Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy

A Promising Compound for Green Multiresponsive Materials Based on Acyl Carrier Protein

A gel that exhibits intrinsically multiple-responsive behavior was prepared from an oligopeptide and studied. ACP(65-74) is an active decapeptide fragment of acyl carrier protein. We investigated 3% w/v ACP(65-74)-NH2 self-healing physical gels in water, glycerol carbonate (GC), and their mixtures. The morphology was investigated by optical, birefringence, and confocal laser scanning microscopy, circular dichroism, Fourier transform infrared, and fluorescence spectroscopy experiments. We found that all samples possess pH responsiveness with fully reversible sol-to-gel transitions. The rheological properties depend on the temperature and solvent composition. The temperature dependence of the gels in water shows a peculiar behavior that is similar to that of thermoresponsive polymer solutions. The results reveal the presence of several β-sheet structures and amyloid aggregates, offering valuable insights into the fibrillation mechanism of amyloids in different solvent media.

Enabling High Activation of Glucose-6-Phosphate Dehydrogenase Activity Through Liquid Condensate Formation and Compression

Droplet formation via liquid-liquid phase separation is thought to be involved in the regulation of various biological processes, including enzymatic reactions. We investigated a glycolytic enzymatic reaction, the conversion of glucose-6-phosphate to 6-phospho-D-glucono-1,5-lactone with concomitant reduction of NADP+ to NADPH both in the absence and presence of dynamically controlled liquid droplet formation. Here, the nucleotide serves as substrate as well as the scaffold required for the formation of liquid droplets. To further expand the process parameter space, temperature and pressure dependent measurements were performed. Incorporation of the reactants in the liquid droplet phase led to a boost in enzymatic activity, which was most pronounced at medium-high pressures. The crowded environment of the droplet phase induced a marked increase of the affinity of the enzyme and substrate. An increase in turnover number in the droplet phase at high pressure contributed to a further strong increase in catalytic efficiency. Enzyme systems that are dynamically coupled to liquid condensate formation may be the key to deciphering many biochemical reactions. Expanding the process parameter space by adjusting temperature and pressure conditions can be a means to further increase the efficiency of industrial enzyme utilization and help uncover regulatory mechanisms adopted by extremophiles.

H2 production under stress: [FeFe]‑hydrogenases reveal strong stability in high pressure environments

Hydrogenases are a diverse group of metalloenzymes that catalyze the conversion of H2 into protons and electrons and the reverse reaction. A subgroup is formed by the [FeFe]‑hydrogenases, which are the most efficient enzymes of microbes for catalytic H2 conversion. We have determined the stability and activity of two [FeFe]‑hydrogenases under high temperature and pressure conditions employing FTIR spectroscopy and the high-pressure stopped-flow methodology in combination with fast UV/Vis detection. Our data show high temperature stability and an increase in activity up to the unfolding temperatures of the enzymes. Remarkably, both enzymes reveal a very high pressure stability of their structure, even up to pressures of several kbars. Their high pressure-stability enables high enzymatic activity up to 2 kbar, which largely exceeds the pressure limit encountered by organisms in the deep sea and sub-seafloor on Earth.

Designed modular protein hydrogels for biofabrication

Designing proteins that fold and assemble over different length scales provides a way to tailor the mechanical properties and biological performance of hydrogels. In this study, we designed modular proteins that self-assemble into fibrillar networks and, as a result, form hydrogel materials with novel properties. We incorporated distinct functionalities by connecting separate self-assembling (A block) and cell-binding (B block) domains into single macromolecules. The number of self-assembling domains affects the rigidity of the fibers and the final storage modulus G' of the materials. The mechanical properties of the hydrogels could be tuned over a broad range (G' = 0.1 - 10 kPa), making them suitable for the cultivation and differentiation of multiple cell types, including cortical neurons and human mesenchymal stem cells. Moreover, we confirmed the bioavailability of cell attachment domains in the hydrogels that can be further tailored for specific cell types or other biological applications. Finally, we demonstrate the versatility of the designed proteins for application in biofabrication as 3D scaffolds that support cell growth and guide their function. STATEMENT OF SIGNIFICANCE: Designed proteins that enable the decoupling of biophysical and biochemical properties within the final material could enable modular biomaterial engineering. In this context, we present a designed modular protein platform that integrates self-assembling domains (A blocks) and cell-binding domains (B blocks) within a single biopolymer. The linking of assembly domains and cell-binding domains this way provided independent tuning of mechanical properties and inclusion of biofunctional domains. We demonstrate the use of this platform for biofabrication, including neural cell culture and 3D printing of scaffolds for mesenchymal stem cell culture and differentiation. Overall, this work highlights how informed design of biopolymer sequences can enable the modular design of protein-based hydrogels with independently tunable biophysical and biochemical properties.

A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones

Following the development of modern genome sequencing technologies, the investigation of museum osteological finds is increasingly informative and popular. Viable protocols to help preserve these collections from exceedingly invasive analyses, would allow greater access to the specimens for scientific research. The main aim of this work is to survey skeletal tissues, specifically petrous bones and roots of teeth, using infrared spectroscopy as a prescreening method to assess the bone quality for molecular analyses. This approach could overcome the major problem of identifying useful genetic material in archaeological bone collections without resorting to demanding, time consuming and expensive laboratory studies. A minimally invasive sampling of archaeological bones was developed and bone structural and compositional changes were examined, linking isotopic and genetic data to infrared spectra. The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period.

Modulation of protein-saccharide interactions by deep-sea osmolytes under high pressure stress

Deep-sea organisms must cope with high hydrostatic pressures (HHP) up to the kbar regime to control their biomolecular processes. To alleviate the adverse effects of HHP on protein stability most organisms use high amounts of osmolytes. Little is known about the effects of these high concentrations on ligand binding. We studied the effect of the deep-sea osmolytes trimethylamine-N-oxide, glycine, and glycine betaine on the binding between lysozyme and the tri-saccharide NAG3, employing experimental and theoretical tools to reveal the combined effect of osmolytes and HHP on the conformational dynamics, hydration changes, and thermodynamics of the binding process. Due to their different chemical makeup, these cosolutes modulate the protein-sugar interaction in different ways, leading to significant changes in the binding constant and its pressure dependence. These findings suggest that deep-sea organisms may down- and up-regulate reactions in response to HHP stress by altering the concentration and type of the intracellular osmolyte.

Influence of the Sequence Motive Repeating Number on Protein Folding in Spider Silk Protein Films

Like multiblock copolymers, spider silk proteins are built of repetitive sequence motives. One prominent repetitive motif is based on the consensus sequence of spidroin 4 of the spider Araneus diadematus ADF4. The number x of the repeating sequence motives (C) determines the molecular weight of the recombinant ADF4-based, engineered spider silk protein denoted as eADF4(Cx). eADF4(Cx) can be used as a model for intrinsically disordered proteins (IDP) and to elucidate their folding. Herein, the influence of the variation of the sequence motive repeating number x (x = 1, 2, 4, 8, 16) on the protein folding within eADF4(Cx) films was investigated. eADF4(Cx) films were cast from 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) solutions onto planar silicon model substrates, revealing mainly helical or random coil structure. Upon treatment with methanol vapor (ptm), the formation of crystalline β-sheets was triggered. Dichroic Fourier-transform infrared (FTIR) spectroscopy, circular dichroism, spectroscopic ellipsometry, atomic force microscopy, grazing-incidence small-angle X-ray scattering (GISAXS), grazing-incidence wide-angle X-ray scattering (GIWAXS), and electrokinetic and contact angle measurements were used to get information concerning the secondary structure and folding kinetics, orientation of β-sheets, the ratio of parallel/antiparallel β-sheets, domain sizes and distributions, surface topography, surface potential, hydrophobicity and the film integrity under water. Significant differences in the final β-sheet content, the share of antiparallel β-sheet structures, film integrity, surface potential, and isoelectric points between eADF4(Cx) with x = 1, 2 and eADF4(Cx) with x = 4, 8, 16 gave new insights in the molecular weight-dependent structure formation and film properties of IDP systems. GISAXS and kinetic measurements confirmed a relation between β-sheet crystal growth rate and final β-sheet crystal size. Further, competing effects of reduced diffusibility hindering accelerated crystal growth and enhanced backfolding promoting accelerated crystal growth with increasing molecular weight were discussed.

Biomineralization in Barnacle Base Plate in Association with Adhesive Cement Protein

Barnacles strongly attach to various underwater substrates by depositing and curing a proteinaceous cement that forms a permanent adhesive layer. The protein MrCP20 present within the calcareous base plate of the acorn barnacle Megabalanus rosa (M. rosa) was investigated for its role in regulating biomineralization and growth of the barnacle base plate, as well as the influence of the mineral on the protein structure and corresponding functional role. Calcium carbonate (CaCO3) growth on gold surfaces modified by 11-mercaptoundecanoic acid (MUA/Au) with or without the protein was followed using quartz crystal microbalance with dissipation monitoring (QCM-D), and the grown crystal polymorph was identified by Raman spectroscopy. It is found that MrCP20 either in solution or on the surface affects the kinetics of nucleation and growth of crystals and stabilizes the metastable vaterite polymorph of CaCO3. A comparative study of mass uptake calculated by applying the Sauerbrey equation to the QCM-D data and quantitative X-ray photoelectron spectroscopy determined that the final surface density of the crystals as well as the crystallization kinetics are influenced by MrCP20. In addition, polarization modulation infrared reflection-absorption spectroscopy of MrCP20 established that, during crystal growth, the content of β-sheet structures in MrCP20 increases, in line with the formation of amyloid-like fibrils. The results provide insights into the molecular mechanisms by which MrCP20 regulates the biomineralization of the barnacle base plate, while favoring fibril formation, which is advantageous for other functional roles such as adhesion and cohesion.

Optimization of Water Lentil (Duckweed) Leaf Protein Purification: Identification, Structure, and Foaming Properties

Water lentil, commonly known as duckweed, is an aquatic plant with great agronomic potential, as it can double its biomass in less than 24 h and contains up to 45% leaf proteins on a dry matter basis. However, extracting proteins from leaves is an arduous process due to the complexity of the matrix, which limits their uses in the food industry. In this study, water lentil protein extraction by solubilization was maximized using response surface methodology. By heating at 80 °C at pH 11 with a water lentil powder concentration of 2% or 4% for 2 h, up to 77.8% of total proteins were solubilized. Then, by precipitating the solubilized proteins at pH 4, a protein purity of 57.6% combined with a total protein yield of 60.0% was achieved. To the best of our knowledge, this is the highest leaf protein extraction yield reported in the literature with such protein purity. Proteomics analyses showed that the protein concentrate was composed of around 85.0% RubisCO, and protein structure analyses using ATR-FTIR and DSC were linked to a high protein solubility in water at pH 7. Moreover, a 1.5% protein solution of the protein concentrate at pH 7 showed excellent foaming properties compared to a 10.3% protein egg white solution. It had a superior foaming capacity (194% vs. 122%, respectively) for the same foaming stability after 60 min, which confirms water lentil proteins' potential for human nutrition and food formulation.

Development of a Novel Histatin-5 Mucoadhesive Gel for the Treatment of Oral Mucositis: In Vitro Characterization and In Vivo Evaluation

Antimicrobial peptides have appeared to be promising candidates for therapeutic purposes due to their broad antimicrobial activity and non-toxicity. Histatin-5 (Hst-5) is a notable salivary antimicrobial peptide that exhibited therapeutic properties in the oral cavity. Oral mucositis is an acute inflammation of the oral cavity, following cancer therapy. The current treatment methods of oral mucositis have low effectiveness. The aim of this study was to design, formulate and characterize a mucoadhesive gel delivery system for Hst-5 usage in the treatment of oral mucositis. Carbopol 934 and hydroxypropyl methylcellulose (HPMC) have been used in the development of a Hst-5 mucoadhesive gel that was optimized by using Box-Behnken design. The optimized formulation was evaluated in-vitro, based on mucoadhesive strength, viscoelasticity, spreadability, release rate, peptide secondary structure analysis, antimicrobial activity, and storage stability. The efficacy of Hst-5 gel was assessed in vivo in a chemotherapy-induced mucositis model. The results showed a sustained release of Hst-5 from the new formulation. Hst-5 gel exerted antimicrobial activity against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Candida albicans. The histopathological, immunohistochemical and statistical analysis showed that the Hst-5 gel had wound healing activity in vivo. The findings of this study indicate that the mentioned compound possesses promising potential as a novel and efficient therapeutic agent in managing oral mucositis. Moreover, the results suggest that the compound is commercially feasible for further development and utilization.

Multiple Carbon Morphologies Derived from Polyion Complex-Based Double Hydrophilic Block Copolymers as Templates and Phenol as a Carbon Precursor

This study demonstrates the multiple carbon morphology forming abilities of two dissimilar polyion complex (PIC)-based double hydrophilic block copolymers (DHBC) along with three different phenol concentrations when subjecting the blend in aqueous media via a hydrothermal-assisted carbonization strategy. The morphological transition from worm-like to spherical along with granular is found for the blend of oppositely charged poly(ethylene glycol) (PEG)-conjugated poly(amino acid) block copolymers, PEG-poly(l-lysine) (PEG-PLys) and PEG-poly(glutamic acid) (PEG-PGlu), along with three different concentrations of phenol. In contrast, after mixing the combination of PEG-PLys and PEG-poly(aspartic acid) (PEG-PAsp) separately with three different phenol contents, elliptical to irregular to spherical structural transition occurred. Fourier transform infrared and circular dichroism spectroscopic studies indicated that the formation of worm-like hybrid micellar structures is attributed to the presence of the β-sheet structure, whereas spherical-shaped hybrid micellar structures are formed due to the existence of α-helix and random coil structures. We discuss the mechanism for the secondary structure-induced morphology formation based on the theory related to the packing parameter, which is commonly used for analyzing the shape of the micellar structures. Secondary structures of the PIC-based DHBC system are responsible for forming multiple carbon morphologies, whereas these structures are absent in the case of the amphiphilic block copolymer (ABC) system. Furthermore, ABC-based template methods require organic solvent, ultrasonication, and a prolonged solvent evaporation process to obtain multiple carbon morphologies. Scanning electron microscopy observations suggested there is no significant morphological change even after subjecting the hybrid micelles to carbonization at elevated temperatures. Raman scattering studies revealed that the degree of graphitization and the graphitic crystallite domain size of the carbonized sample depend on the phenol content. Carbon materials exhibited the highest specific surface area of 579 m² g^-1 along with a pore volume of 0.398 cc g^-1, and this observation suggests that the prepared carbons are porous. Our findings illustrate the facile and effective strategy to fabricate the multiple carbon morphologies that can be used as potential candidates for energy storage applications.

Effect of the Electric Field on the Biomineralization of Collagen

Collagen/hydroxyapatite hybrids are promising biomimetic materials that can replace or temporarily substitute bone tissues. The process of biomineralization was carried out through a double diffusion system. The methodological principle consisted in applying an electric field on the incubation medium to promote the opposite migration of ions into collagen membranes to form hydroxyapatite (HA) on the collagen membrane. Two physically separated solutions were used for the incubation medium, one rich in phosphate ions and the other in calcium ions, and their effects were evaluated against the traditional mineralization in Simulated Body Fluid (SBF). Pre-polarization of the organic membranes and the effect of incubation time on the biomineralization process were also assessed by FTIR and Raman spectroscopies.Our results demonstrated that the membrane pre-polarization significantly accelerated the mineralization process on collagen. On the other side, it was found that the application of the electric field influenced the collagen structure and its interactions with the mineral phase. The increment of the mineralization degree enhanced the photoluminescence properties of the collagen/HA materials, while the conductivity and the dielectric constant were reduced. These results might provide a useful approach for future applications in manufacturing biomimetic bone-like materials.

Despite their structural similarities, the cytosolic isoforms of human Hsp90 show different behaviour in thermal unfolding due to their conformation: An FTIR study

Heat shock proteins 90 (Hsp90) are chaperones that promote the proper folding of other proteins under high temperature stress situations. Hsp90s are highly conserved and ubiquitous proteins, and in mammalian cells, they are localized in the cytoplasm, endoplasmic reticulum, and mitochondria. Cytoplasmic Hsp90 are named Hsp90α and Hsp90β and differ mainly in their expression pattern: Hsp90α is expressed under stress conditions, while Hsp90β is a constitutive protein. Structurally, both share the same characteristics by presenting three well-conserved domains, one of which, the N-terminal domain, has a binding site for ATP to which various drugs targeting this protein, including radicicol, can bind. The protein is mainly found in dimeric form and adopts different conformations depending on the presence of ligands, co-chaperones and client proteins. In this study, some aspects of structure and thermal unfolding of cytoplasmic human Hsp90 were analysed by infrared spectroscopy. The effect on Hsp90β of binding with a non-hydrolysable ATP analogue and radicicol was also examined. The results obtained showed that despite the high similarity in secondary structure the two isoforms exhibit substantial differences in their behaviour during thermal unfolding, as Hsp90α exhibits higher thermal stability, slower denaturation process and different event sequence during unfolding. Ligand binding strongly stabilizes Hsp90β and slightly modifies the secondary structure of the protein as well. Most likely, these structural and thermostability characteristics are closely related to the conformational cycling of the chaperone and its propensity to exist in monomer or dimer form.

Bulk Biopolyelectrolyte Complexes from Homopolypeptides: Solid "Salt Bridges"

Salt bridges, pairings between oppositely charged amino acids, are dispersed throughout proteins to assist folding and interactions. Biopolyelectrolyte complexes (BioPECs) were made between the homopolypeptides poly-l-arginine (PLR) and poly-l-lysine (PLK) with sodium triphosphate (STPP), as well as from polypeptide-only combinations. Viscoelastic measurements on these high salt bridge density materials showed many were solid, even glassy, in nature. Although the polypeptide-phosphate complexes had similar moduli at room temperature, the PLR-STPP complex displayed an unusual melting event above 70 °C not seen in PLK-STPP. This event was supported with differential scanning calorimetry. Infrared spectroscopy showed the PLK-STPP system contained β-sheets, while PLR-STPP did not. Stoichiometric, macroscopic BioPECs of PLR and PLK with poly-l-aspartic acid (PLD) and poly-l-glutamic acid (PLE) were made. PLR-PLD was found to undergo a melting event similar to that in PLR-STPP. ATR-FTIR studies showed that BioPECs made with PLD do not contain β-sheets, while those composed of PLE do. This work illustrates an expanded palette of unique properties from these biomaterials, such as strong viscoelastic differences between PECs containing PLE and PLD, even though they differ by only one carbon on the side chain.

Non-Invasive Disease Specific Biomarker Detection Using Infrared Spectroscopy: A Review

Many life-threatening diseases remain obscure in their early disease stages. Symptoms appear only at the advanced stage when the survival rate is poor. A non-invasive diagnostic tool may be able to identify disease even at the asymptotic stage and save lives. Volatile metabolites-based diagnostics hold a lot of promise to fulfil this demand. Many experimental techniques are being developed to establish a reliable non-invasive diagnostic tool; however, none of them are yet able to fulfil clinicians' demands. Infrared spectroscopy-based gaseous biofluid analysis demonstrated promising results to fulfil clinicians' expectations. The recent development of the standard operating procedure (SOP), sample measurement, and data analysis techniques for infrared spectroscopy are summarized in this review article. It has also outlined the applicability of infrared spectroscopy to identify the specific biomarkers for diseases such as diabetes, acute gastritis caused by bacterial infection, cerebral palsy, and prostate cancer.

Residue-specific binding of Ni(II) ions influences the structure and aggregation of amyloid beta (Aβ) peptides

Alzheimer's disease (AD) is the most common cause of dementia worldwide. AD brains display deposits of insoluble amyloid plaques consisting mainly of aggregated amyloid-β (Aβ) peptides, and Aβ oligomers are likely a toxic species in AD pathology. AD patients display altered metal homeostasis, and AD plaques show elevated concentrations of metals such as Cu, Fe, and Zn. Yet, the metal chemistry in AD pathology remains unclear. Ni(II) ions are known to interact with Aβ peptides, but the nature and effects of such interactions are unknown. Here, we use numerous biophysical methods-mainly spectroscopy and imaging techniques-to characterize Aβ/Ni(II) interactions in vitro, for different Aβ variants: Aβ(1-40), Aβ(1-40)(H6A, H13A, H14A), Aβ(4-40), and Aβ(1-42). We show for the first time that Ni(II) ions display specific binding to the N-terminal segment of full-length Aβ monomers. Equimolar amounts of Ni(II) ions retard Aβ aggregation and direct it towards non-structured aggregates. The His6, His13, and His14 residues are implicated as binding ligands, and the Ni(II)·Aβ binding affinity is in the low µM range. The redox-active Ni(II) ions induce formation of dityrosine cross-links via redox chemistry, thereby creating covalent Aβ dimers. In aqueous buffer Ni(II) ions promote formation of beta sheet structure in Aβ monomers, while in a membrane-mimicking environment (SDS micelles) coil-coil helix interactions appear to be induced. For SDS-stabilized Aβ oligomers, Ni(II) ions direct the oligomers towards larger sizes and more diverse (heterogeneous) populations. All of these structural rearrangements may be relevant for the Aβ aggregation processes that are involved in AD brain pathology.

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222

Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length. This article is protected by copyright. All rights reserved.

Ultrasonic process affecting interactions between sodium caseinate and whey proteins

Ultrasound has been widely explored for several applications, such as emulsification or structural modification of food materials such as proteins. In this work, the effect of ultrasound on the control of whey proteins (WPI) aggregation was evaluated in the presence of sodium caseinate (NaCas). Solutions of NaCas, WPI and both (1:1) were treated with ultrasound under different power and time conditions and were initially evaluated in terms of particle size distribution, charge density, pH and polyacrylamide gel electrophoresis. Three pairs of conditions were adopted to provide the same energy density - A1 (450 W / 300 s, 6750 MJ/m³), A2 (150 W / 900 s, 6750 MJ/m³), A3 (600 W / 300 s, 900 MJ/m³), A4 (202.5 W / 900 s, 9112.5 MJ/m³), A5 (742.5 W / 300 s, 11137.5 MJ/m³) and A6 (247.5 W / 900 s, 11137.5 MJ/m³). Best conditions of transmitted energy - A1, A3 and A5 - were studied for surface hydrophobicity, circular dichroism and infrared spectroscopy. The decrease of surface hydrophobicity of NaCas:WPI mixtures pointed to a protective effect of NaCas against WPI denaturation, confirmed by the presence of more ordered structures by FTIR analysis that were not observed in the absence of NaCas. Finally, the effect of these structural changes on the gelation capacity of the ultrasound-treated proteins was assessed. Ultrasound was able to reduce the stress at rupture from 1988.59 Pa (control) to 1655.31 Pa (A3) and 1871.24 Pa (A5), and more markedly increase the Young modulus from 113.69 kPa (control) to 243.30 kPa (A3) and 392.44 kPa (A5). This study identified that higher power values with shorter times were able to provide greater protein changes that affected gelation properties, showing that the modulation of ultrasound conditions can produce ingredients with different techno-functional properties.

Combined Neutrase-Alcalase Protein Hydrolysates from Hazelnut Meal, a Potential Functional Food Ingredient

Consumers' interest in functional foods has significantly increased in the past few years. Hazelnut meal, the main valuable byproduct of the hazelnut oil industry, is a rich source of proteins and bioactive peptides and thus has great potential to become a valuable functional ingredient. In this study, hazelnut protein hydrolysates obtained by a single or combined hydrolysis by Alcalase and Neutrase were mainly characterized for their physicochemical properties (SDS-PAGE, particle size distribution, Fourier-transform infrared (FTIR) spectroscopy, molecular weight distribution, etc.) and potential antiobesity effect (Free fatty acid (FFA) release inhibition), antioxidant activity (DPPH and ABTS methods), and emulsifying properties. The impact of a microfluidization pretreatment was also investigated. The combination of Alcalase with Neutrase permitted the highest degree of hydrolysis (DH; 15.57 ± 0.0%) of hazelnut protein isolate, which resulted in hydrolysates with the highest amount of low-molecular-weight peptides, as indicated by size exclusion chromatography (SEC) and SDS-PAGE. There was a positive correlation between the DH and the inhibition of FFA release by pancreatic lipase (PL), with a significant positive effect of microfluidization when followed by Alcalase hydrolysis. Microfluidization enhanced the emulsifying activity index (EAI) of protein isolates and hydrolysates. Low hydrolysis by Neutrase had the best effect on the EAI (84.32 ± 1.43 (NH) and 88.04 ± 2.22 m²/g (MFNH)), while a negative correlation between the emulsifying stability index (ESI) and the DH was observed. Again, the combined Alcalase-Neutrase hydrolysates displayed the highest radical scavenging activities (96.63 ± 1.06% DPPH and 98.31 ± 0.46% ABTS). FTIR results showed that the application of microfluidization caused the unfolding of the protein structure. The individual or combined application of the Alcalase and Neutrase enzymes caused a switch from the β-sheet organization of the proteins to α-helix structures. In conclusion, hazelnut meal may be a good source of bioactive and functional peptides. The control of its enzymatic hydrolysis, together with an appropriate pretreatment such as microfluidization, may be crucial to achieve the best suitable activity.

Study of fluorescence spectroscopy and molecular mechanisms for the interaction of Hg2+ ions and R-phycoerythrin from marine algae (Porphyra yezoensis)

Heavy metal is a worldwide hazardous material, and many efforts were made to detect them sensitively and selectively. R-phycoerythrin (R-PE), a marine fluorescent protein, is abundant in red algae and participates in photosynthesis. In this work, the fluorescence spectroscopy and molecular mechanism of Hg2+ ions and R-PE were further explored through fluorescence spectrum measurements, time-resolved fluorescence lifetimes, peak fitting of Fourier transform infrared spectroscopy, and molecular docking simulation in this study. It was proved by fluorescent spectrum measurements that Hg2+ ions could lead to static fluorescence quenching. Besides, the interaction was a spontaneous and exothermic process driven by hydrogen bond and Van der Waals (VDW) force. Importantly, Hg2+ ions bound to 78LYS and 82CYS on the α chain and 73CYS and 82CYS on the β chain, which resulted in the structural changes of the peptide chain and affected the secondary structure contents of R-PE. This study further explained the effect of Hg2+ ions on marine fluorescent protein R-PE.

Molecular dynamics simulations of the adsorption of an intrinsically disordered protein: Force field and water model evaluation in comparison with experiments

This study investigates possible structural changes of an intrinsically disordered protein (IDP) when it adsorbs to a solid surface. Experiments on IDPs primarily result in ensemble averages due to their high dynamics. Therefore, molecular dynamics (MD) simulations are crucial for obtaining more detailed information on the atomistic and molecular levels. An evaluation of seven different force field and water model combinations have been applied: (A) CHARMM36IDPSFF + CHARMM-modified TIP3P, (B) CHARMM36IDPSFF + TIP4P-D, (C) CHARMM36m + CHARMM-modified TIP3P, (D) AMBER99SB-ILDN + TIP3P, (E) AMBER99SB-ILDN + TIP4P-D, (F) AMBERff03ws + TIP4P/2005, and (G) AMBER99SB-disp + disp-water. The results have been qualitatively compared with those of small-angle X-ray scattering, synchrotron radiation circular dichroism spectroscopy, and attenuated total reflectance Fourier transform infrared spectroscopy. The model IDP corresponds to the first 33 amino acids of the N-terminal of the magnesium transporter A (MgtA) and is denoted as KEIF. With a net charge of +3, KEIF is found to adsorb to the anionic synthetic clay mineral Laponite^® due to the increase in entropy from the concomitant release of counterions from the surface. The experimental results show that the peptide is largely disordered with a random coil conformation, whereas the helical content (α- and/or 3₁₀-helices) increased upon adsorption. MD simulations corroborate these findings and further reveal an increase in polyproline II helices and an extension of the peptide conformation in the adsorbed state. In addition, the simulations provided atomistic resolution of the adsorbed ensemble of structures, where the arginine residues had a high propensity to form hydrogen bonds with the surface. Simulations B, E, and G showed significantly better agreement with experiments than the other simulations. Particularly noteworthy is the discovery that B and E with TIP4P-D water had superior performance to their corresponding simulations A and D with TIP3P-type water. Thus, this study shows the importance of the water model when simulating IDPs and has also provided an insight into the structural changes of surface-active IDPs induced by adsorption, which may play an important role in their function.

μ-FTIR, μ-Raman, and SERS Analysis of Amide I Spectral Region in Oral Biofluid Samples during Orthodontic Treatment

Gingival crevicular fluid (GCF) is a site-specific exudate deriving from the epithelium lining of the gingival sulcus. GCF analysis provides a simple and noninvasive diagnostic procedure to follow-up periodontal and bone remodeling in response to diseases or mechanical stimuli such as orthodontic tooth movement (OTM). In recent years, the use of vibrational spectroscopies such as Fourier Transform Infrared and Raman microspectroscopy and Surface-Enhanced Raman spectroscopy contributed to characterizing changes in GCF during fixed orthodontic treatment. Amide I band plays a relevant role in the analysis of these changes. The aim of this study was to investigate the spectroscopy response of Amide I depending on the OTM process duration. A model based on Gaussian-Lorentzian curves was used to analyze the infrared spectra, while only Lorentzian functions were used for Raman and SERS spectra. Changes induced by the OTM process in subcomponents of the Amide I band were determined and ascribed to secondary structure modification occurring in proteins. The vibrational spectroscopies allow us to efficiently monitor the effects of the orthodontic force application, thus gaining increasing attention as tools for individual patient personalization in clinical practice.

ATR-FTIR Biosensors for Antibody Detection and Analysis

Quality control of drug products is of paramount importance in the pharmaceutical world. It ensures product safety, efficiency, and consistency. In the case of complex biomolecules such as therapeutic proteins, small variations in bioprocess parameters can induce substantial variations in terms of structure, impacting the drug product quality. Conditions for obtaining highly reproducible grafting of 11-mercaptoundecanoic acid were determined. On that basis, we developed an easy-to-use, cost effective, and timesaving biosensor based on ATR-FTIR spectroscopy able to detect immunoglobulins during their production. A germanium crystal, used as an internal reflection element (IRE) for FTIR spectroscopy, was covalently coated with immunoglobulin-binding proteins. This thereby functionalized surface could bind only immunoglobulins present in complex media such as culture media or biopharmaceutical products. The potential subsequent analysis of their structure by ATR-FTIR spectroscopy makes this biosensor a powerful tool to monitor the production of biotherapeutics and assess important critical quality attributes (CQAs) such as high-order structure and aggregation level.

Functional Delineation of a Protein-Membrane Interaction Hotspot Site on the HIV-1 Neutralizing Antibody 10E8

Antibody engagement with the membrane-proximal external region (MPER) of the envelope glycoprotein (Env) of HIV-1 constitutes a distinctive molecular recognition phenomenon, the full appreciation of which is crucial for understanding the mechanisms that underlie the broad neutralization of the virus. Recognition of the HIV-1 Env antigen seems to depend on two specific features developed by antibodies with MPER specificity: (i) a large cavity at the antigen-binding site that holds the epitope amphipathic helix; and (ii) a membrane-accommodating Fab surface that engages with viral phospholipids. Thus, besides the main Fab-peptide interaction, molecular recognition of MPER depends on semi-specific (electrostatic and hydrophobic) interactions with membranes and, reportedly, on specific binding to the phospholipid head groups. Here, based on available cryo-EM structures of Fab-Env complexes of the anti-MPER antibody 10E8, we sought to delineate the functional antibody-membrane interface using as the defining criterion the neutralization potency and binding affinity improvements induced by Arg substitutions. This rational, Arg-based mutagenesis strategy revealed the position-dependent contribution of electrostatic interactions upon inclusion of Arg-s at the CDR1, CDR2 or FR3 of the Fab light chain. Moreover, the contribution of the most effective Arg-s increased the potency enhancement induced by inclusion of a hydrophobic-at-interface Phe at position 100c of the heavy chain CDR3. In combination, the potency and affinity improvements by Arg residues delineated a protein-membrane interaction site, whose surface and position support a possible mechanism of action for 10E8-induced neutralization. Functional delineation of membrane-interacting patches could open new lines of research to optimize antibodies of therapeutic interest that target integral membrane epitopes.

Metabolic Fingerprint Analysis of Cytochrome b5-producing E. coli N4830-1 Using FT-IR Spectroscopy

Optimization of recombinant protein expression in bacteria is an important task in order to increase protein yield while maintaining the structural fidelity of the product. In this study, we employ Fourier transform infrared (FT-IR) spectroscopy as a high throughput metabolic fingerprinting approach to optimize and monitor cytochrome b₅ (CYT b₅) production in Escherichia coli N4830-1, as the heterologous host. Cyt b₅ was introduced as a plasmid with between 0 and 6 copies under a strong promoter. The FT-IR spectroscopy results combined with multivariate chemometric analysis illustrated discriminations among culture conditions as well as revealing features that correlated to the different cytb₅ gene copy numbers. The second derivative of the FT-IR spectral data allowed for the quantitative detection of Cyt b₅ directly inside the intact cells without the need for extraction, and highlighted changes in protein secondary structure that was directly correlated to the cytb₅ gene copy number and protein content, and was in complete agreement with quantitative findings of standard traditional techniques such as SDS–PAGE and western blot analysis.

Effect of Nonisoprene Degradation and Naturally Occurring Network during Maturation on the Properties of Natural Rubber

It well-known that the superior performance of natural rubber (NR) compared to its synthetic counterpart mainly derives from nonisoprene components and naturally occurring network, which varies during the progress of the maturation and thereby results in technically graded rubber with different properties. However, identifying the roles of these two factors in the forming of excellent performance of NR is still a challenge as they change simultaneously during the maturation process. Here, influences of naturally occurring networking and nonisoprene degradation on the components, structures and properties of NR were systematically investigated by tailored treatments of maturation. It was found that the maturation-induced formation of natural network structure contributes to the increase in initial plastic value, Mooney viscosity and gel content for un-crosslinked NR, while the decomposition of nonisoprene components plays a dominant role in improving the mechanical properties of vulcanized NR. Stress-strain curve and Mooney-Rivlin analysis demonstrate that the biodegradation of the nonisoprene components significantly boost the vulcanization process, which significantly increases the number of chemical cross-link networks and effective cross-link density of the material, greatly improving the mechanical properties of NR vulcanizates. This resulted in the tensile strength of TSR 10CV being able to reach 22.6 MPa, which is significantly improved compared to 15.8 MPa of TSR 3CV. Evidenced by tubular model fitting, the increase in chemical cross-linking points effectively reduces the movable radius of the molecular chain under dynamic loading, making the molecular chain more difficult to move, which suppresses the entropy change under dynamic loading and consequently endows NR excellent dynamic mechanical properties. This resulted in a significant decrease in the temperature rising of TSR 10CV to 3.3 °C, while the temperature rising of TSR 3CV was still as high as 14.5 °C. As a minor factor, the naturally occurring network improves the mechanical properties of vulcanizates in the form of sacrificial bonds.

The mechanism for thermal-enhanced chaperone-like activity of α-crystallin against UV irradiation-induced aggregation of γD-crystallin

Exposure to solar UV irradiation damages γ-crystallin, leading to cataract formation via aggregation. α-Crystallin, as a small heat-shock protein (sHsps), efficiently suppresses this irreversible aggregation by selectively binding the denatured γ-crystallin monomer. In this study, liquid chromatography tandem mass spectrometry (LC-MS) was used to evaluate UV-325 nm irradiation-induced photodamage of human γD-crystallin in the presence of bovine α-crystallin, atomic force microscope (AFM) and dynamic light scattering (DLS) techniques were used to detect the quaternary structure changes of α-crystallin oligomer, and Fourier transform infrared (FTIR) spectroscopy and temperature-jump (T-jump) nanosecond time-resolved IR absorbance difference spectroscopy were used to probe the secondary structure changes of bovine α-crystallin. We find that the thermal-induced subunit dissociation of α-crystallin oligomer involves the breaking of hydrogen bonds at the dimeric interface, leading to three different spectral components at varied temperature regions as resolved from temperature-dependent IR spectra. Under UV-325 nm irradiation, unfolded γD-crystallin binds to the dissociated α-crystallin subunit to form αγ-complex, then follows the reassociation of αγ-complex to the partially dissociated α-crystallin oligomer. This prevents the aggregation of denatured γD-crystallin. The formation of the γD-bound α-crystallin oligomer is further confirmed by AFM and DLS analysis, which reveals an obvious size expansion in the reassociated αγ-oligomers. In addition, UV-325 nm irradiation causes a peptide bond cleavage of γD-crystallin at Ala158 in presence of α-crystallin. Our results suggest a very effective protection mechanism for subunits dissociated from α-crystallin oligomers against UV irradiation-induced aggregation of γD-crystallin, at an expense of a loss of a short C-terminal peptide in γD-crystallin.

Effects of Electrospun Potato Protein-Maltodextrin Mixtures and Thermal Glycation on Trypsin Inhibitor Activity

Fibers of potato protein and polysaccharides were obtained by needleless electrospinning. Mixtures of maltodextrin DE2 (dextrose equivalent) (0.8 g/mL), DE21 (0.1 g/mL), and different concentrations of potato protein (0.05, 0.1, 0.15, and 0.2 g/mL) were used for fiber production. Glycation was performed via the Maillard reaction after thermal treatment (0/6/12/24/48 h, 65 °C, 75% relative humidity). The effects of electrospinning and heating on trypsin inhibitor activity (IA) were studied. The results of the IA assay showed that electrospinning and glycation caused significant differences in IA among blends, heating times, and the interaction of blend and heating time (p < 0.001). The higher the protein content in the fibers, the higher the IA. The lowest IA was found in the mixture with the lowest protein content after 48 h. In other blends, the minimum IAs were found between 6 and 12 h of heating. The determination of the free lysine groups showed a nonsignificant decrease after heating. However, higher free lysine groups per protein (6.3−9.5 g/100 g) were found in unheated fibers than in the potato protein isolate (6.0 ± 0.5 g/100 g). The amide I and amide II regions, detected by the Fourier transform infrared spectra, showed only a slight shift after heating.

Influence of Urea and Dimethyl Sulfoxide on K-Peptide Fibrillation

Protein fibrillation leads to formation of amyloids-linear aggregates that are hallmarks of many serious diseases, including Alzheimer's and Parkinson's diseases. In this work, we investigate the fibrillation of a short peptide (K-peptide) from the amyloidogenic core of hen egg white lysozyme in the presence of dimethyl sulfoxide or urea. During the studies, a variety of spectroscopic methods were used: fluorescence spectroscopy and the Thioflavin T assay, circular dichroism, Fourier-transform infrared spectroscopy, optical density measurements, dynamic light scattering and intrinsic fluorescence. Additionally, the presence of amyloids was confirmed by atomic force microscopy. The obtained results show that the K-peptide is highly prone to form fibrillar aggregates. The measurements also confirm the weak impact of dimethyl sulfoxide on peptide fibrillation and distinct influence of urea. We believe that the K-peptide has higher amyloidogenic propensity than the whole protein, i.e., hen egg white lysozyme, most likely due to the lack of the first step of amyloidogenesis-partial unfolding of the native structure. Urea influences the second step of K-peptide amyloidogenesis, i.e., folding into amyloids.

Macrophage Polarization Profiling on Native and Regenerated Silk Biomaterials

We investigated the plasticity and polarization of THP-1 cells on native and regenerated silk-based biomaterials to address the basic paradigm of immune response. Here, we report redox kinetics, adhesion morphology, and nitric oxide release patterns to identify specific subtypes of macrophages at different time points. Water-annealed silk film and native fibrous braids from Bombyx mori silkworms showed higher anti-inflammatory cytokine profiles or M2 subtypes (as evidenced by the enhanced expression of interleukin-10, interleukin-13, and interleukin-4). Ethanol-treated Bombyx mori silk films and Antheraea mylitta braids exhibited higher levels of pro-inflammatory cytokines or the M1 subtype (as evidenced by enhanced expression of interleukin-1, interleukin-6, interleukin-8, interferon-γ, TNF-α, and GM-CSF) in contact with healthy THP monocytes for 14 days; such a long study is unprecedented. Cytokine microarray analysis revealed the transition (M0-M1, M1-M2), plasticity, and stable phenotype of THP-1 cells in a variable stage in contact with different physicochemical properties of silk-based biomaterials. The detailed immunogenicity in the context of the physicochemical properties of native and regenerative silk-based biomaterials will enable us to accurately predict the possibility of a pro-/anti-inflammatory response. It will helps to predict the in vivo reprogramming and avoid fibrosis formation to enhance their clinical translational potential.

Enhancing the Kinetic Stability of Polymeric Nanomicelles (PLGA) Using Nano-Montmorillonite for Effective Targeting of Cancer Tumors

The toxic profile of chemical cross-linkers used in enhancing the stability of self-assembled nanomicelles made of amphiphilic polymeric materials hinders their use in clinical applications. This study was aimed to use the layered structure of Na-montmorillonite (MMT) as a stabilizer for nanomicelles made of poly(d,l-lactide-co-glycolide) (PLGA) amphiphilic polymer. The size of Na-MMT was reduced below 40 nm (nano-MMT) by processing in an attritor prior to its incorporation with PLGA. Hybrid PLGA nano-MMT (PM) nanoparticles (NPs) were prepared using dialysis nanoprecipitation. The size distribution was measured using dynamic light scattering (DLS). Loading 1250 μg of the model drug molecule curcumin to PM (PMC) resulted in obtaining 88 nm-sized particles, suitable for passive targeting of cancer tumors. The structure of nano-MMT and its position in PMC were investigated using FT-IR, differential scanning chalorimetry (DSC), XRF, XRD, ESEM, and EDAX assays, all of which showed the exfoliated structure of nano-MMT incorporated with both hydrophilic and hydrophobic blocks of PLGA. Curcumin was mutually loaded to PLGA and nano-MMT. This firm incorporation caused a serious extension in the release of curcumin from PMC compared to PLGA (PC). Fitting the release profile to different mathematical models showed the remarkable role of nano-MMT in surface modification of PLGA NPs. The ex vivo dynamic model showed the enhanced stability of PMC in simulated blood flow, while cytotoxicity assays showed that nano-MMT does not aggravate the good toxic profile of PLGA but improves the anticancer effect of payload. Nano-MMT could be used as an effective nontoxic stabilizer agent for self-assembled NPs.

Multiple surface interaction mechanisms direct the anchoring, co-aggregation and formation of dual-species biofilm between Candida albicans and Helicobacter pylori

Introduction

Polymicrobial biofilms have a significant impact on pathogenesis of infectious microorganisms. Many human diseases are affected by colonization of multi-species communities affecting negatively the treatments and increase the risks for the health. In particular, in the epithelium of the stomach co-existence between C. albicans and H. pylori has been described, which has been associated to a synergistic effect on ulcer pathogenesis.

Objective

The objective of this work was to advance in the understanding of surface interaction between H. pylori and C. albicans for the formation of polymicrobial biofilms.

Methods

Studies of microbial surfaces both bacterium, yeast and co-cultures of them were carried out by infrared spectroscopy, deconvolution analysis, transmission and scanning electron microscopies, and optic microscopy. Additional methods were used to contrast the results as dynamic light scattering, contact angle, agarose gel electrophoresis and gene amplification.

Results

Several surface interaction mechanisms promote the anchoring of H. pylori on C. albicans, cell co-aggregation, and polymicrobial biofilm formation, main identified interactions were: (i) hydrophobic interactions between non-polar peptide chains and lipid structures, characterized by θ_w among 84.9 ± 1.6 (γ = 22.78 mJ/m² with 95.3 of dispersive contribution) and 76.6 ± 3.8 (γ = 17.34 mJ/m², 40.2 of dispersive contribution) for C. albicans and H. pylori, respectively, (ii) hydrogen bonds between surface components of yeast and bacterium (e.g., -S-H⋅⋅⋅NH₂- or -S-H⋅⋅⋅O[bond, double bond]CO-) and (iii) thiol-mediated surface interactions identified by displacements to lower wavenumbers (Δv = 5 cm^-1). Evidence of internalization and electrostatic interactions were not evidenced. All observations were congruent with the biofilm formation, including the identification of small-size biostructures (i.e., 122-459 nm) associated with extracellular proteins, extracellular DNA, or outer membrane vesicles were observed characteristic of biofilm formation.

Conclusion

It is concluded that biofilm is formed by co-aggregation after anchoring of H. pylori on C. albicans. Several surface interactions were associated with the prevalence of H. pylori, the possibility to find C. albicans in the stomach epithelium infected by H. pylori, but also, strength interactions could be interfering in experimental observations associated with bacterial-DNA detection in culture mixtures.

Interaction of Prion Peptides with DNA Structures

Prion protein aggregation is known to be modulated by macromolecules including nucleic acids. To clarify the role of nucleic acids in PrP pathology, we investigated the interaction between nucleic acids and the prion peptide (PrP)-a synthetic prion protein model peptide resembling a portion of the human prion protein in structure and function spanning amino acid residues 106-126. We used synthetic DNA lattices and natural DNA duplexes extracted from salmon (sDNA) bound with PrP and studied their interaction using distinct physical measurements. The formation of DNA lattices with PrP was visualized by atomic force microscopy (AFM) to investigate the influence of the PrP. PrP inhibited the growth of the double-crossover (DX) lattices significantly compared to the control peptide (CoP). We also conducted optical measurements such as ultraviolet-visible (UV-Vis), circular dichroism (CD), and Fourier transform infrared (FTIR) spectroscopies to validate the interaction between PrP and DNA immediately (D0) and after a 30-day incubation (D30) period. UV-Vis spectra showed variation in the absorbance intensities, specific for the binding of CoP and PrP to DNA. The CD analysis revealed the presence of various secondary structures, such as α-helices and β-sheets, in PrP- and PrP-bound sDNA complexes. The PrP-sDNA interaction was confirmed using FTIR by the change and shift of the absorption peak intensity and the alteration of PrP secondary structures in the presence of DNA. The cytotoxic effects of the PrP-bound sDNA complexes were assessed by a cytotoxicity assay in human neuroblastoma cells in culture. It confirmed that PrP with sDNA was less cytotoxic than CoP. This study provides new applications for DNA molecules by investigating their effect in complex with aggregated proteins. Our study unequivocally showed the beneficial effect of the interaction between DNA and the pathological prion protein. It therefore provides valuable information to exploit this effect in the development of potential therapeutics. Moreover, our work might serve as a basis for further studies investigating the role of DNA interactions with other amyloidogenic proteins.

Characterization of the Conformational Properties of Soluble and Insoluble Proteins by Fourier Transform Infrared Spectroscopy

The FTIR (micro-)spectroscopy method applied to the study of the structural properties of different soluble and insoluble proteins will be illustrated. In particular, we will discuss the procedure to analyze proteins in form of hydrated films and in solution by means of attenuated total reflection (ATR) measurements. Moreover, we will describe the procedure to characterize bacterial inclusion bodies (IBs) and amyloid deposits within human tissues by means of FTIR microspectroscopy.

Characterization of an exopolysaccharide (EPS-3A) produced by Streptococcus thermophilus ZJUIDS-2-01 isolated from traditional yak yogurt

Yak yogurt, one of the naturally fermented dairy products prepared by local herdsmen in the Qinghai-Tibet Plateau, contains a diverse array of microorganisms. We isolated and identified a novel Streptococcus thermophilus strain, ZJUIDS-2-01, from the traditional yak yogurt. We further purified and carried out detailed structural, physiochemical, and bioactivity studies of an exopolysaccharide (EPS-3A) produced by S. thermophilus ZJUIDS-2-01. The weight-average molecular weight (Mw) of EPS-3A was estimated to be 1.38 × 10⁶ Da by High-Performance Gel Permeation Chromatography (HPGPC). The monosaccharide analysis established its composition to be glucose, galactose, N-acetyl-D-galactosamine, and rhamnose in a ratio of 5.2:2.5:6.4:1.0. The molecular structure of EPS-3A was determined by the combination of permethylation analysis, FT-IR, and NMR spectroscopic techniques. The ζ-potential measurements indicated that EPS-3A had a pKa value of ~4.40. The DSC yielded a melting point (T_m) of 80.4 °C and enthalpy change (ΔH) of 578 J/g for EPS-3A, comparable to those of the xanthan gum (XG), a commercial EPS. EPS-3A exhibited better O/W emulsion stability and flocculating capacity than XG. Furthermore, it also demonstrated similar antioxidant activity to XG and promising in vitro antibacterial properties. This work evidenced that EPS-3A derived from S. thermophilus ZJUIDS-2-01 holds the potential for food and industrial applications.

Truncation-Driven Lateral Association of α-Synuclein Hinders Amyloid Clearance by the Hsp70-Based Disaggregase

The aggregation of α-synuclein is the hallmark of a collective of neurodegenerative disorders known as synucleinopathies. The tendency to aggregate of this protein, the toxicity of its aggregation intermediates and the ability of the cellular protein quality control system to clear these intermediates seems to be regulated, among other factors, by post-translational modifications (PTMs). Among these modifications, we consider herein proteolysis at both the N- and C-terminal regions of α-synuclein as a factor that could modulate disassembly of toxic amyloids by the human disaggregase, a combination of the chaperones Hsc70, DnaJB1 and Apg2. We find that, in contrast to aggregates of the protein lacking the N-terminus, which can be solubilized as efficiently as those of the WT protein, the deletion of the C-terminal domain, either in a recombinant context or as a consequence of calpain treatment, impaired Hsc70-mediated amyloid disassembly. Progressive removal of the negative charges at the C-terminal region induces lateral association of fibrils and type B* oligomers, precluding chaperone action. We propose that truncation-driven aggregate clumping impairs the mechanical action of chaperones, which includes fast protofilament unzipping coupled to depolymerization. Inhibition of the chaperone-mediated clearance of C-truncated species could explain their exacerbated toxicity and higher propensity to deposit found in vivo.

(De)stabilization of Alpha-Synuclein Fibrillary Aggregation by Charged and Uncharged Surfactants

Parkinson’s disease (PD) is the second most common neurodegenerative disorder. An important hallmark of PD involves the pathological aggregation of proteins in structures known as Lewy bodies. The major component of these proteinaceous inclusions is alpha (α)-synuclein. In different conditions, α-synuclein can assume conformations rich in either α-helix or β-sheets. The mechanisms of α-synuclein misfolding, aggregation, and fibrillation remain unknown, but it is thought that β-sheet conformation of α-synuclein is responsible for its associated toxic mechanisms. To gain fundamental insights into the process of α-synuclein misfolding and aggregation, the secondary structure of this protein in the presence of charged and non-charged surfactant solutions was characterized. The selected surfactants were (anionic) sodium dodecyl sulphate (SDS), (cationic) cetyltrimethylammonium chloride (CTAC), and (uncharged) octyl β-D-glucopyranoside (OG). The effect of surfactants in α-synuclein misfolding was assessed by ultra-structural analyses, in vitro aggregation assays, and secondary structure analyses. The α-synuclein aggregation in the presence of negatively charged SDS suggests that SDS-monomer complexes stimulate the aggregation process. A reduction in the electrostatic repulsion between N- and C-terminal and in the hydrophobic interactions between the NAC (non-amyloid beta component) region and the C-terminal seems to be important to undergo aggregation. Fourier transform infrared spectroscopy (FTIR) measurements show that β-sheet structures comprise the assembly of the fibrils.

Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

UV Resonance Raman explores protein structural modification upon fibrillation and ligand interaction

Amyloids are proteinaceous deposits considered an underlying pathological hallmark of several degenerative diseases. The mechanism of amyloid formation and its inhibition still represent challenging issues, especially when protein structure cannot be investigated by classical biophysical techniques as for the intrinsically disordered proteins (IDPs). In this view, the need to find an alternative way for providing molecular and structural information regarding IDPs prompted us to set a novel, to our knowledge, approach focused on UV Resonance Raman (UVRR) spectroscopy. To test its applicability, we study the fibrillation of hen-egg white lysozyme (HEWL) and insulin as well as their interaction with resveratrol, employing also intrinsic fluorescence spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The increasing of the β-sheet structure content at the end of protein fibrillation probed by FTIR occurs simultaneously with a major solvent exposure of tryptophan (Trp) and tyrosine (Tyr) residues of HEWL and insulin, respectively, as revealed by UVRR and intrinsic fluorescence spectroscopy. However, because the latter technique is successfully used when proteins naturally contain Trp residues, it shows poor performances in the case of insulin, and the information regarding its tertiary structure is exclusively provided by UVRR spectroscopy. The presence of an increased concentration of resveratrol induces mild changes in the secondary structure of both protein fibrils while remodeling HEWL fibril length and promoting the formation of amorphous aggregates in the case of insulin. Although the intrinsic fluorescence spectra of proteins are hidden by resveratrol signal, UVRR Trp and Tyr bands are resonantly enhanced, showing a good sensitivity to the presence of resveratrol and marking a modification in the noncovalent interactions in which they are involved. Our findings demonstrate that UVRR is successfully employed in the study of aggregation-prone proteins and of their interaction with ligands, especially in the case of Trp-lacking proteins.

Protein Structural Denaturation Evaluated by MCR-ALS of Protein Microarray FTIR Spectra

The loss of native structure is common in proteins. Among others, aggregation is one structural modification of particular importance as it is a major concern for the efficiency and safety of biotherapeutic proteins. Yet, recognizing the structural features associated with intermolecular bridging in a high-throughput manner remains a challenge. We combined here the use of protein microarrays spotted at a density of ca 2500 samples per cm² and Fourier transform infrared (FTIR) imaging to analyze structural modifications in a set of 85 proteins characterized by widely different secondary structure contents, submitted or not to mild denaturing conditions. Multivariate curve resolution alternating least squares (MCR-ALS) was used to model a new spectral component appearing in the protein set subject to denaturing conditions. In the native protein set, 6 components were found to be sufficient to obtain good modeling of the spectra. Furthermore, their shape allowed them to be assigned to α-helix, β-sheet, and other structures. Their content in each protein was correlated with the known secondary structure, confirming these assignments. In the denatured proteins, a new component was necessary and modeled by MCR-ALS. This new component could be assigned to the intermolecular β-sheet, bridging protein molecules. MCR-ALS, therefore, unveiled a potential spectroscopic marker of protein aggregation and allowed a semiquantitative evaluation of its content. Insight into other structural rearrangements was also obtained.

All-or-none amyloid disassembly via chaperone-triggered fibril unzipping favors clearance of α-synuclein toxic species

α-synuclein aggregation is present in Parkinson's disease and other neuropathologies. Among the assemblies that populate the amyloid formation process, oligomers and short fibrils are the most cytotoxic. The human Hsc70-based disaggregase system can resolve α-synuclein fibrils, but its ability to target other toxic assemblies has not been studied. Here, we show that this chaperone system preferentially disaggregates toxic oligomers and short fibrils, while its activity against large, less toxic amyloids is severely impaired. Biochemical and kinetic characterization of the disassembly process reveals that this behavior is the result of an all-or-none abrupt solubilization of individual aggregates. High-speed atomic force microscopy explicitly shows that disassembly starts with the destabilization of the tips and rapidly progresses to completion through protofilament unzipping and depolymerization without accumulation of harmful oligomeric intermediates. Our data provide molecular insights into the selective processing of toxic amyloids, which is critical to identify potential therapeutic targets against increasingly prevalent neurodegenerative disorders.

Cryogenic activity and stability of benzaldehyde lyase enzyme in lipidic mesophases-nanoconfined water

Phytantriol-based lipidic mesophases (LMs) are introduced as a platform for cryoenzymology, which relies on the presence of liquid water in LMs at subzero temperatures. After incorporation into LMs, the model enzyme Benzaldehyde lyase (BAL) shows high cryogenic stability and activity. In contrast, BAL in bulk solution undergoes significant secondary structural transitions caused by low temperatures (cold denaturation), demonstrating the potential of this approach to enable in meso cryoenzymology.

Normal mode calculation and infrared spectroscopy of proteins in water solution: Relationship between amide I transition dipole strength and secondary structure

Dipole Strength (DS) of the amides has gained a renewed interest in chemical physics since it provides an important tool to disclose the on-site vibrational energy distributions. Apart from earlier experimental efforts on polypeptides, little is still known about DS in complex proteins. We accurately measured the Fourier Transform Infrared absorption spectra of nine proteins in water solution obtaining their Molar Extinction Coefficient in the amide I and II spectral region. Our results show that the amide I DS value depends on the protein secondary structure, being that of the α-rich and unstructured proteins lower by a factor of 2 than that of the β-rich proteins. The average DS for amino acids in α and β secondary structures confirms this finding. Normal Mode calculation and Molecular Dynamics were performed and used as tools for data analysis and interpretation. The present outcomes corroborate the hypothesis that antiparallel β-sheet environment is more prone to delocalize the on-site CO stretching vibration through coupling mechanisms between carbonyl groups, whereas α-helix structures are energetically less stable to permit vibrational mode delocalization.