatidylcholine membrane lipid with a coarse grain model.
4. The method according to claim 1 , wherein (3) comprises performing the molecular dynamics simulation under constant pressure and temperature conditions.
5. The method according to claim 3 , wherein (1) further comprises representing the dimyristoyl-sn-glycero-phosphatidylcholine membrane lipid with at least 1000 coarse grain molecules and at least 5000 sites.
6. The method according to claim 5 , wherein (3) comprises performing the molecular dynamics simulation under constant pressure conditions.
7. The method according to claim 3 , wherein (1) comprises:
(a) representing triplets of carbon atoms in hydrocarbons and their accompanying hydrogen atoms as spherical objects;
(b) linking hydrocarbon sites together to form chains using stretching and bending potentials; and
(c) representing triplets of water molecules as spherical objects.
8. The method according to claim 7 , wherein (1) further comprises:
(d) representing a choline backbone as a first spherical object;
(e) representing a phosphate backbone as a second spherical object; and
(f) representing a glycerol backbone as a third spherical object.
9. The method according to claim 1 , wherein (2) comprises generating the initial bilayer-like structure from a disordered group of the coarse grain models.
10. The method according to claim 1 , wherein (3) comprises conducting the molecular dynamics simulation in a canonical ensemble using Nosé-Hoover chain lengths of 4.
11. The method according to claim 1 , wherein (3) comprises performing a multiple time step molecular dynamics simulation using a three stage RESPA integration of equations in motion.
12. The method according to claim 1 , wherein (3) comprises:
(a) conducting the molecular dynamics simulation in a canonical ensemble using Nosé-Hoover chain lengths of 4; and
(b) performing a multiple time step molecular dynamics simulation using a three stage RESPA integration of equations in motion.