RSC Advances  

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Biophysics articles published in the last 6 months

26 items - Showing page 1 of 2
Open Access Paper

Silver nanoparticles alter the dimerization of Aβ42 studied by REMD simulations

The dimerization of the Aβ42 peptide is inhibited by the silver nanoparticle.

Graphical abstract: Silver nanoparticles alter the dimerization of Aβ42 studied by REMD simulations
Open Access Paper

Pregnenolone derivatives for the treatment of Alzheimer's disease: synthesis, and in vitro inhibition of amyloid β1–42 peptide aggregation, acetylcholinesterase and carbonic anhydrase-II

Pregnenolone-based derivatives have been synthesized to inhibit the protofibril formation in order to reduce Aβ1–42 production and prevent its aggregation.

Graphical abstract: Pregnenolone derivatives for the treatment of Alzheimer's disease: synthesis, and in vitro inhibition of amyloid β1–42 peptide aggregation, acetylcholinesterase and carbonic anhydrase-II
Open Access Paper

Mechanics of biomimetic free-standing lipid membranes: insights into the elasticity of complex lipid compositions

In this study, we prepare pore-spanning membranes that mimic the composition of plasma membranes and perform force spectroscopy indentation measurements to unravel mechanistic insights depending on lipid composition.

Graphical abstract: Mechanics of biomimetic free-standing lipid membranes: insights into the elasticity of complex lipid compositions
Open Access Paper

Rational design of a lysosome-targeted fluorescent probe for monitoring the generation of hydroxyl radicals in ferroptosis pathways

A novel hydrocyanine-based turn-on fluorescence probe HCy-Lyso, with excellent lysosome-targeting ability and ˙OH-responsive efficiency, has been applied for monitoring the variation in lysosomal ˙OH levels during ferroptosis.

Graphical abstract: Rational design of a lysosome-targeted fluorescent probe for monitoring the generation of hydroxyl radicals in ferroptosis pathways
Open Access Paper

The inhibition of fibril formation of lysozyme by sucrose and trehalose

WAXS displays a significant difference due to the presence of amyloid fibrils in the absence of sugar.

Graphical abstract: The inhibition of fibril formation of lysozyme by sucrose and trehalose
Open Access Paper

A novel fluorescence probe for simultaneous detection of mitochondrial viscosity in hepatic ischemia reperfusion injury models

A versatile probe with mitochondria targeting, PN, for detection of viscosity alteration in HIRI mouse model was fabricated. PN had high sensitivity and selectivity, and with a large Stokes shift (∼190 nm) for viscosity. PN is expected to be used for early diagnosis and treatment assessment of HIRI disease, and also provides diagnostic basis for other related diseases.

Graphical abstract: A novel fluorescence probe for simultaneous detection of mitochondrial viscosity in hepatic ischemia reperfusion injury models
Open Access Review Article

Cancer cell membrane-coated nanoparticles: a promising anti-tumor bionic platform

This review summarized the function of cancer cell membranes and comprehensively discussed the preparation of cancer cell membrane-coated nanoparticles (CCM-NPs) and their application in anti-tumor therapy. The graphical abstract figure was drawn by Figdraw (https://www.figdraw.com).

Graphical abstract: Cancer cell membrane-coated nanoparticles: a promising anti-tumor bionic platform
From the themed collection: 2024 Reviews in RSC Advances
Open Access Paper

Analysing the effect caused by increasing the molecular volume in M1-AChR receptor agonists and antagonists: a structural and computational study

Two QSAR models which correlates the interaction energy and structural features of agonists and antagonists of M1-AChR.

Graphical abstract: Analysing the effect caused by increasing the molecular volume in M1-AChR receptor agonists and antagonists: a structural and computational study
Open Access Paper

Silica-coated LiYF4:Yb3+, Tm3+ upconverting nanoparticles are non-toxic and activate minor stress responses in mammalian cells

Silica-coated lanthanide-doped upconverting nanoparticles (UCNPs) are internalized by mammalian cells. The bipyramidal UCNPs are non-toxic and elicit minor stress responses in a cell type-dependent fashion.

Graphical abstract: Silica-coated LiYF4:Yb3+, Tm3+ upconverting nanoparticles are non-toxic and activate minor stress responses in mammalian cells
Open Access Review Article

Clicking in harmony: exploring the bio-orthogonal overlap in click chemistry

The fundamentals of bio-orthogonal click chemistry are investigated, while exploring mechanistic intricacies, demonstrating the adaptability and promise of this methodology.

Graphical abstract: Clicking in harmony: exploring the bio-orthogonal overlap in click chemistry
From the themed collection: 2024 Reviews in RSC Advances
Open Access Paper

Lipid nanodiscs spontaneously formed by an amphiphilic polymethacrylate derivative as an efficient nanocarrier for molecular delivery to intact cells

Lipid nanodisc is a promising nano-carrier for molecular delivery that efficiently delivers hydrophobic molecules to intact cells.

Graphical abstract: Lipid nanodiscs spontaneously formed by an amphiphilic polymethacrylate derivative as an efficient nanocarrier for molecular delivery to intact cells
Open Access Paper

Single molecule technique unveils the role of electrostatic interactions in ssDNA–gp32 molecular complex stability

A single-molecule electrophysiology assay was employed using an α-HL nanopore to test the stability of ssDNA and gp32 SSB–protein, in different salt conditions. Low salt and the presence of Zn2+ increases ssDNA–gp32 complex stability.

Graphical abstract: Single molecule technique unveils the role of electrostatic interactions in ssDNA–gp32 molecular complex stability
Open Access Paper

Exploring protein–ligand binding affinity prediction with electron density-based geometric deep learning

A deep learning approach centered on electron density is suggested for predicting the binding affility between proteins and ligands. The approach is thoroughly assessed using various pertinent benchmarks.

Graphical abstract: Exploring protein–ligand binding affinity prediction with electron density-based geometric deep learning
Open Access Paper

De novo designed aliphatic and aromatic peptides assemble into amyloid-like cytotoxic supramolecular nanofibrils

De novo designed aliphatic and aromatic peptides form biomimetic supramolecular nanofibrils illuminating the intricacies of the pathogenic amyloid assemblies.

Graphical abstract: De novo designed aliphatic and aromatic peptides assemble into amyloid-like cytotoxic supramolecular nanofibrils
Open Access Paper

Fluorescence photobleaching and recovery of fluorescein sodium in carbomer film

The recovery rate of the fluorescein sodium-loaded carbomer film following a prolonged bleaching process demonstrates a conspicuous deceleration at elevated concentrations.

Graphical abstract: Fluorescence photobleaching and recovery of fluorescein sodium in carbomer film
Open Access Paper

Functionalising silk hydrogels with hetero- and homotypic nanoparticles

Despite many reports detailing silk hydrogels, the development of composite silk hydrogels with homotypic and heterotypic silk nanoparticles and their impact on material mechanics and biology have remained largely unexplored.

Graphical abstract: Functionalising silk hydrogels with hetero- and homotypic nanoparticles
Open Access Paper

LEGO-lipophosphonoxins: length of hydrophobic module affects permeabilizing activity in target membranes of different phospholipid composition

We developed modular antimicrobial compounds capable of inducing cytoplasmic membrane perforation. This structure–activity relationship study focuses on the role of the length of their alkenyl hydrophobic module.

Graphical abstract: LEGO-lipophosphonoxins: length of hydrophobic module affects permeabilizing activity in target membranes of different phospholipid composition
Open Access Paper

Insights into colistin-mediated fluorescence labelling of bacterial LPS

Indirect labelling of the lipopolysaccharide of Gram-negative bacteria by fluorescence turn-on signalling and computational calculations.

Graphical abstract: Insights into colistin-mediated fluorescence labelling of bacterial LPS
Open Access Paper

Asymmetric Michael addition catalysed by copper–amyloid complexes

Amyloid proteins displaying a copper histidine-brace offer designable scaffolds for efficient and asymmetric chemical reactions.

Graphical abstract: Asymmetric Michael addition catalysed by copper–amyloid complexes
Open Access Paper

Elucidating arsenic-bound proteins in the protein data bank: data mining and amino acid cross-validation through Raman spectroscopy

Decoding arsenic's impact: data mining protein structures in the protein data bank through amino acid mapping.

Graphical abstract: Elucidating arsenic-bound proteins in the protein data bank: data mining and amino acid cross-validation through Raman spectroscopy
Open Access Review Article

Stabilization challenges and aggregation in protein-based therapeutics in the pharmaceutical industry

In this review, we have discussed some features of protein aggregation during production, formulation and storage as well as stabilization strategies in protein engineering and computational methods to prevent aggregation.

Graphical abstract: Stabilization challenges and aggregation in protein-based therapeutics in the pharmaceutical industry
From the themed collection: 2023 Reviews in RSC Advances
Open Access Paper

In silico description of the adsorption of cell signaling pathway proteins ovalbumin, glutathione, LC3, TLR4, ASC PYCARD, PI3K and NF-Kβ on 7.0 nm gold nanoparticles: obtaining their Lennard-Jones-like potentials through docking and molecular mechanics

Classical interaction energies as a function of the distance between the AuNP and proteins have Lennard-Jones-like potentials.

Graphical abstract: In silico description of the adsorption of cell signaling pathway proteins ovalbumin, glutathione, LC3, TLR4, ASC PYCARD, PI3K and NF-Kβ on 7.0 nm gold nanoparticles: obtaining their Lennard-Jones-like potentials through docking and molecular mechanics
Open Access Paper

Unsupervised deep learning for molecular dynamics simulations: a novel analysis of protein–ligand interactions in SARS-CoV-2 Mpro

Using SARS-CoV-2 Mpro as a case study, Wasserstein distance and dimension reduction are applied to the analysis of MD data of flexible complexes. The resulting embedding map correlates ligand-induced conformational differences and binding affinity.

Graphical abstract: Unsupervised deep learning for molecular dynamics simulations: a novel analysis of protein–ligand interactions in SARS-CoV-2 Mpro
Open Access Paper

Modeling selectivity of antimicrobial peptides: how it depends on the presence of host cells and cell density

Antimicrobial peptides (AMPs), naturally-occurring peptide antibiotics, are known to attack bacteria selectively over the host cells.

Graphical abstract: Modeling selectivity of antimicrobial peptides: how it depends on the presence of host cells and cell density
Open Access Paper

Binding interactions of hydrophobically-modified flavonols with β-glucosidase: fluorescence spectroscopy and molecular modelling study

Binding interactions of fluorescent flavonols with the β-glucosidase enzyme are studied using fluorescence spectroscopy in combination with molecular docking and molecular dynamics simulations.

Graphical abstract: Binding interactions of hydrophobically-modified flavonols with β-glucosidase: fluorescence spectroscopy and molecular modelling study
26 items - Showing page 1 of 2

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