Designing soft nanomaterials via the self assembly of functionalized icosahedral viral capsid nanoparticles

2014 ◽  
Vol 30 (1) ◽  
pp. 141-150 ◽  
Author(s):  
Vidyalakshmi Chockalingam Muthukumar ◽  
Leebyn Chong ◽  
Meenakshi Dutt
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Viral Capsid ◽  
Image Position

Abstract

Identification of a major intermediate along the self-assembly pathway of an icosahedral viral capsid by using an analytical model of a spherical patch

Soft Matter ◽  
2016 ◽  
Vol 12 (32) ◽  
pp. 6728-6736 ◽  
Author(s):  
Didier Law-Hine ◽  
Mehdi Zeghal ◽  
Stéphane Bressanelli ◽  
Doru Constantin ◽  
Guillaume Tresset
Keyword(s):  
Analytical Model ◽  
Self Assembly ◽  
The Self ◽  
Viral Capsid ◽  
Assembly Pathway

scholarly journals Hot Spots and Their Contribution to the Self-Assembly of the Viral Capsid: In Silico Prediction and Analysis

2019 ◽  
Vol 20 (23) ◽  
pp. 5966 ◽  
Author(s):  
Armando Díaz-Valle ◽  
José Marcos Falcón-González ◽  
Mauricio Carrillo-Tripp
Keyword(s):  
Free Energy ◽  
Self Assembly ◽  
Hot Spots ◽  
Binding Free Energy ◽  
Hot Spot ◽  
Free Energy Calculations ◽  
The Self ◽  
Viral Capsid ◽  
Macromolecular Complex ◽  
Single Mutation

The viral capsid is a macromolecular complex formed by a defined number of self-assembled proteins, which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein–protein interactions (PPI) drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the PPI hot spot hypothesis, we present a conservation-based methodology to identify those interface residues hypothesized to be crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate the predictions through a rigorous physical framework which integrates molecular dynamics simulations and free energy calculations by Umbrella sampling and the potential of mean force using an all-atom molecular representation of the capsid proteins of an icosahedral virus in an explicit solvent. Our results show that a single mutation in any of the structure-conserved hot spots significantly perturbs the quaternary protein–protein interaction, decreasing the absolute value of the binding free energy, without altering the protein’s secondary nor tertiary structure. Our conservation-based hot spot prediction methodology can lead to strategies to rationally modulate the capsid’s thermodynamic properties.

scholarly journals Hot-spots and their contribution to the self-assembly of the viral capsid: in-vitro validation

2019 ◽  
Author(s):  
Alejandra Gabriela Valdez-Lara ◽  
Mariana Andrade-Medina ◽  
Josué Alejandro Alemán-Vilis ◽  
Aldo Adrián Pérez-Montoya ◽  
Nayely Pineda-Aguilar ◽  
...  
Keyword(s):  
Self Assembly ◽  
Hot Spots ◽  
Point Mutations ◽  
The Self ◽  
Viral Capsid ◽  
Single Mutation ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle ◽  
Interface Residues

AbstractThe viral capsid is a macromolecular complex formed by self-assembled proteins (CPs) which, in many cases, are biopolymers with an identical amino acid sequence. Specific CP-CP interactions drive the capsid self-assembly process. However, it is believed that only a small set of protein-protein interface residues significantly contribute to the formation of the capsid; the so-called “hot-spots”. Here, we investigate the effect of in-vitro point-mutations on the Bromoviridae family structure-conserved interface residues of the icosahedral Cowpea Chlorotic Mottle Virus, previously hypothesized as hot-spots. We study the self-assembly of those mutated recombinant CPs for the formation of capsids by Thermal Shift Assay (TSA). We show that the TSA biophysical technique is a reliable way to characterize capsid assembly. Our results show that point-mutations on non-conserved interface residues produce capsids indistinguishable from the wild-type. In contrast, a single mutation on structure-conserved residues E176 or V189 prevents the formation of the capsid while maintaining the tertiary fold of the CP. Our findings provide experimental evidence of the in-silico conservation-based hot-spot prediction accuracy. As a whole, our methodology provides a framework that could aid in the rational development of molecules to inhibit virus formation, or advance capsid bioengineering to design for their stability, function and applications.

scholarly journals Hot-spots and their contribution to the self-assembly of the viral capsid: in-silico prediction and analysis

2019 ◽  
Author(s):  
Armando Díaz-Valle ◽  
José Marcos Falcón-González ◽  
Mauricio Carrillo-Tripp
Keyword(s):  
Free Energy ◽  
Self Assembly ◽  
Hot Spots ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
The Self ◽  
Atomic Scale ◽  
Viral Capsid ◽  
Macromolecular Complex ◽  
Single Mutation

AbstractIn order to rationally design biopolymers that mimic biological functions, first, we need to elucidate the molecular mechanisms followed by nature. For example, the viral capsid is a macromolecular complex formed by self-assembled proteins which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein-protein interactions drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the hot-spot hypothesis, we propose a conservation-based methodology to identify those interface residues that are crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate our predictions by computational free energy calculations using an atomic-scale molecular model of an icosahedral virus. Our results show that a single mutation in any of the hot-spots significantly perturbs the quaternary interaction, decreasing the absolute value of the binding free energy, without altering the tertiary structure. Our methodology can lead to a strategy to rationally modulate the capsid’s thermodynamic properties.

Phase separation of a nematic liquid crystal in the self-assembly of lysozyme in a drying aqueous solution drop

2019 ◽  
Vol 9 (01) ◽  
pp. 150-158 ◽  
Author(s):  
Anusuya Pal ◽  
Amalesh Gope ◽  
Rumani Kafle ◽  
Germano S. Iannacchione
Keyword(s):  
Aqueous Solution ◽  
Liquid Crystal ◽  
Phase Separation ◽  
Nematic Liquid Crystal ◽  
Self Assembly ◽  
The Self ◽  
Image Position

Abstract

Synthetic approaches to construct viral capsid-like spherical nanomaterials

2018 ◽  
Vol 54 (65) ◽  
pp. 8944-8959 ◽  
Author(s):  
Kazunori Matsuura
Keyword(s):  
Self Assembly ◽  
Recent Progress ◽  
The Self ◽  
Viral Capsid ◽  
Feature Article ◽  
Synthetic Approaches

This feature article describes recent progress in synthetic strategies to construct viral capsid-like spherical nanomaterials using the self-assembly of peptides and/or proteins.

The Nature of Rapidly Extracted Phycocyanin from the Blue-Green Alga Plectonema Boryanum

1971 ◽  
Vol 29 ◽  
pp. 366-367
Author(s):  
M. Kessel ◽  
R. MacColl
Keyword(s):  
Self Assembly ◽  
Analytical Ultracentrifugation ◽  
Uranyl Acetate ◽  
The Self ◽  
Major Protein ◽  
Subunit Structure ◽  
Blue Green Alga ◽  
Thin Sections ◽  
Blue Green Algae ◽  
Cacodylate Buffer

The major protein of the blue-green algae is the biliprotein, C-phycocyanin (Amax = 620 nm), which is presumed to exist in the cell in the form of distinct aggregates called phycobilisomes. The self-assembly of C-phycocyanin from monomer to hexamer has been extensively studied, but the proposed next step in the assembly of a phycobilisome, the formation of 19s subunits, is completely unknown. We have used electron microscopy and analytical ultracentrifugation in combination with a method for rapid and gentle extraction of phycocyanin to study its subunit structure and assembly.To establish the existence of phycobilisomes, cells of P. boryanum in the log phase of growth, growing at a light intensity of 200 foot candles, were fixed in 2% glutaraldehyde in 0.1M cacodylate buffer, pH 7.0, for 3 hours at 4°C. The cells were post-fixed in 1% OsO4 in the same buffer overnight. Material was stained for 1 hour in uranyl acetate (1%), dehydrated and embedded in araldite and examined in thin sections.

Interrelationship of the cellular distribution and secretion of regular structure (RS) protein in Bacillus licheniformis nm 105

1992 ◽  
Vol 50 (1) ◽  
pp. 712-713
Author(s):  
Xiaorong Zhu ◽  
Richard McVeigh ◽  
Bijan K. Ghosh
Keyword(s):  
Alkaline Phosphatase ◽  
Bacillus Licheniformis ◽  
Self Assembly ◽  
Gel Electrophoresis ◽  
Culture Supernatant ◽  
Regular Structure ◽  
The Self ◽  
Cellular Distribution ◽  
Structural Protein ◽  
Laboratory Cultures

A mutant of Bacillus licheniformis 749/C, NM 105 exhibits some notable properties, e.g., arrest of alkaline phosphatase secretion and overexpression and hypersecretion of RS protein. Although RS is known to be widely distributed in many microbes, it is rarely found, with a few exceptions, in laboratory cultures of microorganisms. RS protein is a structural protein and has the unusual properties to form aggregate. This characteristic may have been responsible for the self assembly of RS into regular tetragonal structures. Another uncommon characteristic of RS is that enhanced synthesis and secretion which occurs when the cells cease to grow. Assembled RS protein with a tetragonal structure is not seen inside cells at any stage of cell growth including cells in the stationary phase of growth. Gel electrophoresis of the culture supernatant shows a very large amount of RS protein in the stationary culture of the B. licheniformis. It seems, Therefore, that the RS protein is cotranslationally secreted and self assembled on the envelope surface.

Nanoscale Self-Assembly Using Ion and Electron Beam Techniques: A Rapid Review

MRS Advances ◽  
2020 ◽  
Vol 5 (64) ◽  
pp. 3507-3520
Author(s):  
Chunhui Dai ◽  
Kriti Agarwal ◽  
Jeong-Hyun Cho
Keyword(s):  
Electron Beam ◽  
Self Assembly ◽  
Ion Beam ◽  
Three Dimensional ◽  
The Self ◽  
Stress Generation ◽  
Rapid Review ◽  
High Yield ◽  
3D Nanostructures ◽  
Self Assembled

AbstractNanoscale self-assembly, as a technique to transform two-dimensional (2D) planar patterns into three-dimensional (3D) nanoscale architectures, has achieved tremendous success in the past decade. However, an assembly process at nanoscale is easily affected by small unavoidable variations in sample conditions and reaction environment, resulting in a low yield. Recently, in-situ monitored self-assembly based on ion and electron irradiation has stood out as a promising candidate to overcome this limitation. The usage of ion and electron beam allows stress generation and real-time observation simultaneously, which significantly enhances the controllability of self-assembly. This enables the realization of various complex 3D nanostructures with a high yield. The additional dimension of the self-assembled 3D nanostructures opens the possibility to explore novel properties that cannot be demonstrated in 2D planar patterns. Here, we present a rapid review on the recent achievements and challenges in nanoscale self-assembly using electron and ion beam techniques, followed by a discussion of the novel optical properties achieved in the self-assembled 3D nanostructures.

Bottom-up Evolution from Disks to High-Genus Polymersomes

2018 ◽  
Author(s):  
Claudia Contini ◽  
Russell Pearson ◽  
Linge Wang ◽  
Lea Messager ◽  
Jens Gaitzsch ◽  
...  
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Amphiphilic Copolymers ◽  
Chain Entanglement ◽  
Bottom Up ◽  
New Approach ◽  
High Genus ◽  
Transmission Electron ◽  
Minimal Radius ◽  
Stop Flow

<div><div><div><p>We report the design of polymersomes using a bottom-up approach where the self-assembly of amphiphilic copolymers poly(2-(methacryloyloxy) ethyl phosphorylcholine)–poly(2-(diisopropylamino) ethyl methacrylate) (PMPC-PDPA) into membranes is tuned using pH and temperature. We study this process in detail using transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and stop-flow ab- sorbance disclosing the molecular and supramolecular anatomy of each structure observed. We report a clear evolution from disk micelles to vesicle to high-genus vesicles where each passage is controlled by pH switch or temperature. We show that the process can be rationalised adapting membrane physics theories disclosing important scaling principles that allow the estimation of the vesiculation minimal radius as well as chain entanglement and coupling. This allows us to propose a new approach to generate nanoscale vesicles with genus from 0 to 70 which have been very elusive and difficult to control so far.</p></div></div></div>

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