The infrared absorption of amino acid side chains

Smoking-induced shifts in salivary exosomal cytokines and amino acid profiles as potential early biomarkers for oral cancer

BACKGROUND

Chronic smoking is an established risk factor for oral cancer (OC). The role of tobacco in oral squamous cell cancer (OSCC) emphasizes the need for non-invasive diagnostic approaches to identify early molecular alterations and improve patient outcomes. Salivary exosomes, which contain proteins, lipids, and nucleic acids, accessible and rich in biological content, making them interesting candidate biomarkers.

METHODS

Saliva samples were collected from non-smokers (n = 20), smokers (n = 20), and patients with oral cancer (n = 20). Salivary exosomes were isolated and characterized using various techniques, including estimation of protein concentrations and amino acid profiling using High-Performance Liquid Chromatography (HPLC). Fourier Transform Infrared (FTIR) spectroscopy analyzed protein and amino acid peaks, while enzyme-linked immunosorbent assay (ELISA) measured pro-inflammatory cytokines IL-6 and IL-8.

RESULTS

Elevated levels of salivary exosomal proteins (p = 0.017), IL-6 (p = 0.008), and IL-8 (p = 0.0004), along with significant alterations in amino acid profiles, were observed in smokers compared with non-smokers. Additionally, protein (p = 0.005) and IL-6 (p = 0.004) levels were significantly elevated in oral cancer compared to non-smoker group. FTIR spectroscopy revealed distinct molecular fingerprints in exosomes, highlighting changes in protein and amino acid concentrations and indicating altered metabolism.

CONCLUSION

This comparative cross-sectional study demonstrated that chronic smoking induces significant biochemical changes in salivary exosomes, establishing them as promising non-invasive biomarkers for early oral cancer detection. Elevated pro-inflammatory cytokines IL-6 and IL-8, along with altered amino acid profiles, may create pre-cancerous conditions. Notably, along with altered amino acid profiles, IL-6 levels progressively increase from smoking to oral cancer, highlighting its potential role in cancer progression.

IR Fingerprint of the Intermolecular Hydrogen Bond on Amino Acids and Its Relevance to Chaperone Activity of αB-Crystallin

Intermolecular hydrogen bonds between carboxyl (COO-) and amino groups are a common weak interaction in proteins. Infrared (IR) spectral assignment of such an intermolecular hydrogen bond provides a fingerprint for studying protein-protein interactions as its absorption frequency is affected by the molecular electrostatic environment. Temperature-dependent FTIR and temperature-jump time-resolved IR absorbance difference spectra of several typical amino acids and those of wild type and single-site mutated αB-crystallin were performed. It was found that the antisymmetric vibrational frequency of the COO- groups in amino acids decreases from approximately 1626 to 1610 cm-1 upon the formation of intermolecular hydrogen bonds, which was further supported by DFT calculations, while the IR frequency of the intermolecular hydrogen bonds on the formation of intermolecular hydrogen bonds, which was further supported by DFT calculations, while the IR frequency of the intermolecular hydrogen bonded COO- groups at the αB-crystallin dimeric interface was also observed around 1610 cm-1. With this spectral label, the active site of αB-crystallin, a heat shock molecular chaperone against the UV-light-damaged γD-crystallin was investigated. The active site was found to be localized at an arch loop structure connecting the two β-strands locked by intermolecular hydrogen bonds at the dimeric interface. It is the liberated arch loop after breaking of the intermolecular hydrogen bond locks that binds the damaged γD-crystallin, leading to the observed chaperone-like activity of αB-crystallin.

Bioactive peptides from food waste: New innovative bio-nanocomplexes to enhance cellular uptake and biological effects

Mastitis is the most important bovine disease, causing dramatic economic losses to the dairy industry, worldwide. This study explores the valorization of whey from cows affected by mastitis, through a novel separation approach. Surface Active Maghemite Nanoparticles (SAMNs) were used as magnetic baits to selectively bind bioactive peptides with potential health benefits. Advanced techniques such as HPLC and LC-MS/MS highlighted SAMN capability of isolating a restricted group of peptides, drastically diverging from the control profile (Solid Phase Extraction, SPE) and characterized by a peculiar acidic residue distribution. Most importantly, both magnetically purified and nano-immobilized peptides (SAMN@peptides) showed protective activity against oxidative stress and inflammation, when tested on Caco-2 cells; with SAMN@peptides being associated with the strongest biological effect. SAMNs exhibited excellent characteristics, they are environmentally sustainable, and their synthesis is cost-effective prompting at a scalable and selective tool for capturing bioactive peptides, with potential applications in functional foods and nutraceuticals.

Lipid Coating Modulates Effects of Nanoceria on Oxidative Metabolism in Human Embryonic Lung Fibroblasts: A Case of Cardiolipin

The unique redox properties of nanoscale cerium dioxide determine its diverse application in biology and medicine as a regulator of oxidative metabolism. Lipid modifiers of the nanoparticle surface change their biochemical properties and bioavailability. Complexes with lipids can be formed upon contact of the nanoparticles with the membrane. The effects of lipid coating on nanoceria have not been studied yet. Here, we assessed the effect of bare and cardiolipin-coated CeO2 on the expression of oxidative metabolism genes in human embryonic lung fibroblasts. Cell viability, mitochondrial activity, intracellular reactive oxygen species, NOX4, NRF2, and NF-κB expression, oxidative DNA damage/repair, autophagy, and cell proliferation were studied. We used an MTT assay, fluorescence microscopy, real-time reverse transcription polymerase chain reaction, and flow cytometry. At a concentration of 1.5 μM, bare and cardiolipin-coated nanoceria penetrated into cells within 1-3 h. Cell survival, mitochondrial activity, and the proliferative effect were similar for bare and cardiolipin-coated nanoceria. Intracellular ROS, activation of NOX4, NRF2, and NF-kB, DNA oxidative damage, and DNA break/repair were different. Cardiolipin-coated nanoceria induced intracellular oxidative stress and short-term activation of these genes and DNA damage/break/repair. Unlike bare nanoceria, cardiolipin-coated nanoceria induced autophagy. Thus, the effects of cardiolipin-coated nanoceria are determined by both the nanoceria itself and cardiolipin. Presumably, the differences in properties are due to lipid peroxidation of cardiolipin. This effect needs to be taken into account when developing nanoceria-based drugs targeting mitochondria.

Anti-amyloidogenic hexapeptide-coated gold nanoparticles for enhanced inhibition of amyloid formation: A promising therapeutic approach

Under specific external stimulus, misfolded and natively disordered globular proteins undergo irreversible transformation into pathogenic β-sheet-rich insoluble fibrillar structure, and deposition of theses fibrils in cells and tissues leads to disorders like Alzheimer's, Dementia, Type II diabetes, and many more. Here, we have developed a positively-charged Arg-containing hexapeptide, SqP7, and elucidated its anti-amyloidogenic propensity on in vitro HEWL amyloid formation under acidic and neutral fibrillation conditions using computational tools and several biophysical techniques. SqP7, at a five-fold molar excess, displayed excellent amyloid inhibition capability at both pH conditions (~83 % and 72 % inhibition under acidic and neutral fibrillation conditions, respectively), and was further chosen as a coating agent on gold nanoparticles. This was done to investigate whether coating of this peptide on gold nanoparticles has any effect on its anti-amyloidogenic efficiency and effective inhibition concentration. The synthesized SqP7-coated gold nanoparticles were characterized to be spherical and highly-dispersed having a mean diameter of 9.12 ± 2.08 nm. The anti-amyloidogenic capability of the synthesized SqP7-coated gold nanoparticles was further evaluated, and a 10-fold reduction in the effective inhibition concentration of SqP7 was observed. This peptide‑gold nanoparticle based integrated approach can lead to the development of highly effective therapeutics for amyloid-related diseases, offering improved prevention and treatment options.

Effects of enzyme-induced carbonate precipitation (EICP) with different urease sources on the zinc remediation

Enzyme-induced carbonate precipitation (EICP) has been studied in the remediation of heavy metals in recent years. This study aims to investigate the impact of EICP with jack bean urease (JU) and sword bean urease (SU) on the Zn2+ remediation. The results show that relatively high concentration of organic molecules in SU can protect urease from deactivation and absorb Zn2+. For the treatment subject to 1 mmol/L of Zn2+ without calcium chloride added, the final NH4+ conversion efficiency and Zn2+ immobilization percentage for the SU group are 95 % and 95.1 % higher than those for JU group, respectively. For the treatment with calcium chloride added, SU group can produce enough CO32-, contributing to over 99 % formation of CaCO3. The CaCO3 can decrease Zn2+ concentration through the physical absorption. The highest Zn2+ immobilization percentage (98.9 %) can be achieved using SU with 0.5 mol/L calcium chloride. The XRD, FTIR and SEM-EDS analysis also show that CaCO3, ZnCO3, and Zn(OH)2 can be generated, and the organic molecules in SU and CaCO3 can adsorb Zn2+. SU is recommended as the catalyzer to immobilize Zn2+. The mechanism of Zn2+ immobilization can be understood as bio-mineralization to form ZnCO3 and Zn(OH)2, as well as adsorption by organic molecules in SU and CaCO3.

Formation mechanism of iron-catechol complexes in the colored periostracum of Corbicula spp

The shell color of Corbicula clams, which are globally distributed, is roughly divided into yellowish and blackish depending on the environmental conditions of the sediment. The formation of an iron-L-3,4-dihydroxyphenylalanine (DOPA) complex in a thin organic layer, called the periostracum, on a calcareous layer causes the blackening of the clamshell. However, the iron-DOPA complex formation mechanism is unclear. To reveal how the iron is transported from the aquatic environment to the periostracum, cross-sectional analyses of the shell were conducted using an electron probe microanalyzer and Raman spectroscopy to investigate the distribution and structure of iron in the shell. Iron was only present in the periostracum, excluding deposition, and all iron was in the form of an iron-DOPA complex. Attenuated total reflection infrared spectroscopy and oxygen K-edge X-ray absorption fine structure spectroscopy revealed that the molecular structure of the native periostracum is independent of shell color. These results indicate that dissolved iron-organic complexes diffuse from the aqueous environment to the periostracum, forming iron-DOPA complex through ligand exchange. Because the iron-DOPA complex color depends on the pH, the shell color can serve as a historical indicator of the shell's growth environment.

Use of FTIR to study secondary structure of texturized plant proteins by high moisture extrusion cooking, a comprehensive review

Fourier-Transform Infrared spectroscopy (FTIR) is often used by researchers to understand the texturization mechanisms of plant proteins. High Moisture Extrusion-Cooking (HMEC) is the main process used for their texturization by heating, mechanical shearing, and subsequent cooling of a high-moisture mixture, which causes denaturation and restructuration of proteins, resulting in an anisotropic product, commonly called "meat analog". Researchers try to link the properties of extrudates to the secondary conformation of proteins, which are supposed to aggregate and align in the flow direction within the die. This review will attempt to show the reasons for studying the secondary structures of plant proteins in HMEC-textured products, and compare and discuss the different methods applied to prepare samples and analyze them by FTIR. A focus will be put on the different methods of spectra analysis (i.e., peak deconvolution, and reference tables used), for which a total of around 60 scientific papers have been carefully analyzed to illustrate the disparity of reference tables used in the literature. A discussion will summarize the various hypotheses currently found in the literature, and provided by FTIR to explain the texturization mechanisms of plant proteins through HMEC. Finally, advice such as comparing results with other amide bands and other analysis methods and following published procedures, are provided as an outlook for future improvements in FTIR data quality, processing and interpretation.

Optimizing lipopeptide bioactivity: The impact of non-ionic surfactant dressing

The aim of the research is to increase the applicability of lipopeptides as drugs. To this end, non-ionic triblock copolymers, namely poloxamers, were applied. The physico-chemical properties of poloxamers vary depending on the length of the blocks. In our study, we experimented with different types and systematically investigated the variation of the critical micelle concentration (CMC) of poloxamers at 25 and 37 °C in different media. In addition, the cytotoxicity of the different poloxamer micelles on three different cell lines was evaluated, and based on the results, Plur104, Plur123, and Plur127 were selected. Fatty acid elongated derivatives of a short antibacterial peptide (pL1), a medium-sized anticancer peptide (pCM15), and a branched-chain vaccine antigen (pATIPC) were used as lipopeptide models, and their formulations with the selected poloxamers were investigated. The solubility and homogeneity of the lipopeptides were significantly increased, and dynamic light scattering (DLS) measurements showed the formation of small particles of around 20 nm, which were well reproducible and storable. Similar homogenous micelle formation was observed after freeze-drying and reconstitution with water. The pL1 lipopeptide, formulated with the selected poloxamers, exhibited enhanced antibacterial activity with significantly reduced haemolytic side effects. The pCM15 peptide, when incorporated into poloxamer micelles, showed significantly enhanced cytotoxicity against tumor cells. Additionally, the internalization rate of poloxamer-formulated pATIPC peptide by antigen-presenting model cells exceeded that of the unformulated peptide. Our results demonstrate the potential of poloxamers as promising tools for the formulation of lipopeptides and for the optimization of their selectivity.

Disassembly of self-assembling peptide hydrogels as a versatile method for cell extraction and manipulation

Self-assembling peptide hydrogels (SAPHs) are increasingly being used as two-dimensional (2D) cell culture substrates and three-dimensional (3D) matrices due to their tunable properties and biomimicry of native tissues. Despite these advantages, SAPHs often represent an end-point in cell culture, as isolating cells from them leads to low yields and disruption of cells, limiting their use and post-culture analyses. Here, we report on a protocol designed to easily and effectively disassemble peptide amphiphile (PA) SAPHs to retrieve 3D encapsulated cells with high viability and minimal disruption. Due to the pivotal role played by salt ions in SAPH gelation, tetrasodium ethylenediaminetetraacetic acid (Na4EDTA) was used as metal chelator to sequester ions participating in PA self-assembly and induce a rapid, efficient, clean, and gentle gel-to-sol transition. We characterise PA disassembly from the nano- to the macro-scale, provide mechanistic and practical insights into the PA disassembly mechanism, and assess the potential use of the process. As proof-of-concept, we isolated different cell types from cell-laden PA hydrogels and demonstrated the possibility to perform downstream biological analyses including cell re-plating, gene analysis, and flow cytometry with high reproducibility and no material interference. Our work offers new opportunities for the use of SAPHs in cell culture and the potential use of cells cultured on SAPHs, in applications such as cell expansion, analysis of in vitro models, cell therapies, and regenerative medicine.

Probing the Interplay of Protein Self-Assembly and Covalent Bond Formation in Photo-Crosslinked Silk Fibroin Hydrogels

Covalent crosslinking of silk fibroin via native tyrosine residues has been extensively explored; however, while these materials are very promising for biomedical, optical, soft robotics, and sensor applications, their structure and mechanical properties are unstable over time. This instability results in spontaneous silk self-assembly and stiffening over time, a process that is poorly understood. This study investigates the interplay between self-assembly and di-tyrosine bond formation in silk hydrogels photo-crosslinked using ruthenium (Ru) and sodium persulfate (SPS) with visible light. The effects of silk concentration, molecular weight, Ru/SPS concentration, and solvent conditions are examined. The Ru/SPS system enables rapid crosslinking, achieving gelation within seconds and incorporating over 90% of silk into the network, even at very low protein concentrations (≥0.75% wt/v). A model emerges where silk self-assembly both before and after crosslinking affects protein phase separation, mesoscale structure, and dynamic changes in the hydrogel network over time. Silk concentration has the greatest impact on hydrogel properties, with higher silk concentration hydrogels experiencing two orders of magnitude increase in stiffness within 1 week. This new understanding and ability to tune hydrogel properties and dynamic stiffening aids in developing advanced materials for 4D biofabrication, sensing, 3D cancer models, drug delivery, and soft robotics.

Boosting stability: a hierarchical approach for self-assembling peptide structures

The primary objective of this study was to implement a hierarchical approach to enhance the conformational stability of a selected group of peptides by incorporating trans-(1S,2S)-2-aminocyclopentanecarboxylic acid (trans-ACPC). The influence of residue mutation on the peptide structures was investigated using circular dichroism, analytical ultracentrifugation, and vibrational spectroscopy. The resulting nanostructures were examined via transmission electron microscopy. The incorporation of trans-ACPC led to increased conformational stability and self-assembling propensity in peptides containing constrained β-amino acid residues.

Infrared Spectroscopy of SARS-CoV-2 Viral Protein: from Receptor Binding Domain to Spike Protein

Spike (S) glycoprotein is the largest structural protein of SARS-CoV-2 virus and the main one involved in anchoring of the host receptor ACE2 through the receptor binding domain (RBD). S protein secondary structure is of great interest for shedding light on various aspects, from functionality to pathogenesis, finally to spectral fingerprint for the design of optical biosensors. In this paper, the secondary structure of SARS-CoV-2 S protein and its constituting components, namely RBD, S1 and S2 regions, are investigated at serological pH by measuring their amide I infrared absorption bands through Attenuated Total Reflection Infrared (ATR-IR) spectroscopy. Experimental data in combination with MultiFOLD predictions, Define Secondary Structure of Proteins (DSSP) web server and Gravy value calculations, provide a comprehensive understanding of RBD, S1, S2, and S proteins in terms of their secondary structure content, conformational order, and interaction with the solvent.

De Novo Design and Characterization of Amphiphilic Peptides with Basic Side Chains for Tailored Interfacial Chemistries

Lysine-leucine (LK) peptides have been used as model systems and platforms for 2D material design for decades. LK peptides are amphiphilic sequences designed to bind and fold at hydrophobic surfaces through hydrophobic leucine side chains and hydrophilic lysine side chains extending into the aqueous subphase. The hydrophobic periodicity of the sequence dictates the secondary structure at the interface. This robust design makes them ideal candidates for controlling interfacial chemistry. This study presents the de novo design and characterization of two novel peptides: LRα14 and LHα14, which substitute lysine with arginine and histidine, respectively, in the helical LKα14 sequence. This modification is intended to expand the LK peptide platform to a new basic interfacial chemistry. We explore the stability of the new LRα14 and LHα14 designs with respect to changes in pH and salt concentration in bulk solution and at the interface using circular dichroism (UV-CD) and vibrational sum-frequency generation spectroscopy, respectively. Notably, the structural stability of the peptides remains unaffected across a wide range of pH and ionic strength values. At the same time, the variation of side-chain chemistry leads to a wide spectrum of interfacial water structures. By extension of the LK platform to include arginine and histidine, this study broadens the toolbox for designing tailored interfacial chemistries with applications in material and biomedical sciences.

Structure and Intercalation of Cysteine-Asparagine-Serine Peptide into Montmorillonite as an Anti-Inflammatory Agent Preparation-A DFT Study

Peptides are receiving significant attention in pharmaceutical sciences due to their applications as anti-inflammatory drugs; however, many aspects of their interactions and mechanisms at the molecular level are not well-known. This work explores the molecular structure of two peptides-(i) cysteine (Cys)-asparagine (Asn)-serine (Ser) (CNS) as a molecule in the gas phase and solvated in water in zwitterion form, and (ii) the crystal structure of the dipeptide serine-asparagine (SN), a reliable peptide indication whose experimental cell parameters are well known. A search was performed by means of atomistic calculations based on density functional theory (DFT). These calculations matched the experimental crystal structure of SN, validating the CNS results and useful for assignments of our experimental spectroscopic IR bands. Our calculations also explore the intercalation of CNS into the interlayer space of montmorillonite (MNT). Our quantum mechanical calculations show that the conformations of these peptides change significantly during intercalation into the confined interlayer space of MNT. This intercalation is energetically favorable, indicating that this process can be a useful preparation for therapeutic anti-inflammatory applications and showing high stability and controlled release processes.

Improved L-Asparaginase Properties and Reusability by Immobilization onto Functionalized Carbon Xerogels

Enzyme immobilization can offer a range of significant advantages, including reusability, and increased selectivity, stability, and activity. In this work, a central composite design (CCD) of experiments and response surface methodology (RSM) were used to study, for the first time, the L-asparaginase (ASNase) immobilization onto functionalized carbon xerogels (CXs). The best results were achieved using CXs obtained by hydrothermal oxidation with nitric acid and subsequent heat treatment in a nitrogen flow at 600 °C (CX-OX-600). Under the optimal conditions (81 min of contact time, pH 6.2 and 0.36 g/L of ASNase), an immobilization yield (IY) of 100 % and relative recovered activity (RRA) of 103 % were achieved. The kinetic parameters obtained also indicate a 1.25-fold increase in the affinity of ASNase towards the substrate after immobilization. Moreover, the immobilized enzyme retained 97 % of its initial activity after 6 consecutive reaction cycles. All these outcomes confirm the promising properties of functionalized CXs as support for ASNase, bringing new insights into the development of an efficient and stable immobilization platform for use in the pharmaceutical industry, food industry, and biosensors.

Dual electro-/pH-responsive nanoparticle/hydrogel system for controlled delivery of anticancer peptide

An electro-chemo-responsive carrier has been engineered for the controlled release of a highly hydrophilic anticancer peptide, CR(NMe)EKA (Cys-Arg- N-methyl-Glu-Lys-Ala). Remotely controlled on demand release of CR(NMe)EKA, loaded in electro-responsive poly(3,4-ethylenedioxythiophene) (PEDOT) nanoparticles, has been achieved by applying electrical stimuli consisting of constant positive (+0.50 V) or negative voltages (-0.50 V) at pre-defined time intervals. In addition, after loading CR(NMe)EKA/PEDOT nanoparticles into an injectable pH responsive hydrogel formed by phenylboronic acid grafted to chitosan (PBA-CS), the efficiency of the controlled peptide release has increased approximately by a factor of 2.6. The hydration ratio of such hydrogel is significantly lower in acidic environments than in neutral and basic media, which has been attributed to the dissociation of the boronate bonds between polymer chains. Hence, the electro-controlled peptide release from PBA-CS/CR(NMe)EKA/PEDOT hydrogels, in the acidic environment of tumors, combines the effects of the oxidation and reduction of PEDOT chains on the interactions with the peptide and the carrier, with the peptide concentration gradient at the interface between the collapsed hydrogel and the release medium. Furthermore, the peptide released by electro-stimulation preserved its bioactivity assessed by promoting human prostate cancer cells death. Overall, this work is a promising attempt to develop a carrier platform for small hydrophilic anticancer peptides, which delivery rationale is synergistically regulated by the electrical and pH responsiveness of the carrier.

Label-free colorimetric analysis strategies based on adsorption-responsive surface-enhanced photochromic phenomena of tungsten(VI) oxide nanoparticles for amino acids

Herein, we present a colorimetric detection method based on the surface-enhanced photochromic phenomenon of tungsten (VI) oxide (WO3) nanocolloid particles for α-amino acid (AA) molecules, including L-aspartic acid (Asp), L-glutamic acid (Glu), L-histidine (His), L-isoleucine (Ile), L-leucine (Leu), L-lysine (Lys), L-phenylalanine (Phe), and L-valine (Val). The UV-induced photochromic phenomena in the AA/WO3 binary aqueous systems were investigated using UV-Vis absorption spectrometry. The adsorption properties of the AA molecules on the surface of the WO3 nanocolloid particles have been identified using a combination of adsorption isotherm analysis and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. A good linear correlation between the concentration of the AAs adsorbed on the surface of the WO3 nanocolloid particles and the initial photochromic coloration rate in the corresponding UV-irradiated WO3 colloidal aqueous solution was obtained with over three orders of magnitude, indicating that the surface-enhanced photochromic phenomenon of the WO3 nanocolloid particle can be used to detect the AA molecules. In addition, based on the results of the UV-Vis absorption, ATR-FTIR, and adsorption isotherm analyses, we have experimentally demonstrated that the AA/WO3 binary aqueous system with inner-sphere adsorbed Ile, Leu, Lys, or Val molecules on the surface of the WO3 nanocolloid particles exhibits a more significant surface-enhanced photochromic phenomenon than the system with outer-sphere adsorbed Asp, Glu, His, or Phe molecules. The strong inner-sphere adsorption of the AA molecules successfully improved the limit of detection. This study provides valuable insights into a "label-free" colorimetric assay system based on the surface-enhanced photochromic phenomenon of the WO3 nanocolloid probe.

Antioxidant Marine Hydrolysates Isolated from Tuna Mixed Byproducts: An Example of Fishery Side Streams Upcycling

The aim of this research is to propose simple and scalable processes to obtain bioactive peptides extensively hydrolyzed starting from a tuna mixed biomass. The upcycling of this powdered biomass is challenging since it comes from the unsorted industrial side streams of the tuna canning process (cooked residues from fillet trimming) after a patented mild dehydration useful for preventing its degradation until its exploitation. Two different protocols were proposed, with and without the inclusion of an exogenous enzyme (Enzymatic-Assisted Extraction, EAE), with no relevant differences in yields (24% vs. 22%) and a comparable amino acid composition. Nevertheless, the former protocol (with EAE) provided peptides with an average molecular weight of 1.3 kDa, and the second one (without EAE) provided peptides with an average molecular weight of 2.2 kDa. The two corresponding types of tuna protein hydrolysates (Enzymatic Hydrolysates (EH) and Non-Enzymatic Hydrolysates (NEH)) were characterized by proximate compositions, pH, color profile, amino acid analysis, FTIR spectra, and molecular weight distribution. In addition, several biological analyses were performed to assess their potential use as nutraceutical supplements: special attention has been paid to antioxidant activity using three different methods to quantify it. EH showed the most promising antioxidant activity which could be exploited also in other fields (e.g., biomaterials, cosmetics).

Solvent induced amyloid polymorphism and the uncovering of the elusive class 3 amyloid topology

Aggregation-prone-motifs (APRs) of proteins are short segments, which - as isolated peptides - form diverse amyloid-like crystals. We introduce two APRs - designed variants of the incretin mimetic Exendin-4 - that both display crystal-phase polymorphism. Crystallographic and spectroscopic analysis revealed that a single amino-acid substitution can greatly reduce topological variability: while LYIQWL can form both parallel and anti-parallel β-sheets, LYIQNL selects only the former. We also found that the parallel/anti-parallel switch of LYIQWL can be induced by simply changing the crystallization temperature. One crystal form of LYIQNL was found to belong to the class 3 topology, an arrangement previously not encountered among proteinogenic systems. We also show that subtle environmental changes lead to crystalline assemblies with different topologies, but similar interfaces. Spectroscopic measurements showed that polymorphism is already apparent in the solution state. Our results suggest that the temperature-, sequence- and environmental sensitivity of physiological amyloids is reflected in assemblies of the APR segments, which, complete with the new class 3 crystal form, effectively sample all the originally proposed basic topologies of amyloid-like aggregates.

Suppressing sidechain modes and improving structural resolution for 2D IR spectroscopy via vibrational lifetimes

Vibrational spectroscopy of protein structure often utilizes 13C18O-labeling of backbone carbonyls to further increase structural resolution. However, sidechains such as arginine, aspartate, and glutamate absorb within the same spectral region, complicating the analysis of isotope-labeled peaks. In this study, we report that the waiting time between pump and probe pulses in two-dimensional infrared spectroscopy can be used to suppress sidechain modes in favor of backbone amide I' modes based on differences in vibrational lifetimes. Furthermore, differences in the lifetimes of 13C18O-amide I' modes can aid in the assignment of secondary structure for labeled residues. Using model disordered and β-sheet peptides, it was determined that while β-sheets exhibit a longer lifetime than disordered structures, amide I' modes in both secondary structures exhibit longer lifetimes than sidechain modes. Overall, this work demonstrates that collecting 2D IR data at delayed waiting times, based on differences in vibrational lifetime between modes, can be used to effectively suppress interfering sidechain modes and further identify secondary structures.

Higher Order Structure Characterization of Two Interdomain Disulfide Bond Variants of a Bispecific Monoclonal Antibody

Characterization and understanding of protein higher order structure (HOS) is essential at all stages of biologics development. Here, two folding variants of a bispecific monoclonal antibody, the correctly folded form and an alternative configuration with reduced potency, were characterized by several HOS characterization techniques. Specifically, differential scanning calorimetry (DSC), circular dichroism (CD), Fourier-transform infrared spectroscopy (FTIR), Raman and Raman optical activity (ROA) spectroscopy were used together to elucidate the impacts of disulfide bond scrambling in the fused scFv domains on the structure and thermal stability of the antibody. This study illustrates the importance of selecting appropriate biophysical characterization techniques based on the nature and magnitude of the HOS change.

Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells

The ability to track minute changes of a single amino acid residue in a cellular environment is causing a paradigm shift in the attempt to fully understand the responses of biomolecules that are highly sensitive to their environment. Detecting early protein dynamics in living cells is crucial to understanding their mechanisms, such as those of photosynthetic proteins. Here, we elucidate the light response of the microbial chloride pump NmHR from the marine bacterium Nonlabens marinus, located in the membrane of living Escherichia coli cells, using nanosecond time-resolved UV/vis and IR absorption spectroscopy over the time range from nanoseconds to seconds. Transient structural changes of the retinal cofactor and the surrounding apoprotein are recorded using light-induced time-resolved UV/vis and IR difference spectroscopy. Of particular note, we have resolved the kinetics of the transient deprotonation of a single cysteine residue during the photocycle of NmHR out of the manifold of molecular vibrations of the cells. These findings are of high general relevance, given the successful development of optogenetic tools from photoreceptors to interfere with enzymatic and neuronal pathways in living organisms using light pulses as a noninvasive trigger.

Optical fiber-based open source low cost portable spectrometer system

This article explores the development of a small, compact fiber-based spectrometer system designed to overcome the limitations of standard spectrometers, such as the high cost and restricted accessibility. Operated by a Raspberry Pi, the fiber-based spectrometer system uses the increased computing power to provide versatile modes of operation and powerful data processing, while maintaining a small size. Specifically crafted for basic chemistry and biology lab setups, where fibers allow measurements in different conditions, and customization enables fluorescence, light scattering, and absorption measurements. The system is adaptable and versatile, offering ease of modification and adaptation for a broad range of applications.

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

3D Printing Silk Fibroin/Polyacrylamide Triple-Network Composite Hydrogels with Stretchability, Conductivity, and Strain-Sensing Ability as Bionic Electronic Skins

Electronic skins have received increasing attention due to their great application potential in wearable electronics. Meanwhile, tremendous efforts are still needed for the fabrication of multifunctional composite hydrogels with complex structures for electronic skins via simple methods. In this work, a novel three-dimensional (3D) printing composite hydrogel with stretchability, conductivity, and strain-sensing ability is produced using a one-step photocuring method to achieve a dual-signal response of the electronic skin. The composite hydrogel exhibits a triple-network structure composed of silk microfibers (SMF), regenerated silk fibroin (RSF), and polyacrylamide (PAM). The establishment of triple networks is based on the electrostatic interaction between SMF and RSF, as well as the chemically cross-linked RSF and PAM. Thanks to its specific structure and components, the composite hydrogel possesses enhanced mechanical properties (elastic modulus of 140 kPa, compressive stress of 21 MPa, and compression modulus of 600 kPa) and 3D printability while retaining stretchability and flexibility. The interaction between negatively charged SMF and cations in phosphate-buffered saline endows the composite hydrogel with good conductivity and strain-sensing ability after immersion in a low-concentration (10 mM) salt solution. Moreover, the 3D printing composite hydrogel scaffold successfully realizes real-time monitoring. Therefore, the proposed hydrogel-based ionic sensor is promising for skin tissue engineering, real-time monitoring, soft robotics, and human-machine interfaces.

Furosemide Derails Human Lysozyme Fibrillation by Interacting with Aggregation Hot Spots: A Biophysical Comprehension

Kidney-associated human lysozyme amyloidosis leads to renal impairments;thus, patients are often prescribed furosemide. Based on this fact, the effect of furosemide on induced human lysozyme fibrillation, in vitro, is evaluated by spectroscopic, calorimetric, computational, and cellular-based assays/methods. Results show that furosemide increases the lag phase and decreases the apparent rate of aggregation of human lysozyme, thereby decelerating the nucleation phase and amyloid fibril formation, as confirmed by the decrease in the level of Thioflavin-T fluorescence. Fewer entities of hydrodynamic radii of ∼171 nm instead of amyloid fibrils (∼412 nm) are detected in human lysozyme in the presence of furosemide by dynamic light scattering. Moreover, furosemide decreases the extent of conversion of the α/β structure of human lysozyme into a predominant β-sheet. The isothermal titration calorimetry established that furosemide forms a complex with human lysozyme, which was also confirmed through fluorescence quenching and computational studies. Also, human lysozyme lytic activity is inhibited competitively by furosemide due to the involvement of amino acid residues of the active site in catalysis, as well as complex formation. Conclusively, furosemide interacts with Gln58, Ile59, Asn60, Ala108, and Trp109 of aggregation-prone regions 2 and 4 of human lysozyme, thereby masking its sites of aggregation and generating only lower-order entities that are less toxic to red blood cells than the fibrils. Thus, furosemide slows the progression of amyloid fibrillation in human lysozyme.

Human serum albumin directed formation of cadmium telluride quantum dots: Applications in biosensing, anti-bacterial activities and cell cytotoxicity measurements

Although cadmium-based quantum dots (QDs) are highly promising candidates for numerous biological applications, their intrinsic toxicity limits their pertinency in living systems. Surface functionalization of QDs with appropriate molecules could reduce the toxicity level. Herein, we have synthesized the smaller sized (1-5 nm) aqueous-compatible biogenic CdTe QDs using human serum albumin (HSA) as a surface passivating agent via a greener approach. HSA-functionalized CdTe QDs have been explored in multiple in vitro sensing and biological applications, namely, (1) sensing, (2) anti-bacterial and (3) anti-cancer properties. Using CdTe-HSA QDs as a fluorescence probe, a simple fluorometric method has been developed for highly sensitive and selective detection of blood marker bilirubin and hazardous Hg2+ ion with a limit of detection (LOD) of 3.38 and 0.53 ng/mL, respectively. CdTe-HSA QDs also acts as a sensor for standard antibiotics, tetracycline and rifampicin with LOD values of 41.34 and 114.99 ng/mL, respectively. Nano-sized biogenic CdTe-HSA QDs have shown promising anti-bacterial activities against both gram-negative, E. coli and gram-positive, E. faecalis strains confirming more effectiveness against E. faecalis strains. The treatment of human cervical cancer cell lines (HeLa cells) with the synthesized QDs reflected the proficient cytotoxic properties of QDs.

Cyclodextrin-Assisted Surface-Enhanced Photochromic Phenomena of Tungsten(VI) Oxide Nanoparticles for Label-Free Colorimetric Detection of Phenylalanine

Herein are presented the results of experiments designed to evaluate the effectiveness of host-guest interactions in improving the sensitivity of colorimetric detection based on surface-enhanced photochromic phenomena of tungsten(VI) oxide (WO3) nanocolloid particles. The UV-induced photochromic coloration of WO3 nanocolloid particles in the presence of aromatic α-amino acid (AA), l-phenylalanine (Phe) or l-2-phenylglycine (Phg), and heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin (TMβCDx) in an aqueous system was investigated using UV-vis absorption spectrometry. The characteristics of the adsorption modes and configurations of AAs on the WO3 surface have also been identified by using a combination of adsorption isotherm analysis and attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). A distinct linear relationship was observed between the concentration of AAs adsorbed on the WO3 nanocolloid particles and the initial photochromic coloration rate in the corresponding UV-irradiated colloidal WO3 in aqueous media, indicating that a simple and sensitive quantification of AAs can be achieved from UV-induced WO3 photochromic coloration without any complicated preprocessing. The proposed colorimetric assay in the Phe/TMβCDx/WO3 ternary aqueous system had a linear range of 1 × 10-8 to 1 × 10-4 mol dm-3 for Phe detection, with a limit of detection of 8.3 × 10-9 mol dm-3. The combined results from UV-vis absorption, ATR-FTIR, and adsorption isotherm experiments conclusively indicated that the TMβCDx-complexed Phe molecules in the Phe/TMβCDx/WO3 ternary aqueous system are preferentially and strongly inner-sphere adsorbed on the WO3 surface, resulting in a more significant surface-enhanced photochromic phenomenon. The findings in this study provided intriguing insights into the design and development of the "label-free" colorimetric assay system based on the surface-enhanced photochromic phenomenon of the WO3 nanocolloid probe.

Is the A-1 Pigment in Photosystem I Part of P700? A (P700+-P700) FTIR Difference Spectroscopy Study of A-1 Mutants

The involvement of the second pair of chlorophylls, termed A-1A and A-1B, in light-induced electron transfer in photosystem I (PSI) is currently debated. Asparagines at PsaA600 and PsaB582 are involved in coordinating the A-1B and A-1A pigments, respectively. Here we have mutated these asparagine residues to methionine in two single mutants and a double mutant in PSI from Synechocystis sp. PCC 6803, which we term NA600M, NB582M, and NA600M/NB582M mutants. (P700+-P700) FTIR difference spectra (DS) at 293 K were obtained for the wild-type and the three mutant PSI samples. The wild-type and mutant FTIR DS differ considerably. This difference indicates that the observed changes in the (P700+-P700) FTIR DS cannot be due to only the PA and PB pigments of P700. Comparison of the wild-type and mutant FTIR DS allows the assignment of different features to both A-1 pigments in the FTIR DS for wild-type PSI and assesses how these features shift upon cation formation and upon mutation. While the exact role the A-1 pigments play in the species we call P700 is unclear, we demonstrate that the vibrational modes of the A-1A and A-1B pigments are modified upon P700+ formation. Previously, we showed that the A-1 pigments contribute to P700 in green algae. In this manuscript, we demonstrate that this is also the case in cyanobacterial PSI. The nature of the mutation-induced changes in algal and cyanobacterial PSI is similar and can be considered within the same framework, suggesting a universality in the nature of P700 in different photosynthetic organisms.

Regenerated Fiber's Ideal Target: Comparable to Natural Fiber

The toughness of silk naturally obtained from spiders and silkworms exceeds that of all other natural and man-made fibers. These insects transform aqueous protein feedstocks into mechanically specialized materials, which represents an engineering phenomenon that has developed over millions of years of natural evolution. Silkworms have become a new research hotspot due to the difficulties in collecting spider silk and other challenges. According to continuous research on the natural spinning process of the silkworm, it is possible to divide the main aspects of bionic spinning into two main segments: the solvent and behavior. This work focuses on the various methods currently used for the spinning of artificial silk fibers to replicate natural silk fibers, providing new insights based on changes in the fiber properties and production processes over time.

Screening, separation and identification of metal-chelating peptides for nutritional, cosmetics and pharmaceutical applications

Metal-chelating peptides, which form metal-peptide coordination complexes with various metal ions, can be used as biofunctional ingredients notably to enhance human health and prevent diseases. This review aims to discuss recent insights into food-derived metal-chelating peptides, the strategies set up for their discovery, their study, and identification. After understanding the overall properties of metal-chelating peptides, their production from food-derived protein sources and their potential applications will be discussed, particularly in nutritional, cosmetics and pharmaceutical fields. In addition, the review provides an overview of the last decades of progress in discovering food-derived metal-chelating peptides, addressing several screening, separation and identification methodologies. Furthermore, it emphasizes the methods used to assess peptide-metal interaction, allowing for better understanding of chemical and thermodynamic parameters associated with the formation of peptide-metal coordination complexes, as well as the specific amino acid residues that play important roles in the metal ion coordination.

Differentiation of protein types extracted from tilapia byproducts by FTIR spectroscopy combined with chemometric analysis and their antioxidant protein hydrolysates

This research aimed to characterize protein types including sarcoplasmic protein (SP), myofibrillar protein (MP), and alkali-aided protein extract (AP) prepared from tilapia byproducts using water, 0.6 M NaCl, and alkaline solution (pH 11), respectively compared to freeze-dried minced tilapia muscle (CONTROL). Principal component analysis was performed from second derivative FTIR spectra to differentiate protein type. The AP mostly contained β-sheet structure and had low total sulfhydryl content and surface hydrophobicity. SP can be distinguished from MP by the loading plots of the FTIR bands representing the α-helical structure. While the bands for lipids and β-sheet of protein were noted for differentiating AP from CONTROL. After being hydrolyzed by Protease G6, the AP hydrolysate disclosed the highest ABTS radical scavenging activity, while the SP hydrolysate revealed the strongest metal chelating ability. Thus, an understanding of how fish processing waste can be utilized in the production of antioxidant protein hydrolysates has been achieved.

Glycation of tilapia protein hydrolysate decreases cellular antioxidant activity upon in vitro gastrointestinal digestion

Changes in structural characteristics and antioxidant activity of tilapia hydrolysate glycated with glucose, fructose, or xylose at 90 °C for 12 h, and following in vitro gastrointestinal (GI) digestion were investigated. Fourier-transformed infrared (FTIR) band between 1,800 and 1,400 cm-1 confirmed the structural modifications of hydrolysate under glycations. Glycation drastically increased ATBS · + and ONOO - scavenging activities (p < 0.05) as well as ferric-reducing antioxidant power (FRAP). Xylose was the most effective sugar for glycation, yielding the highest chemical antioxidant activities (p < 0.05). However, glycated hydrolysates exhibited lower cellular antioxidant activity (CAA) on HepG2 cell when compared to hydrolysates. The extensive glycation of hydrolysates resulted in lower GI digestibility as confirmed by the FTIR spectra of C[bond, double bond]O, C-N, N-H, C-C, C-O, and C-H stretching vibrations. Glycation of tilapia hydrolysates only improved chemical antioxidant activities, but alleviated CAA, especially upon simulated GI digestion.

Elucidating the Signal Transduction Mechanism of the Blue-Light-Regulated Photoreceptor YtvA: From Photoactivation to Downstream Regulation

The blue-light photoreceptor YtvA from Bacillus subtilis has an N-terminal flavin mononucleotide (FMN)-binding light-oxygen-voltage (LOV) domain that is fused to a C-terminal sulfate transporter and anti-σ factor antagonist (STAS) output domain. To interrogate the signal transduction pathway that leads to photoactivation, the STAS domain was replaced with a histidine kinase, so that photoexcitation of the flavin could be directly correlated with biological activity. N94, a conserved Asn that is hydrogen bonded to the FMN C2═O group, was replaced with Ala, Asp, and Ser residues to explore the role of this residue in triggering the structural dynamics that activate the output domain. Femtosecond to millisecond time-resolved multiple probe spectroscopy coupled with a fluorescence polarization assay revealed that the loss of the hydrogen bond between N94 and the C2═O group decoupled changes in the protein structure from photoexcitation. In addition, alterations in N94 also decreased the stability of the Cys-FMN adduct formed in the light-activated state by up to a factor of ∼25. Collectively, these studies shed light on the role of the hydrogen bonding network in the LOV β-scaffold in signal transduction.

From a Droplet to a Fibril and from a Fibril to a Droplet: Intertwined Transition Pathways in Highly Dynamic Enzyme-Modulated Peptide-Adenosine Triphosphate Systems

Many cellular coassemblies of proteins and polynucleotides facilitate liquid-liquid phase separation (LLPS) and the subsequent self-assembly of disease-associated amyloid fibrils within the liquid droplets. Here, we explore the dynamics of coupled phase and conformational transitions of model adenosine triphosphate (ATP)-binding peptides, ACC1-13Kn, consisting of the potent amyloidogenic fragment of insulin's A-chain (ACC1-13) merged with oligolysine segments of various lengths (Kn, n = 16, 24, 40). The self-assembly of ATP-stabilized amyloid fibrils is preceded by LLPS for peptides with sufficiently long oligolysine segments. The two-component droplets and fibrils are in dynamic equilibria with free ATP and monomeric peptides, which makes them susceptible to ATP-hydrolyzing apyrase and ACC1-13Kn-digesting proteinase K. Both enzymes are capable of rapid disassembly of amyloid fibrils, producing either monomers of the peptide (apyrase) or free ATP released together with cleaved-off oligolysine segments (proteinase K). In the latter case, the enzyme-sequestered Kn segments form subsequent droplets with the co-released ATP, resulting in an unusual fibril-to-droplet transition. In support of the highly dynamic nature of the aggregate-monomer equilibria, addition of superstoichiometric amounts of free peptide to the ACC1-13Kn-ATP coaggregate causes its disassembly. Our results show that the droplet state is not merely an intermediate phase on the pathway to the amyloid aggregate but may also constitute the final phase of a complex amyloidogenic protein misfolding scenario rich in highly degraded protein fragments incompetent to transition again into fibrils.

Biomolecular fingerprints of the effect of zoledronic acid on prostate cancer stem cells: Comparison of 2D and 3D cell culture models

Revealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research.

Mechanism of Proton Transfer through the D1-E65/D2-E312 Gate during Photosynthetic Water Oxidation

In photosystem II, the D1-E65/D2-E312 dyad in the Cl-1 channel has been proposed to play a pivotal role in proton transfer during water oxidation. However, the precise mechanism remains elusive. Here, the proton transfer mechanism within the Cl-1 channel was investigated using quantum mechanics/molecular mechanics calculations. The molecular vibration of the E65/E312 dyad and its deuteration effect revealed that the recently suggested stepwise proton transfer, i.e., initial proton release from the dyad followed by slow reprotonation, does not occur in the Cl-1 channel. Instead, proton transfer is proposed to take place via a conformational change at the E65/E312 dyad, acting as a gate. In its closed form, a proton is trapped within the dyad, preventing forward proton transfer. This closed form converts into the open form, where protonated D1-E65 provides a hydrogen bond to the water network, thereby facilitating fast Grotthuss-type proton transfer.

Small organic molecules containing amorphous calcium phosphate: synthesis, characterization and transformation

As the primary solid phase, amorphous calcium phosphate (ACP) is a pivotal precursor in cellular biomineralization. The intrinsic interplay between ACP and Howard factor underscores the significance of understanding their association for advancing biomimetic ACP development. While organic compounds play established roles in biomineralization, this study presents the synthesis of ACP with naturally occurring organic compounds (ascorbate, glutamate, and itaconate) ubiquitously found in mitochondria and vital for bone remodeling and healing. The developed ACP with organic compounds was meticulously characterized using XRD, FTIR, and solid-state 13C and 31P NMR. The morphological analysis revealed the characteristic spherical morphology with particle size close to 20 nm of all synthesized ACP variants. Notably, the type of organic compound strongly influences true density, specific surface area, particle size, and transformation. The in vitro analysis was performed with MC3T3-E1 cells, indicating the highest cell viability with ACP_ASC (ascorbate), followed by ACP_ITA (itaconate). The lowest cell viability was observed with 10 %w/v of ACP_GLU (glutamate); however, 1 %w/v of ACP_GLU was cytocompatible. Further, the effect of small organic molecules on the transformation of ACP to low crystalline apatite (Ap) was examined in Milli-Q® water, PBS, and α-MEM.

Solvent-Induced Transient Self-Assembly of Peptide Gels: Gelator-Solvent Reactions and Material Properties Correlation

Herein, we introduce a new methodology for designing transient organogels that offers tunability of the mechanical properties simply by matching the protective groups of the precursor to that of the solvent. We developed solvent-induced transient materials in which the solvent chemically participates in a set of reactions and actively supports the assembly event. The activation of a single precursor by an acid (accelerator) yields the formation of two distinct gelators and induces gelation. The interconversion cycle is supplied by the secondary solvent (originating from hydrolysis of the primary solvent by the accelerator), which then progressively solubilizes the gel network. We show that this gelation method offers a direct correlation between the mechanical and transient properties by modifying the chemical structure of the precursors and the presence of an accelerator in the system. Such a method paves the way for the design of self-abolishing and mechanically tunable materials for targeted purposes. The biocompatibility and versatility of amino acid-based gelators can offer a wide range of biomaterials for applications requiring a controllable and definite lifetime such as drug delivery platforms exhibiting a burst release or self-abolishing cell culture substrates.

The Enrichment of Whey Protein Isolate Hydrogels with Poly-γ-Glutamic Acid Promotes the Proliferation and Osteogenic Differentiation of Preosteoblasts

Osseous disease accounts for over half of chronic pathologies, but there is a limited supply of autografts, the gold standard; hence, there is a demand for new synthetic biomaterials. Herein, we present the use of a promising, new dairy-derived biomaterial: whey protein isolate (WPI) in the form of hydrogels, modified with the addition of different concentrations of the biotechnologically produced protein-like polymeric substance poly-γ-glutamic acid (γ-PGA) as a potential scaffold for tissue regeneration. Raman spectroscopic analysis demonstrated the successful creation of WPI-γ-PGA hydrogels. A cytotoxicity assessment using preosteoblastic cells demonstrated that the hydrogels were noncytotoxic and supported cell proliferation from day 3 to 14. All γ-PGA-containing scaffold compositions strongly promoted cell attachment and the formation of dense interconnected cell layers. Cell viability was significantly increased on γ-PGA-containing scaffolds on day 14 compared to WPI control scaffolds. Significantly, the cells showed markers of osteogenic differentiation; they synthesised increasing amounts of collagen over time, and cells showed significantly enhanced alkaline phosphatase activity at day 7 and higher levels of calcium for matrix mineralization at days 14 and 21 on the γ-PGA-containing scaffolds. These results demonstrated the potential of WPI-γ-PGA hydrogels as scaffolds for bone regeneration.

Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy

We present structural models for three different amyloid fibril polymorphs prepared from amylin20-29 (sequence SNNFGAILSS) and amyloid-β25-35 (Aβ25-35) (sequence GSNKGAIIGLM) peptides. These models are based on the amide C=O bond and Ramachandran ψ-dihedral angle data from Raman spectroscopy, which were used as structural constraints to guide molecular dynamics (MD) simulations. The resulting structural models indicate that the basic structural motif of amylin20-29 and Aβ25-35 fibrils is extended β-strands. Our data indicate that amylin20-29 forms both antiparallel and parallel β-sheet fibril polymorphs, while Aβ25-35 forms a parallel β-sheet fibril structure. Overall, our work lays the foundation for using Raman spectroscopy in conjunction with MD simulations to determine detailed molecular-level structural models of amyloid fibrils in a manner that complements gold-standard techniques, such as solid-state nuclear magnetic resonance and cryogenic electron microscopy.

Staphylococcus aureus functional amyloids catalyze degradation of β-lactam antibiotics

Antibiotic resistance of bacteria is considered one of the most alarming developments in modern medicine. While varied pathways for bacteria acquiring antibiotic resistance have been identified, there still are open questions concerning the mechanisms underlying resistance. Here, we show that alpha phenol-soluble modulins (PSMαs), functional bacterial amyloids secreted by Staphylococcus aureus, catalyze hydrolysis of β-lactams, a prominent class of antibiotic compounds. Specifically, we show that PSMα2 and, particularly, PSMα3 catalyze hydrolysis of the amide-like bond of the four membered β-lactam ring of nitrocefin, an antibiotic β-lactam surrogate. Examination of the catalytic activities of several PSMα3 variants allowed mapping of the active sites on the amyloid fibrils' surface, specifically underscoring the key roles of the cross-α fibril organization, and the combined electrostatic and nucleophilic functions of the lysine arrays. Molecular dynamics simulations further illuminate the structural features of β-lactam association upon the fibril surface. Complementary experimental data underscore the generality of the functional amyloid-mediated catalytic phenomenon, demonstrating hydrolysis of clinically employed β-lactams by PSMα3 fibrils, and illustrating antibiotic degradation in actual S. aureus biofilms and live bacteria environments. Overall, this study unveils functional amyloids as catalytic agents inducing degradation of β-lactam antibiotics, underlying possible antibiotic resistance mechanisms associated with bacterial biofilms.

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.

Extracting accurate infrared lineshapes from weak vibrational probes at low concentrations

Fourier-transform infrared (FTIR) spectroscopy using vibrational probes is an ideal tool to detect changes in structure and local environments within biological molecules. However, challenges arise when dealing with weak infrared probes, such as thiocyanates, due to their inherent low signal strengths and overlap with solvent bands. In this protocol we demonstrate:•A streamlined approach for the precise extraction of weak infrared absorption lineshapes from a strong solvent background.•A protocol combining a spectral filter, background modeling, and subtraction.•Our methodology successfully extracts the CN stretching mode peak from methyl thiocyanate at remarkably low concentrations (0.25 mM) in water, previously a challenge for FTIR spectroscopy.This approach offers valuable insights and tools for more accurate FTIR measurements using weak vibrational probes. This enhanced precision can potentially enable new approaches to enhance our understanding of protein structure and dynamics in solution.

Copper-flavonoid family of complexes involved in alkaline phosphatase activation

The flavonoid naringenin and a family of naringenin derivative Cu(II) complexes having phenanthroline-based second ligands were selected to study alkaline phosphatase activation. This enzyme plays a critical role in tissue formation, increasing the inorganic phosphate formation, favoring mineralization, and being essential to producing bone mineralization. The effects of those compounds on the function and structure of the enzyme were evaluated by kinetic measurements, fluorescence, FTIR, and UV-Vis spectroscopies. The results showed that naringenin did not affect alkaline phosphatase activity, having a value of the Michaelis-Menten-constant close to the enzyme (Km = 3.07 × 10-6). The binary complex, Cu(II)-naringenin, and the ternary complex Cu(II)-naringenin-phenanthroline behaved as an enzyme activator in all the concentrations range used in this study. Those complexes increased in c.a. 1.9% the catalytic efficiency concerning enzyme and naringenin. The ternary complex Cu(II)-naringenin-bathophenanthroline, provokes an activator mixed effect, dependent on the substrate concentrations. The different kinetic behavior can be correlated with different conformational changes observed under the interaction with ALP. Fluorescence experiments showed a raising of the binding constant with temperature. FTIR determinations showed that the complex with bathophenanthroline modifies the ALP structure but maintains the helical structure. The other copper complexes provoked a structural unfolding, decreasing the α-helix content. None of them affect the dephosphorylation enzyme ability. Even though the interactions and structural modifications on ALP are different, it is evident that the presence of copper favors enzymatic activity. The observed electrostatic interactions probably benefit the dissociation of the bound phosphate. The results suggest potential biological applications for the studied compounds.

Stretching vibrational frequencies and pKa differences in H-bond networks of protein environments

The experimentally measured stretching vibrational frequencies of O-D [νO-D(donor)] and C=O [νC=O(donor)] H-bond donor groups can provide valuable information about the H-bonds in proteins. Here, using a quantum mechanical/molecular mechanical approach, the relationship between these vibrational frequencies and the difference in pKa values between H-bond donor and acceptor groups [ΔpKa(donor … acceptor)] in bacteriorhodopsin and photoactive yellow protein environments was investigated. The results show that νO-D(donor) is correlated with ΔpKa(donor … acceptor), regardless of the specific protein environment. νC=O(donor) is also correlated with ΔpKa(donor … acceptor), although the correlation is weak because the C=O bond does not have a proton. Importantly, the shifts in νO-D(donor) and νC=O(donor) are not caused by changes in pKa(donor) alone, but rather by changes in ΔpKa(donor … acceptor). Specifically, a decrease in ΔpKa(donor … acceptor) can lead to proton release from the H-bond donor group toward the acceptor group, resulting in shifts in the vibrational frequencies of the protein environment. These findings suggest that changes in the stretching vibrational frequencies, in particular νO-D(donor), can be used to monitor proton transfer in protein environments.

Self-Assembly and Cytocompatibility of Amino Acid Conjugates Containing a Novel Water-Soluble Aromatic Protecting Group

There has been considerable interest in peptides in which the Fmoc (9-fluorenylmethoxycarbonyl) protecting group is retained at the N-terminus, since this bulky aromatic group can drive self-assembly, and Fmoc-peptides are biocompatible and have applications in cell culture biomaterials. Recently, analogues of new amino acids with 2,7-disulfo-9-fluorenylmethoxycarbonyl (Smoc) protecting groups have been developed for water-based peptide synthesis. Here, we report on the self-assembly and biocompatibility of Smoc-Ala, Smoc-Phe and Smoc-Arg as examples of Smoc conjugates to aliphatic, aromatic, and charged amino acids, respectively. Self-assembly occurs at concentrations above the critical aggregation concentration (CAC). Cryo-TEM imaging and SAXS reveal the presence of nanosheet, nanoribbon or nanotube structures, and spectroscopic methods (ThT fluorescence circular dichroism and FTIR) show the presence of β-sheet secondary structure, although Smoc-Ala solutions contain significant unaggregated monomer content. Smoc shows self-fluorescence, which was used to determine CAC values of the Smoc-amino acids from fluorescence assays. Smoc fluorescence was also exploited in confocal microscopy imaging with fibroblast cells, which revealed its uptake into the cytoplasm. The biocompatibility of these Smoc-amino acids was found to be excellent with zero cytotoxicity (in fact increased metabolism) to fibroblasts at low concentration.

CLIP-Seq analysis enables the design of protective ribosomal RNA bait oligonucleotides against C9ORF72 ALS/FTD poly-GR pathophysiology

Amyotrophic lateral sclerosis and frontotemporal dementia patients with a hexanucleotide repeat expansion in C9ORF72 (C9-HRE) accumulate poly-GR and poly-PR aggregates. The pathogenicity of these arginine-rich dipeptide repeats (R-DPRs) is thought to be driven by their propensity to bind low-complexity domains of multivalent proteins. However, the ability of R-DPRs to bind native RNA and the significance of this interaction remain unclear. Here, we used computational and experimental approaches to characterize the physicochemical properties of R-DPRs and their interaction with RNA. We find that poly-GR predominantly binds ribosomal RNA (rRNA) in cells and exhibits an interaction that is predicted to be energetically stronger than that for associated ribosomal proteins. Critically, modified rRNA "bait" oligonucleotides restore poly-GR-associated ribosomal deficits and ameliorate poly-GR toxicity in patient neurons and Drosophila models. Our work strengthens the hypothesis that ribosomal function is impaired by R-DPRs, highlights a role for direct rRNA binding in mediating ribosomal dysfunction, and presents a strategy for protecting against C9-HRE pathophysiological mechanisms.

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.