Understanding the Phase Behavior of Coarse-Grained Model Lipid Bilayers through Computational Calorimetry

Abstract

We study the phase behavior of saturated lipids as a function of temperature and tail length for two coarse-grained models: the soft-repulsive model typically employed with dissipative particle dynamics (DPD) and the MARTINI model. We characterize the simulated transitions through changes in structural properties, and we introduce a computational method to monitor changes in enthalpy, as is done experimentally with differential scanning calorimetry. The lipid system experimentally presents four different bilayer phasessubgel, gel, ripple, and fluidand the DPD model describes all of these phases structurally while MARTINI describes a single orderÀdisorder transition between the gel and the fluid phases. Given both models' varying degrees of success in displaying accurate structural and thermodynamic signatures, there is an overall satisfying extent of agreement for the coarse-grained models. We also study the lipid dynamics displayed by these models for the various phases, discussing this dynamics with relation to fidelity to experiment and computational efficiency.

PSII–LHCII Supercomplex Organizations in Photosynthetic Membrane by Coarse-Grained Simulation

“…For the CG model of lipid bilayer, we coarse-grained the whole lipid molecule into two CG beads -namely, the hydrophilic and hydrophobic beads (right panel of Figure 1b), based on a CG model derived from dissipative particle 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 7 dynamics (middle panel of Figure 1b). [29][30][31] This CG scheme for the PSII-LHCII supercomplexes and lipid bilayer allowed us to model the order/disorder packings of PSII-LHCII supramolecular structures under various free-LHCII (M):PSII (C 2 S 2 ) ratios, protein packing fractions, and temperatures of the thylakoid membrane with lateral size of 0.5 × 0.5 µm 2 , see Figure 1c, thereby providing direct comparisons with experimental results. Note that the spatial resolution of the CG model in the present study is good for studying the supramolecular organizations in the thylakoid membrane, and therefore, is too coarse for taking the orientation dependencies of moderately-bound-LHCII trimmer association/dissociation with the PSII complexes.…”

“…1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 The CG model for lipid bilayer in the present study was based on a CG model derived from dissipative particle dynamics. [29][30][31] In order to accommodate lipid CG particle sizes with those of PSII-LHCII CG beads, further coarse-graining is required. We further coarse-grained the hydrophobic and hydrophilic parts of a lipid molecule into two CG beads, namely, hydrophilic (bead f) and hydrophobic (bead g) beads.…”

Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods

“…11 Although many MC and MD simulations have been performed to study micelle formation from the self-assembly of amphiphiles, limited studies have been performed on the systematic examination of bilayer phase behavior as a function of temperature. 1,[20][21][22][23][24][25][26] Of those studies, conventional MD or MC methods, along with temperature quenching, have been used as the main simulation techniques to induce phase transitions. In addition, these studies all use visual inspection or calculation of order parameters to support the structural phase transition as a function of the system temperature; however, more recently, the calculation of the heat capacity (C v ) has been used as a more direct signature of the phase transition.…”

“…In addition, these studies all use visual inspection or calculation of order parameters to support the structural phase transition as a function of the system temperature; however, more recently, the calculation of the heat capacity (C v ) has been used as a more direct signature of the phase transition. Rodgers et al 20 reported the first attempt to characterize the phase transition of a solvated amphiphilic model by monitoring changes in enthalpy with a computational calorimetry approach developed based on a dissipative particle dynamics (DPD) model. Almost simultaneously, Nagai et al 21 reported the application of replica-exchange MD (REMD) to an explicit atom simulation of a small dipalmitoylphosphatidylcholine (DPPC) bilayer system using the coarse-grained (CG) Martini force field, with enthalpy tracking for the calculation of heat capacity.…”

Coarse-grained simulation of transmembrane peptides in the gel phase

“…The resulting, coarse-grained, model can advance much faster in time, allowing the study of much slower, or larger-scale, processes [16]. Simulations of lipid membranes using extremely coarse-grained models, in which each particle represents many atoms, are much more efficient [10,17,18] and have given considerable insight into the interaction between embedded proteins [19][20][21][22][23].…”