scholarly journals Self-Assembly of Tail Tube Protein of Bacteriophage vB_EcoS_NBD2 into Extremely Long Polytubes in E. coli and S. cerevisiae

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 208 ◽  
Author(s):  
Aliona Špakova ◽  
Eugenijus Šimoliūnas ◽  
Raminta Batiuškaitė ◽  
Simonas Pajeda ◽  
Rolandas Meškys ◽  
...  
Keyword(s):  
Self Assembly ◽  
Tail Length ◽  
Cell Protein ◽  
Tubular Structures ◽  
E Coli ◽  
Physical Conditions ◽  
Self Assembling ◽  
Phage Proteins ◽  
Purification Protocol

Nucleotides, peptides and proteins serve as a scaffold material for self-assembling nanostructures. In this study, the production of siphovirus vB_EcoS_NBD2 (NBD2) recombinant tail tube protein gp39 reached approximately 33% and 27% of the total cell protein level in Escherichia coli and Saccharomyces cerevisiae expression systems, respectively. A simple purification protocol allowed us to produce a recombinant gp39 protein with 85%–90% purity. The yield of gp39 was 2.9 ± 0.36 mg/g of wet E. coli cells and 0.85 ± 0.33 mg/g for S. cerevisiae cells. The recombinant gp39 self-assembled into well-ordered tubular structures (polytubes) in vivo in the absence of other phage proteins. The diameter of these structures was the same as the diameter of the tail of phage NBD2 (~12 nm). The length of these structures varied from 0.1 µm to >3.95 µm, which is 23-fold the normal NBD2 tail length. Stability analysis demonstrated that the polytubes could withstand various chemical and physical conditions. These polytubes show the potential to be used as a nanomaterial in various fields of science.

scholarly journals Dnm1 forms spirals that are structurally tailored to fit mitochondria

2005 ◽  
Vol 170 (7) ◽  
pp. 1021-1027 ◽  
Author(s):  
Elena Ingerman ◽  
Edward M. Perkins ◽  
Michael Marino ◽  
Jason A. Mears ◽  
J. Michael McCaffery ◽  
...  
Keyword(s):  
Self Assembly ◽  
Membrane Dynamics ◽  
Nucleotide Hydrolysis ◽  
Mitochondrial Division ◽  
Cellular Processes ◽  
Self Assembling ◽  
Related Proteins ◽  
Rate Limiting ◽  
Common Function

Dynamin-related proteins (DRPs) are large self-assembling GTPases whose common function is to regulate membrane dynamics in a variety of cellular processes. Dnm1, which is a yeast DRP (Drp1/Dlp1 in humans), is required for mitochondrial division, but its mechanism is unknown. We provide evidence that Dnm1 likely functions through self-assembly to drive the membrane constriction event that is associated with mitochondrial division. Two regulatory features of Dnm1 self-assembly were also identified. Dnm1 self-assembly proceeded through a rate-limiting nucleation step, and nucleotide hydrolysis by assembled Dnm1 structures was highly cooperative with respect to GTP. Dnm1 formed extended spirals, which possessed diameters greater than those of dynamin-1 spirals but whose sizes, remarkably, were equal to those of mitochondrial constriction sites in vivo. These data suggest that Dnm1 has evolved to form structures that fit the dimensions of mitochondria.

MOLECULE-UP FABRICATION AND MANIPULATION OF LIPID NANOTUBES

2002 ◽  
Vol 01 (05n06) ◽  
pp. 465-469 ◽  
Author(s):  
TOSHIMI SHIMIZU ◽  
GEORGE JOHN ◽  
AKIHIRO FUKAGAWA ◽  
KOHZO ITO ◽  
HIROSHI FRUSAWA
Keyword(s):  
Optical Tweezers ◽  
Self Assembly ◽  
Flexural Rigidity ◽  
Combinatorial Approach ◽  
Tubular Structures ◽  
Self Assembling ◽  
Degree Of Unsaturation ◽  
Hydrophobic Chain ◽  
Rational Control ◽  
Lipid Nanotube

Self-assembling behavior of both a cardanol-appended glycolipid mixture and the fractionated four components has been examined in aqueous solutions. The cardanyl glucoside mixture differing in the degree of unsaturation in the hydrophobic chain was found to self-assemble in water to form open-ended nanotube structures with 10–15 nm inner diameters. The pure saturated homologue produced twisted helical ribbons through self-assembly, whereas the monoene derivative gave tubular structures. The rational control of helical and tubular morphologies has been achieved by a combinatorial approach through the binary self-assembly of the saturated and monoene derivatives. The flexural rigidity of a single lipid nanotube was first evaluated using optical tweezers manipulation and then compared with that of natural microtubules.

scholarly journals Lipid membranes trigger misfolding and self-assembly of amyloid β 42 protein into aggregates

2019 ◽  
Author(s):  
Siddhartha Banerjee ◽  
Mohtadin Hashemi ◽  
Karen Zagorski ◽  
Yuri L. Lyubchenko
Keyword(s):  
Self Assembly ◽  
Lipid Membranes ◽  
Membrane Surface ◽  
Amyloid Β ◽  
Test Tube ◽  
Aggregation Process ◽  
Self Assembling ◽  
Nanoscale Aggregates

AbstractThe assembly of polypeptides and proteins into nanoscale aggregates is a phenomenon observed in a vast majority of proteins. Importantly, aggregation of amyloid β (Aβ) proteins is considered as a major cause for the development of Alzheimer’s disease. The process depends on various conditions and typical test-tube experiments require high protein concentration that complicates the translation of results obtained in vitro to understanding the aggregation process in vivo. Here we demonstrate that Aβ42 monomers at the membrane bilayer are capable of self-assembling into aggregates at physiologically low concentrations, and the membrane in this aggregation process plays a role of a catalyst. We applied all-atom molecular dynamics to demonstrate that the interaction with the membrane surface dramatically changes the conformation of Aβ42 protein. As a result, the misfolded Aβ42 rapidly assembles into dimers, trimers and tetramers, so the on-surface aggregation is the mechanism by which amyloid oligomers are produced and spread.

scholarly journals Construction and Characterizations of Antibacterial Surfaces Based on Self-Assembled Monolayer of Antimicrobial Peptides (Pac-525) Derivatives on Gold

Coatings ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1014
Author(s):  
Zijiao Zhang ◽  
Ni Kou ◽  
Weilong Ye ◽  
Shuo Wang ◽  
Jiaju Lu ◽  
...  
Keyword(s):  
Antimicrobial Peptides ◽  
Self Assembly ◽  
The Self ◽  
Self Assembled Monolayer ◽  
E Coli ◽  
Antimicrobial Efficiency ◽  
Gold Substrates ◽  
Self Assembled ◽  
Antibacterial Surfaces

Background: Infection that is related to implanted biomaterials is a serious issue in the clinic. Antimicrobial peptides (AMPs) have been considered as an ideal alternative to traditional antibiotic drugs, for the treatment of infections, while some problems, such as aggregation and protein hydrolysis, are still the dominant concerns that compromise their antimicrobial efficiency in vivo. Methods: In this study, antimicrobial peptides underwent self-assembly on gold substrates, forming good antibacterial surfaces, with stable antibacterial behavior. The antimicrobial ability of AMPs grafted on the surfaces, with or without glycine spaces or a primer layer, was evaluated. Results: Specifically, three Pac-525 derivatives, namely, Ac-CGn-KWRRWVRWI-NH2 (n = 0, 2, or 6) were covalently grafted onto gold substrates via the self-assembling process for inhibiting the growth of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). Furthermore, the alkanethiols HS(CH)10SH were firstly self-assembled into monolayers, as a primer layer (SAM-SH) for the secondary self-assembly of Pac-525 derivatives, to effectively enhance the bactericidal performance of the grafted AMPs. The -(CH)10-S-S-G6Pac derivative was highly effective against S. aureus and E. coli, and reduced the viable amount of E. coli and S. aureus to 0.4% and 33.2%, respectively, after 24 h of contact. In addition, the immobilized AMPs showed good biocompatibility, promoting bone marrow stem cell proliferation. Conclusion: the self-assembled monolayers of the Pac-525 derivatives have great potential as a novel therapeutic method for the treatment of implanted biomaterial infections.

scholarly journals Light-directed trapping of metastable intermediates in a self-assembly process

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Joonsik Seo ◽  
Joonyoung F. Joung ◽  
Sungnam Park ◽  
Young Ji Son ◽  
Jaegeun Noh ◽  
...  
Keyword(s):  
Self Assembly ◽  
Alkyl Chain ◽  
Perylene Diimide ◽  
Chemical Compositions ◽  
Assembly Process ◽  
Supramolecular Framework ◽  
Tubular Structures ◽  
Significant Information ◽  
Self Assembling ◽  
General Method

AbstractSelf-assembly is a dynamic process that often takes place through a stepwise pathway involving formation of kinetically favored metastable intermediates prior to generation of a thermodynamically preferred supramolecular framework. Although trapping intermediates in these pathways can provide significant information about both their nature and the overall self-assembly process, it is a challenging venture without altering temperature, concentrations, chemical compositions and morphologies. Herein, we report a highly efficient and potentially general method for “trapping” metastable intermediates in self-assembly processes that is based on a photopolymerization strategy. By employing a chiral perylene-diimide possessing a diacetylene containing an alkyl chain, we demonstrated that the metastable intermediates, including nanoribbons, nanocoils and nanohelices, can be effectively trapped by using UV promoted polymerization before they form thermodynamic tubular structures. The strategy developed in this study should be applicable to naturally and synthetically abundant alkyl chain containing self-assembling systems.

Molecular self-assembly of a tyroservatide-derived octapeptide and hydroxycamptothecin for enhanced therapeutic efficacy

Nanoscale ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 5094-5102
Author(s):  
Jing Liu ◽  
Can Wu ◽  
Guoru Dai ◽  
Feng Feng ◽  
Yuquan Chi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Therapeutic Efficacy ◽  
Self Assembling

A pure l-amino acid-based molecular hydrogel was designed through conjugation of an anticancer tripeptide tyroservatide (YSV) with a self-assembling moiety, which enhanced therapeutic efficacy of both YSV and hydroxycamptothecin in vitro and in vivo.

scholarly journals Analytical kinetic model of native tandem promoters in E. coli

2021 ◽  
Author(s):  
Vatsala Chauhan ◽  
Mohamed Nasurudeen Mohamed Bahrudeen ◽  
Cristina Santos Dias Palma ◽  
Ines S. C. Baptista ◽  
Bilena Lima de Brito Almeida ◽  
...  
Keyword(s):  
Single Cell ◽  
Step Function ◽  
Single Cell Protein ◽  
Linear Functions ◽  
Cell Protein ◽  
Transcription Start Sites ◽  
E Coli ◽  
Wide Range ◽  
Promoter Occupancy

Closely spaced promoters in tandem formation are abundant in bacteria. We investigated the evolutionary conservation, biological functions, and the RNA and single-cell protein expression of genes regulated by tandem promoters in E. coli. We also studied the sequence (distance between transcription start sites 'dTSS', pause sequences, and distances from oriC) and potential influence of the input transcription factors of these promoters. From this, we propose an analytical model of gene expression based on measured expression dynamics, where RNAP-promoter occupancy times and dTSS are the key regulators of transcription interference due to TSS occlusion by RNAP at one of the promoters (when dTSS ≤ 35 bp) and RNAP occupancy of the downstream promoter (when dTSS > 35 bp). Occlusion and downstream promoter occupancy are modeled as linear functions of occupancy time, while the influence of dTSS is implemented by a continuous step function, fit to in vivo data on mean single-cell protein numbers of 30 natural genes controlled by tandem promoters. The best-fitting step is at 35 bp, matching the length of DNA occupied by RNAP in the open complex formation. This model accurately predicts the squared coefficient of variation and skewness of the natural single-cell protein numbers as a function of dTSS. Additional predictions suggest that promoters in tandem formation can cover a wide range of transcription dynamics within realistic intervals of parameter values. By accurately capturing the dynamics of these promoters, this model can be helpful to predict the dynamics of new promoters and contribute to the expansion of the repertoire of expression dynamics available to synthetic genetic constructs.

scholarly journals Peptide Nanomaterials for Drug Delivery Applications

2020 ◽  
Vol 21 (4) ◽  
pp. 401-412 ◽  
Author(s):  
Sreekanth Pentlavalli ◽  
Sophie Coulter ◽  
Garry Laverty
Keyword(s):  
Drug Delivery ◽  
Self Assembly ◽  
Diverse Range ◽  
Drug Molecules ◽  
Sustained Drug Delivery ◽  
Self Assembling ◽  
Wide Range ◽  
Methods Of Synthesis ◽  
Self Assembled

Self-assembled peptides have been shown to form well-defined nanostructures which display outstanding characteristics for many biomedical applications and especially in controlled drug delivery. Such biomaterials are becoming increasingly popular due to routine, standardized methods of synthesis, high biocompatibility, biodegradability and ease of upscale. Moreover, one can modify the structure at the molecular level to form various nanostructures with a wide range of applications in the field of medicine. Through environmental modifications such as changes in pH and ionic strength and the introduction of enzymes or light, it is possible to trigger self-assembly and design a host of different self-assembled nanostructures. The resulting nanostructures include nanotubes, nanofibers, hydrogels and nanovesicles which all display a diverse range of physico-chemical and mechanical properties. Depending on their design, peptide self-assembling nanostructures can be manufactured with improved biocompatibility and in vivo stability and the ability to encapsulate drugs with the capacity for sustained drug delivery. These molecules can act as carriers for drug molecules to ferry cargo intracellularly and respond to stimuli changes for both hydrophilic and hydrophobic drugs. This review explores the types of self-assembling nanostructures, the effects of external stimuli on and the mechanisms behind the assembly process, and applications for such technology in drug delivery.

Self-assembling RATEA16 peptide nanofiber designed for rapid hemostasis

2020 ◽  
Vol 8 (9) ◽  
pp. 1897-1905 ◽  
Author(s):  
Shuda Wei ◽  
Fangping Chen ◽  
Zhen Geng ◽  
Ruihua Cui ◽  
Yujiao Zhao ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Self Assembly ◽  
Solid Phase ◽  
Phase Method ◽  
Self Assembling ◽  
Solid Phase Method ◽  
Assembly Performance

In this study, we synthesized a novel polypeptide material, RATEA16, by the solid phase method, and investigated the secondary structure, self-assembly performance, gelation ability, biocompatibility and hemostatic efficiency in vitro and in vivo.

Hollow Microcapsules Through Layer-by-Layer Self-Assembly of Chitosan/Alginate on E. coli

MRS Advances ◽  
2020 ◽  
Vol 5 (46-47) ◽  
pp. 2401-2407
Author(s):  
Michael Y. Yitayew ◽  
Maryam Tabrizian
Keyword(s):  
Quantum Dots ◽  
Self Assembly ◽  
Layer By Layer ◽  
E Coli ◽  
Fluorescence Measurements ◽  
Transmission Electron ◽  
Imaging Probes ◽  
Delivery Platform ◽  
20 Nm

AbstractHollow microcapsules prepared via layer-by-layer (LbL) self-assembled polyelectrolytes are prevalent biomaterials in the synthesis of biocompatible delivery systems for drugs, imaging probes, and other macromolecules to control biodistribution and lower toxicity in vivo. The use of LbL self-assembly for the synthesis of these capsules provides several benefits including ease of fabrication, abundance in choice of substrates and coating material, as well as application-specific tunability. This study explores the development of hollow microcapsules by LbL assembly of chitosan and alginate onto live E. coli cells, and also provides a proof-of-concept of this capsule as a delivery platform through the encapsulation of quantum dots as a cargo. The study found that robust bilayers of chitosan/alginate can be formed onto the core substrate (E. coli) containing quantum dots as demonstrated with zeta potential analysis. Confocal microscopy was used to verify cell viability and the internalization of quantum dots into the cells as well as confirmation of the coating using fluorescein-labelled chitosan. Furthermore, transmission electron microscopy (TEM) was used to analyse cells coated with four-bilayers and showed a uniform coating morphology with a capsule thickness of 10-20 nm, which increased to 20-50 nm for hollow capsules after cell lysis. Quantum dot retention in the capsules was demonstrated using fluorescence measurements. Overall, the study shows promising results of a novel fabrication method for hollow microcapsules that uses biocompatible polymers and mild core dissolution conditions using cell templates with applications in sustained release of therapeutics and imaging probes.

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