Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

α-Helical Antimicrobial Peptide Encapsulation and Release from Boron Nitride Nanotubes: A Computational Study.

ABSTRACT:

Introduction

Antimicrobial peptides are potential therapeutics as anti-bacteria, anti-viruses, anti-fungi, or anticancers. However, they suffer from a short half-life and drug resistance which limit their long-term clinical usage.

Methods

Herein, we captured the encapsulation of antimicrobial peptide HA-FD-13 into boron nitride nanotube (BNNT) (20,20) and its release due to subsequent insertion of BNNT (14,14) with molecular dynamics simulation.

Results

The peptide-BNNT (20,20) van der Waals (vdW) interaction energy decreased to -270 kcal·mol^-1 at the end of the simulation (15 ns). However, during the period of 0.2-1.8 ns, when half of the peptide was inside the nanotube, the encapsulation was paused due to an energy barrier in the vicinity of BNNT and subsequently the external intervention, such that the self-adjustment of the peptide allowed full insertion. The free energy of the encapsulation process was -200.12 kcal·mol^-1, suggesting that the insertion procedure occurred spontaneously.

Discussion

Once the BNNT (14,14) entered into the BNNT (20,20), the peptide was completely released after 83.8 ps. This revealed that the vdW interaction between the BNNT (14,14) and BNNT (20,20) was stronger than between BNNT (20,20) and the peptide; therefore, the BNNT (14,14) could act as a piston pushing the peptide outside the BNNT (20,20). Moreover, the sudden drop in the vdW energy between nanotubes to the value of the -1300 Kcal·mol^-1 confirmed the self-insertion of the BNNT (14,14) into the BNNT (20,20) and correspondingly the release of the peptide.

SUBMITTER: Zarghami Dehaghani M

PROVIDER: S-EPMC8238539 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Host-Guest Chemistry in Boron Nitride Nanotubes: Interactions with Polyoxometalates and Mechanism of Encapsulation.

Project description:Boron nitride nanotubes (BNNTs) are an emerging class of molecular container offering new functionalities and possibilities for studying molecules at the nanoscale. Herein, BNNTs are demonstrated as highly effective nanocontainers for polyoxometalate (POM) molecules. The encapsulation of POMs within BNNTs occurs spontaneously at room temperature from an aqueous solution, leading to the self-assembly of a POM@BNNT host-guest system. Analysis of the interactions between the host-nanotube and guest-molecule indicate that Lewis acid-base interactions between W═O groups of the POM (base) and B-atoms of the BNNT lattice (acid) likely play a major role in driving POM encapsulation, with photoactivated electron transfer from BNNTs to POMs in solution also contributing to the process. The transparent nature of the BNNT nanocontainer allows extensive investigation of the guest-molecules by photoluminescence, Raman, UV-vis absorption, and EPR spectroscopies. These studies revealed considerable energy and electron transfer processes between BNNTs and POMs, likely mediated via defect energy states of the BNNTs and resulting in the quenching of BNNT photoluminescence at room temperature, the emergence of new photoluminescence emissions at cryogenic temperatures (<100 K), a photochromic response, and paramagnetic signals from guest-POMs. These phenomena offer a fresh perspective on host-guest interactions at the nanoscale and open pathways for harvesting the functional properties of these hybrid systems.

| S-EPMC9853852 | biostudies-literature

Theoretical Encapsulation of Fluorouracil (5-FU) Anti-Cancer Chemotherapy Drug into Carbon Nanotubes (CNT) and Boron Nitride Nanotubes (BNNT).

Project description:Chemotherapy with anti-cancer drugs is considered the most common approach for killing cancer cells in the human body. However, some barriers such as toxicity and side effects would limit its usage. In this regard, nano-based drug delivery systems have emerged as cost-effective and efficient for sustained and targeted drug delivery. Nanotubes such as carbon nanotubes (CNT) and boron nitride nanotubes (BNNT) are promising nanocarriers that provide the cargo with a large inner volume for encapsulation. However, understanding the insertion process of the anti-cancer drugs into the nanotubes and demonstrating drug-nanotube interactions starts with theoretical analysis. First, interactions parameters of the atoms of 5-FU were quantified from the DREIDING force field. Second, the storage capacity of BNNT (8,8) was simulated to count the number of drugs 5-FU encapsulated inside the cavity of the nanotubes. In terms of the encapsulation process of the one drug 5-FU into nanotubes, it was clarified that the drug 5-FU was more rapidly adsorbed into the cavity of the BNNT compared with the CNT due to the higher van der Waals (vdW) interaction energy between the drug and the BNNT. The obtained values of free energy confirmed that the encapsulation process of the drug inside the CNT and BNNT occurred spontaneously with the free energies of -14 and -25 kcal·mol-1, respectively. However, the lower value of the free energy in the system containing the BNNT unraveled more stability of the encapsulated drug inside the cavity of the BNNT comparing the system having CNT. The encapsulation of Fluorouracil (5-FU) anti-cancer chemotherapy drug (commercial name: Adrucil®) into CNT (8,8) and BNNT (8,8) with the length of 20 Å in an aqueous solution was discussed herein applying molecular dynamics (MD) simulation.

| S-EPMC8398462 | biostudies-literature

Boron Nitride Nanotube as an Antimicrobial Peptide Carrier: A Theoretical Insight.

Project description:IntroductionNanotube-based drug delivery systems have received considerable attention because of their large internal volume to encapsulate the drug and the ability to penetrate tissues, cells, and bacteria. In this regard, understanding the interaction between the drug and the nanotube to evaluate the encapsulation behavior of the drug in the nanotube is of crucial importance.MethodsIn this work, the encapsulation process of the cationic antimicrobial peptide named cRW3 in the biocompatible boron nitride nanotube (BNNT) was investigated under the Canonical ensemble (NVT) by molecular dynamics (MD) simulation.ResultsThe peptide was absorbed into the BNNT by van der Waals (vdW) interaction between cRW3 and the BNNT, in which the vdW interaction decreased during the simulation process and reached the value of -142.7 kcal·mol-1 at 4 ns.DiscussionThe increase in the potential mean force profile of the encapsulated peptide during the pulling process of cRW3 out of the nanotube showed that its insertion into the BNNT occurred spontaneously and that the inserted peptide had the desired stability. The energy barrier at the entrance of the BNNT caused a pause of 0.45 ns when half of the peptide was inside the BNNT during the encapsulation process. Therefore, during this period, the peptide experienced the weakest movement and the smallest conformational changes.

| S-EPMC7939490 | biostudies-literature

Rebar graphene from functionalized boron nitride nanotubes.

Project description:The synthesis of rebar graphene on Cu substrates is described using functionalized boron nitride nanotubes (BNNTs) that were annealed or subjected to chemical vapor deposition (CVD) growth of graphene. Characterization shows that the BNNTs partially unzip and form a reinforcing bar (rebar) network within the graphene layer that enhances the mechanical strength through covalent bonds. The rebar graphene is transferrable to other substrates without polymer assistance. The optical transmittance and conductivity of the hybrid rebar graphene film was tested, and a field effect transistor was fabricated to explore its electrical properties. This method of synthesizing 2D hybrid graphene/BN structures should enable the hybridization of various 1D nanotube and 2D layered structures with enhanced mechanical properties.

| S-EPMC4310641 | biostudies-literature

Achieving Boron-Carbon-Nitrogen Heterostructures by Collision Fusion of Carbon Nanotubes and Boron Nitride Nanotubes.

Project description:Heterostructures may exhibit completely new physical properties that may be otherwise absent in their individual component materials. However, how to precisely grow or assemble desired complex heterostructures is still a significant challenge. In this work, the collision dynamics of a carbon nanotube and a boron nitride nanotube under different collision modes were investigated using the self-consistent-charge density-functional tight-binding molecular dynamics method. The energetic stability and electronic structures of the heterostructure after collision were calculated using the first-principles calculations. Five main collision outcomes are observed, that is, two nanotubes can (1) bounce back, (2) connect, (3) fuse into a defect-free BCN heteronanotube with a larger diameter, (4) form a heteronanoribbon of graphene and hexagonal boron nitride and (5) create serious damage after collision. It was found that both the BCN single-wall nanotube and the heteronanoribbon created by collision are the direct band-gap semiconductors with the band gaps of 0.808 eV and 0.544 eV, respectively. These results indicate that collision fusion is a viable method to create various complex heterostructures with new physical properties.

| S-EPMC10254723 | biostudies-literature

Dynamics of Antimicrobial Peptide Encapsulation in Carbon Nanotubes: The Role of Hydroxylation.

Project description:IntroductionCarbon nanotubes (CNTs) have been widely employed as biomolecule carriers, but there is a need for further functionalization to broaden their therapeutic application in aqueous environments. A few reports have unraveled biomolecule-CNT interactions as a measure of response of the nanocarrier to drug-encapsulation dynamics.MethodsHerein, the dynamics of encapsulation of the antimicrobial peptide HA-FD-13 (accession code 2L24) into CNTs and hydroxylated CNTs (HCNTs) is discussed.ResultsThe van der Waals (vdW) interaction energy of CNT-peptide and HCNT-peptide complexes decreased, reaching -110.6 and -176.8 kcal.Mol-1, respectively, once encapsulation of the peptide inside the CNTs had been completed within 15 ns. The free energy of the two systems decreased to -43.91 and -69.2 kcal.Mol-1 in the same order.DiscussionThe peptide was encased in the HCNTs comparatively more rapidly, due to the presence of both electrostatic and vdW interactions between the peptide and HCNTs. However, the peptide remained encapsulated throughout the vdW interaction in both systems. The negative values of the free energy of the two systems showed that the encapsulation process had occurred spontaneously. Of note, the lower free energy in the HCNT system suggested more stable peptide encapsulation.

| S-EPMC8765279 | biostudies-literature

Chemical affinity and dispersibility of boron nitride nanotubes.

Project description:Boron nitride nanotubes (BNNTs) are electrically insulating nanoparticles that display highly competitive elastic modulus and thermal conductivity. Long presented as potential fillers for nanocomposite applications, their poor dispersibility in most commodity polymers has, however, limited their spread. In this work, the chemical affinity of purified BNNTs, measured in terms of Hansen solubility parameters (HSP), were obtained through sedimentation tests in a wide set of organic solvents, taking into account relative sedimentation time. The parameters obtained were {δ d; δ p; δ h} = {16.8; 10.7; 14.7} ± {0.3; 0.9; 0.3} MPa1/2, with a Hildebrand parameter, δ t = 24.7 MPa1/2 and a sphere radius of 5.4 MPa1/2. The solubility parameters were determined considering complete dispersion of the purified nanomaterial, as well as the viscosity and density of the host solvent. These factors, combined with the high purity of the BNNTs, are crucial to minimize the uncertainty of the HSP characterization. Such refined values provide necessary insights both to optimize the solvent casting of unmodified BNNTs, and to orient the surface modification efforts that would be needed to integrate these nanomaterials into a wider range of host matrices.

| S-EPMC9419523 | biostudies-literature

Purification of Boron Nitride Nanotubes Enhances Biological Application Properties.

Project description:Commercially available boron nitride nanotubes (BNNTs) and their purified form (pBNNTs) were dispersed in aqueous solutions with various dispersants, and their cytotoxicity and drug encapsulation capacity were monitored. Our data suggest that pBNNTs showed an average increase in dispersibility of 37.3% in aqueous solution in the presence of 10 different dispersants. In addition, 100 ?g of pBNNTs induced an average decrease in cytotoxicity of 27.4% compared to same amount of BNNTs in normal cell lines. The same amount of pBNNTs can encapsulate 10.4-fold more drug (camptothecin) compared to BNNTs. These data suggest that the purification of BNNTs improves several of their properties, which can be applied to biological experiments and are thus essential in the biological application of BNNTs.

| S-EPMC7073224 | biostudies-literature

Surfactant-assisted individualization and dispersion of boron nitride nanotubes.

Project description:Boron nitride nanotubes (BNNTs) belong to a novel class of material with useful thermal, electronic and optical properties. However, the study and the development of applications of this material requires the formation of stable dispersions of individual BNNTs in water. Here we address the dispersion of BNNT material in water using surfactants with varying properties. The surfactants were compared based on the quantity of BNNTs dispersed and the quality of the dispersions, as visualized by AFM and cryo-TEM. All surfactants produce dispersions of individualized or small bundles of BNNTs. Of the surfactants tested, high molecular weight, nonionic surfactants suspend the most BNNTs, while ionic surfactants remove the most h-BN impurities. The surfactant dispersions were further characterized by ensemble measurements, such as UV absorption and photoluminescence, dynamic light scattering (DLS), and zeta potential to investigate dispersion stability and quality. These techniques provide a facile strategy for testing future BNNT dispersions. The results of this study reveal that BNNT dispersions in aqueous solution can be tuned to fit a specific application through surfactant selection.

| S-EPMC9473271 | biostudies-literature

Dynamic thin film mediated slicing of boron nitride nanotubes.

Project description:A method has been developed to slice boron nitride nanotubes BNNTs under continuous flow in a vortex fluidic device (VFD), along with a method to partially purify the as received BNNT containing material. The latter involves heating the BNNTs to 600 °C followed by dispersing in a 1 : 3 isopropyl alcohol (IPA) and water mixture at 100 °C. The VFD mediated slicing of the BNNTs comprises irradiating the rapidly rotating glass tube (20 mm OD) with a pulsed Nd:YAG laser. Systematically exploring the operating parameter space of the VFD established slicing of ca. 200 μm long purified BNNTs down to 340 nm to 400 nm, in ca. 53% yield, in a 1 : 1 mixture of IPA and water, in the absence of reagents/harsh chemicals, at a flow rate of 0.45 mL min-1, a concentration of 0.1 mg mL-1 BNNTs and an 8.5k rpm rotational speed, with the pulsed laser operating at 1064 nm and 250 mJ per pulse.

| S-EPMC9417105 | 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