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BioRxiv : the Preprint Server For... Jun 2024Folding intermediates mediate both protein folding and the misfolding and aggregation observed in human diseases, including amyotrophic lateral sclerosis (ALS), and are...
Folding intermediates mediate both protein folding and the misfolding and aggregation observed in human diseases, including amyotrophic lateral sclerosis (ALS), and are prime targets for therapeutic interventions. In this study, we identified the core nucleus of structure for a folding intermediate in the second RNA recognition motif (RRM2) of the ALS-linked RNA-binding protein, TDP-43, using a combination of experimental and computational approaches. Urea equilibrium unfolding studies revealed that the RRM2 intermediate state consists of collapsed residual secondary structure localized to the N-terminal half of RRM2, while the C-terminus is largely disordered. Steered molecular dynamics simulations and mutagenesis studies yielded key stabilizing hydrophobic contacts that, when mutated to alanine, severely disrupt the overall fold of RRM2. In combination, these findings suggest a role for this RRM intermediate in normal TDP-43 function as well as serving as a template for misfolding and aggregation through the low stability and non-native secondary structure.
PubMed: 38915526
DOI: 10.1101/2024.06.12.598648 -
Molecular Biology and Evolution Jun 2024Natural proteins are frequently marginally stable, and an increase in environmental temperature can easily lead to unfolding. As a result, protein engineering to improve...
Natural proteins are frequently marginally stable, and an increase in environmental temperature can easily lead to unfolding. As a result, protein engineering to improve protein stability is an area of intensive research. Nonetheless, since there is usually a high degree of structural homology between proteins from thermophilic organisms and their mesophilic counterparts, the identification of structural determinants for thermo-adaptation is challenging. Moreover, in many cases, it has become clear that the success of stabilization strategies is often dependent on the evolutionary history of a protein family. In the last few years, the use of ancestral sequence reconstruction (ASR) as a tool for elucidation of the evolutionary history of functional traits of a protein family have gained strength. Here, we used ASR to trace the evolutionary pathways between mesophilic and thermophilic kinases that participate in the biosynthetic pathway of vitamin B1 in bacteria. By combining biophysics approaches, X-ray crystallography, and molecular dynamic simulations, we found that the thermal stability of these enzymes correlate with their kinetic stability, where the highest thermal/kinetic stability is given by an increase in small hydrophobic amino acids that allow a higher number of interatomic hydrophobic contacts, making this type of interaction the main support for stability in this protein architecture. The results highlight the potential benefits of using ASR to explore the evolutionary history of protein sequence and structure to identify traits responsible for the kinetic and thermal stability of any protein architecture.
PubMed: 38913681
DOI: 10.1093/molbev/msae127 -
International Journal of Pharmaceutics Jun 2024The effect of three commonly used surfactants, poloxamer 188 (P188), polysorbate 20 and 80 (PS20 and PS80), on the stability of a model protein, lactate dehydrogenase...
The effect of three commonly used surfactants, poloxamer 188 (P188), polysorbate 20 and 80 (PS20 and PS80), on the stability of a model protein, lactate dehydrogenase (LDH), was compared in aqueous solutions. In the absence of a surfactant, protein solution revealed a gradual decrease in surface tension as a function of time. The addition of surfactant resulted in a rapid decrease in the surface tension. This suggested that the surface behavior was dictated by the surfactant. PS20 and PS80 were more effective than P188 in preventing LDH adsorption on the solution surface. The advantage of polysorbates over P188 was also evident from the higher LDH tetramer recovery after shaking (room temperature, 30 h), especially when the surfactants were used at concentrations ≤ 0.01 % w/v. However, PS20 and PS80 accelerated protein unfolding during quiescent storage at 40 °C. Based on circular dichroism results, polysorbates perturbed the tertiary structure of LDH but not the secondary structure, while P188 did not impact the protein structure and stability. Polysorbates were more effective in stabilizing LDH against mechanical stress (shaking), but their adverse effects on protein conformational stability need to be carefully evaluated.
PubMed: 38909927
DOI: 10.1016/j.ijpharm.2024.124374 -
Biochimica Et Biophysica Acta.... Jun 2024Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically... (Review)
Review
Iron‑sulfur (FeS) clusters are inorganic protein cofactors that perform essential functions in many physiological processes. Spectroscopic techniques have historically been used to elucidate details of FeS cluster type, their assembly and transfer, and changes in redox and ligand binding properties. Structural probes of protein topology, complex formation, and conformational dynamics are also necessary to fully understand these FeS protein systems. Recent developments in mass spectrometry (MS) instrumentation and methods provide new tools to investigate FeS cluster and structural properties. With the unique advantage of sampling all species in a mixture, MS-based methods can be utilized as a powerful complementary approach to probe native dynamic heterogeneity, interrogate protein folding and unfolding equilibria, and provide extensive insight into protein binding partners within an entire proteome. Here, we highlight key advances in FeS protein studies made possible by MS methodology and contribute an outlook for its role in the field.
PubMed: 38908802
DOI: 10.1016/j.bbamcr.2024.119784 -
International Journal of Biological... Jun 2024The persistent global issues of unsafe food and food waste continue to exist. Microbial contamination stands out as a major cause of losses in perishable foods like...
The persistent global issues of unsafe food and food waste continue to exist. Microbial contamination stands out as a major cause of losses in perishable foods like vegetables and fruits. Herein, we report a self-assembling coating based on disulfide bond cleavage-induced bovine serum albumin (BSA), where the antimicrobial activity of chitosan oligosaccharide (COS) is stably anchored in the coating by electrostatic interactions during the unfolding-aggregation phase of BSA. The intrinsic antimicrobial activity of COS, combined with the positively charged and hydrophobic regions enriched on the BSA coating, significantly disrupts the integrity of bacterial structures. Furthermore, the BSA@COS coating can easily adhere in situ to the grooves on the surface of strawberries through a simple one-step spraying process, extending the shelf life of strawberries and bananas by nearly three times. This makes it a potential economic alternative to current commercial antimicrobial coatings, offering a solution to the rampant global issue of food waste.
PubMed: 38908638
DOI: 10.1016/j.ijbiomac.2024.133330 -
International Journal of Biological... Jun 2024The role of facile curcumin dispersion and its hydrophobic complexation onto GLP, in the form of shell (GLPC-E), core (GLPE-C) and with synergy (GLP-ECE), on the protein...
The role of facile curcumin dispersion and its hydrophobic complexation onto GLP, in the form of shell (GLPC-E), core (GLPE-C) and with synergy (GLP-ECE), on the protein interfacial and emulsion stabilization was investigated. Turbiscan instability index, microrheological elasticity, viscosity and solid-liquid balance values showed that the O/W emulsion stability was in the order of GLP-E < GLPC-E < GLPE-C < GLP-ECE. GLP-ECE also gave the most reduced D (Xue et al., 2019; Zhang et al., 2022 [3,4]) (8.11 ± 0.14 μm) with lowest indexes of flocculation (2.80 ± 0.05 %) and coalescence (2.83 ± 0.10 %) at day 5. Interfacial shear rheology suggested the GLP-curcumin complexation fortified the GLP interfacial gelling and then the efficiency as steric stabilizer, especially of core-shell complexation (14.2 mPa.m) that showed the most sufficient in-plane protein interaction against strain. Dilatational elasticity and desorption observation revealed the synergistic curcumin complexation facilitated GLP unfolding and macromolecular association at O/W interface, as was also verified from SEM image and surface hydrophobicity (from 36.23 to 76.04). Overall, this study firstly reported the facile curcumin bi-physic dispersion and GLP complexation in improving the emulsion stabilizing efficiency of the protein by advancing its interfacial stabilization.
PubMed: 38908636
DOI: 10.1016/j.ijbiomac.2024.133324 -
International Journal of Biological... Jun 2024Understanding how shear affects whey protein stability is crucial to deal with typical industrial issues occurring at the bulk solution/surface interface, such as...
Understanding how shear affects whey protein stability is crucial to deal with typical industrial issues occurring at the bulk solution/surface interface, such as fouling during heat treatments. However, at the state of the art, this effect remains unclear, contrary to that of temperature. This article presents a novel strategy to study the impact of shear rate and concentration on the accumulation of whey protein surficial deposits. It consists in applying a range of shear rates (0-200 s) at controlled temperature (65 °C) on whey protein solutions (5-10 wt%) by a parallel plate rheometer equipped with a glass disc, thus allowing the off-line characterization of the deposits by microscopy. Our results highlight an unequivocal effect of increasing shear stress. At 5 wt%, it fosters the formation of primary deposits (≈ 10 μm), whereas at 10 wt% it results in the development of complex branched structures (≈ 50 μm) especially for shear rates ranging from 140 s to 200 s. Based on the classification by size of the observed populations, we discuss possible hypotheses for the deposit growth kinetics, involving the interplay of different physico-chemical protein-surface interactions and paving the way to future further investigations.
PubMed: 38908625
DOI: 10.1016/j.ijbiomac.2024.133291 -
Food Chemistry Jun 2024In this study, chlorogenic acid (CA), piceatannol (PIC), epigallocatechin-3-gallate (EGCG) and ferulic acid (FA) was selected to explore the influence of polyphenol on...
In this study, chlorogenic acid (CA), piceatannol (PIC), epigallocatechin-3-gallate (EGCG) and ferulic acid (FA) was selected to explore the influence of polyphenol on the structural properties of wheat germ albumin (WGA) and wheat germ globulin (WGG). The emulsifying properties of the emulsions prepared by WGA-EGCG complex were also evaluated. The results indicated that all polyphenols could significantly enhance the antioxidant capacity of WGA and WGG. In particular, EGCG increased the ratio of random coil in WGA and WGG, resulting in protein unfolding and shifting from an order to disorder structure. In addition, lipid oxidation and protein oxidation of the soybean oil emulsion was significantly slowed down by WGA-EGCG. The stability of the emulsions under various environmental stress and the storage time was significantly improved by WGA-EGCG. These findings can provide a reference for expanding the application of wheat germ protein in food industry.
PubMed: 38908242
DOI: 10.1016/j.foodchem.2024.140129 -
Nucleic Acids Research Jun 2024i-Motifs (iMs) are non-canonical, four-stranded secondary structures formed by stacking of hemi-protonated CH+·C base pairs in cytosine-rich DNA sequences,...
i-Motifs (iMs) are non-canonical, four-stranded secondary structures formed by stacking of hemi-protonated CH+·C base pairs in cytosine-rich DNA sequences, predominantly at pH < 7. The presence of iM structures in cells was a matter of debate until the recent development of iM-specific antibody, iMab, which was instrumental for several studies that suggested the existence of iMs in live cells and their putative biological roles. We assessed the interaction of iMab with cytosine-rich oligonucleotides by biolayer interferometry (BLI), pull-down assay and bulk-FRET experiments. Our results suggest that binding of iMab to DNA oligonucleotides is governed by the presence of runs of at least two consecutive cytosines and is generally increased in acidic conditions, irrespectively of the capacity of the sequence to adopt, or not, an iM structure. Moreover, the results of the bulk-FRET assay indicate that interaction with iMab results in unfolding of iM structures even in acidic conditions, similarly to what has been observed with hnRNP K, well-studied single-stranded DNA binding protein. Taken together, our results strongly suggest that iMab actually binds to blocks of 2-3 cytosines in single-stranded DNA, and call for more careful interpretation of results obtained with this antibody.
PubMed: 38908025
DOI: 10.1093/nar/gkae531 -
Langmuir : the ACS Journal of Surfaces... Jun 2024Optical tweezers (OT) have evolved into powerful single molecule force spectroscopy tools to investigate protein folding-unfolding dynamics. To stretch a protein of...
Optical tweezers (OT) have evolved into powerful single molecule force spectroscopy tools to investigate protein folding-unfolding dynamics. To stretch a protein of interest using OT, the protein must be flanked with two double stranded DNA (dsDNA) handles. However, coupling dsDNA handles to the protein is often of low yield, representing a bottleneck in OT experiments. Here, we report a handle-free, all-protein-based OT method for investigating protein folding/unfolding dynamics. In this new method, we employed disordered elastin-like polypeptides (ELPs) as a molecular linker and the mechanically stable cohesin-dockerin (Coh-Doc) pair as the prey-bait system to enable the efficient capture and stretching of individual protein molecules. This novel approach was validated by using model proteins NuG2 and RTX-v, yielding experimental results comparable to those obtained by using the dsDNA handle approach. This new method provides a streamlined and efficient OT approach to investigate the folding-unfolding dynamics of proteins at the single molecule level, thus expanding the toolbox of OT-based single molecule force spectroscopy.
PubMed: 38899455
DOI: 10.1021/acs.langmuir.4c01711