Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

Patmanidis, Ilias; Vries, Alex H. de; Wassenaar, Tsjerk A.; Wang, Wenjun; Portale, Giuseppe; Marrink, Siewert J.

doi:10.1039/d0cp03282d

Cited by 18 publications

(29 citation statements)

References 71 publications

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“…The boundary distance of the DWNTs of 13.6 ± 0.4 nm agrees with the values published in the literature 6 , 13 , 21 , 22 . The wall thickness, evaluated from the difference between the boundary distances of DWNTs and flash-diluted NTs, is (13.6–10.2)/2 = 1.7 nm, which agrees well with the size of C8S3 molecule (∼2 nm) 23 considering the interdigitating aliphatic tails 21 .…”

Section: Resultssupporting

confidence: 90%

Cryogenic TEM imaging of artificial light harvesting complexes outside equilibrium

Krishnaswamy

Gabrovski

Patmanidis

et al. 2022

Sci Rep

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The energy transport in natural light-harvesting complexes can be explored in laboratory conditions via self-assembled supramolecular structures. One such structure arises from the amphiphilic dye C8S3 molecules, which self-assemble in an aqueous medium to a double-wall cylindrical nanotube reminiscent of natural light-harvesting complexes found in green sulphur bacteria. In this paper, we report a way to investigate the structure of inner nanotubes (NTs) alone by dissolving the outer NTs in a microfluidic setting. The resulting thermodynamically unstable system was rapidly frozen, preventing the reassembly of the outer NT from the dissolved molecules, and imaged using cryogenic transmission electron microscopy (cryo-TEM). The experimental cryo-TEM images and the molecular structure were compared by simulating high-resolution TEM images, which were based on the molecular modelling of C8S3 NTs. We found that the inner NT with outer walls removed during the flash-dilution process had a similar size to the parent double-walled NTs. Moreover, no structural inhomogeneity was observed in the inner NT after flash-dilution. This opens up exciting possibilities for functionalisation of inner NTs before the reassembly of the outer NT occurs, which can be broadly extended to modify the intra-architecture of other self-assembled nanostructures.

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Section: Resultssupporting

confidence: 90%

Cryogenic TEM imaging of artificial light harvesting complexes outside equilibrium

Krishnaswamy

Gabrovski

Patmanidis

et al. 2022

Sci Rep

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“…A large number of biological phenomena are now accessible for computational analysis, ranging from biomolecular dynamics, enzymatic processes, and virus assembly to the structure of small organelles [ 12 , 13 , 14 ], making computer simulation techniques an indispensable tool. Additionally, they are used for biomolecular engineering and drug design [ 15 , 16 , 17 , 18 ], Nevertheless, all computational methods have their strength in specific ranges of time and length scales, while they are inapplicable outside these ranges. Therefore, for many biological processes, several of these methods must be put into play.…”

Section: Methodsmentioning

confidence: 99%

Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Pezeshkian

Shillcock

Ipsen

2021

Toxins

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Many bacteria secrete toxic protein complexes that modify and disrupt essential processes in the infected cell that can lead to cell death. To conduct their action, these toxins often need to cross the cell membrane and reach a specific substrate inside the cell. The investigation of these protein complexes is essential not only for understanding their biological functions but also for the rational design of targeted drug delivery vehicles that must navigate across the cell membrane to deliver their therapeutic payload. Despite the immense advances in experimental techniques, the investigations of the toxin entry mechanism have remained challenging. Computer simulations are robust complementary tools that allow for the exploration of biological processes in exceptional detail. In this review, we first highlight the strength of computational methods, with a special focus on all-atom molecular dynamics, coarse-grained, and mesoscopic models, for exploring different stages of the toxin protein entry mechanism. We then summarize recent developments that are significantly advancing our understanding, notably of the glycolipid–lectin (GL-Lect) endocytosis of bacterial Shiga and cholera toxins. The methods discussed here are also applicable to the design of membrane-penetrating nanoparticles and the study of the phenomenon of protein phase separation at the surface of the membrane. Finally, we discuss other likely routes for future development.

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“…Furthermore, nanotubes and a nanotube bundle with length ∼50 nm (∼3650-6000 and ∼16000 molecules, respectively) were constructed and solvated in rectangular boxes. The C8S3 nanotubes were constructed by creating 2D-lattices from an initial unit cell and, then, rolling the lattices into cylindrical shapes 20,21 . The initial unit cell was obtained from the crystal structure of a cyanine dye with the same aromatic core as the C8S3 molecule 32 , and the original molecules were replaced with C8S3 molecules at CG level.…”

Section: Simulations -Cgmentioning

confidence: 99%

“…The diameters of the designed systems ranged from 12 to 17 nm, close to the reported experimental values in the literature for the nanotube diameter vary from 13 to 17 nm 10,46 . Previous atomistic MD studies showed that preformed nanotubes with different diameter can be stable, as long as the nanotube thickness and the initial monomer arrangement is reasonable 20,21 . All systems were constructed with an initial double-wall thickness of ∼2.5 nm, which remained roughly the same in all simulations.…”

Section: Preformed Nanotubesmentioning

confidence: 99%

“…In this study, we were interested in 1,1'-dioctyl-3,3'-bis(2-sulfopropyl)-5,5',6,6'-tetrachloro-benzimida-carbocyanine (C8S3) (see Figure 1c), which forms double-walled nanotubes [14][15][16][17][18] (see Figure 1d). C8S3 aggregates have been previously studied with MD simulation by testing the stability of different types of aggregates and their optical properties [19][20][21] . These studies were limited to simulations of preformed aggregates, that do not necessarily allow the molecules to rearrange and explore a large portion of the available configurational space.…”

Section: Introductionmentioning

confidence: 99%

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Modelling structural properties of cyanine dye nanotubes at coarse-grained level

Patmanidis

Souza

Sami

et al. 2022

Preprint

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Self-assembly is a ubiquitous process spanning from biomolecular aggregates to nanomaterials. Even though the resulting aggregates can be studied through experimental techniques, the dynamic pathways of the process and the molecular details of the final structures are not necessarily easy to resolve. Consequently, rational design of self-assembling aggregates and their properties remains extremely challenging. At the same time, modelling the self-assembly with computational methods is not trivial, because its spatio-temporal scales are usually beyond the limits of all-atom based simulations. The use of coarse-grained (CG) models can alleviate this limitation, but usually suffers from the lack of optimised parameters for the molecular constituents. In this work, we describe the procedure of parametrizing a CG Martini model for a cyanine dye (C8S3) that self-assembles into hollow double-walled nanotubes. We optimised the model based on quantum mechanics calculations and all-atom reference simulations, in combination with available experimental data. Then, we performed random self-assembly simulations and the performance of our model was tested on preformed assemblies. Our simulations provide information on the time-dependent local arrangement of this cyanine dye, when aggregates are being formed. Furthermore, we provide guidelines for designing and optimising parameters for similar self-assembling nanomaterials.

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Structural characterization of supramolecular hollow nanotubes with atomistic simulations and SAXS

Abstract: Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers. Here, we study an amphiphilic cyanine dye (C8S3) that is...

Cited by 18 publications

References 71 publications

Cryogenic TEM imaging of artificial light harvesting complexes outside equilibrium

Cryogenic TEM imaging of artificial light harvesting complexes outside equilibrium

Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Modelling structural properties of cyanine dye nanotubes at coarse-grained level

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