Temperature Effect on the Nanostructureof SDS Micelles in Water

Hammouda, Boualem

doi:10.6028/jres.118.008

Cited by 174 publications

(153 citation statements)

References 14 publications

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“…R g : radius of gyration. Again, this is in line with previously published data [8,11,13,20,21,24,48]. The ability of the hydrocarbon subunits to be surrounded by water molecules has subsequently been evaluated.…”

Section: The Micelle Inner Structuresupporting

confidence: 78%

“…Indeed, many experimental studies have been performed to determine the size and shape of SDS micelles, as well as their aggregation number [6][7][8][9][10], the dynamics of the hydrocarbon chains [11][12][13], or the solvent penetration within the hydrophobic inner core [14,15]. However, the interpretation of experimental results is often modeldependent, making theoretical studies of micelles a crucial stage to obtain relevant molecular pictures.…”

Section: Introductionmentioning

confidence: 99%

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Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

2014

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Sodium dodecyl sulfate (SDS) is a well-known anionic detergent widely used in both experimental and theoretical investigations. Many molecular dynamics (MD) simulation have been performed on the SDS molecule at coarse-grained (CG), united-atom (UA), and all-atom (AA) resolutions. However, these simulations are usually based on general parameters determined from large sets of molecules, and as a result, peculiar molecular specificities are often poorly represented. In addition, the parameters (ideal bond lengths, angles, dihedrals and charge distribution) differ according to the resolution, highlighting a lack of coherence. We therefore propose a new set of parameters for CG, UA, and AA resolutions based on a high quantum mechanics (QM) level optimization of the detergent structure and the charge distribution. For the first time, QM-optimized parameters were directly applied to build the AA, UA, and CG model of the SDS molecule, leading to a more coherent description. As a test case, MD simulations were then performed on SDS preformed micelles as previous experimental and theoretical investigations allow direct comparison with our new sets of parameters. While all three models yield similar macromolecular properties (size, shape, and accessible surface) perfectly matching previous results, the attribution of more coherent parameters to SDS enables the description of the specific interactions inside and outside the micelle. These more consistent parameters can now be used to accurately describe new multi-scale systems involving the SDS molecule.

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Section: The Micelle Inner Structuresupporting

confidence: 78%

Section: Introductionmentioning

confidence: 99%

Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

2014

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“…In general, higher temperature and higher voltage results in faster clearing of the tissue, but may lead to a higher risk of sample, epitope, or fluorescence loss (see also ref. 23 for detailed characterization of the effect of temperature on SDS micelle sizes).…”

Section: Methodsmentioning

confidence: 99%

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

Tomer¹,

Li²,

Hsueh³

et al. 2014

Nat Protoc

745

886

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CLARITY is a method for chemical transformation of intact biological tissues into a hydrogeltissue hybrid, which becomes amenable to interrogation with light and macromolecular labels while retaining fine structure and native biological molecules. This emerging accessibility of information from large intact samples has created both new opportunities and new challenges. Here we describe next-generation protocols spanning multiple dimensions of the CLARITY workflow, ranging from a novel approach to simple, reliable, and efficient lipid removal without electrophoretic instrumentation (passive CLARITY), to optimized objectives and integration with light-sheet optics (CLARITY-optimized light-sheet microscopy or COLM) for accelerating data collection from clarified samples by several orders of magnitude while maintaining or increasing quality and resolution. These methods may find application in the structural and molecular analysis of large assembled biological systems such as the intact mammalian brain.

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“…For SDS in aqueous medium, the average micelle volume decreases, but the total number of micelles increases as the temperature rises 50 . It is hypothesized that smaller micelles may more readily diffuse through the tissue-hydrogel matrix, and thus increasing the temperature of the clearing bath will accelerate lipid extraction.…”

Section: Introductionmentioning

confidence: 99%

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

et al. 2015

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To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1–2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.

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Temperature Effect on the Nanostructureof SDS Micelles in Water

Cited by 174 publications

References 14 publications

Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

Multiscale molecular dynamics simulations of sodium dodecyl sulfate micelles: from coarse-grained to all-atom resolution

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

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