Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods

Protopine and Allocryptopine Interactions with Plasma Proteins

A comprehensive study of the interactions of human serum albumin (HSA) and α-1-acid glycoprotein (AAG) with two isoquinoline alkaloids, i.e., allocryptopine (ACP) and protopine (PP), was performed. The UV-Vis spectroscopy, molecular docking, competitive binding assays, and circular dichroism (CD) spectroscopy were used for the investigations. The results showed that ACP and PP form spontaneous and stable complexes with HSA and AAG, with ACP displaying a stronger affinity towards both proteins. Molecular docking studies revealed the preferential binding of ACP and PP to specific sites within HSA, with site 2 (IIIA) being identified as the favored location for both alkaloids. This was supported by competitive binding assays using markers specific to HSA's drug binding sites. Similarly, for AAG, a decrease in fluorescence intensity upon addition of the alkaloids to AAG/quinaldine red (QR) complexes indicated the replacement of the marker by the alkaloids, with ACP showing a greater extent of replacement than PP. CD spectroscopy showed that the proteins' structures remained largely unchanged, suggesting that the formation of complexes did not significantly perturb the overall spatial configuration of these macromolecules. These findings are crucial for advancing the knowledge on the natural product-protein interactions and the future design of isoquinoline alkaloid-based therapeutics.

Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation

Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.

Self-assembly of heterochiral, aliphatic dipeptides with Leu

This work describes the self-assembly behavior of heterochiral, aliphatic dipeptides, l-Leu-d-Xaa (Xaa = Ala, Val, Ile, Leu), in green solvents such as acetonitrile (MeCN) and buffered water at neutral pH. Interestingly, water plays a structuring role because at 1% v/v, it enables dipeptide self-assembly in MeCN to yield organogels, which then undergo transition towards crystals. Other organic solvents and oils were tested for gelation, and metastable gels were formed in tetrahydrofuran, although at high peptide concentration (80 mM). Single-crystal X-ray diffraction revealed the dipeptides' supramolecular packing modes in amphipathic layers, as opposed to water channels reported for the homochiral Leu-Leu, or hydrophobic columns reported for homochiral Leu-Val and Leu-Ile.

Recent Advances in the Field of Amino Acid-Conjugated Aminoferrocenes-A Personal Perspective

The development of turn-based inhibitors of protein-protein interactions has attracted considerable attention in medicinal chemistry. Our group has synthesized a series of peptides derived from an amino-functionalized ferrocene to investigate their potential to mimic protein turn structures. Detailed DFT and spectroscopic studies (IR, NMR, CD) have shown that, for peptides, the backbone chirality and bulkiness of the amino acid side chains determine the hydrogen-bond pattern, allowing tuning of the size of the preferred hydrogen-bonded ring in turn-folded structures. However, their biological potential is more dependent on their lipophilicity. In addition, our pioneering work on the chiroptical properties of aminoferrocene-containing peptides enables the correlation of their geometry with the sign of the CD signal in the absorption region of the ferrocene chromophore. These studies have opened up the possibility of using aminoferrocene and its derivatives as chirooptical probes for the determination of various chirality elements, such as the central chirality of amino acids and the helicity of peptide sequences.

Probing protein aggregation through spectroscopic insights and multimodal approaches: A comprehensive review for counteracting neurodegenerative disorders

Aberrant accumulation of protein misfolding can cause aggregation and fibrillation and is one of the primary characteristic features of neurodegenerative diseases. Because they are disordered, misfolded, and aggregated proteins pose a significant setback in drug designing. The structural study of intermediate steps in these kinds of aggregated proteins will allow us to determine the conformational changes as well as the probable pathways encompassing various neurodegenerative disorders. The analysis of protein aggregates involved in neurodegenerative diseases relies on a diverse toolkit of biophysical techniques, encompassing both morphological and non-morphological methods. Additionally, Thioflavin T (ThT) assays and Circular Dichroism (CD) spectroscopy facilitate investigations into aggregation kinetics and secondary structure alterations. The collective application of these biophysical techniques empowers researchers to comprehensively unravel the intricate nature of protein aggregates associated with neurodegeneration. Furthermore, the topics covered in this review have summed up a handful of well-established techniques used for the structural analysis of protein aggregation. This multifaceted approach advances our fundamental understanding of the underlying mechanisms driving neurodegenerative diseases and informs potential therapeutic strategies.

Peptide Extract from Red Kidney Beans, Phaseolus vulgaris (Fabaceae), Shows Promising Antimicrobial, Antibiofilm, and Quorum Sensing Inhibitory Effects

The rapid spread of multidrug-resistant bacteria has led to an increased risk of infectious diseases. Pseudomonas aeruginosa, in particular, poses a significant obstacle due to its propensity to rapidly acquire resistance to conventional antibiotics. This has resulted in an urgent need for the development of new classes of antibiotics that do not induce resistance. Antimicrobial peptides (AMPs) have been studied as potential small-molecule antibiotics due to their unique mode of action. In this study, peptides were extracted from the seeds of Phaseolus vulgaris (Fabaceae), and the antimicrobial activities of the extract were evaluated using microbroth dilution against five different microorganisms. The extract showed antimicrobial activity against all tested organisms with minimum inhibitory concentrations (MIC) of 2.5 mg/mL, except for Candida albicans and Pseudomonas aeruginosa, which had MICs of 1.25 mg/mL. The extract was also bacteriostatic for all tested organisms. The crude peptide extract from Phaseolus vulgaris was further studied for its antibiofilm activity against Pseudomonas aeruginosa, a common nosocomial pathogen associated with biofilm formation. The extract showed good antibiofilm activity at 1/2 MIC. The extract also inhibited the expression of pyocyanin and pyoverdine (virulence factors of P. aeruginosa whose expression is mediated by quorum sensing) by 82% and 66%, respectively. These results suggest that the peptide mix from Phaseolus vulgaris may inhibit biofilm formation and virulence factor expression by interfering with cell-to-cell communication in Pseudomonas aeruginosa. The ability of the extract to inhibit the growth and biofilm formation of all tested organisms indicates its potential as an antimicrobial agent that could be further studied for drug discovery.

Effect of Natural Osmolytes on Recombinant Tau Monomer: Propensity of Oligomerization and Aggregation

The pathological misfolding and aggregation of the microtubule associated protein tau (MAPT), a full length Tau2N4R with 441aa, is considered the principal disease relevant constituent in tauopathies including Alzheimer's disease (AD) with an imbalanced ratio in 3R/4R isoforms. The exact cellular fluid composition, properties, and changes that coincide with tau misfolding, seed formation, and propagation events remain obscure. The proteostasis network, along with the associated osmolytes, is responsible for maintaining the presence of tau in its native structure or dealing with misfolding. In this study, for the first time, the roles of natural brain osmolytes are being investigated for their potential effects on regulating the conformational stability of the tau monomer (tauM) and its propensity to aggregate or disaggregate. Herein, the effects of physiological osmolytes myo-inositol, taurine, trimethyl amine oxide (TMAO), betaine, sorbitol, glycerophosphocholine (GPC), and citrulline on tau's aggregation state were investigated. The overall results indicate the ability of sorbitol and GPC to maintain the monomeric form and prevent aggregation of tau, whereas myo-inositol, taurine, TMAO, betaine, and citrulline promote tau aggregation to different degrees, as revealed by protein morphology in atomic force microscopy images. Biochemical and biophysical methods also revealed that tau proteins adopt different conformations under the influence of these osmolytes. TauM in the presence of all osmolytes expressed no toxicity when tested by a lactate dehydrogenase assay. Investigating the conformational stability of tau in the presence of osmolytes may provide a better understanding of the complex nature of tau aggregation in AD and the protective and/or chaotropic nature of osmolytes.

Experimental techniques for detecting and evaluating the amyloid fibrils

Amyloid fibrils are insoluble proteins with intricate β-sheet structures associated with various human diseases, including Parkinson's, Alzheimer's, and prion diseases. Proteins can form aggregates when their structure is misfolded, resulting in highly organized amyloid fibrils or amorphous aggregates. The formation of protein aggregates is a promising research field for mitigating diseases and the pharmaceutical and food industries. It is important to monitor and minimize the appearance of aggregates in these protein products. Several methods exist to assess protein aggregation, that includes from basic investigations to advanced biophysical techniques. Physicochemical parameters such as molecular weight, conformation, structure, and dimension are examined to study aggregation. There is an urgent need to develop methods for the detection of protein aggregation and amyloid fibril formation both in vitro and in vivo. This chapter focuses on a comprehensive discussion of the methods used to characterize and evaluate aggregates and amyloid fibrils.

Neural network informed photon filtering reduces fluorescence correlation spectroscopy artifacts

Fluorescence correlation spectroscopy (FCS) techniques are well-established tools to investigate molecular dynamics in confocal and super-resolution microscopy. In practice, users often need to handle a variety of sample- or hardware-related artifacts, an example being peak artifacts created by bright, slow-moving clusters. Approaches to address peak artifacts exist, but measurements suffering from severe artifacts are typically nonanalyzable. Here, we trained a one-dimensional U-Net to automatically identify peak artifacts in fluorescence time series and then analyzed the purified, nonartifactual fluctuations by time-series editing. We show that, in samples with peak artifacts, the transit time and particle number distributions can be restored in simulations and validated the approach in two independent biological experiments. We propose that it is adaptable for other FCS artifacts, such as detector dropout, membrane movement, or photobleaching. In conclusion, this simulation-based, automated, open-source pipeline makes measurements analyzable that previously had to be discarded and extends every FCS user's experimental toolbox.

Invitro anti-biofilm activity and the artificial chaperone activity of quinoline-based ionic liquids

The maintenance of protein conformation under stressful conditions is one of the prevailing challenges. This has led to a rapid growth in the ingenious protein therapies, in the past few decades, prioritizing the investigation of the structure and function of proteins in novel environments. Ionic Liquids (ILs) are currently dominating the biomedical industry, by endowing great solubility and stability to bio-molecules, especially proteins. Recently, researchers have devoted their attention towards the artificial chaperone activity of several classes of ILs. Thus, comprehending the long-term as well as momentary stability of protein conformation in IL formulations is an absolute necessity. In this context, we present the activity of quinoline-based ionic liquids (ILs) as artificial cheperones against time-dependent, self induced fibril formation in Bovine Serum Albumin (BSA). Herein, a series of quinoline-based ILs were synthesized and characterized. The structural and morphological changes induced in BSA in the presence and absence of these ILs are corroborated using several spectroscopic measurements and in-silico studies. The anti-microbial and antibiofilm activity of these compounds demonstrating their medicinal properties is substantiated in this study. Furthermore, the present research also gives an account of the toxicity of these compounds under in vivo conditions, using C. elegans as the model organism.

Preparation of pH-sensitive nanogels bioconjugated with shark antibodies (VNAR) for targeted drug delivery with potential applications in colon cancer therapies

Cancer is the second leading cause of death worldwide. To combat this disease, novel and specialized therapeutic systems are urgently needed. This is the first study to explore a system that combines shark variable domain (Fv) of new antigen receptor (VNAR) antibodies (hereinafter VNARs), PEGylated nanogels (pH-sensitive poly(N,N-diethylaminoethyl methacrylate, PDEAEM), and the anticancer drug 5-fluorouracil (5-FU) to explore its potential applications in colon cancer therapies. Nanogels were functionalized in a scalable reaction with an N-hydroxysuccinimide (NHS)-terminated polyethylene glycol derivative and bioconjugated with shark antibodies. Dynamic light scattering measurements indicated the presence of monodispersed nanogels (74 to 236 nm). All systems maintained the pH-sensitive capacity to increase in size as pH decreased. This has direct implications for the release kinetics of 5-FU, which was released faster at pH 5 than at pH 7.4. After bioconjugation, the ELISA results indicated VNAR presence and carcinoembryonic antigen (CEA) recognition. In vitro evaluations of HCT-116 colon cancer cells indicated that functionalized empty nanogels are not cytotoxic and when loaded with 5-FU, the cytotoxic effect of the drug is preserved. A 15% reduction in cell viability was observed after two hours of contact with bioconjugated nanogels when compared to what was observed with non-bioconjugated nanogels. The prepared nanogel system shows potential as an effective and site-specific nanocarrier with promising applications in in vivo studies of colon cancer therapies.

Direct Imaging of "Patch-Clasping" and Relaxation in Robust and Flexible Nanoparticle Assemblies

Polymer patching on inorganic nanoparticles (NPs) enables multifunctionality and directed self-assembly into nonclosely packed optical and mechanical metamaterials. However, experimental demonstration of such assemblies has been scant due to challenges in leveraging patch-induced NP-NP attractions and understanding NP self-assembly dynamics. Here we use low-dose liquid-phase transmission electron microscopy to visualize the dynamic behaviors of tip-patched triangular nanoprisms upon patch-clasping, where polymer patches interpenetrate to form cohesive bonds that connect NPs. Notably, these bonds are longitudinally robust but rotationally flexible. Patch-clasping is found to allow highly selective tip-tip assembly, interconversion between dimeric bowtie and sawtooth configurations, and collective structural relaxation of NP networks. The integration of single particle tracking, polymer physics theory, and molecular dynamics simulation reveals the macromolecular origin of patch-clasping-induced NP dynamics. Our experiment-computation integration can aid the design of stimuli-responsive nanomaterials, such as topological metamaterials for chiral sensors, waveguides, and nanoantennas.

Assembly Requirements for the Construction of Large-Scale Binary Protein Structures

The precise assembly of multiple biomacromolecules into well-defined structures and materials is of great importance for various biomedical and nanobiotechnological applications. In this study, we investigate the assembly requirements for two-component materials using charged protein nanocages as building blocks. To achieve this, we designed several variants of ferritin nanocages to determine the surface characteristics necessary for the formation of large-scale binary three-dimensional (3D) assemblies. These nanocage variants were employed in protein crystallization experiments and macromolecular crystallography analyses, complemented by computational methods. Through the screening of nanocage variant combinations at various ionic strengths, we identified three essential features for successful assembly: (1) the presence of a favored crystal contact region, (2) the presence of a charged patch not involved in crystal contacts, and (3) sufficient distinctiveness between the nanocages. Surprisingly, the absence of noncrystal contact mediating patches had a detrimental effect on the assemblies, highlighting their unexpected importance. Intriguingly, we observed the formation of not only binary structures but also both negatively and positively charged unitary structures under previously exclusively binary conditions. Overall, our findings will inform future design strategies by providing some design rules, showcasing the utility of supercharging symmetric building blocks in facilitating the assembly of biomacromolecules into large-scale binary 3D assemblies.

Injectable cell-laden silk acid hydrogel

This study presents an injectable cell-laden hydrogel system based on silk acid, a carboxylated derivative of natural silk fibroin, which exhibits promising applications in biomedicine. The hydrogel is produced under physiological conditions (37 °C and pH 7.4) via physical crosslinking. Notably, the hydrogel demonstrates remarkable cytocompatibility, enabling efficient cell encapsulation, and exhibits good injectability. These promising results strongly indicate the potential of silk acid hydrogel for transformative applications, including 3D cell culture, targeted cell delivery, and tissue engineering.

Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity

This study investigates the ability of bovine serum albumin (BSA) to act as an extracellular chaperone (EC) on human hemoglobin (Hb) at a pH of 7.4. The best temperature for studying this behavior was determined by analyzing Hb's aggregation kinetics at multiple temperatures. 55 °C was chosen as the optimal temperature for forming Hb amyloids. BSA was then tested at various concentrations (20-100 μM) to assess its chaperone-like activity on Hb at 55 °C. At a concentration of 100 μM, BSA exhibits chaperone-like activity with a client protein:BSA ratio of 1:10. The high ratio implies that the chaperone activity of BSA is favored by the effects of macromolecular crowding. The results showed that BSA has the potential to inhibit Hb's dissociation into alpha and beta subunits and protein aggregation by inhibiting secondary nucleation. BSA also causes the depolymerization of fibrils over time. The results were validated using molecular docking and all-atom molecular dynamics simulations. MD analysis such as RMSD, RMSF, Rg, SASA, Hydrogen bond, PCA, Free energy landscape (FEL) revealed that the stability of hemoglobin is greater when it is bound to BSA compared to unbound state. The study suggests that BSA can potentially bind to Hb dimers and reduce excitonic interactions, which reduces Hb aggregation. These results are consistent with the aggregation kinetics experiments.Communicated by Ramaswamy H. Sarma.

Integrated spectroscopic and MD simulation approach to decipher the effect of pH on the structure function of Staphylococcus aureus thymidine kinase

Staphylococcus aureus is a major human pathogen responsible for a variety of clinical infections, becoming increasingly resistant to antibiotics. To address this challenge, there is a need to identify new cellular targets and innovative approaches to expand treatment options. One such target is thymidine kinase (TK), a crucial enzyme in the pyrimidine salvage pathway, which plays a key role in the phosphorylation of thymidine, an essential component in DNA synthesis and repair. In this study, we have successfully cloned, expressed, and purified the TK protein. A comprehensive investigation into how different pH levels affect the structure and functional activity of TK, using a combination of spectroscopy, classical molecular dynamics simulations, and enzyme activity assays was conducted. Our study revealed that variation in pH disrupts secondary and tertiary structures of TK with noticeable aggregate formation at pH 5.0. Enzyme activity studies demonstrated that TK exhibited its maximum kinase activity within the physiological pH range. These findings strongly suggest a connection between structural changes and enzymatic activity, which was further supported by the agreement between the spectroscopic features we measured and the results of our MD simulations. Our study provides a deeper insight into the structural features of TK, which could potentially be harnessed for the development of therapeutic strategies aimed at combatting infectious diseases. Conformational dynamics plays an essential role in the design and development of effective inhibitors. Considering the effects of pH on the conformational dynamics of TK, our findings may be implicated in the development of potent and selective inhibitors.Communicated by Ramaswamy H. Sarma.

Single Gold Nanobipyramids Sensing the Chirality of Amyloids

Plasmonic nanoparticles, due to their sensitivity to small changes in their closest environment and plasmon resonance, can sense the chirality of the surrounding molecules. Therefore, plasmonic nanoparticles can be applied as a next-generation biosensor for peptides or proteins. In this work, we explore the interaction between chiral, ordered protein aggregates (amyloids) and small gold nanobipyramids. We show how the morphology, structure, and chiroptical properties of amyloids induce circular dichroism in the plasmon resonance wavelengths from individual plasmonic nanoparticles upon binding to the chiral amyloid template. Moreover, using the data from microscopic and spectroscopic analyses of formed heterostructures, we propose the most probable mechanism behind the induction of chirality in this system and discuss which specific feature of insulin protein aggregates is sensed by nanobipyramids.

Correcting Ultraviolet-Visible Spectra for Baseline Artifacts

Rayleigh and Mie light scattering from particulates, soluble protein aggregates, or large proteins can lead to inaccuracy of concentration measurements using ultraviolet (UV) spectroscopy and Beer's Law. While a number of light scattering correction equations have been proposed in the literature, they can also lead to incorrect values if samples vary in particulate and/or soluble aggregate levels or depart in other ways from which the equations were developed. We propose a curve-fitting baseline subtraction approach based on fundamental Rayleigh and Mie scattering equations which also factors in instrument baseline artifacts. We validated this Rayleigh-Mie correction against a wide variety of positive and negative controls, including protein size standards, protein aggregates induced by forced degradation, lentivirus and polystyrene nanospheres.

Application of spectroscopic techniques combined with chemometrics to the authenticity and quality attributes of rice

Rice is a staple food for two-thirds of the world's population and is grown in over a hundred countries around the world. Due to its large scale, it is vulnerable to adulteration. In addition, the quality attribute of rice is an important factor affecting the circulation and price, which is also paid more and more attention. The combination of spectroscopy and chemometrics enables rapid detection of authenticity and quality attributes in rice. This article described the application of seven spectroscopic techniques combined with chemometrics to the rice industry. For a long time, near-infrared spectroscopy and linear chemometric methods (e.g., PLSR and PLS-DA) have been widely used in the rice industry. Although some studies have achieved good accuracy, with models in many studies having greater than 90% accuracy. However, higher accuracy and stability were more likely to be obtained using multiple spectroscopic techniques, nonlinear chemometric methods, and key wavelength selection algorithms. Future research should develop larger rice databases to include more rice varieties and larger amounts of rice depending on the type of rice, and then combine various spectroscopic techniques, nonlinear chemometric methods, and key wavelength selection algorithms. This article provided a reference for a more efficient and accurate determination of rice quality and authenticity.

A novel filter-assisted protein precipitation (FAPP) based sample pre-treatment method for LC-MS peptide mapping for biosimilar characterization

Establishing analytical and functional comparability serves as the foundation of biosimilar development. A critical part of this exercise is sequence similarity search and categorization of post-translational modifications (PTMs), often by peptide mapping using liquid chromatography-mass spectrometry (LC-MS). When performing bottom-up proteomic sample preparation, efficient digestion of the protein and extraction of peptides for subsequent mass spectrometric analysis can be a challenge. Conventional sample preparation strategies face the risk of allowing interference of chemicals which are essential for extraction but are likely to interfere with digestion, resulting in complex chromatographic profiles due to semi-cleavages, insufficient peptide cleavages, and other unwanted reactions. Further, peptide cleanup through commonly used immobilized C-18 pipette tips can cause significant peptide loss as well as variability in individual peptide yields, thereby causing artifacts of various product-related modifications. In this study, we proposed a simple enzymatic digestion technique by incorporating different molecular weight filters and protein precipitation, with the objective to minimize interference of denaturing, reducing, and alkylating agents throughout overnight digestion. As a result, the need for peptide cleanup is significantly reduced and results in higher peptide yield. The proposed FAPP approach outperformed the conventional method across multiple metrics including, 30% more peptides, 8.19% more fully digested peptides, 14% higher sequence coverage rate, and 11.82% more site-specific alterations. Quantitative and qualitative repeatability of the proposed approach have been demonstrated. It can be concluded that the filter-assisted protein precipitation (FAPP) protocol proposed in this study offers an effective substitute for the traditional approach.

Investigating the aggregation perspective of Dengue virus proteome

Dengue viruses are human pathogens that are transmitted through mosquitoes. Apart from the typical symptoms associated with viral fevers, DENV infections are known to cause several neurological complications such as meningitis, encephalitis, intracranial haemorrhage, retinopathies along with the more severe, and sometimes fatal, vascular leakage and dengue shock syndrome. This study was designed to investigate, in detail, the predicted viral protein aggregation prone regions among all serotypes. Further, in order to understand the cross-talk between viral protein aggregation and aggregation of cellular proteins, cross-seeding experiments between the DENV NS1 (1-30), corresponding to the β-roll domain and the diabetes hallmark protein, amylin, were performed. Various techniques such as fluorescence spectroscopy, circular dichroism, atomic force microscopy and immunoblotting have been employed for this. We observe that the DENV proteomes have many predicted APRs and the NS1 (1-30) of DENV1-3, 2K and capsid anchor of DENV2 and DENV4 are capable of forming amyloids, in vitro. Further, the DENV NS1 (1-30), aggregates are also able to cross-seed and enhance amylin aggregation and vice-versa. This knowledge may lead to an opportunity for designing suitable inhibitors of protein aggregation that may be beneficial for viral infections and comorbidities.

The unusual properties of lactoferrin during its nascent phase

Lactoferrin, a multifunctional iron-binding protein containing 16 disulfides, is actively studied for its antibacterial and anti-carcinogenic properties. However, scarce information is nowadays available about its oxidative folding starting from the reduced and unfolded status. This study discovers unusual properties when this protein is examined in its reduced molten globule-like conformation. Using kinetic, CD and fluorescence analyses together with mass spectrometry, we found that a few cysteines display astonishing hyper-reactivity toward different thiol reagents. In details, four cysteines (i.e. 668, 64, 512 and 424) display thousands of times higher reactivity toward GSSG but normal against other natural disulfides. The formation of these four mixed-disulfides with glutathione probably represents the first step of its folding in vivo. A widespread low pKa decreases the reactivity of other 14 cysteines toward GSSG limiting their involvement in the early phase of the oxidative folding. The origin of this hyper-reactivity was due to transient lactoferrin-GSSG complex, as supported by fluorescence experiments. Lactoferrin represents another disulfide containing protein in addition to albumin, lysozyme, ribonuclease, chymotrypsinogen, and trypsinogen which shows cysteines with an extraordinary and specific hyper-reactivity toward GSSG confirming the discovery of a fascinating new feature of proteins in their nascent phase.

Protein aggregation and neurodegenerative disease: Structural outlook for the novel therapeutics

Before the controversial approval of humanized monoclonal antibody lecanemab, which binds to the soluble amyloid-β protofibrils, all the treatments available earlier, for Alzheimer's disease (AD) were symptomatic. The researchers are still struggling to find a breakthrough in AD therapeutic medicine, which is partially attributable to lack in understanding of the structural information associated with the intrinsically disordered proteins and amyloids. One of the major challenges in this area of research is to understand the structural diversity of intrinsically disordered proteins under in vitro conditions. Therefore, in this review, we have summarized the in vitro applications of biophysical methods, which are aimed to shed some light on the heterogeneity, pathogenicity, structures and mechanisms of the intrinsically disordered protein aggregates associated with proteinopathies including AD. This review will also rationalize some of the strategies in modulating disease-relevant pathogenic protein entities by small molecules using structural biology approaches and biophysical characterization. We have also highlighted tools and techniques to simulate the in vivo conditions for native and cytotoxic tau/amyloids assemblies, urge new chemical approaches to replicate tau/amyloids assemblies similar to those in vivo conditions, in addition to designing novel potential drugs.

Protein aggregation: Consequences, mechanism, characterization and inhibitory strategies

Proteins play a major role in the regulation of various cellular functions including the synthesis of structural components. But proteins are stable under physiological conditions only. A slight variation in environmental conditions can cost them huge in terms of conformational stability ultimately leading to aggregation. Under normal conditions, aggregated proteins are degraded or removed from the cell by a quality control system including ubiquitin-proteasomal machinery and autophagy. But they are burdened under diseased conditions or are impaired by the aggregated proteins leading to the generation of toxicity. The misfolding and aggregation of protein such as amyloid-β, α-synuclein, human lysozyme etc., are responsible for certain diseases including Alzheimer, Parkinson, and non- neuropathic systemic amyloidosis respectively. Extensive research has been done to find the therapeutics for such diseases but till now we have got only symptomatic treatment that will reduce the disease severity but will not target the initial formation of nucleus responsible for disease progression and propagation. Hence there is an urgent need to develop the drugs targeting the cause of the disease. For this, a wide knowledge related to misfolding and aggregation under the same heading is required as described in this review alongwith the strategies hypothesized and implemented till now. This will contribute a lot to the work of researchers in the field of neuroscience.

Bioaffinity Nanoprobes for Foodborne Pathogen Sensing

Bioaffinity nanoprobes are a type of biosensor that utilize the specific binding properties of biological molecules, such as antibodies, enzymes, and nucleic acids, for the detection of foodborne pathogens. These probes serve as nanosensors and can provide highly specific and sensitive detection of pathogens in food samples, making them an attractive option for food safety testing. The advantages of bioaffinity nanoprobes include their ability to detect low levels of pathogens, rapid analysis time, and cost-effectiveness. However, limitations include the need for specialized equipment and the potential for cross-reactivity with other biological molecules. Current research efforts focus on optimizing the performance of bioaffinity probes and expanding their application in the food industry. This article discusses relevant analytical methods, such as surface plasmon resonance (SPR) analysis, Fluorescence Resonance Energy Transfer (FRET) measurements, circular dichroism, and flow cytometry, that are used to evaluate the efficacy of bioaffinity nanoprobes. Additionally, it discusses advances in the development and application of biosensors in monitoring foodborne pathogens.

Kaleidoscope megamolecules synthesis and application using self-assembly technology

The megamolecules with high ordered structures play an important role in chemical biology and biomedical engineering. Self-assembly, a long-discovered but very appealing technique, could induce many reactions between biomacromolecules and organic linking molecules, such as an enzyme domain and its covalent inhibitors. Enzyme and its small-molecule inhibitors have achieved many successes in medical application, which realize the catalysis process and theranostic function. By employing the protein engineering technology, the building blocks of enzyme fusion protein and small molecule linker can be assembled into a novel architecture with the specified organization and conformation. Molecular level recognition of enzyme domain could provide both covalent reaction sites and structural skeleton for the functional fusion protein. In this review, we will discuss the range of tools available to combine functional domains by using the recombinant protein technology, which can assemble them into precisely specified architectures/valences and develop the kaleidoscope megamolecules for catalytic and medical application.

Cation-π Interaction Trigger Supramolecular Hydrogelation of Peptide Amphiphiles

As an important noncovalent interaction, cation-π interaction plays an essential role in a broad area of biology and chemistry. Despite extensive studies in protein stability and molecular recognition, the utilization of cation-π interaction as a major driving force to construct supramolecular hydrogel remains uncharted. Here, a series of peptide amphiphiles are designed with cation-π interaction pairs that can self-assemble into supramolecular hydrogel under physiological condition. The influence of cation-π interaction is thoroughly investigated on peptide folding propensity, morphology, and rigidity of the resultant hydrogel. Computational and experimental results confirm that cation-π interaction could serve as a major driving force to trigger peptide folding, resultant β-hairpin peptide self-assembled into fibril-rich hydrogel. Furthermore, the designed peptides exhibit high efficacy on cytosolic protein delivery. As the first case of using cation-π interactions to trigger peptide self-assembly and hydrogelation, this work provides a novel strategy to generate supramolecular biomaterials.

Understanding the activity of glucose oxidase after exposure to organic solvents

Long-term stability of enzymes in organic solvents is one of the most challenging problems in modern biotechnology and chemical industries. However, the resistance of enzymes to organic solvents is not very well understood so far. Herein, the effects of apolar, chlorinated, and polar organic solvents on the activity and structure of glucose oxidase from Aspergillus niger were systemically investigated using spectrophotometric activity assay of this enzyme and absorption and chiroptical spectroscopy. Molecular dynamics simulations and correlation of the activity with properties of the organic solvents were employed to understand the effects of organic solvents on the enzyme. The experimental and theoretical results showed that apolar solvents reduce the enzyme activity because they facilitate its aggregation through inter-enzymatic salt bridges. Moreover, polar solvents strongly coordinate with amino acid residues in the glucose binding pocket and prevent binding of the substrates. We found that this enzyme is stable in pure apolar and chlorinated solvents and these solvents can be used for the functionalization of its residues. This work provides an in depth understanding at the molecular level of the impact of various pure organic solvents on the structure and dynamics of glucose oxidase and the regulation of its catalytic activity.

Selective vitamins as potential options for dietary therapeutic interventions: In silico and In vitro insights from mutant C terminal fragment of FGA

We have used an integrated computational approach to explore the role of vitamin C and vitamin D in preventing aggregation of Fibrinogen A alpha-chain (FGA^cter) protein responsible for renal amyloidosis. We modelled structures of E524K / E526K mutants of FGA^cter protein and examined the potential interactions of these mutants with vitamin C and vitamin D3. Interaction of these vitamins at the amyloidogenic site may prevent the intermolecular interaction required for amyloid formation. The binding free energy values of vitamin C and vitamin D3 for E524K FGA^cter and E526K FGA^cter are - 67.12 ± 30.46 kJ/mole and - 79.45 ± 26.12 kJ/mol, respectively. Experimental studies using Congo red absorption, aggregation index studies and AFM imaging show encouraging results. The AFM images of E526K FGA^cter contained more extensive and higher protofibril aggregates, whereas, in the presence of vitamin D3, small monomeric and oligomeric aggregates were observed. Overall, the works provide interesting results about vitamin C and D role in preventing renal amyloidosis.

A Blue/NIR ratiometric fluorescent probe for intracellular detection of Tyrosinase and the inhibitor screening

A novel ratiometric fluorescent tyrosinase assay is developed based on hybrid nano-assembly of gold nanocluster and tyrosine-containing peptides. The AuNCs@YCY nano-probe (AYNP) is fabricated through the hydrophobic interactions and π-π stacking between the tyrosine residues of the Tyr-Cys-Tyr tripeptide (YCY) and the ligands on the surfaces of AuNCs under the near-isoelectric pH value. The resulted AYNP shows distinct fluorescence responses, spontaneous turn-on of the blue emission and turn-off of the near-infrared emission, with a single wavelength excitation. It is demonstrated that the enhancement and quenching are due to the production of pheomelanin and dopaquinone structures, respectively, induced by tyrosinase oxidation. The internal referencing system provides the tyrosinase assay with superior sensitivity and a detection limit as low as 6.3 U L^-1 could be achieved. The experimental results also demonstrate the excellent selectivity, good photo-stability, and both in vitro and cellular applications of AYNP. This assay technique is low-cost, easy to prepare, and shows excellent potential as a novel melanoma clinical diagnostic platform and a tyrosinase inhibitor screening tool.

Structural and functional properties of collagen isolated from lumpfish and starfish using isoelectric precipitation vs salting out

The possibility of replacing the very time and resource demanding salting out (SO) method with isoelectric precipitation (IP) during collagen extraction from common starfish and lumpfish was investigated. The effect of IP on yield, structural and functional properties of the collagens was therefore compared with SO. Application of IP resulted in a higher or similar collagen mass yield compared with SO from starfish and lumpfish, respectively. However, the purity of collagens recovered with IP was lower than those recovered with SO. Replacing SO with IP did not affect polypeptide pattern and tropohelical structural integrity of collagen from the two resources as revealed with SDS-PAGE and FTIR analysis. Thermal stability and fibril formation capacity of collagens recovered with IP were also well preserved. Overall, the results showed that the IP can be a promising resource smart alternative for the classic SO precipitation during collagen extraction from marine resources.

The pH-responsive precipitation-redissolution of the CspB fusion protein, CspB50TEV-Teriparatide, triggered by changes in secondary structure

Cell surface protein B (CspB) fusion proteins can undergo reversible pH-responsive precipitation-redissolution. A pH-responsive precipitation-redissolution of CspB tag purification (pPRCP) method was established for protein purification using this property. However, the mechanism of the pH-responsive precipitation of CspB fusion proteins is unknown, which has made it difficult to set process parameters for pPRCP. In this study, we investigated the mechanism of the pH-responsive precipitation of CspB fusion proteins using CspB50TEV-Teriparatide (CspB-teri) as a model. As expected, CspB-Teri was reversibly precipitated at acidic pH. By contrast, CspB-Teri was not precipitated under unfolding conditions induced by trifluoroethanol, urea, or guanidine hydrochloride, even at acidic pH. The conformation of CspB-Teri changed to a β-sheet-rich structure as the pH decreased, followed by the formation of intermolecular interactions, which caused precipitation. The particle size of the CspB-Teri precipitate increased in a protein concentration-dependent manner. These results indicated that the pH-responsive precipitation of CspB-Teri is triggered by the formation of a β-sheet structure in response to decreasing pH, and the growth of the precipitate particles occurred through intermolecular interactions.

A Diphenylalanine Based Pentapeptide with Fibrillating Self-Assembling Properties

Peptides and their related compounds can self-assemble into diverse nanostructures of different shapes and sizes in response to various stimuli such as pH, temperature or ionic strength. Here we report the synthesis and characterization of a lysozyme derived pentapeptide and its ability to build well-defined fibrillar structures. Lysozyme FESNF peptide fragment was synthesized by solid phase peptide synthesis using the Fmoc/t-Bu strategy, purified by analytical high-performance liquid chromatography (HPLC) and its molecular weight was confirmed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Spectroscopic features of this pentapeptide were investigated by UV-visible spectroscopy and fluorimetry showing the pattern of marginal phenylalanine residues within the peptide sequence. Self-assembling properties were determined using atomic force microscopy (AFM), aggregation index and thioflavin T assay (ThT). FESNF generating fibrillar structures observed by AFM and aggregation propensity were primarily influenced by pH conditions. Moreover, the experimental data were confirmed by molecular dynamics simulation studies. The obtained fibrils will be used next to explore their potential to act as support material for medical and cosmetic application.

Heating-mediated purification of active FGF21 and structure-based design of its variant with enhanced potency

Fibroblast growth factor 21 (FGF21) has pharmaceutical potential against obesity-related metabolic disorders, including non-alcoholic fatty liver disease. Since thermal stability is a desirable factor for therapeutic proteins, we investigated the thermal behavior of human FGF21. FGF21 remained soluble after heating; thus, we examined its temperature-induced structural changes using circular dichroism (CD). FGF21 showed inter-convertible temperature-specific CD spectra. The CD spectrum at 100 °C returned to that at 20 °C when the heated FGF21 solution was cooled. Through loop swapping, the connecting loop between β10 and β12 in FGF21 was revealed to be associated with the unique thermal behavior of FGF21. According to surface plasmon resonance (SPR) experiments, in vitro cell-based assays, and model high-fat diet (HFD)-induced obesity studies, heated FGF21 maintained biological activities that were comparable to those of non-heated and commercial FGF21s. Based on sequence comparison and structural analysis, five point-mutations were introduced into FGF21. Compared with the wild type, the heated FGF21 variant displayed improved therapeutic potential in terms of body weight loss, the levels of hepatic triglycerides and lipids, and the degree of vacuolization of liver in HFD-fed mice.

Comprehensive study upon physicochemical properties of bio-ZnO NCs

In this study, for the first time, the comparison of commercially available chemical ZnO NCs and bio-ZnO NCs produced extracellularly by two different probiotic isolates (Latilactobacillus curvatus MEVP1 [OM736187] and Limosilactobacillus fermentum MEVP2 [OM736188]) were performed. All types of ZnO formulations were characterized by comprehensive interdisciplinary approach including various instrumental techniques in order to obtain nanocomposites with suitable properties for further applications, i.e. biomedical. Based on the X- ray diffraction analysis results, all tested nanoparticles exhibited the wurtzite structure with an average crystalline size distribution of 21.1 nm (CHEM_ZnO NCs), 13.2 nm (1C_ZnO NCs) and 12.9 nm (4a_ZnO NCs). The microscopy approach with use of broad range of detectors (SE, BF, HAADF) revealed the core-shell structure of bio-ZnO NCs, compared to the chemical one. The nanoparticles core of 1C and 4a_ZnO NCs are coated by the specific organic deposit coming from the metabolites produced by two probiotic strains, L. fermentum and L. curvatus. Vibrational infrared spectroscopy, photoluminescence (PL) and mass spectrometry (LDI-TOF-MS) have been used to monitor the ZnO NCs surface chemistry and allowed for better description of bio-NCs organic coating composition (amino acids residues). The characterized ZnO formulations were then assessed for their photocatalytic properties against methylene blue (MB). Both types of bio-ZnO NCs exhibited good photocatalytic activity, however, the effect of CHEM_ZnO NCs was more potent than bio-ZnO NCs. Finally, the colloidal stability of the tested nanoparticles were investigated based on the zeta potential (ZP) and hydrodynamic diameter measurements in dependence of the nanocomposites concentration and investigation time. During the biosynthesis of nano-ZnO, the increment of pH from 5.7 to around 8 were observed which suggested possible contribution of zinc aquacomplexes and carboxyl-rich compounds resulted in conversion of zinc tetrahydroxy ion complex to ZnO NCs. Overall results in present study suggest that used accessible source such us probiotic strains, L. fermentum and L. curvatus, for extracellular bio-ZnO NCs synthesis are of high interest. What is important, no significant differences between organic deposit (e.g. metabolites) produced by tested strains were noticed-both of them allowed to form the nanoparticles with natural origin coating. In comparison to chemical ZnO NCs, those synthetized via microbiological route are promising material with further biological potential once have shown high stability during 7 days.

Polybrominated diphenyl ethers interact with the key protein involved in carbohydrate metabolism in rice

Rice exposed to organic pollutants such as polybrominated diphenyl ethers (PBDEs) usually experiences reduced biomass and increased soluble sugar content. This study showed that 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47) led to increased glucose, fructose, and sucrose in rice leaves, accompanied by decreased photosynthetic rate and biomass. In order to identify the key enzyme that BDE-47 interacted with, a diazirine-alkynyl photoaffinity probe was designed, and photoaffinity labeling based chemoproteomics was conducted. Among all differentially expressed proteins, fructose-1, 6-bisphosphate aldolase (FBA) involved in carbohydrate metabolism was most likely the target protein of BDE-47. Spectral techniques and molecular docking analysis further revealed that the pollutant-protein interaction was driven by hydrophobic force. BDE-47 inhibited FBA catalytic efficiency by competing with its substrate, fructose-1, 6-diphosphate (F-1, 6-P), leading to soluble sugar accumulation, photosynthetic rate decline and biomass reduction. This study unraveled the influencing mechanism of PBDEs on rice by combining the novel photoaffinity labeling-based chemoproteomics with conventional proteomics. The improved knowledge on direct interaction between organic pollutants and proteins will help alleviate the harmful effects of soil pollution on plants.

Determination of Conformational and Functional Stability of Potential Plague Vaccine Candidate in Formulation

Generally, protein-based vaccines are available in liquid form and are highly susceptible to instability under elevated temperature changes including freezing conditions. There is a need to create a convenient formulation of protein/peptides that can be stored at ambient conditions without loss of activity or production of adverse effects. The efficiency of naturally occurring biocompatible polymer dextran in improving the shelf-life and biological activity of a highly thermally unstable plague vaccine candidate protein called Low Calcium Response V antigen (LcrV), which can be stored at room temperature (30 ± 2 °C), has been evaluated. To determine the preferential interactions with molecular-level insight into solvent-protein interactions, analytical techniques such asspectroscopy, particle size distribution, gel electrophoresis, microscopy, and thermal analysis have been performed along with the evaluation of humoral immune response, invivo. The analytical methods demonstrate the structural stability of the LcrV protein by expressing its interaction with the excipients in the formulation. The invivo studies elicited the biological activity of the formulated antigen with a significantly higher humoral immune response (p-value = 0.047) when compared to the native, adjuvanted antigen. We propose dextran as a potential biopolymer with its co-excipient sodium chloride (NaCl) to provide protein compactness, i.e., prevent protein unfolding by molecular crowding or masking mechanism using preferential hydrophobic interaction for up to three weeks at room temperature (30 ± 2 °C).

Bioprocessing of recombinant proteins from Escherichia coli inclusion bodies: insights from structure-function relationship for novel applications

The formation of inclusion bodies (IBs) during expression of recombinant therapeutic proteins using E. coli is a significant hurdle in producing high-quality, safe, and efficacious medicines. The improved understanding of the structure-function relationship of the IBs has resulted in the development of novel biotechnologies that have streamlined the isolation, solubilization, refolding, and purification of the active functional proteins from the bacterial IBs. Together, this overall effort promises to radically improve the scope of experimental biology of therapeutic protein production and expand new prospects in IBs usage. Notably, the IBs are increasingly used for applications in more pristine areas such as drug delivery and material sciences. In this review, we intend to provide a comprehensive picture of the bio-processing of bacterial IBs, including assessing critical gaps that still need to be addressed and potential solutions to overcome them. We expect this review to be a useful resource for those working in the area of protein refolding and therapeutic protein production.

Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a

Double-PHD fingers 3 (DPF3) is a BAF-associated human epigenetic regulator, which is increasingly recognised as a major contributor to various pathological contexts, such as cardiac defects, cancer, and neurodegenerative diseases. Recently, we unveiled that its two isoforms (DPF3b and DPF3a) are amyloidogenic intrinsically disordered proteins. DPF3 isoforms differ from their C-terminal region (C-TERb and C-TERa), containing zinc fingers and disordered domains. Herein, we investigated the disorder aggregation properties of C-TER isoforms. In agreement with the predictions, spectroscopy highlighted a lack of a highly ordered structure, especially for C-TERa. Over a few days, both C-TERs were shown to spontaneously assemble into similar antiparallel and parallel β-sheet-rich fibrils. Altered metal homeostasis being a neurodegeneration hallmark, we also assessed the influence of divalent metal cations, namely Cu²⁺, Mg²⁺, Ni²⁺, and Zn²⁺, on the C-TER aggregation pathway. Circular dichroism revealed that metal binding does not impair the formation of β-sheets, though metal-specific tertiary structure modifications were observed. Through intrinsic and extrinsic fluorescence, we found that metal cations differently affect C-TERb and C-TERa. Cu²⁺ and Ni²⁺ have a strong inhibitory effect on the aggregation of both isoforms, whereas Mg²⁺ impedes C-TERb fibrillation and, on the contrary, enhances that of C-TERa. Upon Zn²⁺ binding, C-TERb aggregation is also hindered, and the amyloid autofluorescence of C-TERa is remarkably red-shifted. Using electron microscopy, we confirmed that the metal-induced spectral changes are related to the morphological diversity of the aggregates. While metal-treated C-TERb formed breakable and fragmented filaments, C-TERa fibrils retained their flexibility and packing properties in the presence of Mg²⁺ and Zn²⁺ cations.

Understanding the Role of Self-Assembly and Interaction with Biological Membranes of Short Cationic Lipopeptides in the Effective Design of New Antibiotics

This study investigates short cationic antimicrobial lipopeptides composed of 2-4 amino acid residues and C12-C18 fatty acids attached to the N-terminal part of the peptides. The findings were discussed in the context of the relationship among biological activity, self-assembly, stability, and membrane interactions. All the lipopeptides showed the ability to self-assemble in PBS solution. In most cases, the critical aggregation concentration (CAC) much surpassed the minimal inhibitory concentration (MIC) values, suggesting that monomers are the main active form of lipopeptides. The introduction of β-alanine into the peptide sequence resulted in a compound with a high propensity to fibrillate, which increased the peptide stability and activity against S. epidermidis and C. albicans and reduced the cytotoxicity against human keratinocytes. The results of our study indicated that the target of action of lipopeptides is the bacterial membrane. Interestingly, the type of peptide counterion may affect the degree of penetration of the lipid bilayer. In addition, the binding of the lipopeptide to the membrane of Gram-negative bacteria may lead to the release of calcium ions necessary for stabilization of the lipopolysaccharide layer.

Integrating-Sphere-Assisted Resonance Synchronous Spectroscopy for the Quantification of Material Double-Beam UV-Vis Absorption and Scattering Extinction

Integrating spheres (IS) have been used extensively for the characterization of light absorption in turbid samples. However, converting the IS-based sample absorption coefficient to the UV-vis absorbance quantified with a double-beam UV-vis spectrophotometer is challenging. Herein, we report an integrating-sphere-assisted resonance synchronous (ISARS) spectroscopy method performed with conventional spectrofluorometers equipped with an integrating-sphere accessory. Mathematical models and experimental procedures for quantifying the sample, solvent, and instrument-baseline ISARS intensity spectra were provided. A three-parameter analytical model has been developed for correlating the ISARS-based UV-vis absorbance and the absorbance measured with double-beam instruments. This ISARS method enables the quantitative separation of light absorption and scattering contribution to the sample UV-vis extinction spectrum measured with double-beam UV-vis spectrophotometers. Example applications of this ISARS technique are demonstrated with a series of representative samples differing significantly in their optical complexities, from approximately pure absorbers, pure scatterers, to simultaneous light absorbers, scatterers, and emitters under resonance excitation and detection conditions.

The Anfinsen Dogma: Intriguing Details Sixty-Five Years Later

The pioneering experiments of Anfinsen on the oxidative folding of RNase have been revisited discovering some details, which update the statement of his dogma and shed new light on the leading role of the correct disulfide in the attainment of the native structure. CD analysis, mass spectrometry, fluorescence spectroscopy and enzyme activity indicate that native disulfides drive the formation of the secondary and tertiary structures that cannot be entirely formed in their absence. This opposes a common opinion that these structures are first formed and then stabilized by the native disulfides. Our results also indicate that a spontaneous re-oxidation of a reduced RNase cannot produce a complete recovery of activity, as described by many textbooks; this can be obtained only in the presence of a reshuffling solution such as GSH/GSSG.

Effect of pH on Diclofenac–Lysozyme Interaction: Structural and Functional Aspect

As a nonsteroidal antiinflammatory drug, diclofenac (DCF) is used in the treatment of a variety of human ailments. It has already been reported that the use of this class of drugs for a longer duration is associated with numerous side effects such as cardiovascular implications, reno-medullary complications, etc. In the present study, the effect of DCF on the structure, stability, and function of lysozyme was studied. The study was designed to examine the effect of DCF only at various pH values. Heat-induced denaturation of lysozyme was analyzed in the presence and absence of various molar concentrations of DCF at different pH values. The values of thermodynamic parameters, the midpoint of denaturation (T_m), enthalpy change at T_m (ΔH_m), constant pressure heat capacity change (ΔC_p), and Gibbs energy change at 25°C (ΔG_D^o), thus obtained under a given set of conditions (pH and molar concentration of DCF), demonstrated the following 1) DCF destabilized lysozyme with respect of T_m and ΔG_D^o at all the pH values, 2) the magnitude of protein destabilization is lesser at acidic pH than at physiological pH, 3) structural changes in lysozyme are less projecting at pH 2.0 than at pH 7.0, and 4) quenching is observed at both pH values. Furthermore, the process of protein destabilization in the presence of DCF is entropically driven.

Comparative Assessment of the Structural Features of Originator Recombinant Human Follitropin Alfa Versus Recombinant Human Follitropin Alfa Biosimilar Preparations Approved in Non-European Regions

Although the full primary structures of the alfa and beta subunits of reference r-hFSH-alfa and its biosimilars are identical, cell context-dependent differences in the expressing cell lines and manufacturing process can lead to variations in glycosylation profiles. In the present study, we compared the structural features of reference r-hFSH-alfa with those of five biosimilar preparations approved in different global regions outside Europe (Primapur^®, Jin Sai Heng^®, Follitrope^®, Folisurge^®, and Corneumon^®) with respect to glycosylation, macro- and microheterogeneity, and other post-translational modifications and higher order structure. The mean proportion of N-glycosylation-site occupancy was highest in reference r-hFSH-alfa, decreasing sequentially in Primapur, Jin Sai Heng, Corneumon, Follisurge and Follitrope, respectively. The level of antennarity showed slightly higher complexity in Corneumon, Primapur and Follitrope versus reference r-hFSH-alfa, whereas Jin Sai Heng and Folisurge were aligned with reference r-hFSH-alfa across all N-glycosylation sites. Sialylation level was higher in Corneumon and Follitrope, but small differences were detected in other biosimilar preparations compared with reference r-hFSH-alfa. Jin Sai Heng showed higher levels of N-glyconeuramic acid than the other preparations. Minor differences in oxidation levels were seen among the different products. Therefore, in summary, we identified var ious differences in N-glycosylation occupancy, antennarity, sialylation and oxidation between reference r-hFSH-alfa and the biosimilar preparations analyzed.

Multipoint Immobilization at the Inert Center of Urease on Homofunctional Diazo-Activated Silica Gel: A Way of Restoring Room-Temperature Catalytic Sustainability for Perennial Utilization

At present, enzyme immobilization is a big issue. It improves enzyme stability, activity, specificity, or selectivity, particularly the enantioselectivity compared to the native enzymes, and by solving the separation problem, it helps in recovering the catalyst with good reusability as desired in vitro. Motivated by these facts, in this work, Jack bean urease (JBU) is immobilized on three-dimensional (3D)-network silica gel (SG) via multipoint covalent bonding employing dimethyldichlorosilane (DMDCS) and p-nitrophenol, respectively, as the second-generation silane-coupling reagent and spacer. The homofunctional diazo group appearing at the functionalized SG unit cell makes a diazo linkage at the inert center, the ortho position of the phenolic-OH of the tyrosine moiety, where all of the amino, thiol, phenol, imidazole, carboxy, etc., groups of the enzyme residues, including those that belong to the active site, remain intact. The coupling process, analyzed using field emission scanning electron microscopy (FESEM), energy-dispersive X-ray analysis (EDX), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR) spectroscopy, ultraviolet-visible spectroscopy (UV-vis), and fluorescence spectroscopy, occurs without molecular aggregation in borate buffer at pH 8.8 ± 0.4, which is much higher than the iso-electric point (pH 5.1) of the macromolecule where it becomes soluble. Eventually, the immobilization is maximize and also the native-enzyme activities are restored remarkably. The immobilized catalyst converts urea (0.0625-0.15 mmol L^-1) to ammonia appreciably (94.50 ± 1.5%) at 27 °C, and the efficiency is well comparable to that of the native enzyme (93.0 ± 0.4%). The efficiency gradually diminishes, coming down to 50% at the 40th cycle, and the enzyme returns to its native conformation within 72 h in tris-EDTA borate buffer at 27 °C for the next 40 cycles of reuse and so on. The efficiency becomes hindered by 8-10% in every 5th subsequent reuse to reach 50% on the 30th reuse, resulting in room-temperature catalytic sustainability of 90 days. The catalytic performances are well restored in rice extract and coconut water.

Antamanide Analogs as Potential Inhibitors of Tyrosinase

The tyrosinase enzyme, which catalyzes the hydroxylation of monophenols and the oxidation of o-diphenols, is typically involved in the synthesis of the dark product melanin starting from the amino acid tyrosine. Contributing to the browning of plant and fruit tissues and to the hyperpigmentation of the skin, leading to melasma or age spots, the research of possible tyrosinase inhibitors has attracted much interest in agri-food, cosmetic, and medicinal industries. In this study, we analyzed the capability of antamanide, a mushroom bioactive cyclic decapeptide, and some of its glycine derivatives, compared to that of pseudostellarin A, a known tyrosinase inhibitor, to hinder tyrosinase activity by using a spectrophotometric method. Additionally, computational docking studies were performed in order to elucidate the interactions occurring with the tyrosinase catalytic site. Our results show that antamanide did not exert any inhibitory activity. On the contrary, the three glycine derivatives AG9, AG6, and AOG9, which differ from each other by the position of a glycine that substitutes phenylalanine in the parent molecule, improving water solubility and flexibility, showed tyrosinase inhibition by spectrophotometric assays. Analytical data were confirmed by computational studies.

Cost-effective Purification of Membrane Proteins using a Dual-detergent Strategy

Understanding the mechanisms of membrane protein function is critical for biomedical research and drug discovery as membrane proteins constitute ∼30% of the proteins encoded by the genomes of both lower and higher organisms and are targets for two-thirds of approved drugs worldwide. Significant progress has been made in engineering host expression systems for large-scale production of membrane proteins and in determining their three-dimensional high-resolution structures. Despite these efforts, the study of membrane proteins at the atomic level is challenging due to poor expression and extraction, low yields of functional protein, and the complexity and heterogeneity of source membranes. Structural and spectroscopic studies of any membrane protein require that the protein be extracted from its native membranes into a membrane-mimetic stable environment, which is often achieved by the use of detergents. Unfortunately, there is no magic detergent that can extract all membrane proteins and successful extraction often requires a thorough screen of detergents. Furthermore, membrane protein purification in general and the detergents used are very expensive, which puts a financial constraint on sophisticated membrane protein studies. To overcome this hurdle, a dual-detergent strategy has recently been developed and successfully applied to purify various classes of pure, stable, and functionally relevant membrane proteins in a cost-effective manner. This strategy uses an inexpensive detergent for solubilization of the desired protein from membranes and a second detergent during protein purification. In the Basic Protocol, we describe the dual-detergent strategy to significantly reduce the overall purification cost of a bacterial membrane protein using the magnesium ion channel MgtE as an example. Support Protocols are also provided for selecting a suitable E. coli strain for protein expression and the optimal detergent(s) for membrane protein solubilization. © 2022 Wiley Periodicals LLC. Basic Protocol: Expression, membrane solubilization, and cost-effective purification of MgtE Support Protocol 1: Selecting a suitable E. coli strain for optimal protein expression Support Protocol 2: Identification of suitable detergents for membrane protein solubilization.

Functionalization of Glucose Oxidase in Organic Solvent: Towards Direct Electrical Communication across Enzyme-Electrode Interface

Enzymatic biosensors based on glucose oxidase has been proven to be one of the effective strategies for the detection of glucose and contributed to health improvements. Therefore, research and debates to date are ongoing in an attempt to find the most effective way to detect this analyte using this enzyme as the recognition center. The 3rd generation biosensors using direct electron transfer (DET) type enzymes are a great way towards practical devices. In this work, we developed a simple method for the functionalization of glucose oxidase with redoxable ferrocene groups in chloroform. The enzyme retained its activity after storage in this organic solvent and after the functionalization procedures. This enzyme functionalization strategy was employed to develop the biosensing monolayer-based platforms for the detection of glucose utilizing the quasi-DET mechanism. As a result of an electrochemical regeneration of the catalytic center, the formation of harmful H₂O₂ is minimized during enzymatic electrocatalysis.