Multi-Scale Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer (original) (raw)
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A positional interpolation/extrapolation method for the mapping of coarse-grained (CG) to atomistic (AT) resolution is presented and tested for single-component micelles formed by lysophospholipids of different chain length. The target CG nanoaggregates were self-assembled from random mixtures of surfactants in explicit MARTINI water and equilibrated by molecular dynamics simulations, at the microsecond time scale. The ambiguity inherent in the definition of the CG particles was explored by mapping the same CG structures to AT resolution surfactants of different size. After the conversion, the obtained AT micelles were simulated for 250 ns and the resulting trajectories were analyzed in detail. The mean lifetime of the surfactant-solvent interactions as well as the lateral diffusion coefficients of the surfactant molecules within the micellar aggregates were obtained for the first time. The results suggest that the individual molecules within the micelle behave like lipids in a fluid membrane. The employed mapping back method is efficient and versatile, as it can be applied to diverse combinations of force fields and systems with a minimum of code development. In a general context, this work illustrates the power of multiscale molecular dynamics simulations for the generation and subsequent examination of self-assembled structures, including the fine characterization of structural and dynamic properties of the resulting aggregate.
Epitoanyag - Journal of Silicate Based and Composite Materials, 2010
Better understanding of the forces between modified or unmodified nanoparticles would be beneficial for developing new strategies for the production of engineered nanoparticle suspensions, as well as for predicting their fate and transport in the environment. Molecularlevel simulations, such as Molecular Dynamics can be useful for understanding the interactions between colloidal nanoparticles, but simulations of very large systems are constrained by the long calculation times and require enormous computer resources. A new computation approach that combines series of cycles of Rigid Body Dynamics and Molecular Dynamics has been applied to the study of the interaction of a lysophospholipidic micelle with polyacrylic acid. The results obtained show that the method makes it possible to reach a stationary interaction structure quite rapidly. The method is ready to be applied to the study of the interaction of a wide range of nanoparticles of industrial, environmental or biological interest via a widely-used and freelyaccessible computer code.
Langmuir, 2011
The amphiphilic nature of surfactants makes them prone to their spontaneous aggregation and self-organization in a variety of supramolecular forms such as micelles, vesicles, emulsions, and liquid crystals. The micelle shape in solution can be controlled by different factors including temperature, concentration, additives, and ionic strength. Variation of these parameters may result in modifications of micellar structure and eventually in geometrical transitions. It is demonstrated experimentally that micelles can adopt various shapes: spheres, discs, ellipsoids, or rods, and that at low concentrations of nonionic surfactants the micelles formed are close to spherical. The increase of concentration may lead to two effects: 2,3 either to a growth in the number of spherical aggregates with minor changes of their size or to the registration of a second critical concentration of micellization (CMC) characterizing the transition to rod-like assemblies.
Molecular dynamics simulations as a tool for accurate determination of surfactant micelle properties
Langmuir : the ACS journal of surfaces and colloids, 2017
Molecular dynamics (MD) simulations were used to characterize the equilibrium size, shape, hydration, and self-assembly of dodecylphosphocholine (DPC) and dodecyl-β-D-maltoside (DDM) micelles. We show that DPC molecules self-assemble to form micelles with sizes within the range reported in the experimental literature. The equilibrium shape of DPC and DDM micelles as well as associated micellar radii are in agreement with small angle X-ray scattering (SAXS) experiments and theoretical packing parameters. In addition, we show that hydration of the micelle interior is limited; however, flexibility of the acyl chains leads to dynamic encounters with the solvated outer shell of the micelle, providing an explanation for long-standing differences in models of micelle hydration. Altogether, our results provide fundamental understanding of physical characteristics of micelles that can be utilized to study other types of detergents and proteomicelle complexes.
The energy profile of self-assembly process of DLPE, DLPS, DOPE, DOPS, DLiPE, and DLiPS in water was investigated by a coarse-grained molecular dynamics simulation using NAMD package. The self-assembly process was initiated from random configurations. The simulation was carried out for 160 ns. This study presented proof that there were three major self-assembled arrangements which became visible for a certain duration when the simulation took place, that is, liposome, deformed liposome, and planar bilayer. The energy profile that shows plateau at the time of these structures emerge confirmed their stability therein. Our findings have highlighted the idea that liposomes and deformed liposomes are metastable phases which eventually will turn into planar bilayer, the stable one.
Molecular Dynamics Simulations of a Characteristic DPC Micelle in Water
Journal of Chemical Theory and Computation, 2012
We present the first comparative molecular dynamics investigation for a dodecylphosphocholine (DPC) micelle performed in condensed phase using the CHARMM36, GROMOS53A6, GROMOS54A7, and GROMOS53A6/Berger force fields and a set of parameters developed anew. Our potential consists of newly derived RESP atomic charges, which are associated with the Amber99SB force field developed for proteins. This new potential is expressly designed for simulations of peptides and transmembrane proteins in a micellar environment. To validate this new ensemble, molecular dynamics simulations of a DPC micelle composed of 54 monomers were carried out in explicit water using a "self-assembling" approach. Characteristic micellar properties such as aggregation kinetic, volume, size, shape, surface area, internal structure, surfactant conformation, and hydration were thoroughly examined and compared with experiments. Derived RESP charge values combined with parameters taken from Amber99SB reproduce reasonably well important structural properties and experimental data compared to the other tested force fields. However, the headgroup and alkyl chain conformations or the micelle hydration simulated with the Amber99SB force field display some differences. In particular, we show that Amber99SB slightly overestimates the trans population of the alkyl Csp 3 − Csp 3 −Csp 3 −Csp 3 dihedral angle (i.e., CCCC) and reduces the flexibility of the DPC alkyl chain. In agreement with experiments and previously published studies, the DPC micelle shows a slightly ellipsoidal shape with a radius of gyration of ∼17 Å for the different potentials evaluated. The surface of contact between the DPC headgroup and water molecules represents between 70% and 80% of the total micelle surface independently of the force field considered. Finally, molecular dynamics simulations show that water molecules form various hydrogen-bond patterns with the surfactant headgroup, as noted previously for phospholipids with a phosphatidylcholine headgroup. Figure 1. DPC surfactant with the atom-numbering scheme used in this work. Hydrogen atoms are omitted for clarity. Article pubs.acs.org/JCTC
Structure of cationic surfactant micelles from molecular simulations of self-assembly
2010
Molecular dynamics simulations of self-assembly of n-decyltrimethylammonium bromide surfactants were performed using an atomistic model, and a detailed analysis of the spontaneously formed micellar aggregates was carried out. This allowed for a detailed study of the structure of cationic surfactant micelles free from any a priori assumptions regarding their size and shape. Atomic radial distribution functions, radial density profiles and bivariate water orientation distributions were computed. Together, they show the presence of a dry micelle core, with a hydrophobic environment similar to a liquid alkane, a well-defined head-group layer at the interface, and an outer layer of strongly bound bromide counterions. Water molecules penetrate the micelle as far as the innermost head site, adopting a sequence of orientations that is akin to that observed at planar interfaces with vapor or immiscible organic solvents. Water molecules at the exterior of the micelle are highly polarized by the electrical double-layer formed by cationic head-groups and bromide anions, orienting themselves with their dipole vector pointing towards the micelle core.
Molecular Dynamics Simulation of the Kinetics of Spontaneous Micelle Formation
The Journal of Physical Chemistry B, 2000
Using an atom based force field, molecular dynamics (MD) simulations of 54 dodecylphosphocholine (DPC) surfactant molecules in water at two different concentrations above the critical micelle concentration have been performed. Starting from a random distribution of surfactants, we observed the spontaneous aggregation of the surfactants into a single micelle. At the higher DPC concentration (0.46 M) the surfactants aggregated into a worm-like micelle within 1 ns, whereas at lower concentration (0.12 M) they aggregated on a slower time scale (∼12 ns) into a spherical micelle. The difference in the final aggregate is a direct consequence of the system achieving the lowest free energy configuration for a given quantity of surfactant within the periodic boundary conditions. The simulation at low surfactant concentration was repeated three times in order to obtain statistics on the rate of aggregation. It was found that the aggregation occurs at a (virtually) constant rate with a rate constant of k ) 1 × 10 -4 ps -1 . This is an unexpected result. On the basis of Monte Carlo simulations of a stochastic description of the system, using diffusion rates and cluster radii as determined by separate MD simulations of single DPC clusters, a lower rate constant which diminishes in the course of the aggregation process had been predicted. Neglect of hydrodynamic interactions, of long-range hydrophobic interactions, or of spatial correlations in the stochastic approach might account for the descrepancies with the more accurate MD simulations.
Journal of Physics: Condensed Matter, 2002
Molecular dynamics simulations using a coarse-grained (CG) model for dimyristoyl-phosphatidyl-choline and water molecules have been carried out to follow the self-assembly process of a Langmuir monolayer. We expand on a previous study of the characteristics of the CG model where we compare the rotational and translational constants of the present model to those of an all-atom (AA) model, and find that the rotational and translational timescales are up to two orders of magnitude faster than in an AA model. We then apply the model to the self-assembly of a Langmuir monolayer. The initial randomly distributed system, which consists of 80 lipids and 5000 water sites, quickly self-assembles into two Langmuir monolayers and a micelle in the bulk water region. The micelle slowly diffuses towards and fuses with one of the interfacial monolayers, leaving the final equilibrated state with a Langmuir monolayer at each of the two air/water interfaces. The effective speed-up gained from the CG approach gives access to timescales and spatial scales that are much larger than those currently accessible with AA models.