scholarly journals Geometrical frustration as a potential design principle for peptide-based assemblies

2017 ◽  
Vol 7 (6) ◽  
pp. 20160141 ◽  
Author(s):  
Tao Jiang ◽  
Elizabeth L. Magnotti ◽  
Vincent P. Conticello
Keyword(s):  
Self Assembly ◽  
Rational Design ◽  
Structural Parameters ◽  
Two Dimensional ◽  
Protein Assemblies ◽  
Geometrical Frustration ◽  
Protein Motifs ◽  
Planar Shapes ◽  
And Function

Two-dimensional peptide and protein assemblies have been the focus of increased scientific research as they display significant potential for the creation of functional nanomaterials. Soluble subunits derived from a variety of protein motifs have been demonstrated to self-assemble into structurally defined nanosheets under environmentally benign conditions in which the components often retain their native structure and function. These types of two-dimensional assemblies may have an advantage for nanofabrication in that their extended planar shapes can be more straightforwardly incorporated into the current formats of nanoscale devices. However, significant challenges remain in the fabrication of these materials, particularly in devising methods to control the size, shape and internal structure of the resultant materials. Geometrical frustration may be envisioned as a possible mechanism to exert control over these structural parameters through rational design. While this objective has yet to be realized in practice, we discuss in this article the potential role of geometrical frustration as a principle to rationalize unusual self-assembly behaviour in several examples of two-dimensional peptide assemblies.

scholarly journals The Adenomatous polyposis coli tumour suppressor is essential for Axin complex assembly and function and opposes Axin's interaction with Dishevelled

Open Biology ◽  
2011 ◽  
Vol 1 (3) ◽  
pp. 110013 ◽  
Author(s):  
Carolina Mendoza-Topaz ◽  
Juliusz Mieszczanek ◽  
Mariann Bienz
Keyword(s):  
Adenomatous Polyposis Coli ◽  
Self Assembly ◽  
Wnt Signalling ◽  
Tumour Suppressor ◽  
Adenomatous Polyposis ◽  
Polyposis Coli ◽  
Protein Assemblies ◽  
Membrane Recruitment ◽  
And Function

Most cases of colorectal cancer are linked to mutational inactivation of the Adenomatous polyposis coli (APC) tumour suppressor. APC downregulates Wnt signalling by enabling Axin to promote the degradation of the Wnt signalling effector β-catenin (Armadillo in flies). This depends on Axin's DIX domain whose polymerization allows it to form dynamic protein assemblies (‘degradasomes’). Axin is inactivated upon Wnt signalling, by heteropolymerization with the DIX domain of Dishevelled, which recruits it into membrane-associated ‘signalosomes’. How APC promotes Axin's function is unclear, especially as it has been reported that APC's function can be bypassed by overexpression of Axin. Examining apc null mutant Drosophila tissues, we discovered that APC is required for Axin degradasome assembly, itself essential for Armadillo downregulation. Degradasome assembly is also attenuated in APC mutant cancer cells. Notably, Axin becomes prone to Dishevelled-dependent plasma membrane recruitment in the absence of APC, indicating a crucial role of APC in opposing the interaction of Axin with Dishevelled. Indeed, co-expression experiments reveal that APC displaces Dishevelled from Axin assemblies, promoting degradasome over signalosome formation in the absence of Wnts. APC thus empowers Axin to function in two ways—by enabling its DIX-dependent self-assembly, and by opposing its DIX-dependent copolymerization with Dishevelled and consequent inactivation.

scholarly journals Inversion of Potential Vorticity Density

2017 ◽  
Vol 74 (3) ◽  
pp. 801-807 ◽  
Author(s):  
Joseph Egger ◽  
Klaus-Peter Hoinka ◽  
Thomas Spengler
Keyword(s):  
Boundary Conditions ◽  
Potential Vorticity ◽  
Potential Temperature ◽  
Two Dimensional ◽  
Dimensional Problem ◽  
Absolute Vorticity ◽  
Vertical Vector ◽  
The North ◽  
And Function

Abstract Inversion of potential vorticity density with absolute vorticity and function η is explored in η coordinates. This density is shown to be the component of absolute vorticity associated with the vertical vector of the covariant basis of η coordinates. This implies that inversion of in η coordinates is a two-dimensional problem in hydrostatic flow. Examples of inversions are presented for (θ is potential temperature) and (p is pressure) with satisfactory results for domains covering the North Pole. The role of the boundary conditions is investigated and piecewise inversions are performed as well. The results shed new light on the interpretation of potential vorticity inversions.

scholarly journals Multiscale Molecular Modelling of ATP-fueled Supramolecular Polymerisation and Depolymerisation

2020 ◽  
Author(s):  
Claudio Perego ◽  
Luca Pesce ◽  
Riccardo Capelli ◽  
Subi J. George ◽  
Giovanni M. Pavan
Keyword(s):  
Molecular Modelling ◽  
Self Assembly ◽  
Rational Design ◽  
Atp Hydrolysis ◽  
Grand Challenge ◽  
Molecular Systems ◽  
Artificial Materials ◽  
Profound Knowledge ◽  
General Aspects

Fuel-regulated self-assembly is a key principle by which Nature creates spatiotemporally controlled materials and dynamic molecular systems that are in continuous communication (molecular exchange) with the external environment. Designing artificial materials that self-assemble and disassemble via conversion/consumption of a chemical fuel is a grand challenge in supramolecular chemistry, which requires a profound knowledge of the factors governing these complex systems. Here we focus on recently reported metal-coordinated monomers that polymerise in the presence of ATP and depolymerise upon ATP hydrolysis, exploring their fuel-regulated self-assembly/disassembly via multiscale molecular modelling. We use all-atom simulations to assess the role of ATP in stabilising these monomers in assemblies, and we then build on a minimalistic model to investigate their fuel-driven polymerization and depolymerization on a higher scale. In this way, we elucidate general aspects of fuel-regulated self-assembly that are important toward the rational design of new types of bioinspired materials.

scholarly journals In situ imaging of two-dimensional surface growth reveals the prevalence and role of defects in zeolite crystallization

2020 ◽  
Vol 117 (46) ◽  
pp. 28632-28639
Author(s):  
Madhuresh K. Choudhary ◽  
Rishabh Jain ◽  
Jeffrey D. Rimer
Keyword(s):  
Silica Nanoparticles ◽  
Rational Design ◽  
Surface Defects ◽  
Surface Growth ◽  
Two Dimensional ◽  
Crystal Surfaces ◽  
Structure Directing Agent ◽  
Layered Growth

Zeolite crystallization predominantly occurs by nonclassical pathways involving the attachment of complex (alumino)silicate precursors to crystal surfaces, yet recurrent images of fully crystalline materials with layered surfaces are evidence of classical growth by molecule attachment. Here we use in situ atomic force microscopy to monitor three distinct mechanisms of two-dimensional (2D) growth of zeolite A where we show that layer nucleation from surface defects is the most common pathway. Direct observation of defects was made possible by the identification of conditions promoting layered growth, which correlates to the use of sodium as an inorganic structure-directing agent, whereas its replacement with an organic results in a nonclassical mode of growth that obscures 2D layers and markedly slows the rate of crystallization. In situ measurements of layered growth reveal that undissolved silica nanoparticles in the synthesis medium can incorporate into advancing steps on crystal surfaces to generate defects (i.e., amorphous silica occlusions) that largely go undetected in literature. Nanoparticle occlusion in natural and synthetic crystals is a topic of wide-ranging interest owing to its relevance in fields spanning from biomineralization to the rational design of functional nanocomposites. In this study, we provide unprecedented insight into zeolite surface growth by molecule addition through time-resolved microscopy that directly captures the occlusion of silica nanoparticles and highlights the prevalent role of defects in zeolite crystallization.

scholarly journals Synergistic role of nucleotides and lipids for the self-assembly of Shs1 septin oligomers

2020 ◽  
Vol 477 (14) ◽  
pp. 2697-2714
Author(s):  
Cyntia Taveneau ◽  
Rémi Blanc ◽  
Gérard Péhau-Arnaudet ◽  
Aurélie Di Cicco ◽  
Aurélie Bertin
Keyword(s):  
Self Assembly ◽  
Structural Organization ◽  
Electron Tomography ◽  
Budding Yeast ◽  
The Self ◽  
Two Dimensional ◽  
Molecular Polymorphism ◽  
Cryo Electron Tomography ◽  
First Time

Budding yeast septins are essential for cell division and polarity. Septins assemble as palindromic linear octameric complexes. The function and ultra-structural organization of septins are finely governed by their molecular polymorphism. In particular, in budding yeast, the end subunit can stand either as Shs1 or Cdc11. We have dissected, here, for the first time, the behavior of the Shs1 protomer bound to membranes at nanometer resolution, in complex with the other septins. Using electron microscopy, we have shown that on membranes, Shs1 protomers self-assemble into rings, bundles, filaments or two-dimensional gauzes. Using a set of specific mutants we have demonstrated a synergistic role of both nucleotides and lipids for the organization and oligomerization of budding yeast septins. Besides, cryo-electron tomography assays show that vesicles are deformed by the interaction between Shs1 oligomers and lipids. The Shs1–Shs1 interface is stabilized by the presence of phosphoinositides, allowing the visualization of micrometric long filaments formed by Shs1 protomers. In addition, molecular modeling experiments have revealed a potential molecular mechanism regarding the selectivity of septin subunits for phosphoinositide lipids.

scholarly journals How Does SUMO Participate in Spindle Organization?

Cells ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 801
Author(s):  
Abrieu ◽  
Liakopoulos
Keyword(s):  
Dna Repair ◽  
Protein Assemblies ◽  
Cellular Mechanisms ◽  
Future Directions ◽  
Kinetochore Assembly ◽  
Associated Proteins ◽  
Long Time ◽  
And Function ◽  
Dependent Processes

The ubiquitin-like protein SUMO is a regulator involved in most cellular mechanisms. Recent studies have discovered new modes of function for this protein. Of particular interest is the ability of SUMO to organize proteins in larger assemblies, as well as the role of SUMO-dependent ubiquitylation in their disassembly. These mechanisms have been largely described in the context of DNA repair, transcriptional regulation, or signaling, while much less is known on how SUMO facilitates organization of microtubule-dependent processes during mitosis. Remarkably however, SUMO has been known for a long time to modify kinetochore proteins, while more recently, extensive proteomic screens have identified a large number of microtubule- and spindle-associated proteins that are SUMOylated. The aim of this review is to focus on the possible role of SUMOylation in organization of the spindle and kinetochore complexes. We summarize mitotic and microtubule/spindle-associated proteins that have been identified as SUMO conjugates and present examples regarding their regulation by SUMO. Moreover, we discuss the possible contribution of SUMOylation in organization of larger protein assemblies on the spindle, as well as the role of SUMO-targeted ubiquitylation in control of kinetochore assembly and function. Finally, we propose future directions regarding the study of SUMOylation in regulation of spindle organization and examine the potential of SUMO and SUMO-mediated degradation as target for antimitotic-based therapies.

Insights on the dual role of two-dimensional materials as catalysts and supports for energy and environmental catalysis

2021 ◽  
Author(s):  
Li Xin Chen ◽  
Zhi Wen Chen ◽  
Ming Jiang ◽  
Zhuole Lu ◽  
Chan Gao ◽  
...  
Keyword(s):  
Rational Design ◽  
2D Materials ◽  
Dual Role ◽  
Environmental Catalysis ◽  
Two Dimensional ◽  
Dual Roles ◽  
Two Dimensional Materials

The application of 2D materials in catalysis has great potential, opportunities, and challenges. The dual roles (catalysts and supports) of 2D materials determine different strategies for rational design of 2D-based catalysts.

Rational Design and Self-Assembly of Two-Dimensional, Dodecagonal DNA Quasicrystals

2019 ◽  
Vol 141 (10) ◽  
pp. 4248-4251 ◽  
Author(s):  
Longfei Liu ◽  
Zhe Li ◽  
Yulin Li ◽  
Chengde Mao
Keyword(s):  
Self Assembly ◽  
Rational Design ◽  
Two Dimensional

scholarly journals Engineering Peptide-Based Polyelectrolyte Complexes with Increased Hydrophobicity

Molecules ◽  
2019 ◽  
Vol 24 (5) ◽  
pp. 868 ◽  
Author(s):  
Sara Tabandeh ◽  
Lorraine Leon
Keyword(s):  
Charge Density ◽  
Self Assembly ◽  
Rational Design ◽  
Hydrophobicity Index ◽  
Polyelectrolyte Complexes ◽  
Polyelectrolyte Complexation ◽  
Future Work ◽  
Oppositely Charged ◽  
H And F Nmr

Polyelectrolyte complexation is a versatile platform for the design of self-assembled materials. Here we use rational design to create ionic hydrophobically-patterned peptides that allow us to precisely explore the role of hydrophobicity on electrostatic self-assembly. Polycations and polyanions were designed and synthesized with an alternating sequence of d- and l-chiral patterns of lysine or glutamic acid with either glycine, alanine or leucine due to their increasing hydrophobicity index, respectively. Two motifs were considered for the oppositely charged patterned peptides; one with equal residues of charged and uncharged amino acids and the other with increased charge density. Mass spectroscopy, circular dichroism, H- and F-NMR spectroscopy were used to characterize the polypeptides. Polyelectrolyte complexes (PECs) formed using the sequences were characterized using turbidity measurements, optical microscopy and infrared spectroscopy. Our results show that the critical salt concentration, a key measure of PEC stability, increased with both increasing charge density as well as hydrophobicity. Furthermore, by increasing the hydrophobicity, the amount of PEC formed increased with temperature, contrary to purely ionic PECs. Lastly, we assessed the encapsulation behavior of these materials using a hydrophobic dye. Concluding that encapsulation efficiency increased with hydrophobic content of the complexes providing insight for future work on the application of these materials for drug delivery.

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