Charged membranes under confinement induced by polymer-, salt-, or ionic liquid solutions

Dvir, Tom; Fink, Lea; Asor, Roi; Schilt, Yael; Steinar, Ariel; Raviv, Uri

doi:10.1039/c3sm51916c

Cited by 28 publications

(50 citation statements)

References 38 publications

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“…Similar trends were also found for other lipid lamellar phases by when increasing salt concentration. 39,40 Eq. 1 is constant is generally referred to the disjoining pressure, it is commonly observed in osmotic stress experiments for water thicknesses above 2-3 nm and it can be described by the necessary force to overcome hydration forces.…”

Section: Resultsmentioning

confidence: 99%

Primary and Secondary Hydration Forces between Interdigitated Membranes Composed of Bolaform Microbial Glucolipids

Baccile

Cristiglio

2020

Langmuir

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To better understand lipid membranes in living organisms, the study of intermolecular forces using the osmotic pressure technique applied to model lipid membranes has constituted the ground knowledge in the field since four decades. However, the study of intermolecular forces in lipid systems other than phospholipids, like glycolipids, has gained a certain interest only recently. Even in this case, the work generally focus on the study of membrane glycolipids, but little is known on new forms of non-membrane functional compounds, like pH-responsive bolaform glycolipids. This works explores, through the osmotic stress method involving an adiabatic humidity chamber coupled to neutron diffraction, the short-range (< 2 nm) intermolecular forces of membranes entirely composed of interdigitated glucolipids.Experiments are performed at pH 6, when the glucolipid is partially negatively charged and for which we explore the effect of low (16 mM) and high (100 mM) ionic strength. We find that this system is characterized by primary and secondary hydration regimes, respectively insensitive and sensitive to ionic strength and with typical decay lengths of 1 = 0.37 ± 0.12 nm and 2 =1.97 ± 0.78 nm.

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Section: Resultsmentioning

confidence: 99%

Primary and Secondary Hydration Forces between Interdigitated Membranes Composed of Bolaform Microbial Glucolipids

Baccile

Cristiglio

2020

Langmuir

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“…It is also well known fact that ionic liquids can generate certain extent of osmotic stress in solution, which is achieved due to the reduction in the dielectric permittivity of the solution2656. Here it is pertinent to mention that Mel'nikov et al suggested an enhancement in electrostatic attraction between DNA and counter ion due to the lowering of dielectric permittivity26.…”

Section: Discussionmentioning

confidence: 99%

A Green Solvent Induced DNA Package

Satpathi

Sengupta

Hridya

et al. 2015

Sci Rep

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Mechanistic details of DNA compaction is essential blue print for gene regulation in living organisms. Many in vitro studies have been implemented using several compaction agents. However, these compacting agents may have some kinds of cytotoxic effects to the cells. To minimize this aspect, several research works had been performed, but people have never focused green solvent, i.e. room temperature ionic liquid as DNA compaction agent. To the best of our knowledge, this is the first ever report where we have shown that guanidinium tris(pentafluoroethyl)trifluorophosphate (Gua-IL) acts as a DNA compacting agent. The compaction ability of Gua-IL has been verified by different spectroscopic techniques, like steady state emission, circular dichroism, dynamic light scattering and UV melting. Notably, we have extensively probed this compaction by Gua-IL through field emission scanning electron microscopy (FE-SEM) and fluorescence microscopy images. We also have discussed the plausible compaction mechanism process of DNA by Gua-IL. Our results suggest that Gua-IL forms a micellar kind of self aggregation above a certain concentration (≥1 mM), which instigates this compaction process. This study divulges the specific details of DNA compaction mechanism by a new class of compaction agent, which is highly biodegradable and eco friendly in nature.

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“…The challenge of structural biophysics is to determine the high-resolution structure of large self-assembled complexes, made of many subunits, in their biologically relevant solution conditions. Solution small-and wide-angle X-ray scattering (SAXS/WAXS) methods are one of the important labelfree and highly sensitive bulk methods for investigating the structure and interactions between complex molecular constructs (Rädler et al, 1997;Koltover et al, 1998;Schilt et al, 2016;Dvir et al, 2014;Dvir et al, 2013;Chung et al, 2015;Chung et al, 2016;Lotan et al, 2016;Ojeda-Lopez et al, 2014;Moshe et al, 2013;Saper et al, 2012;Steiner et al, 2012;Szekely et al, 2011a;Szekely et al, 2011b;Choi et al, 2009;Choi et al, 2016;Wong et al, 2000;Deek et al, 2013;Beck et al, 2010;Kornreich et al, 2016;Shaharabani et al, 2016;Ginsburg et al, 2017;Asor et al, 2017;Fink et al, 2017a). With modern synchrotron facilities the temporal and spatial resolution of these methods has been greatly improved Kler et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

Ginsburg¹,

Ben-Nun²,

Asor³

et al. 2018

Preprint

Self Cite

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<div>In this paper, we present our new computer program, D+, which uses the reciprocal-grid (RG) algorithm to efficiently compute X-ray scattering curves from solutions of complex structures at high-resolution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and by repeating this process for all the leaves and nodes of the tree. For very large structures, a Hybrid method can be used to avoid numerical artifacts. In the Hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. We present how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a protein data bank (PDB) file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. In addition, a python wrapper is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, we present a large number of tests and compare the results of D+ with other programs when possible and demonstrate the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number. D+ and its source code are freely available (https://scholars.huji.ac.il/uriraviv/software/d-software) for academic users and developers. </div>

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Charged membranes under confinement induced by polymer-, salt-, or ionic liquid solutions

Cited by 28 publications

References 38 publications

Primary and Secondary Hydration Forces between Interdigitated Membranes Composed of Bolaform Microbial Glucolipids

Primary and Secondary Hydration Forces between Interdigitated Membranes Composed of Bolaform Microbial Glucolipids

A Green Solvent Induced DNA Package

D+: Software for High-Resolution Hierarchical Modeling of Solution X-Ray Scattering from Complex Structures

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