Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations.

ABSTRACT: Micelles play an important role in both experimental and computational studies of the effect of lipid interactions on biological systems. The spherical geometry and the dynamical behavior of micelles makes generating micelle structures for use in molecular simulations challenging. An easy tool for generating simulation-ready micelle models, covering a broad range of lipids, is highly desirable. Here, we present a new Web server, Micelle Maker, which can provide equilibrated micelle models as a direct input for subsequent molecular dynamics simulations from a broad range of lipids (currently 25 lipid types, including 24 glycolipids). The Web server, which is available at http://www.micellemaker.net, uses error checking routines to prevent clashes during the initial placement of the lipids and uses AMBER's GLYCAM library for generating minimized or equilibrated micelle models, but the resulting structures can be used as starting points for simulations with any force field or simulation package. Extensive validation simulations with an overall simulation time of 12 μs using eight micelle models where assembly information is available show that all of the micelles remain very stable over the whole simulation time. Finally, we discuss the advantages of Micelle Maker relative to other approaches in the field.

SUBMITTER: Kruger DM

PROVIDER: S-EPMC5579539 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Micelles with ultralow critical micelle concentration as carriers for drug delivery.

Project description:Conventional micellar carriers disassemble into free surfactants when diluted at concentrations below the critical micelle concentration (CMC). This limits the bioavailability in vivo of injected hydrophobic drugs encapsulated in micellar systems. Here, we show that a micelle comprising a superhydrophilic zwitterionic polymer domain and a superhydrophobic lipid domain has an undetectable CMC below 10-6 mM-a value that is orders of magnitude lower than the CMCs (>10-3 mM) of typical micellar systems. We also show that zwitterionic moieties or zwitterionic polymers added to a micelle solution stabilize the micelles at concentrations below their inherent CMC. In a mouse model of melanoma, ultralow-CMC micelles encapsulating docetaxel led to the complete eradication of tumours, whereas conventional docetaxel micellar formulations did not reverse tumour growth. Ultralow-CMC micelles might become next-generation carriers for drug delivery.

| S-EPMC6553490 | biostudies-literature

Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters.

Project description:In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers? compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids? topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (md.mdp). The data is associated with the research article "Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner" (Róg et al., 2016) [3].

| S-EPMC5063793 | biostudies-literature

Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets.

Project description:SummaryDifferential Expression Gene Explorer (DrEdGE) is a web-based tool that guides genomicists through easily creating interactive online data visualizations, which colleagues can query according to their own conditions to discover genes, samples or patterns of interest. We demonstrate DrEdGE's features with three example websites generated from publicly available datasets-human neuronal tissue, mouse embryonic tissue and Caenorhabditis elegans whole embryos. DrEdGE increases the utility of large genomics datasets by removing technical obstacles to independent exploration.Availability and implementationFreely available at http://dredge.bio.unc.edu.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC7178403 | biostudies-literature

The Amyloid as a Ribbon-Like Micelle in Contrast to Spherical Micelles Represented by Globular Proteins.

Project description:Selected amyloid structures available in the Protein Data Bank have been subjected to a comparative analysis. Classification is based on the distribution of hydrophobicity in amyloids that differ with respect to sequence, chain length, the distribution of beta folds, protofibril structure, and the arrangement of protofibrils in each superfibril. The study set includes the following amyloids: A? (1-42), which is listed as A? (15-40) and carries the D23N mutation, and A? (11-42) and A? (1-40), both of which carry the E22? mutation, tau amyloid, and ?-synuclein. Based on the fuzzy oil drop model (FOD), we determined that, despite their conformational diversity, all presented amyloids adopt a similar structural pattern that can be described as a ribbon-like micelle. The same model, when applied to globular proteins, results in structures referred to as "globular micelles," emerging as a result of interactions between the proteins' constituent residues and the aqueous solvent. Due to their composition, amyloids are unable to attain entropically favorable globular forms and instead attempt to limit contact between hydrophobic residues and water by producing elongated structures. Such structures typically contain quasi hydrophobic cores that stretch along the fibril's long axis. Similar properties are commonly found in ribbon-like micelles, with alternating bands of high and low hydrophobicity emerging as the fibrils increase in length. Thus, while globular proteins are generally consistent with a 3D Gaussian distribution of hydrophobicity, the distribution instead conforms to a 2D Gaussian distribution in amyloid fibrils.

| S-EPMC6930452 | biostudies-literature

Structural determination of Abeta25-35 micelles by molecular dynamics simulations.

Project description:Amyloid-beta (Abeta) peptides and other amyloidogenic proteins can form a wide range of soluble oligomers of varied morphologies at the early aggregation stage, and some of these oligomers are biologically relevant to the pathogenesis of Alzheimer's disease. Spherical micelle-like oligomers have been often observed for many different types of amyloids. Here, we report a hybrid computational approach to systematically construct, search, optimize, and rank soluble micelle-like Abeta25-35 structures with different side-chain packings at the atomic level. Simulations reveal for the first time, to our knowledge, that two Abeta micelles with antiparallel peptide organization and distinct surface hydrophobicity display high structural stability. Stable micelles experience a slow secondary structural transition from turn to alpha-helix. Energetic analysis coupled with computational mutagenesis reveals that van der Waals and solvation energies play a more pronounced role in stabilizing the micelles, whereas the electrostatic energies present a stable but minor energetic contribution to peptide assemblies. Modeled Abeta micelles with shapes and dimensions similar to those of experimentally derived spherical structures also provide detailed information about the roles of structural dynamics and transition in the formation of amyloid fibrils. The strong binding affinity of our micelles to antibodies implies that micelles may be a biologically relevant species.

| S-EPMC2905084 | biostudies-literature

Genome Annotation and Curation Using MAKER and MAKER-P.

Project description:This unit describes how to use the genome annotation and curation tools MAKER and MAKER-P to annotate protein-coding and noncoding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality metrics to annotations from other pipelines, and map existing annotations to a new assembly. MAKER and MAKER-P can rapidly annotate genomes of any size, and scale to match available computational resources.

| S-EPMC4286374 | biostudies-literature

CHARMM-GUI PACE CG Builder for solution, micelle, and bilayer coarse-grained simulations.

Project description:Coarse-grained (CG) and multiscale simulations are widely used to study large biological systems. However, preparing the simulation system is time-consuming when the system has multiple components, because each component must be arranged carefully as in protein/micelle or protein/bilayer systems. We have developed CHARMM-GUI PACE CG Builder for building solution, micelle, and bilayer systems using the PACE force field, a united-atom (UA) model for proteins, and the Martini CG force field for water, ions, and lipids. The robustness of PACE CG Builder is validated by simulations of various systems in solution (α3D, fibronectin, and lysozyme), micelles (Pf1, DAP12-NKG2C, OmpA, and DHPC-only micelle), and bilayers (GpA, OmpA, VDAC, MscL, OmpF, and lipid-only bilayers for six lipids). The micelle's radius of gyration, the bilayer thickness, and the per-lipid area in bilayers are comparable to the values from previous all-atom and CG simulations. Most tested proteins have root-mean squared deviations of less than 3 Å. We expect PACE CG Builder to be a useful tool for modeling/refining large, complex biological systems at the mixed UA/CG level.

| S-EPMC3985889 | biostudies-literature

Tuning small molecule release from polymer micelles: Varying H2S release through cross linking in the micelle core.

Project description:Polymer micelles, used extensively as vehicles in the delivery of active pharmaceutical ingredients, represent a versatile polymer architecture in drug delivery systems. We hypothesized that degree of crosslinking in the hydrophobic core of amphiphilic block copolymer micelles could be used to tune the rate of release of the biological signaling gas (gasotransmitter) hydrogen sulfide (H2S), a potential therapeutic. To test this hypothesis, we first synthesized amphiphilic block copolymers of the structure PEG-b-P(FBEA) (PEG = poly(ethylene glycol), FBEA = 2-(4-formylbenzoyloxy)ethyl acrylate). Using a modified arm-first approach, we then varied the crosslinking percentage in the core-forming block via addition of a 'O,O'-alkanediyl bis(hydroxylamine) crosslinking agent. We followed incorporation of the crosslinker by 1H NMR spectroscopy, monitoring the appearance of the oxime signal resulting from reaction of pendant aryl aldehydes on the block copolymer with hydroxylamines on the crosslinker, which revealed crosslinking percentages of 5, 10, and 15%. We then installed H2S-releasing S-aroylthiooxime (SATO) groups on the crosslinked polymers, yielding micelles with SATO units in their hydrophobic cores after self-assembly in water. H2S release studies in water, using cysteine (Cys) as a trigger to induce H2S release from the SATO groups in the micelle core, revealed increasing half-lives of H2S release, from 117 ± 6 min to 210 ± 30 min, with increasing crosslinking density in the micelle core. This result was consistent with our hypothesis, and we speculate that core crosslinking limits the rate of Cys diffusion into the micelle core, decreasing the release rate. This method for tuning the release of covalently linked small molecules through modulation of micelle core crosslinking density may extend beyond H2S to other drug delivery systems where precise control of release rate is needed.

| S-EPMC7643851 | biostudies-literature

How Detergents Dissolve Polymeric Micelles: Kinetic Pathways of Hybrid Micelle Formation in SDS and Block Copolymer Mixtures.

Project description:Mixtures of amphiphilic polymers and surfactants are used in a wide range of applications, e.g., pharmaceuticals, detergents, cosmetics, and drug delivery systems. Still, many questions remain on how the structure and, in particular, the kinetics of block copolymer micelles are affected in the presence of surfactants and what controls the solubilization kinetics. In this work, we have studied the stability and solubilization kinetics of block copolymer micelles upon the addition of the surfactant sodium dodecyl sulfate (SDS) using small-angle X-ray/neutron scattering. The ability of the surfactant to dissolve polymer micelles or form mixed micelles has been investigated using two types of amphiphilic polymers, poly(ethylene-alt-propylene)-poly(ethylene oxide) (PEP1-PEO20) and n-alkyl-functionalized PEO (C28-PEO5). The exchange kinetics of C28-PEO5 micelles are in the order of hours, while PEP1-PEO20 micelles are known to be frozen on a practical timescale. In this work, we show that the addition of SDS to PEP1-PEO20 provides virtually no solubilization, even after an extended period of time. However, upon adding SDS to C28-PEO5 micelles, we observe micellar dissolution and formation of mixed micelles occurring on the timescale of hours. Using a coexistence model of mixed and neat micelles, the SAXS data were analyzed to provide detailed structural parameters over time. First, we observe a fast fragmentation/fission step followed by a slow reorganization process. The latter process is essentially independent of concentration at low volume fraction but is greatly accelerated at larger concentrations. This might indicate a crossover from a predominance of molecular exchange to fusion/fission processes.

| S-EPMC7660944 | biostudies-literature

Simulations of the confinement of ubiquitin in self-assembled reverse micelles.

Project description:We describe the effects of confinement on the structure, hydration, and the internal dynamics of ubiquitin encapsulated in reverse micelles (RM). We performed molecular dynamics simulations of the encapsulation of ubiquitin into self-assembled protein/surfactant reverse micelles to study the positioning and interactions of the protein with the RM and found that ubiquitin binds to the RM interface at low salt concentrations. The same hydrophobic patch that is recognized by ubiquitin binding domains in vivo is found to make direct contact with the surfactant head groups, hydrophobic tails, and the iso-octane solvent. The fast backbone N-H relaxation dynamics show that the fluctuations of the protein encapsulated in the RM are reduced when compared to the protein in bulk. This reduction in fluctuations can be explained by the direct interactions of ubiquitin with the surfactant and by the reduced hydration environment within the RM. At high concentrations of excess salt, the protein does not bind strongly to the RM interface and the fast backbone dynamics are similar to that of the protein in bulk. Our simulations demonstrate that the confinement of protein can result in altered protein dynamics due to the interactions between the protein and the surfactant.

| S-EPMC3133568 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data