scholarly journals Heterotypic Supramolecular Hydrogels Formed by Noncovalent Interactions in Inflammasomes

Molecules ◽  
2020 ◽  
Vol 26 (1) ◽  
pp. 77
Author(s):  
Adrianna N. Shy ◽  
Huaimin Wang ◽  
Zhaoqianqi Feng ◽  
Bing Xu
Keyword(s):  
Self Assembly ◽  
Electrostatic Interactions ◽  
Structural Information ◽  
Noncovalent Interactions ◽  
Protein Structures ◽  
Peptide Sequence ◽  
Binding Motifs ◽  
Self Assembling ◽  
Transmission Electron ◽  
Peptide Materials

The advance of structural biology has revealed numerous noncovalent interactions between peptide sequences in protein structures, but such information is less explored for developing peptide materials. Here we report the formation of heterotypic peptide hydrogels by the two binding motifs revealed by the structures of an inflammasome. Specifically, conjugating a self-assembling motif to the positively or negatively charged peptide sequence from the ASCPYD filaments of inflammasome produces the solutions of the peptides. The addition of the peptides of the oppositely charged and complementary peptides to the corresponding peptide solution produces the heterotypic hydrogels. Rheology measurement shows that ratios of the complementary peptides affect the viscoelasticity of the resulted hydrogel. Circular dichroism indicates that the addition of the complementary peptides results in electrostatic interactions that modulate self-assembly. Transmission electron microscopy reveals that the ratio of the complementary peptides controls the morphology of the heterotypic peptide assemblies. This work illustrates a rational, biomimetic approach that uses the structural information from the protein data base (PDB) for developing heterotypic peptide materials via self-assembly.

scholarly journals Computationally designed peptides for self-assembly of nanostructured lattices

2016 ◽  
Vol 2 (9) ◽  
pp. e1600307 ◽  
Author(s):  
Huixi Violet Zhang ◽  
Frank Polzer ◽  
Michael J. Haider ◽  
Yu Tian ◽  
Jose A. Villegas ◽  
...  
Keyword(s):  
Self Assembly ◽  
Noncovalent Interactions ◽  
Building Blocks ◽  
Covalent Modification ◽  
Amino Acid Sequences ◽  
Peptide Sequence ◽  
Self Assembling ◽  
Transmission Electron ◽  
Wide Range ◽  
Micrometer Scale

Folded peptides present complex exterior surfaces specified by their amino acid sequences, and the control of these surfaces offers high-precision routes to self-assembling materials. The complexity of peptide structure and the subtlety of noncovalent interactions make the design of predetermined nanostructures difficult. Computational methods can facilitate this design and are used here to determine 29-residue peptides that form tetrahelical bundles that, in turn, serve as building blocks for lattice-forming materials. Four distinct assemblies were engineered. Peptide bundle exterior amino acids were designed in the context of three different interbundle lattices in addition to one design to produce bundles isolated in solution. Solution assembly produced three different types of lattice-forming materials that exhibited varying degrees of agreement with the chosen lattices used in the design of each sequence. Transmission electron microscopy revealed the nanostructure of the sheetlike nanomaterials. In contrast, the peptide sequence designed to form isolated, soluble, tetrameric bundles remained dispersed and did not form any higher-order assembled nanostructure. Small-angle neutron scattering confirmed the formation of soluble bundles with the designed size. In the lattice-forming nanostructures, the solution assembly process is robust with respect to variation of solution conditions (pH and temperature) and covalent modification of the computationally designed peptides. Solution conditions can be used to control micrometer-scale morphology of the assemblies. The findings illustrate that, with careful control of molecular structure and solution conditions, a single peptide motif can be versatile enough to yield a wide range of self-assembled lattice morphologies across many length scales (1 to 1000 nm).

Self Assembling Nanostructured Delivery Vehicles for Biochemically Reactive Pairs

1994 ◽  
Vol 351 ◽  
Author(s):  
Nir Kossovsky ◽  
A. Gelman ◽  
H.J. Hnatyszyn ◽  
E. Sponsler ◽  
G.-M. Chow
Keyword(s):  
Physical Properties ◽  
Self Assembly ◽  
Materials Science ◽  
Technology Development ◽  
Biological Behavior ◽  
X Ray Diffraction ◽  
Self Assembling ◽  
Transmission Electron ◽  
Carbon Ceramic

ABSTRACTIntrigued by the deceptive simplicity and beauty of macromolecular self-assembly, our laboratory began studying models of self-assembly using solids, glasses, and colloidal substrates. These studies have defined a fundamental new colloidal material for supporting members of a biochemically reactive pair.The technology, a molecular transportation assembly, is based on preformed carbon ceramic nanoparticles and self assembled calcium-phosphate dihydrate particles to which glassy carbohydrates are then applied as a nanometer thick surface coating. This carbohydrate coated core functions as a dehydroprotectant and stabilizes surface immobilized members of a biochemically reactive pair. The final product, therefore, consists of three layers. The core is comprised of the ceramic, the second layer is the dehydroprotectant carbohydrate adhesive, and the surface layer is the biochemically reactive molecule for which delivery is desired.We have characterized many of the physical properties of this system and have evaluated the utility of this delivery technology in vitro and in animal models. Physical characterization has included standard and high resolution transmission electron microscopy, electron and x-ray diffraction and ζ potential analysis. Functional assays of the ability of the system to act as a nanoscale dehydroprotecting delivery vehicle have been performed on viral antigens, hemoglobin, and insulin. By all measures at present, the favorable physical properties and biological behavior of the molecular transportation assembly point to an exciting new interdisciplinary area of technology development in materials science, chemistry and biology.

scholarly journals Nanohydrogels Based on Self-Assembly of Cationic Pullulan and Anionic Dextran Derivatives for Efficient Delivery of Piroxicam

Pharmaceutics ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 622 ◽  
Author(s):  
Dorota Lachowicz ◽  
Przemyslaw Mielczarek ◽  
Roma Wirecka ◽  
Katarzyna Berent ◽  
Anna Karewicz ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Self Assembly ◽  
Electrostatic Interactions ◽  
Dextran Sulfate ◽  
Force Microscopy ◽  
Grafting Reaction ◽  
Atomic Force ◽  
Transmission Electron ◽  
Efficient Delivery ◽  
Model Drug

A cationic derivative of pullulan was obtained by grafting reaction and used together with dextran sulfate to form polysaccharide-based nanohydrogel cross-linked via electrostatic interactions between polyions. Due to the polycation-polyanion interactions nanohydrogel particles were formed instantly and spontaneously in water. The nanoparticles were colloidally stable and their size and surface charge could be controlled by the polycation/polyanion ratio. The morphology of the obtained particles was visualized by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and atomic force microscopy (AFM). The resulting structures were spherical, with hydrodynamic diameters in the range of 100–150 nm. The binding constant (Ka) of a model drug, piroxicam, to the cationic pullulan (C-PUL) was determined by spectrophotometric measurements. The value of Ka was calculated according to the Benesi—Hildebrand equation to be (3.6 ± 0.2) × 103 M−1. After binding to cationic pullulan, piroxicam was effectively entrapped inside the nanohydrogel particles and released in a controlled way. The obtained system was efficiently taken up by cells and was shown to be biocompatible.

scholarly journals An investigation into the nano-/micro-architecture of electrospun poly (ε-caprolactone) and self-assembling peptide fibers

MRS Advances ◽  
2016 ◽  
Vol 1 (11) ◽  
pp. 711-716 ◽  
Author(s):  
Robabeh Gharaei ◽  
Giuseppe Tronci ◽  
Robert P. Davies ◽  
Parikshit Goswami ◽  
Stephen J. Russell
Keyword(s):  
Self Assembly ◽  
Mechanical Stability ◽  
Porous Scaffold ◽  
Fiber Formation ◽  
Peptide Sequence ◽  
Diagnostic Tools ◽  
Great Promise ◽  
Electrospinning Technique ◽  
Fibrous Scaffold ◽  
Self Assembling

ABSTRACTSelf-assembling peptides (SAPs) have the ability to spontaneously assemble into ordered nanostructures enabling the manufacture of ‘designer’ nanomaterials. The reversible molecular association of SAPs has been shown to offer great promise in therapeutics via for example, the design of biomimetic assemblies for hard tissue regeneration. This could be further exploited for novel nano/micro diagnostic tools. However, self-assembled peptide gels are often associated with inherent weak and transient mechanical properties. Their incorporation into polymeric matrices has been considered as a potential strategy to enhance their mechanical stability. This study focuses on the incorporation of an 11-residue peptide, P11-8 (peptide sequence: CH3CO-Gln-Gln-Arg-Phe-Orn-Trp-Orn-Phe-Glu-Gln-Gln-NH2) within a fibrous scaffold of poly (ε-caprolactone) (PCL). In this study an electrospinning technique was used to fabricate a biomimetic porous scaffold out of a solution of P11-8 and PCL which resulted in a biphasic structure composed of submicron fibers (diameter of 100-700 nm) and nanofibers (diameter of 10-100 nm). The internal morphology of the fabric and its micro-structure can be easily controlled by changing the peptide concentration. The secondary conformation of P11-8 was investigated in the as-spun fibers by ATR-FTIR spectroscopy and it is shown that peptide self-assembly into β-sheet tapes has taken place during fiber formation and the deposition of the fibrous web.

Copolymer Nanoparticles Prepared by Self-Assembly of Poly(ethylene glycol) and Poly-γ-Glutamic Acid and its Characteristics

2013 ◽  
Vol 662 ◽  
pp. 136-139
Author(s):  
Ge Yang ◽  
Ke Shuai Lu ◽  
Xue Yan Su
Keyword(s):  
Ethylene Glycol ◽  
Glutamic Acid ◽  
Size Distribution ◽  
Self Assembly ◽  
Aqueous Media ◽  
Poly Ethylene Glycol ◽  
Polyelectrolyte Complexes ◽  
Self Assembling ◽  
Transmission Electron ◽  
Poly Ethylene

The paper describes the preparation and characterization of novel biodegradable nanoparticles based on self-assembly of poly-gamma-glutamic acid (γ-PGA) and poly(ethylene glycol) (PEG). The nanosystems were stable in aqueous media at low pH conditions. Solubility of the systems was determined by turbidity measurements. The particle size and the size distribution of the polyelectrolyte complexes were identified by dynamic lightscattering and transmission electron microscopy.It was found that the size and size distribution of the nanosystems depends on the concentrations of γ-PGA and PEG solutions and their ratio as well as on the pH of the mixture and the order of addition. The diameter of individual particles was in the range of 30–270 nm. measured by TEM, and the average hydrodynamic diameters were between 130 and 300 nm. These biodegradable, self-assembling stable nanocomplexes might be useful for several biomedical applications.

scholarly journals Self-assembling Peptide Discovery: Overcoming Human Bias With Machine Learning

2021 ◽  
Author(s):  
Rohit Batra ◽  
Troy Loeffler ◽  
Henry Chan ◽  
Srilok Sriniva ◽  
Honggang Cui ◽  
...  
Keyword(s):  
Machine Learning ◽  
Self Assembly ◽  
Search Space ◽  
Sequence Length ◽  
Monte Carlo Tree Search ◽  
Self Assembling ◽  
Naturally Occurring ◽  
Peptide Materials ◽  
Dynamics Simulations ◽  
Better Than

Abstract Peptide materials have a wide array of functions from tissue engineering, surface coatings to catalysis and sensing. This class of biopolymer is composed of a sequence, comprised of 20 naturally occurring amino acids whose arrangement dictate the peptide functionality. While it is highly desirable to tailor the amino acid sequence, a small increase in their sequence length leads to dramatic increase in the possible candidates (e.g., from tripeptide = 20^3 or 8,000 peptides to a pentapeptide = 20^5 or 3.2 M). Traditionally, peptide design is guided by the use of structural propensity tables, hydrophobicity scales, or other desired properties and typically yields <10 peptides per study, barely scraping the surface of the search space. These approaches, driven by human expertise and intuition, are not easily scalable and are riddled with human bias. Here, we introduce a machine learning workflow that combines Monte Carlo tree search and random forest, with molecular dynamics simulations to develop a fully autonomous computational search engine (named, AI-expert) to discover peptide sequences with high potential for self-assembly (as a representative target functionality). We demonstrate the efficacy of the AI-expert to efficiently search large spaces of tripeptides and pentapeptides. Subsequent experiments on the proposed peptide sequences are performed to compare the predictability of the AI-expert with those of human experts. The AI performs on-par or better than human experts and suggests several non-intuitive sequences with high self-assembly propensity, outlining its potential to overcome human bias and accelerate peptide discovery.

scholarly journals Biocatalysis of d,l-Peptide Nanofibrillar Hydrogel

Molecules ◽  
2020 ◽  
Vol 25 (13) ◽  
pp. 2995 ◽  
Author(s):  
Tiziano Carlomagno ◽  
Maria C. Cringoli ◽  
Slavko Kralj ◽  
Marina Kurbasic ◽  
Paolo Fornasiero ◽  
...  
Keyword(s):  
Self Assembly ◽  
Solid Phase ◽  
Building Blocks ◽  
Cd Spectroscopy ◽  
Tem Analysis ◽  
Design Rules ◽  
Self Assembling ◽  
Transmission Electron ◽  
Oscillatory Rheometry ◽  
The Many

Self-assembling peptides are attracting wide interest as biodegradable building blocks to achieve functional nanomaterials that do not persist in the environment. Amongst the many applications, biocatalysis is gaining momentum, although a clear structure-to-activity relationship is still lacking. This work applied emerging design rules to the heterochiral octapeptide sequence His–Leu–DLeu–Ile–His–Leu–DLeu–Ile for self-assembly into nanofibrils that, at higher concentration, give rise to a supramolecular hydrogel for the mimicry of esterase-like activity. The peptide was synthesized by solid-phase and purified by HPLC, while its identity was confirmed by 1H-NMR and electrospray ionization (ESI)-MS. The hydrogel formed by this peptide was studied with oscillatory rheometry, and the supramolecular behavior of the peptide was investigated with transmission electron microscopy (TEM) analysis, circular dichroism (CD) spectroscopy, thioflavin T amyloid fluorescence assay, and attenuated total reflectance (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The biocatalytic activity was studied by monitoring the hydrolysis of p-nitrophenyl acetate (pNPA) at neutral pH, and the reaction kinetics followed an apparent Michaelis–Menten model, for which a Lineweaver–Burk plot was produced to determine its enzymatic parameters for a comparison with the literature. Finally, LC–MS analysis was conducted on a series of experiments to evaluate the extent of, if any, undesired peptide acetylation at the N-terminus. In conclusion, we provide new insights that allow gaining a clearer picture of self-assembling peptide design rules for biocatalysis.

scholarly journals Self-Assembling Behavior of pH-Responsive Peptide A6K without End-Capping

Molecules ◽  
2020 ◽  
Vol 25 (9) ◽  
pp. 2017
Author(s):  
Peng Zhang ◽  
Fenghuan Wang ◽  
Yuxuan Wang ◽  
Shuangyang Li ◽  
Sai Wen
Keyword(s):  
Self Assembly ◽  
Md Simulation ◽  
Block Structure ◽  
Distribution Model ◽  
Ph Responsive ◽  
Random Coils ◽  
Self Assembling ◽  
C Terminus ◽  
Transmission Electron ◽  
End Capping

A short self-assembly peptide A6K (H2N−AAAAAAK−OH) with unmodified N− and C−terminus was designed, and the charge distribution model of this short peptide at different pH was established by computer simulation. The pH of the solution was adjusted according to the model and the corresponding self-assembled structure was observed using a transmission electron microscope (TEM). As the pH changes, the peptide will assemble into blocks or nanoribbons, which indicates that the A6K peptide is a pH-responsive peptide. Circular dichroism (CD) and molecular dynamics (MD) simulation showed that the block structure was formed by random coils, while the increase in β-turn content contributes to the formation of intact nanoribbons. A reasonable explanation of the self-assembling structure was made according to the electrostatic distribution model and the effect of electrostatic interaction on self-assembly was investigated. This study laid the foundation for further design of nanomaterials based on pH-responsive peptides.

Structural Characterization of Ordered Phases in Hydrocarbon Dendrimers

1994 ◽  
Vol 351 ◽  
Author(s):  
Christopher J. Buchko ◽  
Atisa Sioshansi ◽  
Zhifu Xu ◽  
Jeffrey S. Moore ◽  
David C. Martin
Keyword(s):  
Structural Characterization ◽  
Rational Design ◽  
Structural Information ◽  
Molecular Architecture ◽  
Thermal Transitions ◽  
Self Assembling ◽  
Transmission Electron ◽  
Ordered Phases ◽  
Construction Of Self

ABSTRACTStructural characterization of phenylacetylene dendrimers (PADs) makes it possible to explore the relationship between molecular architecture and condensed phase organization. The size and geometry of the PAD series is precisely controlled, with phenylacetylene units emanating from a central phenylene in the manner of a tridendron. The branched molecule rapidly increases in size with each synthetic generation. The “shape-persistent” nature of the phenylacetylene molecule makes it ideal for use in the construction of self-assembling supramolecular systems.Transmission electron microscopy (TEM) has been used to identify the crystal structure of lower generation PADs, and wide-angle X-ray studies confirm the decrease in crystallinity with size. Hot stage optical microscopy studies of thermal transitions reveal melting points for lower generation PADs, and an apparent glass transition for the amorphous higher generations. This type of structural information is essential to the rational design of self-assembling materials.

scholarly journals Self-Assembly of Au-Fe3O4 Hybrid Nanoparticles Using a Sol–Gel Pechini Method

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6943
Author(s):  
Jesus G. Ovejero ◽  
Miguel A. Garcia ◽  
Pilar Herrasti
Keyword(s):  
Self Assembly ◽  
Pechini Method ◽  
Sol Gel ◽  
Reaction Times ◽  
Alkaline Media ◽  
Hybrid Nanoparticles ◽  
Self Assembling ◽  
Transmission Electron ◽  
Ir Transmission ◽  
Size And Morphology

The Pechini method has been used as a synthetic route for obtaining self-assembling magnetic and plasmonic nanoparticles in hybrid silica nanostructures. This manuscript evaluates the influence of shaking conditions, reaction time, and pH on the size and morphology of the nanostructures produced. The characterization of the nanomaterials was carried out by transmission electron microscopy (TEM) to evaluate the coating and size of the nanomaterials, Fourier-transform infrared spectroscopy (FT-IR) transmission spectra to evaluate the presence of the different coatings, and thermogravimetric analysis (TGA) curves to determine the amount of coating. The results obtained show that the best conditions to obtain core–satellite nanostructures with homogeneous silica shells and controlled sizes (<200 nm) include the use of slightly alkaline media, the ultrasound activation of silica condensation, and reaction times of around 2 hours. These findings represent an important framework to establish a new general approach for the click chemistry assembling of inorganic nanostructures.

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