RSC Advances
Biophysics articles published in the last
6 months
Silver nanoparticles alter the dimerization of Aβ42 studied by REMD simulations
The dimerization of the Aβ42 peptide is inhibited by the silver nanoparticle.
RSC Adv., 2024,14, 15112-15119
https://doi.org/10.1039/D4RA02197E
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.
RSC Adv., 2024,14, 14742-14757
https://doi.org/10.1039/D4RA01536C
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.
RSC Adv., 2024,14, 13044-13052
https://doi.org/10.1039/D4RA00738G
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.
RSC Adv., 2024,14, 12864-12872
https://doi.org/10.1039/D4RA00562G
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.
RSC Adv., 2024,14, 11921-11931
https://doi.org/10.1039/D4RA01171F
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.
RSC Adv., 2024,14, 11151-11156
https://doi.org/10.1039/D4RA00959B
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).
RSC Adv., 2024,14, 10608-10637
https://doi.org/10.1039/D4RA01026D
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.
RSC Adv., 2024,14, 8615-8640
https://doi.org/10.1039/D3RA07380G
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.
RSC Adv., 2024,14, 8695-8708
https://doi.org/10.1039/D3RA08869C
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.
RSC Adv., 2024,14, 7383-7413
https://doi.org/10.1039/D4RA00494A
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.
RSC Adv., 2024,14, 6127-6134
https://doi.org/10.1039/D3RA07481A
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.
RSC Adv., 2024,14, 5449-5460
https://doi.org/10.1039/D3RA07746B
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.
RSC Adv., 2024,14, 4492-4502
https://doi.org/10.1039/D3RA08650J
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.
RSC Adv., 2024,14, 4382-4388
https://doi.org/10.1039/D3RA07869H
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.
RSC Adv., 2024,14, 3841-3844
https://doi.org/10.1039/D3RA08718B
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.
RSC Adv., 2024,14, 3525-3535
https://doi.org/10.1039/D3RA07634B
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.
RSC Adv., 2024,14, 2745-2756
https://doi.org/10.1039/D3RA07251G
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.
RSC Adv., 2024,14, 2770-2777
https://doi.org/10.1039/D3RA07107C
Asymmetric Michael addition catalysed by copper–amyloid complexes
Amyloid proteins displaying a copper histidine-brace offer designable scaffolds for efficient and asymmetric chemical reactions.
RSC Adv., 2024,14, 206-210
https://doi.org/10.1039/D3RA07900G
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.
RSC Adv., 2023,13, 36261-36279
https://doi.org/10.1039/D3RA05987A
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.
RSC Adv., 2023,13, 35947-35963
https://doi.org/10.1039/D3RA06476J
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.
RSC Adv., 2023,13, 35493-35499
https://doi.org/10.1039/D3RA06180A
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.
RSC Adv., 2023,13, 34249-34261
https://doi.org/10.1039/D3RA06375E
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.
RSC Adv., 2023,13, 34167-34182
https://doi.org/10.1039/D3RA06030F
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.
RSC Adv., 2023,13, 34107-34121
https://doi.org/10.1039/D3RA06276G
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