scholarly journals Classification of self-assembling protein nanoparticle architectures for applications in vaccine design

2017 ◽  
Vol 4 (4) ◽  
pp. 161092 ◽  
Author(s):  
G. Indelicato ◽  
P. Burkhard ◽  
R. Twarock
Keyword(s):  
Self Assembly ◽  
Vaccine Design ◽  
Building Blocks ◽  
Coiled Coils ◽  
Specific Class ◽  
Regular Graphs ◽  
Humoral Immune ◽  
Self Assembling ◽  
Display Systems

We introduce here a mathematical procedure for the structural classification of a specific class of self-assembling protein nanoparticles (SAPNs) that are used as a platform for repetitive antigen display systems. These SAPNs have distinctive geometries as a consequence of the fact that their peptide building blocks are formed from two linked coiled coils that are designed to assemble into trimeric and pentameric clusters. This allows a mathematical description of particle architectures in terms of bipartite (3,5)-regular graphs. Exploiting the relation with fullerene graphs, we provide a complete atlas of SAPN morphologies. The classification enables a detailed understanding of the spectrum of possible particle geometries that can arise in the self-assembly process. Moreover, it provides a toolkit for a systematic exploitation of SAPNs in bioengineering in the context of vaccine design, predicting the density of B-cell epitopes on the SAPN surface, which is critical for a strong humoral immune response.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

scholarly journals Coiled-Coils: The Molecular Zippers that Self-Assemble Protein Nanostructures

2020 ◽  
Vol 21 (10) ◽  
pp. 3584 ◽  
Author(s):  
Won Min Park
Keyword(s):  
Modular Design ◽  
Coiled Coil ◽  
Molecular Complexes ◽  
Building Blocks ◽  
Structural Features ◽  
Coiled Coils ◽  
Design Strategies ◽  
Protein Motifs ◽  
Self Assembling ◽  
Current Design

Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.

scholarly journals Free-standing supramolecular hydrogel objects by reaction-diffusion

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Matija Lovrak ◽  
Wouter E. J. Hendriksen ◽  
Chandan Maity ◽  
Serhii Mytnyk ◽  
Volkert van Steijn ◽  
...  
Keyword(s):  
Structure Formation ◽  
Self Assembly ◽  
Reaction Diffusion ◽  
Building Blocks ◽  
Assembly Process ◽  
Supramolecular Hydrogel ◽  
Free Standing ◽  
Spatial Control ◽  
Self Assembling ◽  
Vast Range

Abstract Self-assembly provides access to a variety of molecular materials, yet spatial control over structure formation remains difficult to achieve. Here we show how reaction–diffusion (RD) can be coupled to a molecular self-assembly process to generate macroscopic free-standing objects with control over shape, size, and functionality. In RD, two or more reactants diffuse from different positions to give rise to spatially defined structures on reaction. We demonstrate that RD can be used to locally control formation and self-assembly of hydrazone molecular gelators from their non-assembling precursors, leading to soft, free-standing hydrogel objects with sizes ranging from several hundred micrometres up to centimeters. Different chemical functionalities and gradients can easily be integrated in the hydrogel objects by using different reactants. Our methodology, together with the vast range of organic reactions and self-assembling building blocks, provides a general approach towards the programmed fabrication of soft microscale objects with controlled functionality and shape.

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.

Functional self-assembling polypeptide bionanomaterials

2012 ◽  
Vol 40 (4) ◽  
pp. 629-634 ◽  
Author(s):  
Tibor Doles ◽  
Sabina Božič ◽  
Helena Gradišar ◽  
Roman Jerala
Keyword(s):  
Self Assembly ◽  
Biological Systems ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Chemical Properties ◽  
Building Blocks ◽  
External Signal ◽  
Form Complex ◽  
Cell Factories ◽  
Self Assembling

Bionanotechnology seeks to modify and design new biopolymers and their applications and uses biological systems as cell factories for the production of nanomaterials. Molecular self-assembly as the main organizing principle of biological systems is also the driving force for the assembly of artificial bionanomaterials. Protein domains and peptides are particularly attractive as building blocks because of their ability to form complex three-dimensional assemblies from a combination of at least two oligomerization domains that have the oligomerization state of at least two and three respectively. In the present paper, we review the application of polypeptide-based material for the formation of material with nanometre-scale pores that can be used for the separation. Use of antiparallel coiled-coil dimerization domains introduces the possibility of modulation of pore size and chemical properties. Assembly or disassembly of bionanomaterials can be regulated by an external signal as demonstrated by the coumermycin-induced dimerization of the gyrase B domain which triggers the formation of polypeptide assembly.

Symmetrical Tris(4,6-diamino-5-methylene-2-pyrimidones): New Building Blocks for Self-Assembly of Hollow Spherical Supramolecules Locked by Hydrogen Bonds

1996 ◽  
Vol 61 (10) ◽  
pp. 1464-1472 ◽  
Author(s):  
Daniel Alexander ◽  
Petr Holý ◽  
Pavel Fiedler ◽  
Zdeněk Havlas ◽  
Jiří Závada
Keyword(s):  
Molecular Modeling ◽  
Hydrogen Bonds ◽  
Gas Phase ◽  
Self Assembly ◽  
Building Blocks ◽  
The Self ◽  
Circumstantial Evidence ◽  
Self Assembling ◽  
Molecular Modeling Study ◽  
Modeling Study

Concise synthesis of the tris(pyrimidones) 1a,b is described. Molecular modeling study demonstrated that both the prepared models 1a,b are capable of self-assembling under formation of spherical dimers locked by 18 hydrogen bonds. Extreme insolubility in all common solvents precluded investigation of the self-assembly in solution. Circumstantial evidence in favor of the self-assembly has been provided in the solid and gas phase.

Capillary And Magnetic Forces For Microscale Self-Assembled Systems

2010 ◽  
Vol 1272 ◽  
Author(s):  
Christopher J. Morris ◽  
Kate E. Laflin ◽  
Brian Isaacson ◽  
Michael Grapes ◽  
David Gracias
Keyword(s):  
Melting Point ◽  
Solder Alloy ◽  
Self Assembly ◽  
Permanent Magnets ◽  
Building Blocks ◽  
Capillary Forces ◽  
Silicon Chips ◽  
Magnetic Forces ◽  
Fundamental Limitations ◽  
Self Assembling

AbstractSelf-assembly is a promising technique to overcome fundamental limitations with integrating, packaging, and generally handling individual electronic-related components with characteristic lengths significantly smaller than 1 mm. Here we briefly summarize the use of capillary and magnetic forces to realize two example microscale systems. In the first example, we use capillary forces from a low melting point solder alloy to integrate 500 μm square, 100 μm thick silicon chips with thermally and chemically sensitive metal-polymer hinge actuators, for potential medical applications. The second example demonstrates a path towards self-assembling 3-D silicon circuits formed out of 280 μm sized building blocks, utilizing both capillary forces from a low melting point solder alloy and magnetic forces from integrated, permanent magnets. In the latter example, the utilization of magnetic forces combined with capillary forces improved the assembly yield to 7.8% over 0.1% achieved previously with capillary forces alone.

Design and Characterization of Nanostructured Biomaterials via the Self-assembly of Lipids

2013 ◽  
Vol 1498 ◽  
pp. 233-238
Author(s):  
Paul Ludford ◽  
Fikret Aydin ◽  
Meenakshi Dutt
Keyword(s):  
Lipid Bilayers ◽  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Building Blocks ◽  
Head Group ◽  
Specific Class ◽  
Multiple Control ◽  
Mesoscopic Simulation ◽  
Lipid Species ◽  
Functionalized Nanotubes

ABSTRACTWe are interested in designing nanostructured biomaterials using nanoscopic building blocks such as functionalized nanotubes and lipid molecules. In our earlier work, we summarized the multiple control parameters which direct the equilibrium morphology of a specific class of nanostructured biomaterials. Individual lipid molecules were composed of a hydrophilic head group and two hydrophobic tails. A bare nanotube encompassed an ABA architecture, with a hydrophobic shaft (B) and two hydrophilic ends (A). We introduced hydrophilic hairs at one end of the tube to enable selective transport through the channel. The dimensions of the nanotube were set to minimize its hydrophobic mismatch with the lipid bilayer. We used a Molecular Dynamics-based mesoscopic simulation technique called Dissipative Particle Dynamics which simultaneously resolves the structure and dynamics of the nanoscopic building blocks and the hybrid aggregate. The amphiphilic lipids and functionalized nanotubes self-assembled into a stable hybrid vesicle or a bicelle in the presence of a hydrophilic solvent. We showed that the morphology of the hybrid structures was directed by factors such as the temperature, the rigidity of the lipid molecules, and the concentration of the nanotubes. Another type of hybrid nanostructured biomaterial could be multi-component lipid bilayers. In this paper, we present approaches to design hybrid nanostructured materials using multiple lipid species with different chemistries and molecular chain stiffness.

Self-Assembly Processes for Organic Led Transport Layers and Electrode Passivation

1999 ◽  
Vol 558 ◽  
Author(s):  
J.E. Malinsky ◽  
W. Li ◽  
Q. Wang ◽  
J. Cui ◽  
H. Chou ◽  
...  
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Hole Transport ◽  
Transport Layer ◽  
Dielectric Films ◽  
Hole Transport Layer ◽  
Use Of Self ◽  
Self Assembling ◽  
Electrode Passivation ◽  
Thin Dielectric Films

ABSTRACTThis contribution describes the use of self-limiting siloxane chemisoroption processes to self-assemble building blocks for the modification of vacuum-deposited organic LED (OLED) devices. One approach consists of the use of self-assembling OLED hole transport materials for application in hybrid self-assembled + vapor deposited two-layer devices. Another approach involves the application of self-limiting, chemisorptive self-assembly techniques to introduce thin dielectric films between the anode and hole transport layer of a vapor deposited two-layer OLED device.

scholarly journals Self-Assembling Drug Formulations with Tunable Permeability and Biodegradability

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6786
Author(s):  
Gulnara Gaynanova ◽  
Leysan Vasileva ◽  
Ruslan Kashapov ◽  
Darya Kuznetsova ◽  
Rushana Kushnazarova ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Self Assembly ◽  
Targeted Delivery ◽  
Building Blocks ◽  
Biological Barriers ◽  
Self Assembling ◽  
Low Toxicity ◽  
Natural Building ◽  
Dynamic Structures ◽  
Supramolecular Aggregates

This review focuses on key topics in the field of drug delivery related to the design of nanocarriers answering the biomedicine criteria, including biocompatibility, biodegradability, low toxicity, and the ability to overcome biological barriers. For these reasons, much attention is paid to the amphiphile-based carriers composed of natural building blocks, lipids, and their structural analogues and synthetic surfactants that are capable of self-assembly with the formation of a variety of supramolecular aggregates. The latter are dynamic structures that can be used as nanocontainers for hydrophobic drugs to increase their solubility and bioavailability. In this section, biodegradable cationic surfactants bearing cleavable fragments are discussed, with ester- and carbamate-containing analogs, as well as amino acid derivatives received special attention. Drug delivery through the biological barriers is a challenging task, which is highlighted by the example of transdermal method of drug administration. In this paper, nonionic surfactants are primarily discussed, including their application for the fabrication of nanocarriers, their surfactant-skin interactions, the mechanisms of modulating their permeability, and the factors controlling drug encapsulation, release, and targeted delivery. Different types of nanocarriers are covered, including niosomes, transfersomes, invasomes and chitosomes, with their morphological specificity, beneficial characteristics and limitations discussed.

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