A Single-Molecule Strategy to Capture Non-native Intramolecular and Intermolecular Protein Disulfide Bridges

Application of atomic force microscopy in the characterization of fruits and vegetables and associated substances toward improvement in quality, preservation, and processing: nanoscale structure and mechanics perspectives

Fruits and vegetables are essential horticultural crops for humans. The quality of fruits and vegetables is critical in determining their nutritional value and edibility, which are decisive to their commercial value. Besides, it is also important to understand the changes in key substances involved in the preservation and processing of fruits and vegetables. Atomic force microscopy (AFM), a powerful technique for investigating biological surfaces, has been widely used to characterize the quality of fruits and vegetables and the substances involved in their preservation and processing from the perspective of nanoscale structure and mechanics. This review summarizes the applications of AFM to investigate the texture, appearance, and nutrients of fruits and vegetables based on structural imaging and force measurements. Additionally, the review highlights the application of AFM in characterizing the morphological and mechanical properties of nanomaterials involved in preserving and processing fruits and vegetables, including films and coatings for preservation, bioactive compounds for processing purposes, nanofiltration membrane for concentration, and nanoencapsulation for delivery of bioactive compounds. Furthermore, the strengths and weaknesses of AFM for characterizing the quality of fruits and vegetables and the substances involved in their preservation and processing are examined, followed by a discussion on the prospects of AFM in this field.

Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales

The reversible unfolding and refolding of proteins is a regulatory mechanism of tissue elasticity and signalling used by cells to sense and adapt to extracellular and intracellular mechanical forces. However, most of these proteins exhibit low mechanical stability, posing technical challenges to the characterization of their conformational dynamics under force. Here, we detail step-by-step instructions for conducting single-protein nanomechanical experiments using ultra-stable magnetic tweezers, which enable the measurement of the equilibrium conformational dynamics of single proteins under physiologically relevant low forces applied over biologically relevant timescales. We report the basic principles determining the functioning of the magnetic tweezer instrument, review the protein design strategy and the fluid chamber preparation and detail the procedure to acquire and analyze the unfolding and refolding trajectories of individual proteins under force. This technique adds to the toolbox of single-molecule nanomechanical techniques and will be of particular interest to those interested in proteins involved in mechanosensing and mechanotransduction. The procedure takes 4 d to complete, plus an additional 6 d for protein cloning and production, requiring basic expertise in molecular biology, surface chemistry and data analysis.

Quinoa protein Pickering emulsion improves the freeze-thaw stability of myofibrillar protein gel: Maintaining protein composition, structure, conformation and digestibility and slowing down protein oxidation

In this work, the effects of quinoa protein Pickering emulsion (QPPE) on protein oxidation, structure and gastrointestinal digestion property of myofibrillar protein gels (MPGs) after freeze-thaw (F-T) cycles are revealed. SDS-PAGE results indicated that 5.0 %-10.0 % QPPE addition slowed down the protein degradation. Meanwhile, 5.0 %-7.5 % QPPE maintained the stability of the protein secondary and tertiary structure of MPGs after F-T cycles. The sulfhydryl group, disulfide bond and dityrosine content increased with QPPE supplementation. The conformations of disulfide bond changed from g-g-t and t-g-t to g-g-g after F-T cycles, and 5.0 %-7.5 % QPPE stabilized the changes of t-g-t conformation. Furthermore, the increase of dityrosine content after F-T cycles was significantly reduced with 7.5 % QPPE addition, indicating its effect to slow down protein oxidation of MPGs. In addition, MPGs with 5.0 % and 7.5 % QPPE showed noticeably higher zeta potential values than other groups, indicating the enhanced electrostatic repulsion and weakened aggregation caused by F-T damage. This work showed that 7.5 % QPPE improved the F-T stability of MPGs and reduced the protein denaturation and oxidation caused by F-T treatments, exerting no side effect on the digestion property of MPGs. QPPE can be used as a green and effective antifreeze in meat industry.

Molecular interpretation of single-molecule force spectroscopy experiments with computational approaches

Single molecule force-spectroscopy techniques have granted access to unprecedented molecular-scale details about biochemical and biological mechanisms. However, the interpretation of the experimental data is often challenging. Computational and simulation approaches (all-atom steered MD simulations in particular) are key to provide molecular details about the associated mechanisms, to help test different hypotheses and to predict experimental results. In this review, particular recent efforts directed towards the molecular interpretation of single-molecule force spectroscopy experiments on proteins and protein-related systems (often in close collaboration with experimental groups) will be presented. These results will be discussed in the broader context of the field, highlighting the recent achievements and the ongoing challenges for computational biophysicists and biochemists. In particular, I will focus on the input gained from molecular simulations approaches to rationalize the origin of the unfolded protein elasticity and the protein conformational behavior under force, to understand how force denaturation differs from chemical, thermal or shear unfolding, and to unravel the molecular details of unfolding events for a variety of systems. I will also discuss the use of models based on Langevin dynamics on a 1-D free-energy surface to understand the effect of protein segmentation on the work exerted by a force, or, at the other end of the spectrum of computational techniques, how quantum calculations can help to understand the reactivity of disulfide bridges exposed to force.