scholarly journals The self assembly of proteins; probing patchy protein interactions

2015 ◽  
Vol 17 (7) ◽  
pp. 5413-5420 ◽  
Author(s):  
Susan James ◽  
Michelle K. Quinn ◽  
Jennifer J. McManus
Keyword(s):  
Phase Diagram ◽  
Thermodynamic Properties ◽  
Protein Interactions ◽  
Self Assembly ◽  
The Self ◽  
Protein Surface ◽  
Competing Interactions ◽  
Diagram Approach

Anisotropy is central to protein self-assembly. The kinetic and thermodynamic properties of proteins in which competing interactions exist due to the anisotropic or patchy nature of the protein surface have been explored using a phase diagram approach.

Simulation study on the assembly of rod-coil diblock copolymers within coil-selective nanoslits

e-Polymers ◽  
2016 ◽  
Vol 16 (4) ◽  
pp. 343-349 ◽  
Author(s):  
Ya-Juan Su ◽  
Ze-Xin Ma ◽  
Jian-Hua Huang
Keyword(s):  
Phase Diagram ◽  
Self Assembly ◽  
Diblock Copolymers ◽  
Dissipative Particle Dynamics ◽  
Orientational Order ◽  
Particle Dynamics ◽  
The Self ◽  
Ordered Structures ◽  
Assembly Structure ◽  
Dynamics Simulations

AbstractDissipative particle dynamics simulations are performed to study the self-assembly of rod-coil (RC) diblock copolymers confined in a slit with two coil-selective surfaces. The effect of rod length and slit thickness on the assembly structure is investigated. A morphological phase diagram as a function of slit thickness and rod length is presented. We observe several ordered structures, such as perpendicular cylinders, parallel cylinders, and puck-shaped structure. In the assembly structures, long-range rod-rod orientational order is observed when the rod length exceeds a critical rod length. Our results show that the coil-selective slit influences the assembly structure as well as the rod orientation of RC diblock copolymers.

Self-assembly of granular spheres under one-dimensional vibration

Soft Matter ◽  
2018 ◽  
Vol 14 (48) ◽  
pp. 9856-9869 ◽  
Author(s):  
Reza Amirifar ◽  
Kejun Dong ◽  
Qinghua Zeng ◽  
Xizhong An
Keyword(s):  
Phase Diagram ◽  
Self Assembly ◽  
The Self ◽  
Sinusoidal Vibration ◽  
One Dimensional

The self-assembly of granular spheres under simple 1D sinusoidal vibration is studied and the correspondingA–fphase diagram is established.

The Origin of the Eukaryotic Cell Based on Conservation of Existing Interfaces

2006 ◽  
Vol 12 (4) ◽  
pp. 513-523 ◽  
Author(s):  
Albert D. G. de Roos
Keyword(s):  
Plasma Membrane ◽  
Protein Interactions ◽  
Self Assembly ◽  
Evolutionary Model ◽  
Lipid Vesicles ◽  
Eukaryotic Cell ◽  
The Self ◽  
Lipid Protein Interactions

Current theories about the origin of the eukaryotic cell all assume that during evolution a prokaryotic cell acquired a nucleus. Here, it is shown that a scenario in which the nucleus acquired a plasma membrane is inherently less complex because existing interfaces remain intact during evolution. Using this scenario, the evolution to the first eukaryotic cell can be modeled in three steps, based on the self-assembly of cellular membranes by lipid-protein interactions. First, the inclusion of chromosomes in a nuclear membrane is mediated by interactions between laminar proteins and lipid vesicles. Second, the formation of a primitive endoplasmic reticulum, or exomembrane, is induced by the expression of intrinsic membrane proteins. Third, a plasma membrane is formed by fusion of exomembrane vesicles on the cytoskeletal protein scaffold. All three self-assembly processes occur both in vivo and in vitro. This new model provides a gradual Darwinistic evolutionary model of the origins of the eukaryotic cell and suggests an inherent ability of an ancestral, primitive genome to induce its own inclusion in a membrane.

scholarly journals Phase Separation of Shell Protein and Enzyme: An Insight into the Biogenesis of a Prokaryotic Metabolosome

2022 ◽  
Author(s):  
Gaurav Kumar ◽  
Sharmistha Sinha
Keyword(s):  
Phase Separation ◽  
Protein Interactions ◽  
Self Assembly ◽  
Bacterial Species ◽  
Protein Structures ◽  
The Self ◽  
Liquid Droplets ◽  
Shell Protein ◽  
Shell Proteins

Bacterial microcompartments are substrate specific metabolic modules that are conditionally expressed in certain bacterial species. These all protein structures have size in the range of 100-150 nm and are formed by the self-assembly of thousands of protein subunits, all encoded by genes belonging to a single operon. The operon contains genes that encode for both enzymes and shell proteins. The shell proteins self-assemble to form the outer coat of the compartment and enzymes are encapsulated within. A perplexing question in MCP biology is to understand the mechanism which governs the formation of these small yet complex assemblages of proteins. In this work we use 1,2-propanediol utilization microcompartments (PduMCP) as a paradigm to identify the factors that drive the self-assembly of MCP proteins. We find that a major shell protein PduBB tend to self-assemble under macromolecular crowded environment and suitable ionic strength. Microscopic visualization and biophysical studies reveal phase separation to be the principle mechanism behind the self-association of shell protein in the presence of salts and macromolecular crowding. The shell protein PduBB interacts with the enzyme diol-dehydratase PduCDE and co-assemble into phase separated liquid droplets. The co-assembly of PduCDE and PduBB results in the enhancement of catalytic activity of the enzyme. A combination of spectroscopic and biochemical techniques shows the relevance of divalent cation Mg2+ in providing stability to intact PduMCP in vivo. Together our results suggest a combination of protein-protein interactions and phase separation guiding the self-assembly of Pdu shell protein and enzyme in solution phase.

scholarly journals Shape-sensitive crystallization in colloidal superball fluids

2015 ◽  
Vol 112 (17) ◽  
pp. 5286-5290 ◽  
Author(s):  
Laura Rossi ◽  
Vishal Soni ◽  
Douglas J. Ashton ◽  
David J. Pine ◽  
Albert P. Philipse ◽  
...  
Keyword(s):  
Phase Diagram ◽  
Self Assembly ◽  
Colloidal Silica ◽  
Solid Phase ◽  
Material Design ◽  
The Self ◽  
Powerful Approach ◽  
The Individual ◽  
Powerful Mechanism ◽  
Shape Of Particles

Guiding the self-assembly of materials by controlling the shape of the individual particle constituents is a powerful approach to material design. We show that colloidal silica superballs crystallize into canted phases in the presence of depletants. Some of these phases are consistent with the so-called “Λ1” lattice that was recently predicted as the densest packing of superdisks. As the size of the depletant is reduced, however, we observe a transition to a square phase. The differences in these entropically stabilized phases result from an interplay between the size of the depletants and the fine structure of the superball shape. We find qualitative agreement of our experimental results both with a phase diagram computed on the basis of the volume accessible to the depletants and with simulations. By using a mixture of depletants, one of which is thermosensitive, we induce solid-to-solid phase transitions between square and canted structures. The use of depletant size to leverage fine features of the shape of particles in driving their self-assembly demonstrates a general and powerful mechanism for engineering novel materials.

Evolution of Carbon Self-Assembly in Colloidal Phase Diagram

2002 ◽  
Vol 739 ◽  
Author(s):  
V. Bouda
Keyword(s):  
Phase Diagram ◽  
Phase Transitions ◽  
Self Assembly ◽  
Colloidal Particles ◽  
Thermal Fluctuation ◽  
Ionic Concentration ◽  
The Self ◽  
Colloidal Systems ◽  
Carbon Particles ◽  
Self Assembled

ABSTRACTThe growth of the self-assembled structure of carbon colloidal particles has been studied [1]. The system of carbon particles was processed in electrical field in polymer melt with controlled ionic concentration. The interpretation of the complex evolution of the self-assembled structure of carbon particles was given in terms of phase transitions of colloidal systems of carbon particles.Interactions between doublets of carbon black (CB) particles are interpreted in terms of DLVO approximation of interaction energy as multiples of average thermal fluctuation kT. Plots of the sum of energy of electrostatic repulsion and energy of van der Waals attraction versus separation between the doublets show the energy barriers to coagulation of high B and the energy wells with the secondary minima of depth W. The colloidal phase transitions appear at critical conjuncture of the concentration of ions in the medium and surface potential on the colloids. Six transition lines determine five phases of the assembly of carbon colloids in the proposed colloidal phase diagram: lateral vapor + axial vapor (vapor), lateral liquid + axial vapor (columnar liquid crystal), lateral liquid + axial liquid (smectic LC), lateral liquid + axial solid (nematic LC), and lateral solid + axial solid (solid).The diagram provides a tool to control the evolution of carbon self-assembly. The eventual morphology depends on the route of the steps of the processing. During the time elapsed in the LC state, the structure can reorganize and the eventual coagulation produces various crystals. On the contrary, the route outside the LC state can produce glass.

scholarly journals Competing Interactions in the Self-Assembly of NC-Ph3-CN Molecules on Cu(111)

2015 ◽  
Vol 119 (45) ◽  
pp. 25442-25448 ◽  
Author(s):  
Giulia E. Pacchioni ◽  
Marina Pivetta ◽  
Harald Brune
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Competing Interactions

scholarly journals Confinement effects on the properties of Janus dimers

2016 ◽  
Vol 18 (41) ◽  
pp. 28740-28746 ◽  
Author(s):  
José Rafael Bordin ◽  
Leandro B. Krott
Keyword(s):  
Thermodynamic Properties ◽  
Self Assembly ◽  
The Self ◽  
Confinement Effects

We show how the confinement between two parallel walls affects the self-assembly, and dynamic and thermodynamic properties of Janus dumbbells.

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.

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