The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes

A new coarse-grain model for molecular dynamics simulation of lipid membranes is presented. Following a simple and conventional approach, lipid molecules are modeled by spherical sites, each representing a group of several atoms. In contrast to common coarse-grain methods, two original (interdependent) features are here adopted. First, the main electrostatics are modeled explicitly by charges and dipoles, which interact realistically through a relative dielectric constant of unity (). Second, water molecules are represented individually through a new parametrization of the simple Stockmayer potential for polar fluids; each water molecule is therefore described by a single spherical site embedded with a point dipole. The force field is shown to accurately reproduce the main physical properties of single-species phospholipid bilayers comprising dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylethanolamine (DOPE) in the liquid crystal phase, as well as distearoylphosphatidylcholine (DSPC) in the liquid crystal and gel phases. Insights are presented into fundamental properties and phenomena that can be difficult or impossible to study with alternative computational or experimental methods. For example, we investigate the internal pressure distribution, dipole potential, lipid diffusion, and spontaneous self-assembly. Simulations lasting up to 1.5 microseconds were conducted for systems of different sizes (128, 512 and 1058 lipids); this also allowed us to identify size-dependent artifacts that are expected to affect membrane simulations in general. Future extensions and applications are discussed, particularly in relation to the methodology's inherent multiscale capabilities

Role of Lipids in Spheroidal High Density Lipoproteins

We study the structure and dynamics of spherical high density lipoprotein (HDL) particles through coarse-grained multi-microsecond molecular dynamics simulations. We simulate both a lipid droplet without the apolipoprotein A-I (apoA-I) and the full HDL particle including two apoA-I molecules surrounding the lipid compartment. The present models are the first ones among computational studies where the size and lipid composition of HDL are realistic, corresponding to human serum HDL. We focus on the role of lipids in HDL structure and dynamics. Particular attention is paid to the assembly of lipids and the influence of lipid-protein interactions on HDL properties. We find that the properties of lipids depend significantly on their location in the particle (core, intermediate region, surface). Unlike the hydrophobic core, the intermediate and surface regions are characterized by prominent conformational lipid order. Yet, not only the conformations but also the dynamics of lipids are found to be distinctly different in the different regions of HDL, highlighting the importance of dynamics in considering the functionalization of HDL. The structure of the lipid droplet close to the HDL-water interface is altered by the presence of apoA-Is, with most prominent changes being observed for cholesterol and polar lipids. For cholesterol, slow trafficking between the surface layer and the regimes underneath is observed. The lipid-protein interactions are strongest for cholesterol, in particular its interaction with hydrophobic residues of apoA-I. Our results reveal that not only hydrophobicity but also conformational entropy of the molecules are the driving forces in the formation of HDL structure. The results provide the first detailed structural model for HDL and its dynamics with and without apoA-I, and indicate how the interplay and competition between entropy and detailed interactions may be used in nanoparticle and drug design through self-assembly

Protracted volitional spawning of pinfish Lagodon rhomboides and changes in egg quality and fatty-acid composition throughout the spawning season

Spawning performance of pinfish Lagodon rhomboides without use of hormonal aids was monitored over an extended season. Nearly three million eggs were obtained from 75 spawns collected over a 90-day consecutive period from a single population of four brood fish (1M:1F). A mean ± s.d. batch fecundity of 30·27 ± 22·64 eggs g−1 female was estimated with 98·0 ± 0·06% of the batch composed of floating eggs which were 1·04 ± 0·04 mm in diameter and 85·71 ± 27·59% fertile. Floating eggs successfully hatched 54·65 ± 29·13% of the time which yielded larvae that were 2·59 ± 0·24 mm in length. Fatty acids within floating eggs were largely represented by polyunsaturated fatty acids (45·30 ± 2·14% of total fatty acids) of which linoleic acid [(c18:2n-6cis) 3·49 ± 1·69% trifluoroacetic acid (TFA)] and docosahexaenoic acid (DHA) [(c22:6n-3) 28·47 ± 1·48% TFA] represented the majority of fatty acids for n-6 and n-3 polyunsaturated fatty acids, respectively. The strongest correlations between fatty acids and hatching success and larval survival to first feeding were observed for the DHA:EPA (eicosapentaenoic acid; c20:5n-3) ratio and total n-6 polyunsaturated fatty-acids levels, respectively. These data demonstrate potential for producers to rely on natural spawns for extensive egg production and provide a baseline for future development of natural spawning protocols of captive L. rhomboides

Performance of Larval Florida Pompano Fed Nauplii of the Calanoid Copepod \u3ci\u3ePseudodiaptomus pelagicus\u3c/i\u3e

The Florida pompano Trachinotus carolinus is a highly prized marine fish species, the larviculture of which currently includes the feeding of live rotifers and nauplii of brine shrimp Artemia spp. However, no previous studies have evaluated the feeding of copepod nauplii. In this study, the growth and survival of Florida pompano larvae fed nauplii of the calanoid copepod Pseudodiaptomus pelagicus were compared with those of larvae fed the standard reference diet of enriched rotifers Brachionus plicatilis. Experiments were conducted during the first 7–9 d posthatch (DPH), a period preceding the provision of Artemia nauplii. Treatments included feeding only copepod nauplii during the first day, the first three days, and on all days, as well as copepod nauplii mixed with rotifers during the entire experiment. In addition, the dietary effects on larval fatty acid composition were examined. Feeding copepod nauplii at a density of 2.0–3.5 nauplii/mL during the first day or the first three days of feeding had advantages over feeding only rotifers. However, after approximately 3 DPH, increased quantities of nauplii were needed to provide sufficient nutrients for growth. This was demonstrated in larvae fed copepod nauplii for the entire trial, for which survival was significantly higher than for the other treatments but for which growth was significantly reduced. Larvae fed a mixture of rotifers and nauplii for the entire trial had survival similar to that of larvae fed only rotifers (∼40%); however, growth was greater in larvae fed the mixed diet, suggesting that there is a nutritional advantage to including copepods in the diet. Fatty acid analyses revealed that increased levels of docosahexaenoic acid were associated with larvae fed copepods, which probably contributed to the observed higher survival and growth. These results indicate that there are multiple benefits to feeding copepods to Florida pompano larvae

Effects of increasing docosahexaenoic acid (DHA) and arachidonic acid (ARA) in brood diets of Monodactylus sebae on fecundity, egg and larval quality, and egg fatty acid composition

The Guinean Fingerfish Monodactylus sebae is a popular euryhaline ornamental fish species with limited aquaculture production. One of the bottlenecks to commercial production is lack of knowledge of the nutritional requirements for broodstock. Therefore, three broodfish diets were formulated and fed to Guinean Fingerfish broodstock to determine their quantitative and qualitative effects on egg production and egg and larval morphology. The dietary treatments consisted of a control, a diet with increased docosahexaenoic acid (DHA), and a diet with increased DHA and arachidonic acid (DHA + ARA). Broodfish fed the DHA + ARA diet spawned more frequently than broodfish fed the DHA diet and those fed the control diet. The greatest egg production was also observed from broodfish fed the DHA + ARA diet. The mean hatching success of floating eggs was not significantly different among diets. The mean egg and oil globule diameters for both floating and sinking eggs were significantly smaller for broodfish fed the DHA + ARA diet rather than the other diets. At both 24 and 48 h, survival was significantly greater for fish fed the control diet than for those fed the DHA and DHA + ARA diets. At both 24 and 48 h posthatch, notochord length was significantly shorter for larvae from broodfish fed the DHA + ARA diet than for larvae from fish fed the control diet. The fatty acid profiles of the eggs closely resembled the fatty acid profiles of the diets with respect to DHA and ARA levels. Guinean Fingerfish females appear to have the ability to regulate the levels of DHA and ARA assimilated into developing eggs, although there is not clear evidence that they can elongate and desaturate C18 fatty acids into DHA and ARA. © American Fisheries Society 2013