Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Self-assembly of protein superstructures by physical interactions under cytoplasm-like conditions.

ABSTRACT: The structure-driven assembly of multimeric protein complexes and the formation of intracellular phase-like protein condensates have been the subject of intense research. However, the assembly of larger superstructures comprising cellular components, such as protein nanoparticles driven by general physical rather than specific biochemical interactions, remains relatively uncharacterized. Here, we use gas vesicles (GVs)-genetically encoded protein nanoparticles that form ordered intracellular clusters-as a model system to study the forces driving multiparticle assembly under cytoplasm-like conditions. Our calculations and experimental results show that the ordered assembly of GVs can be achieved by screening their mutual electrostatic repulsion with electrolytes and creating a crowding force with dissolved macromolecules. The precise balance of these forces results in different packing configurations. Biomacromolecules such as polylysine and DNA are capable of driving GV clustering. These results provide basic insights into how physically driven interactions affect the formation of protein superstructures, offer guidance for manipulating nanoparticle assembly in cellular environments through synthetic biology methods, and inform research on the biotechnology applications of GVs.

SUBMITTER: Yao Y

PROVIDER: S-EPMC8390860 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Metal-mediated self-assembly of protein superstructures: influence of secondary interactions on protein oligomerization and aggregation.

Project description:We have previously demonstrated that non-self-associating protein building blocks can oligomerize to form discrete supramolecular assemblies under the control of metal coordination. We show here that secondary interactions (salt bridges and hydrogen bonds) can be critical in guiding the metal-induced self-assembly of proteins. Crystallographic and hydrodynamic measurements on appropriately engineered cytochrome cb562 variants pinpoint the importance of a single salt-bridging arginine side chain in determining whether the protein monomers form a discrete Zn-induced tetrameric complex or heterogeneous aggregates. The combined ability to direct PPIs through metal coordination and secondary interactions should provide the specificity required for the construction of complex protein superstructures and the selective control of cellular processes that involve protein-protein association reactions.

| S-EPMC2724180 | biostudies-literature

Self-Assembly Protein Superstructures as a Powerful Chemodynamic Therapy Nanoagent for Glioblastoma Treatment.

Project description:Glioblastoma (GBM) remains a formidable challenge in oncology. Chemodynamic therapy (CDT) that triggers tumor cell death by reactive oxygen species (ROS) could open up a new door for GBM treatment. Herein, we report a novel CDT nanoagent. Hemoglobin (Hb) and glucose oxidase (GOx) were employed as powerful CDT catalysts. Instead of encapsulating the proteins in drug delivery nanocarriers, we formulate multimeric superstructures as self-delivery entities by crosslinking techniques. Red blood cell (RBC) membranes are camouflaged on the protein superstructures to promote the delivery across blood-brain barrier. The as-prepared RBC@Hb@GOx nanoparticles (NPs) offer superior biocompatibility, simplified structure, and high accumulation at the tumor site. We successfully demonstrated that the NPs could efficiently produce toxic ROS to kill U87MG cancer cells in vitro and inhibit the growth of GBM tumor in vivo, suggesting that the new CDT nanoagent holds great promise for treating GBM.

| S-EPMC7770858 | biostudies-literature

Unknown aspects of self-assembly of PbS microscale superstructures.

Project description:A lot of interesting and sophisticated examples of nanoparticle (NP) self-assembly (SA) are known. From both fundamental and technological standpoints, this field requires advancements in three principle directions: (a) understanding the mechanism and driving forces of three-dimensional (3D) SA with both nano- and microlevels of organization; (b) understanding disassembly/deconstruction processes; and (c) finding synthetic methods of assembly into continuous superstructures without insulating barriers. From this perspective, we investigated the formation of well-known star-like PbS superstructures and found a number of previously unknown or overlooked aspects that can advance the knowledge of NP self-assembly in these three directions. The primary one is that the formation of large seemingly monocrystalline PbS superstructures with multiple levels of octahedral symmetry can be explained only by SA of small octahedral NPs. We found five distinct periods in the formation PbS hyperbranched stars: (1) nucleation of early PbS NPs with an average diameter of 31 nm; (2) assembly into 100-500 nm octahedral mesocrystals; (3) assembly into 1000-2500 nm hyperbranched stars; (4) assembly and ionic recrystallization into six-arm rods accompanied by disappearance of fine nanoscale structure; (5) deconstruction into rods and cuboctahedral NPs. The switches in assembly patterns between the periods occur due to variable dominance of pattern-determining forces that include van der Waals and electrostatic (charge-charge, dipole-dipole, and polarization) interactions. The superstructure deconstruction is triggered by chemical changes in the deep eutectic solvent (DES) used as the media. PbS superstructures can be excellent models for fundamental studies of nanoscale organization and SA manufacturing of (opto)electronics and energy-harvesting devices which require organization of PbS components at multiple scales.

| S-EPMC3401906 | biostudies-literature

Peptide sequence mediated self-assembly of molybdenum blue nanowheel superstructures.

Project description:The precise control over the formation of complex nanostructures, e.g. polyoxometalates (POMs), at the sub-nanoscale is challenging but critical if non-covalent architectures are to be designed. Combining biologically-evolved systems with inorganic nanostructures could lead to sequence-mediated assembly. Herein, we exploit oligopeptides as multidentate structure-directing ligands via metal-coordination and hydrogen bonded interactions to modulate the self-assembly of POM superstructures. Six oligopeptides (GH, AH, SH, G2H, G4H and G5H) are incorporated into the cavities of Molybdenum Blue (MB) POM nanowheels. It is found that the helicity of the nanowheel can be readily switched (Δ to Λ) by simply altering the N-terminal amino acid on the peptide chain rather than their overall stereochemistry. We also reveal a delicate balance between the Mo-coordination and the hydrogen bonds found within the internal cavity of the inorganic nanowheels which results in the sequence mediated formation of two unprecedented asymmetrical nanowheel frameworks: {Mo122Ce5} and {Mo126Ce4}.

| S-EPMC8179307 | biostudies-literature

Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions.

Project description:Prebiotic phosphorylation of (pre)biological substrates under aqueous conditions is a critical step in the origins of life. Previous investigations have had limited success and/or require unique environments that are incompatible with subsequent generation of the corresponding oligomers or higher-order structures. Here, we demonstrate that diamidophosphate (DAP)-a plausible prebiotic agent produced from trimetaphosphate-efficiently (amido)phosphorylates a wide variety of (pre)biological building blocks (nucleosides/tides, amino acids and lipid precursors) under aqueous (solution/paste) conditions, without the need for a condensing agent. Significantly, higher-order structures (oligonucleotides, peptides and liposomes) are formed under the same phosphorylation reaction conditions. This plausible prebiotic phosphorylation process under similar reaction conditions could enable the systems chemistry of the three classes of (pre)biologically relevant molecules and their oligomers, in a single-pot aqueous environment.

| S-EPMC6295206 | biostudies-literature

Flower-like superstructures of AIE-active tetraphenylethylene through solvophobic controlled self-assembly.

Project description:The development of well-organized structures with high luminescent properties in the solid and aggregated states is of both scientific and technological interest due to their applications in nanotechnology. In this paper we described the synthesis of amphiphilic and dumbbell shaped AIE-active tetraphenylethylene (TPE) derivatives and studied their self-assembly with solvophobic control. Interestingly, both TPE derivatives form a 3D flower-shape supramolecular structure from THF/water solutions at varying water fractions. SEM microscopy was used to visualise step-wise growth of flower-shape assembly. TPE derivatives also show good mechanochromic properties which can be observed in the process of grinding, fuming and heating. These TPE derivative self-assemblies are formed due to two main important properties: (i) the TPE-core along with alkyl chains, optimizing the dispersive interactions within a construct, and (ii) amide-linkage through molecular recognition. We believe such arrangements prevent crystallization and favour the directional growth of flower-shape nanostructures in a 3D fashion.

| S-EPMC5322366 | biostudies-literature

Right handed chiral superstructures from achiral molecules: self-assembly with a twist.

Project description:The induction and development of chiral supramolecular structures from hierarchical self-assembly of achiral compounds is closely related to the evolution of life and the chiral amplification found in nature. Here we show that the combination of achiral tetraphenylethene (TPE) an AIE-active luminophore bearing four long alkyl chains via amide linkage allows the entire process of induction and control of supramolecular chirality into well-defined uniform right-handed twisted superstructures via solvent composition and polarity, i.e. solvophobic effect. We showed that the degree of twist and the pitch of the ribbons can be controlled to one-handed helical structure via solvophobic effects. The twisted superstructure assembly was visualised by scanning electron microscope (SEM) and transmission electron microscopy (TEM), furthermore, circular dichroism (CD) confirms used to determine controlled right-handed assembly. This controlled assembly of an AIE-active molecule can be of practical value; for example, as templates for helical crystallisation, catalysis and a chiral mechanochromic luminescent superstructure formation.

| S-EPMC4616054 | biostudies-literature

Interactions of a Polypeptide with a Protein Nanopore Under Crowding Conditions.

Project description:Molecular crowding, a ubiquitous feature of the cellular environment, has significant implications in the kinetics and equilibrium of biopolymer interactions. In this study, a single charged polypeptide is exposed to competing forces that drive it into a transmembrane protein pore versus forces that pull it outside. Using single-molecule electrophysiology, we provide compelling experimental evidence that the kinetic details of the polypeptide-pore interactions are substantially affected by high concentrations of less-penetrating polyethylene glycols (PEGs). At a polymer concentration above a critical value, the presence of these neutral macromolecular crowders increases the rate constant of association but decreases the rate constant of dissociation, resulting in a stronger polypeptide-pore interaction. Moreover, a larger-molecular weight PEG exhibits a lower rate constant of association but a higher rate constant of dissociation than those values corresponding to a smaller-molecular weight PEG. These outcomes are in accord with a lower diffusion constant of the polypeptide and higher depletion-attraction forces between the polypeptide and transmembrane protein pore under crowding and confinement conditions.

| S-EPMC6482057 | biostudies-literature

Self-assembly of prevascular tissues from endothelial and fibroblast cells under scaffold-free, nonadherent conditions.

Project description:To advance the emerging field of bioengineered prevascularized tissues, we investigated factors that control primary vascular network formation in scaffold-free, high-density cell suspension-derived tissues. Fabricating primary vascular networks in a scaffold-free system requires endothelial cells (ECs) and extracellular matrix (ECM)-producing cells that act together to elaborate a permissive matrix. We report findings on the effects to vascular patterning induced by altering the ratio of human endothelial to human fibroblast cells. Analysis revealed that a 1:4 ratio of ECs to fibroblasts resulted in the synthesis of an ECM permissive for organization of primary vascular networks that recapitulated the pattern of primary vascular networks observed in vivo. Importantly this work highlighted the significance of tension in the organization of vascular networks in prevascularized tissues. To our knowledge our in vitro studies are the first to demonstrate the formation of two distinct vascular patterns in an initially homogenous culture system. Specifically, we demonstrate that within our constructs, vascular networks formed with distinct directional orientations that reflect self-assembly-mediated tension. Further, our studies demonstrate that treatment of prevascularized tissues with matrix-promoting factors such as transforming growth factor beta 1 (TGFβ1) increases tissue strength without altering vascular network patterning. Together, the ability to generate prevascularized tissues from human cells in scaffold-free systems and the ability to enhance the strength of the constructs with matrix-promoting factors represent advances to the potential translational utility of prevascularized tissues both as subcutaneous implants and in surgical scenarios requiring the application of tension to the tissue construct.

| S-EPMC4293139 | biostudies-literature

Amyloid Self-Assembly of Lysozyme in Self-Crowded Conditions: The Formation of a Protein Oligomer Hydrogel.

Project description:A method is designed to quickly form protein hydrogels, based on the self-assembly of highly concentrated lysozyme solutions in acidic conditions. Their properties can be easily modulated by selecting the curing temperature. Molecular insights on the gelation pathway, derived by in situ FTIR spectroscopy, are related to calorimetric and rheological results, providing a consistent picture on structure-property correlations. In these self-crowded samples, the thermal unfolding induces the rapid formation of amyloid aggregates, leading to temperature-dependent quasi-stationary levels of antiparallel cross β-sheet links, attributed to kinetically trapped oligomers. Upon subsequent cooling, thermoreversible hydrogels develop by the formation of interoligomer contacts. Through heating/cooling cycles, the starting solutions can be largely recovered back, due to oligomer-to-monomer dissociation and refolding. Overall, transparent protein hydrogels can be easily formed in self-crowding conditions and their properties explained, considering the formation of interconnected amyloid oligomers. This type of biomaterial might be relevant in different fields, along with analogous systems of a fibrillar nature more commonly considered.

| S-EPMC8023603 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data