Review on the applications of atomic force microscopy imaging in proteins

Visualization of Single Polymer Chains with Atomic Force Microscopy: A Review

Single-chain atomic force microscopy has emerged as a powerful and highly specialized technique, enabling the direct observation and analysis of various isolated polymer chains at the nano and micro scales. This work reviews the most relevant experimental cases utilizing this technique, aiming to shine light on the understanding of the physical appearance of freshly synthesized polymer chains, reveal unique chain conformations and related transitions, decipher the processes of polymer crystallization and self-assembly, study the mechanisms of polymer adsorption and desorption, observe the formation of single-chain nanoparticles, and explore many other related phenomena.

Significant reduction of cell invasiveness in nanoneedle insertion into a living cell with an electron-beam-deposited probe: impacts of probe geometry, speed and vibration

Intracellular probing of living cells using atomic force microscopy (AFM) has advanced significantly, but it requires specially designed nanoprobes to achieve precision and minimize damage. The development of focused ion beam (FIB)-milled nanoprobes enabled this progress, allowing researchers to fabricate long, sharp probes that penetrate cell membranes with reduced force. Although these FIB-milled probes have been crucial in accessing the intracellular environment, they still cause considerable membrane deformation, limiting their effectiveness in detailed measurements. In response, we developed electron beam deposited (EBD) carbon nanoprobes with varying diameters to further reduce penetration force and resulting cell disturbance. Our study reveals that, for probes of the same diameter, EBD carbon nanoprobes inflict significantly less membrane deformation than FIB-milled ones, due to their sharper tip apex. Additionally, reducing the diameter of the EBD nanoprobes further decreased the penetration force and minimized cell disturbance. We also observed that, at similar speeds, EBD nanoprobes consistently caused less damage, emphasizing the importance of both tip geometry and penetration speed in reducing the impact on cells. Oscillating the cantilever during penetration further reduced friction with the membrane, significantly reducing damage. These findings advance the precision and gentleness of intracellular AFM measurements, offering improved methods for studying cellular mechanics while preserving cell viability.

Chemical, structural and antioxidant properties of melanoidins in fish sauce

BACKGROUND

Melanoidins, as a functional component, exhibit antioxidant properties. However, the antioxidant mechanism of melanoidins in fish sauce remains poorly understood. The present study focused on the structural characteristics, microstructure and antioxidant activity of melanoidin substances in fish sauce.

RESULTS

Ultrafiltration and color difference analysis were utilized to confirm the main molecular weight composition of melanoidins. The ultrafiltration component > 10 kDa in fish sauce exhibited the darkest and reddest color, along with the highest content of melanoidins (699.5 mg g-1). The spectral characteristics were consistent with typical melanoidins. Gas chromatography-tandem mass spectrometry and Fourier transform infrared spectroscopy analyses revealed that the melanoidins contained a significant number of oxygen-containing groups, amino compounds, carbohydrates, aromatic compounds and carbonyl compounds (CO), pyrrole (CN), among others. In total, 129 alkanes, 71 esters, nine olefins and two alkynes were identified. The melanoidins (> 10 kDa component) had the strongest antioxidant activity, including a reducing power of 0.8, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical scavenging activity of 67.7% and 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity of 92.4%. Additionally, the melanoidins (> 10 kDa component) had the highest total phenolic content at 48.2 μg gallic acid equivalents mL-1.

CONCLUSION

Melanoidins are important factors affecting the antioxidant activity of fish sauce. There were differences in the structural properties of melanoidin fractions with different molecular weights. © 2024 Society of Chemical Industry.

pH-induced changes in IgE molecules measured by atomic force microscopy

The environment surrounding proteins is tightly linked to its dynamics, which can significantly influence the conformation of proteins. This study focused on the effect of pH conditions on the ultrastructure of Immunoglobulin E (IgE) molecules. Herein, the morphology, height, and area of IgE molecules incubated at different pH were imaged by atomic force microscopy (AFM), and the law of IgE changes induced by pH value was explored. The experiment results indicated that the morphology, height and area of IgE molecules are pH dependent and highly sensitive. In particular, IgE molecules were more likely to present small-sized ellipsoids under acidic conditions, while IgE molecules tend to aggregate into large-sized flower-like structures under alkaline conditions. In addition, it was found that the height of IgE first decreased and then increased with the increase of pH, while the area of IgE increased with the increase of pH. This work provides valuable information for further study of IgE, and the methodological approach used in this study is expected to developed into AFM to investigate the changes of IgE molecules mediated by other physical and chemical factors. RESEARCH HIGHLIGHTS: The ultrastructure of IgE molecules is pH dependent and highly sensitive. IgE molecules were tend to present small-sized ellipsoids under acidic pH. Alkaline pH drives IgE self-assembly into flower-like aggregates.

Exploration on antifreeze potential of thawed drip enzymatic hydrolysates on myofibrillar proteins in pork patties during freeze-thaw cycles

This study explored using small molecular weight hydrolysates from enzymolyzed thawed drip as cryoprotectants to preserve myofibrillar protein quality in pork patties during freeze-thaw cycles. Hydrolysates were added at 0.36 %, 0.72 %, and 1.4 % concentrations, compared to a control with deionized water and a positive control with sorbitol and sucrose. Results indicated that thawed drip hydrolysates significantly reduced thawing loss and cooking loss. Moreover, the color deterioration during the 3rd and 6th freeze-thaw cycles was delayed. Myofibrillar protein denaturation and oxidation in the experimental groups were inhibited, shown by decreased surface hydrophobicity, reduced carbonyl groups and protein surface roughness, and increased free sulfhydryl groups, α-helix content, and protein particle height. The highest hydrolysate concentration (1.4 %) provided the most benefits, performing comparably to the positive control. Correlation analysis confirmed that hydrolysates enhanced both myofibrillar protein and pork quality, offering a promising approach to improve meat resilience against freeze-thaw conditions.

Exploring the interaction mechanism of chlorogenic acid and myoglobin: Insights from structure and molecular dynamics simulation

This study focused on non-covalent complex of myoglobin-chlorogenic acid (Mb-CA) and the changes in conformation, oxidation, and microstructure induced by varying concentrations of CA (10-40 μmol/g Mb). Employing molecular docking and dynamics simulations, further insights into the interaction between Mb and CA were obtained. The findings revealed that different CA concentrations enhanced Mb's thermal stability, while diminishing particle size, solubility, and relative content of metmyoglobin (MetMb%). The optimal interaction occurred at 40 μmol/g Mb. Furthermore, CA exhibited static quenching of Mb, with thermodynamic analysis confirming a 1:1 complex formation. These insights deepen our understanding of interaction between Mb and CA, providing valuable clarity.

L-histidine-assisted ultrasound improved physicochemical properties of myofibrillar proteins under reduced-salt condition - Investigation of underlying mechanisms

The effects of the L-hisdine (L-His)-assisted ultrasound on physicochemical characteristics and conformation of myofibrillar protein (MP) under reduced-salt condition were investigated using spectroscopic analysis, and the binding mechanism between L-His and MP was further elucidated through molecular docking and molecular dynamics (MD) simulations. UV second derivative spectra and intrinsic Try fluorescence spectra revealed that L-His formed a complex with MP and altered the microenvironment of MP. After L-His-assisted ultrasound treatment, MP showed smaller particle size, higher solubility, and more uniform atomic force microscopy image due to the decrease of α-helix content and the subsequent increase in zeta potential, active sulfhydryl content, and surface hydrophobicity. Molecular docking and MD simulations demonstrated the optimal docking pose (minimum binding affinity of -6.78 kcal/mol) and revealed hydrophobic interactions and hydrogen bonds as the main interaction forces between L-His and MP, with several residues (ILE-464, ILE-480, THR-483, ASN-484, GLY-466, ASP-463, PHE-246) identified as binding sites.

Changes in the structure and hydration properties of high-temperature peanut protein induced by cold plasma oxidation

To improve the hydration properties of high-temperature pressed peanut protein isolate (HPPI), we investigated the effect of cold plasma (CP) oxidation on functional and structural properties. Compared to HPPI, the hydrated molecules number and the surface contact angle were significantly decreased at 70 W, from 77.2 × 109 to 17.7 × 109 and from 85.74° to 57.81°, respectively. The reduction of the sulfhydryl content and the increase of the disulfide bond and di-tyrosine content indicated that the structural transformation was affected by the oxidation effect. In terms of structural changes, a stretched tertiary structure, ordered secondary structure, and rough apparent structure were observed after CP treatment. Additionally, the enhancement of surface free energy and group content such as -COOH, -CO and -OH on the surface of HPPI contributed to the formation of hydrated crystal structures. In general, the oxidation effect of CP effectively improved the hydration properties of HPPI and broaden its application field.

Effects of divalent mercury on myosin structure of large yellow croaker and its binding mechanism: Multi-spectroscopies and molecular docking

Heavy metals have long biological half-lives and are therefore a major threat to aquatic organisms, especially fish. Divalent mercury (Hg(II)) is an important form from a toxicological viewpoint. In this paper, we studied the interaction mechanism between large yellow croaker myosin and Hg(II) by multi-spectroscopies and molecular docking. Hg(II) had a positive effect on improving the elasticity of myosin gel, and the constant increase of charge would destroy the gel. Hg(II) caused myosin to aggregate, and the protein's apparent structure rapidly increased in length. The content of α-helix obviously decreased, β-turns and β-sheet increased. The myosin and Hg(II) quenching type was static quenching. Thermodynamic analysis suggested hydrogen bonding and van der Waals forces were the main forces for the combination. The molecular docking further confirmed the mechanism of action. This study provides a theoretical guidance for the preventions and control of marine heavy metals.