Tools and methods for circular dichroism spectroscopy of proteins: a tutorial review

Simulated gastrointestinal digestion of walnut protein yields anti-inflammatory peptides

The impact of the simulated gastrointestinal digestion process on walnut protein and the potential anti-inflammatory properties of its metabolites was studied. Structural changes induced by digestion, notably in α-Helix, β-Turn, and Random Coil configurations, were unveiled. Proteins over 10,000 Da significantly decreased by 35.6 %. Antioxidant activity in these metabolites paralleled increased amino acid content. Molecular docking identified three walnut polypeptides-IPAGTPVYLINR, FQGQLPR, and VVYVLR-with potent anti-inflammatory properties. RMSD and RMSF analysis demonstrated the stable and flexible interaction of these polypeptides with their target proteins. In lipopolysaccharide (LPS)-induced inflammation in normal human colon mucosal epithelial NCM460 cells, these peptides decreased 5-hydroxytryptamine (5-HT), tumor necrosis factor-alpha (TNF-α), and vascular endothelial growth factor (VEGF) expression, while mitigating cell apoptosis and inflammation. Our study offers valuable insights into walnut protein physiology, shedding light on its potential health benefits.

Enhancing the Thermal Stability and Enzyme Activity of Ketopantoate Hydroxymethyltransferase through Interface Modification Engineering

Ketopantoate hydroxymethyltransferase (KPHMT) plays a pivotal role in d-pantothenic acid biosynthesis. Most KPHMTs are homodecamers with low thermal stability, posing challenges for protein engineering and limiting output enhancement. Previously, a high-enzyme activity KPHMT mutant (K25A/E189S) from Corynebacterium glutamicum was screened as mother strain (M0). Building upon this strain, our study focused on interface engineering modifications, employing a multifaceted approach including integrating folding-free energy calculation, B-factor analysis, and conserved site analysis. Preliminary screening led to the selection of five mutants in the interface─E106S, E98T, E98N, S247I, and S247D─showing improved thermal stability, culminating in the double-site mutant M8 (M0-E98N/S247D). M8 exhibited a T1/2 value of 288.79 min at 50 °C, showing a 3.29-fold increase compared to M0. Meanwhile, the Tm value of M8 was elevated from 53.2 to 59.6 °C. Investigations of structural and molecular dynamics simulations revealed alterations in surface electrostatic charge distribution and the formation of increased hydrogen bonds between subunits, contributing to enhanced thermal stability. This investigation corroborates the efficacy of interface engineering modifications in bolstering KPHMT stability while showing its potential for positively impacting industrial d-pantothenic acid synthesis.

The evolutionary novelty of insect defensins: from bacterial killing to toxin neutralization

Insect host defense comprises two complementary dimensions, microbial killing-mediated resistance and microbial toxin neutralization-mediated resilience, both jointly providing protection against pathogen infections. Insect defensins are a class of effectors of innate immunity primarily responsible for resistance to Gram-positive bacteria. Here, we report a newly originated gene from an ancestral defensin via genetic deletion following gene duplication in Drosophila virilis, which confers an enhanced resilience to Gram-positive bacterial infection. This gene encodes an 18-mer arginine-rich peptide (termed DvirARP) with differences from its parent gene in its pattern of expression, structure and function. DvirARP specifically expresses in D. virilis female adults with a constitutive manner. It adopts a novel fold with a 310 helix and a two CXC motif-containing loop stabilized by two disulfide bridges. DvirARP exhibits no activity on the majority of microorganisms tested and only a weak activity against two Gram-positive bacteria. DvirARP knockout flies are viable and have no obvious defect in reproductivity but they are more susceptible to the DvirARP-resistant Staphylococcus aureus infection than the wild type files, which can be attributable to its ability in neutralization of the S. aureus secreted toxins. Phylogenetic distribution analysis reveals that DvirARP is restrictedly present in the Drosophila subgenus, but independent deletion variations also occur in defensins from the Sophophora subgenus, in support of the evolvability of this class of immune effectors. Our work illustrates for the first time how a duplicate resistance-mediated gene evolves an ability to increase the resilience of a subset of Drosophila species against bacterial infection.

Molecular design, construction and analgesic mechanism insights into the novel transdermal fusion peptide ANTP-BgNPB

Toad venom, a traditional Chinese medicine, exhibits remarkable medicinal properties of significant therapeutic value. The peptides present within toad venom possess a wide range of biological functions, yet the neuropeptide B (NPB) and it modification requires further exploration to comprehensively understand its mechanisms of action and potential applications. In this study, a fusion peptide, ANTP-BgNPB, was designed to possess better analgesic properties through the transdermal modification of BgNPB. After optimizing the conditions, the expression of ANTP-BgNPB was successfully induced. The molecular dynamics simulations suggested that the modified protein exhibited improved stability and receptor binding affinity compared to its unmodified form. The analysis of the active site of ANTP-BgNPB and the verification of mutants revealed that GLN3, SER38, and ARG42 were crucial for the protein's recognition and binding with G protein-coupled receptor 7 (GPR7). Moreover, experiments conducted on mice using the hot plate and acetic acid twist body models demonstrated that ANTP-BgNPB was effective in transdermal analgesia. These findings represent significant progress in the development of transdermal delivery medications and could have a significant impact on pain management.

Recombinant multiepitope proteins expressed in Escherichia coli cells and their potential for immunodiagnosis

Recombinant multiepitope proteins (RMPs) are a promising alternative for application in diagnostic tests and, given their wide application in the most diverse diseases, this review article aims to survey the use of these antigens for diagnosis, as well as discuss the main points surrounding these antigens. RMPs usually consisting of linear, immunodominant, and phylogenetically conserved epitopes, has been applied in the experimental diagnosis of various human and animal diseases, such as leishmaniasis, brucellosis, cysticercosis, Chagas disease, hepatitis, leptospirosis, leprosy, filariasis, schistosomiasis, dengue, and COVID-19. The synthetic genes for these epitopes are joined to code a single RMP, either with spacers or fused, with different biochemical properties. The epitopes' high density within the RMPs contributes to a high degree of sensitivity and specificity. The RMPs can also sidestep the need for multiple peptide synthesis or multiple recombinant proteins, reducing costs and enhancing the standardization conditions for immunoassays. Methods such as bioinformatics and circular dichroism have been widely applied in the development of new RMPs, helping to guide their construction and better understand their structure. Several RMPs have been expressed, mainly using the Escherichia coli expression system, highlighting the importance of these cells in the biotechnological field. In fact, technological advances in this area, offering a wide range of different strains to be used, make these cells the most widely used expression platform. RMPs have been experimentally used to diagnose a broad range of illnesses in the laboratory, suggesting they could also be useful for accurate diagnoses commercially. On this point, the RMP method offers a tempting substitute for the production of promising antigens used to assemble commercial diagnostic kits.

Toward Synthetic Intrinsically Disordered Polypeptides (IDPs): Controlled Incorporation of Glycine in the Ring-Opening Polymerization of N-Carboxyanhydrides

Intrinsically disordered proteins (IDPs) do not have a well-defined folded structure but instead behave as extended polymer chains in solution. Many IDPs are rich in glycine residues, which create steric barriers to secondary structuring and protein folding. Inspired by this feature, we have studied how the introduction of glycine residues influences the secondary structure of a model polypeptide, poly(l-glutamic acid), a helical polymer. For this purpose, we carried out ring-opening copolymerization with γ-benzyl-l-glutamate and glycine N-carboxyanhydride (NCA) monomers. We aimed to control the glycine distribution within PBLG by adjusting the reactivity ratios of the two NCAs using different reaction conditions (temperature, solvent). The relationship between those conditions, the monomer distributions, and the secondary structure enabled the design of intrinsically disordered polypeptides when a highly gradient microstructure was achieved in DMSO.

Impact of imperfect data on protein secondary structure estimates from Far-UV circular dichroism spectra

Circular dichroism [CD] is widely used to rapidly assess protein structure. Deconvolution of the far-UV CD spectrum is widely used to quantify the secondary structural elements [SSEs]. Multiple algorithms are available for this. Imperfections in the experimental CD spectra arising from spectral noise, instrument miscalibration, spectral offsets and non-linearity will impact on the accuracy and precision of derived secondary structure estimates. Analytical validation for use in regulated environments, such as biopharmaceuticals, requires that the impact of imperfect data on these estimates be understood. Limited information on the impact of poor data were available. A series of noise-free simulated spectral datasets with modified intensity, wavelength, noise and intensity linearity and offsets were created from entries in the Protein Circular Dichroism Data Bank. These datasets were analysed using the BeStSel, on-line resource to estimate secondary structure. Data imperfections caused significant change in SSEs, but the spectral range is also important. This study emphasises the importance of analytical method validation and justifiable estimates of uncertainty when reporting results. The datasets created are made available as a resource to validate other secondary structure estimation programs.

Copper interaction with cystatin C: effects on protein structure and oligomerization

Human cystatin C (hCC), a small secretory protein, has gained attention beyond its classical role as a cysteine protease inhibitor owing to its potential involvement in neurodegenerative disorders. This study investigates the interaction between copper(II) ions [Cu(II)] and hCC, specifically targeting histidine residues known to participate in metal binding. Through various analytical techniques, including mutagenesis, circular dichroism, fluorescence assays, gel filtration chromatography, and electron microscopy, we evaluated the impact of Cu(II) ions on the structure and oligomerization of hCC. The results show that Cu(II) does not influence the secondary and tertiary structure of the studied hCC variants but affects their stability. To explore the Cu(II)-binding site, nuclear magnetic resonance (NMR) and X-ray studies were conducted. NMR experiments revealed notable changes in signal intensities and linewidths within the region 86His-Asp-Gln-Pro-His90, suggesting its involvement in Cu(II) coordination. Both histidine residues from this fragment were found to serve as a primary anchor of Cu(II) in solution, depending on the structural context and the presence of other Cu(II)-binding agents. The presence of Cu(II) led to significant destabilization and altered thermal stability of the wild-type and H90A variant, confirming differentiation between His residues in Cu(II) binding. In conclusion, this study provides valuable insights into the interaction between Cu(II) and hCC, elucidating the impact of copper ions on protein stability and identifying potential Cu(II)-binding residues. Understanding these interactions enhances our knowledge of the role of copper in neurodegenerative disorders and may facilitate the development of therapeutic strategies targeting copper-mediated processes in protein aggregation and associated pathologies.

Molecular Ballet: Investigating the Complex Interaction between Self-Assembling Dendrimers and Human Serum Albumin via Computational and Experimental Methods

Dendrimers, intricate macromolecules with highly branched nanostructures, offer unique attributes including precise control over size, shape, and functionality, making them promising candidates for a wide range of biomedical applications. The exploration of their interaction with biological environments, particularly human serum albumin (HSA), holds significant importance for biomedical utilization. In this study, the interaction between HSA and a recently developed self-assembling amphiphilic dendrimer (AD) was investigated using various experimental techniques. Fluorescence spectroscopy and isothermal titration calorimetry revealed moderate interactions between the protein and the AD nanomicelles (NMs), primarily attributed to favorable enthalpic contributions arising from electrostatic interactions and hydrogen bonding. Structural analysis indicated minimal changes in HSA upon complexation with the AD NMs, which was further supported by computational simulations demonstrating stable interactions at the atomistic level. These findings provide valuable insights into the binding mechanisms and thermodynamic parameters governing HSA/AD NM interactions, thereby contributing to the understanding of their potential biomedical applications.

Analytical Techniques for Characterizing Tumor-Targeted Antibody-Functionalized Nanoparticles

The specific interaction between cell surface receptors and corresponding antibodies has driven opportunities for developing targeted cancer therapies using nanoparticle systems. It is challenging to design and develop such targeted nanomedicines using antibody ligands, as the final nanoconjugate's specificity hinges on the cohesive functioning of its components. The multicomponent nature of antibody-conjugated nanoparticles also complicates the characterization process. Regardless of the type of nanoparticle, it is essential to perform physicochemical characterization to establish a solid foundation of knowledge and develop suitable preclinical studies. A meaningful physicochemical evaluation of antibody-conjugated nanoparticles should include determining the quantity and orientation of the antibodies, confirming the antibodies' integrity following attachment, and assessing the immunoreactivity of the obtained nanoconjugates. In this review, the authors describe the various techniques (electrophoresis, spectroscopy, colorimetric assays, immunoassays, etc.) used to analyze the physicochemical properties of nanoparticles functionalized with antibodies and discuss the main results.

Spidroin-mimetic Engineered Protein Fibers with High Toughness and Minimized Batch-to-batch Variations through β-sheets Co-assembly

Synthetic spidroin fibers have not yet attained the same level of toughness and stability as natural spider silks due to the complexity of composition and hierarchical structure. Particularly, understanding the intricate interactions between spidroin components in spider fiber is still elusive. Herein, we report modular design and preparation of spidroin-mimetic fibers composed of a conservative C-terminus spidroin module, two different natural β-sheets modules, and a non-spidroin random-coil module. The resulting fibers exhibit a toughness of ~200 MJ/m3, reaching the highest value among the reported artificial spider silks. The interactions between two components of recombinant spidroins facilitate the intermolecular co-assembly of β-sheets, thereby enhancing the mechanical strength and reducing batch-to-batch variability in the dual-component spidroin fibers. Additionally, the dual-component spidroin fibers offer potential applications in implantable or even edible devices. Therefore, our work presents a generic strategy to develop high-performance protein fibers for diverse translations in different scenarios.

A novel thermotolerant L-rhamnose isomerase variant for biocatalytic conversion of D-allulose to D-allose

A novel L-rhamnose isomerase was identified and cloned from an extreme-temperature aquatic habitat metagenome. The deduced amino acid sequence homology suggested the possible source of this metagenomic sequence to be Chloroflexus islandicus. The gene expression was performed in a heterologous host, Escherichia coli, and the recombinant protein L-rhamnose isomerase (L-RIM) was extracted and purified. The catalytic function of L-RIM was characterized for D-allulose to D-allose bioconversion. D-Allose is a sweet, rare sugar molecule with anti-tumour, anti-hypertensive, cryoprotective, and antioxidative properties. The characterization experiments showed L-RIM to be a Co++- or Mn++-dependent metalloenzyme. L-RIM was remarkably active (~ 80%) in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges. Optimal L-RIM activity with D-allulose as the substrate occurred at pH 7.0 and 75 °C. The enzyme was found to be excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively. L-RIM catalysis conducted at slightly acidic pH of 6.0 and 70 °C achieved biosynthesis of about 30 g L-1 from 100 g L-1 D-allulose in 3 h. KEY POINTS: • The present study explored an extreme temperature metagenome to identify a novel gene that encodes a thermostable l-rhamnose isomerase (L-RIM) • L-RIM exhibits substantial (80% or more) activity in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges • L-RIM is excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively.

Extracellular matrix-derived materials for tissue engineering and regenerative medicine: A journey from isolation to characterization and application

Biomaterial choice is an essential step during the development tissue engineering and regenerative medicine (TERM) applications. The selected biomaterial must present properties allowing the physiological-like recapitulation of several processes that lead to the reestablishment of homeostatic tissue or organ function. Biomaterials derived from the extracellular matrix (ECM) present many such properties and their use in the field has been steadily increasing. Considering this growing importance, it becomes imperative to provide a comprehensive overview of ECM biomaterials, encompassing their sourcing, processing, and integration into TERM applications. This review compiles the main strategies used to isolate and process ECM-derived biomaterials as well as different techniques used for its characterization, namely biochemical and chemical, physical, morphological, and biological. Lastly, some of their applications in the TERM field are explored and discussed.

Alleviation of albumin glycation-induced diabetic cardiomyopathy by L-Arginine: Insights into Nrf-2 signaling

In hyperglycemia, accelerated glycation and oxidative stress give rise to many diabetic complications, such as diabetic cardiomyopathy (DCM). Glycated human serum albumin (GHSA) has disturbed structural integrity and hampered functional capabilities. When GHSA accumulates around cardiac cells, Nrf-2 is dysregulated, aiding oxidative stress. L-Arginine (L-Arg) is prescribed to patients with diabetes and cardiovascular diseases. This research contributes to the mechanistic insights on antiglycation and antioxidant potential of L-Arg in alleviating DCM. HSA was glycated with methylglyoxal in the presence of L-Arg (20-640 mM). Structural and functional modifications of HSA were studied. L-Arg and HSA, GHSA interactions, and thermodynamics were determined by steady-state fluorescence. H9c2 cardiomyocytes were given treatments of GHSA-L-Arg along with the inhibitor of the receptor of AGEs. Cellular antioxidant levels, detoxification enzyme activities were measured. Gene, protein expressions, and immunofluorescence data examined the activation and nuclear translocation of Nrf-2 during glycation and oxidative stress. L-Arg protected HSA from glycation-induced structural and functional modifications. The binding affinity of L-Arg was more towards HSA (104 M-1). L-Arg, specifically at lower concentration (20 mM), upregulated Nrf-2 gene, protein expressions and facilitated its nuclear translocation by activating Nrf-2 signaling. The study concluded that L-Arg can be of therapeutic advantage in glycation-induced DCM and associated oxidative stress.

Structural and functional analyses of an L-asparaginase from Geobacillus thermopakistaniensis

Genome sequence of Geobacillus thermopakistaniensis contains an open reading frame annotated as a type II L-asparaginase (ASNaseGt). Critical structural analysis disclosed that ASNaseGt might be a type I L-asparaginase. In order to determine whether it is a type I or type II L-asparaginase, we have performed the structural-functional characterization of the recombinant protein as well as analyzed the localization of ASNaseGt in G. thermopakistaniensis. ASNaseGt exhibited optimal activity at 52 °C and pH 9.5. There was a > 3-fold increase in activity in the presence of β-mercaptoethanol. Apparent Vmax and Km values were 2735 U/mg and 0.35 mM, respectively. ASNaseGt displayed high thermostability with >80 % residual activity even after 6 h of incubation at 55 °C. Recombinant ASNaseGt existed in oligomeric form. Addition of β-mercaptoethanol lowered the degree of oligomerization and displayed that tetrameric form was the most active, with a specific activity of 4300 U/mg. Under physiological conditions, ASNaseGt displayed >50 % of the optimal activity. Localization studies in G. thermopakistaniensis revealed that ASNaseGt is a cytosolic protein. Structural and functional characterization, and localization in G. thermopakistaniensis displayed that ASNaseGt is not a type II but a type I L-asparaginase.

Improving the thermal stability of phytase using core-shell hydrogel beads

A core-shell hydrogel bead system was designed to maintain the catalytic activity of phytase and protect its enzymatic functionality from heat treatment. The designed structure consists of a chitosan-phytase complex core and an alginate-carrageenan hydrogel shell. The core-shell hydrogel was optimized to improve phytase encapsulation efficiency and increase the thermal stability of the encapsulated phytase. After heat treatment, encapsulated phytase retained ∼ 70 % of its catalytic activity and the same secondary structure of free phytase. Fourier transform infrared spectroscopy indicated strong intermolecular interactions between chitosan and phytase in the core, but little interaction between the core and the alginate and κ-carrageenan shell, this supports the structural and functional stability of the phytase. Differential scanning calorimetry confirmed that the designed core-shell structure had a higher melting point. Encapsulating phytase in a core-shell hydrogel bead can enhance the thermal stability of phytase, which broadens the potential applications for phytase delivery.

Rational Design of a Potent Antimicrobial Peptide Based on the Active Region of a Gecko Cathelicidin

The emergence of multidrug-resistant (MDR) bacteria presents a significant challenge to public health, increasing the risk of infections that are resistant to current antibiotic treatment. Antimicrobial peptides (AMPs) offer a promising alternative to conventional antibiotics in the prevention of MDR bacterial infections. In the present study, we identified a novel cathelicidin AMP from Gekko japonicus, which exhibited broad-spectrum antibacterial activity against both Gram-negative and Gram-positive bacteria, with minimal inhibitory concentrations ranging from 2.34 to 4.69 μg/mL. To improve its potential therapeutic application, a series of peptides was synthesized based on the active region of the gecko-derived cathelicidin. The lead peptide (RH-16) showed an antimicrobial activity comparable to that of the parent peptide. Structural characterization revealed that RH-16 adopted an amphipathic α-helical conformation. Furthermore, RH-16 demonstrated neither hemolytic nor cytotoxic activity but effectively killed a wide range of clinically isolated, drug-resistant bacteria. The antimicrobial activity of RH-16 was attributed to the nonspecific targeting of bacterial membranes, leading to rapid bacterial membrane permeabilization and rupture. RH-16 also retained its antibacterial activity in plasma and exhibited mild toxicity in vivo. Notably, RH-16 offered robust protection against skin infection in a murine model. Therefore, this newly identified cathelicidin AMP may be a strong candidate for future pharmacological development targeting multidrug resistance. The use of a rational design approach for isolating the minimal antimicrobial unit may accelerate the transition of natural AMPs to clinically applicable antibacterial agents.

N-terminal truncation (N-) and directional proton transfer in an old yellow enzyme enables tunable efficient producing (R)- or (S)-citronellal

(R)-Citronellal is a valuable molecule as the precursor for the industrial synthesis of (-)-menthol, one of the worldwide best-selling compounds in the flavors and fragrances field. However, its biocatalytic production, even from the optically pure substrate (E)-citral, is inherently limited by the activity of Old Yellow Enzyme (OYE). Herein, we rationally designed a different approach to increase the activity of OYE in biocatalytic production. The activity of OYE from Corynebacterium glutamicum (CgOYE) is increased, as well as superior thermal stability and pH tolerance via truncating the different lengths of regions at N-terminal of CgOYE. Next, we converted the truncation mutant N31-CgOYE, a protein involved in proton transfer for the asymmetric hydrogenation of CC bonds, into highly (R)- and (S)-stereoselective enzymes using only three mutations. The mixture of racemic (E/Z)-citral is reduced into the (R)-citronellal with ee and conversion up to 99 % by the mutant of CgOYE, overcoming the problem of the reduction for the mixtures of (E/Z)-citral in biocatalytic reaction. The present work provides a general and effective strategy for improving the activity of OYE, in which the partially conserved histidine residues provide "tunable gating" for the enantioselectivity for both the (R)- and (S)-isomerases.

Myristoylated GRASP55 dimerizes in the presence of model membranes

The Golgi Reassembly and Stacking Proteins (GRASPs) are engaged in various functions within the cell, both in unconventional secretion mechanisms and structuring and organizing the Golgi apparatus. Understanding their specific role in each situation still requires more structural and functional data at the molecular level. GRASP55 is one of the GRASP members in mammals, anchored to the membrane via the myristoylation of a Gly residue at its N-terminus. Therefore, co-translational modifications, such as myristoylation, are fundamental when considering a strategy to obtain detailed information on the interactions between GRASP55 and membranes. Despite its functional relevance, the N-terminal myristoylation has been underappreciated in the studies reported to date, compromising the previously proposed models for GRASP-membrane interactions. Here, we investigated the synergy between the presence of the membrane and the formation of oligomeric structures of myristoylated GRASP55, using a series of biophysical techniques to perform the structural characterization of the lipidated GRASP55 and its interaction with biological lipid model membranes. Our data fulfill an unexplored gap: the adequate evaluation of the presence of lipidations and lipid membranes on the structure-function dyad of GRASPs.Communicated by Ramaswamy H. Sarma.

New Horizons of Covalent Complex of Plant-Derived Recombinant Human Lactoferrin (OsrhLF) Combined with Different Polyphenols: Formation, Physicochemical Properties, and Gastrointestinal Fate

Four typical dietary polyphenols ((-)-epigallocatechin gallate (EGCG), quinic acid (QA), caffeic acid (CA), and ferulic acid (FA)) were covalently prepared with rice recombinant human lactoferrin (OsrhLF) and bovine lactoferrin (bLF), and their structure and physicochemical properties were investigated, different lycopene emulsions were made by ultrasonic emulsification to analyze gastrointestinal fate. The results indicated that the covalent modification polyphenols changed the secondary/tertiary structure of LF, significantly improving the surface hydrophilicity, thermal stability, and antioxidant activity of LF. Compared with the bLF group, the OsrhLF group was more hydrophilic and the thermal denaturation temperature of the OsrhLF-CA reached 104.4 °C. LF-polyphenol emulsions significantly enhanced the photochemical stability and bioavailability of lycopene and achieved effective encapsulation and protection of lycopene compared to free lycopene, and the OsrhLF-EGCG reached 58.94% lycopene bioavailability. In short, OsrhLF does not differ much from bLF in terms of physicochemical properties and has a strong potential in the field of dietary supplements.

Fluorescence-Based Protein Stability Monitoring-A Review

Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.

Chemically Bonded Pepsin via Its Inert Center to Diazo Functionalized Silica Gel through Multipoint Attachment Mode: A Way of Restoring Biocatalytic Sustainability over "Wider pH" Range

Proteolytic enzymes play a pivotal role in the industry. Still, because of denaturation, the extensive applicability at their level of best catalytic efficiency over a more comprehensive pH range, particularly in alkaline conditions over pH 8, has not been fully developed. On the other hand, enzyme immobilization following a suitable protocol is a long pending issue that determines the conformational stability, specificity, selectivity, enantioselectivity, and activity of the native enzymes at long-range pH. As a bridge between these two findings, in an attempt at a freezing temperature 273-278 K at an alkaline pH, the diazo-functionalized silica gel (SG) surface has been used to rapidly diazo couple pepsin through its inert center, the O-carbon of the phenolic -OH of surface-occupied Tyr residues in a multipoint mode: when all the various protein groups, viz., amino, thiol, phenol, imidazole, carboxy, etc., in the molecular sequence including those belonging to the active sites, remain intact, the inherent inbuilt interactions among themselves remain. Thereby, the macromolecule's global conformation and helicity preserve the status quo. The dimension of the SG-enzyme conjugate confirms as {Si(OSi)4 (H2O)1.03}n {-O-Si(CH3)2-O-C6H4-N═N+}4·{pepsin}·yH2O; where the values of n and y have been determined respectively as 347 and 188. The material performs the catalytic activity much better at 7-8.5 than at pH 2-3.5 and continues for up to six months without any appreciable change.

Characterization of active peptides derived from three leeches and comparison of their anti-thrombotic mechanisms using the tail vein thrombosis model in mice and metabonomics

Background and aims: The increasing incidence of cardiovascular diseases has created an urgent need for safe and effective anti-thrombotic agents. Leech, as a traditional Chinese medicine, has the effect of promoting blood circulation and removing blood stasis, but its real material basis and mechanism of action for the treatment of diseases such as blood stasis and thrombosis have not been reported. Methods: In this study, Whitmania Pigra Whitman (WPW), Hirudo nipponica Whitman (HNW) and Whitmania acranutata Whitman (WAW) were hydrolyzed by biomimetic enzymatic hydrolysis to obtain the active peptides of WPW (APP), the active peptides of HNW (APH) and the active peptides of WAW (APA), respectively. Then their structures were characterized by sykam amino acid analyzer, fourier transform infrared spectrometer (FT-IR), circular dichroism (CD) spectrometer and LC-MS. Next, the anti-thrombotic activities of APP, APH and APA were determined by carrageenan-induced tail vein thrombosis model in mice, and the anti-thrombotic mechanisms of high-dose APP group (HAPP), high-dose APH group (HAPH) and high-dose APA group (HAPA) were explored based on UHPLC-Q-Exactive Orbitrap mass spectrometry. Results: The results showed that the amino acid composition of APP, APH and APA was consistent, and the proportion of each amino acid was few different. The results of FT-IR and CD showed that there were no significant differences in the proportion of secondary structures (such as β-sheet and random coil) and infrared absorption peaks between APP, APH and APA. Mass spectrometry data showed that there were 43 common peptides in APP, APH and APA, indicating that the three have common material basis. APP, APH and APA could significantly inhibit platelet aggregation, reduce black-tail length, whole blood viscosity (WBV), plasma viscosity (PV), and Fibrinogen (FIB), and prolong coagulation time, including activated partial thrombin time (APTT), prothrombin time (PT) and thrombin time (TT). In addition, 24 metabolites were identified as potential biomarkers associated with thrombosis development. Among these, 19, 23, and 20 metabolites were significantly normalized after administration of HAPP, HAPH, and HAPA in the mice, respectively. Furthermore, the intervention mechanism of HAPP, HAPH and HAPA on tail vein thrombosis mainly involved in linoleic acid metabolism, primary bile acid biosynthesis and ether lipid metabolism. Conclusion: Our findings suggest that APP, APH and APA can exert their anti-blood stasis and anti-thrombotic activities by interfering with disordered metabolic pathways in vivo, and there is no significant difference in their efficacies.

New anthracene-based Oxime-Palladium complexes loaded on albumin nanoparticles, in vitro cytotoxicity, mathematical release mechanism studies and biological macromolecules interaction investigation

In this research work, two new palladium complexes [trans-Pd(C15H10NOCH3)2]Cl2 (1) and [cis- Pd(C15H10NOCH3)(PPh3)2Cl]Cl (2) were synthesized using an alkoxyme ligand named isophethalaldoxime. Then structure characterization has been done by FT-IR and different NMR (1H, 13C and 31P) spectroscopy. Then, their interactions with biological macromolecules including deoxyribonucleic acid and bovine serum albumin were studied using various spectroscopic methods such as UV-Vis absorption, fluorescence emission spectroscopy and circular dichroism. The results showed the binding of the prepared complexes to the deoxyribonucleic acid via grooves and different binding sites of bovine serum albumin. Fluorescence emission data showed that the mechanism of extinction of albumin emission by these compounds is static. Competitive titration was performed on albumin with eosin-Y, ibuprofen and digoxin as site markers I, II and III. The antitumor activity and toxicity of these compounds were evaluated on cancer cell lines A549 (leukemia) and K562 by in-vitro cytotoxicity test. The IC50 values showed the good activity of these complexes in inhibiting cancer cells. In the last section, the release mechanism of synthesized complexes from albumin nanoparticles (BNPs) was investigated and theoretical calculations were performed that showed Korsmeyer-Peppas mechanism for complex (1) and Quadratic mechanism for complex (2).

Megahertz detection of spectroscopic polarization by a time-encoded supercontinuum vector beam

We demonstrated a 40-MHz detection of spectroscopic polarization by a supercontinuum vector beam with a wavelength-dependent polarization state. To achieve the high-repetition-rate measurement, we detected the rotation angle of polarization and the spectrum by measuring the temporal waveform using a photodetector after expanding the pulse duration of the supercontinuum vector beam. The spectrum of the supercontinuum vector beam was measured using a spectrometer. We compared it with the temporal waveforms, confirming a good agreement of spectra between the conventional spectrometer and the temporal waveforms. The detection method is useful for many applications requiring high-repetition-rate spectroscopic-polarization measurements, such as the defect inspection of thin optical materials.

Molecular simulation for food protein-ligand interactions: A comprehensive review on principles, current applications, and emerging trends

In recent years, investigations on molecular interaction mechanisms between food proteins and ligands have attracted much interest. The interaction mechanisms can supply much useful information for many fields in the food industry, including nutrient delivery, food processing, auxiliary detection, and others. Molecular simulation has offered extraordinary insights into the interaction mechanisms. It can reflect binding conformation, interaction forces, binding affinity, key residues, and other information that physicochemical experiments cannot reveal in a fast and detailed manner. The simulation results have proven to be consistent with the results of physicochemical experiments. Molecular simulation holds great potential for future applications in the field of food protein-ligand interactions. This review elaborates on the principles of molecular docking and molecular dynamics simulation. Besides, their applications in food protein-ligand interactions are summarized. Furthermore, challenges, perspectives, and trends in molecular simulation of food protein-ligand interactions are proposed. Based on the results of molecular simulation, the mechanisms of interfacial behavior, enzyme-substrate binding, and structural changes during food processing can be reflected, and strategies for hazardous substance detection and food flavor adjustment can be generated. Moreover, molecular simulation can accelerate food development and reduce animal experiments. However, there are still several challenges to applying molecular simulation to food protein-ligand interaction research. The future trends will be a combination of international cooperation and data sharing, quantum mechanics/molecular mechanics, advanced computational techniques, and machine learning, which contribute to promoting food protein-ligand interaction simulation. Overall, the use of molecular simulation to study food protein-ligand interactions has a promising prospect.

Chiral Plasmonic Hybrid Nanostructures: A Gateway to Advanced Chiroptical Materials

Chirality introduces a new dimension of functionality to materials, unlocking new possibilities across various fields. When integrated with plasmonic hybrid nanostructures, this attribute synergizes with plasmonic and other functionalities, resulting in unprecedented chiroptical materials that push the boundaries of the system's capabilities. Recent advancements have illuminated the remarkable chiral light-matter interactions within chiral plasmonic hybrid nanomaterials, allowing for the harnessing of their tunable optical activity and hybrid components. These advancements have led to applications in areas such as chiral sensing, catalysis, and spin optics. Despite these promising developments, there remains a need for a comprehensive synthesis of the current state-of-the-art knowledge, as well as a thorough understanding of the construction techniques and practical applications in this field. This review begins with an exploration of the origins of plasmonic chirality and an overview of the latest advancements in the synthesis of chiral plasmonic hybrid nanostructures. Furthermore, representative emerging categories of hybrid nanomaterials are classified and summarized, elucidating their versatile applications. Finally, the review engages with the fundamental challenges associated with chiral plasmonic hybrid nanostructures and offer insights into the future prospects of this advanced field.

Aqueous Circularly Polarized Luminescence Induced by Homopolypeptide Self-Assembly

Remarkable advances have been achieved in solution self-assembly of polypeptides from the perspective of nanostructures, mechanisms, and applications. Despite the intrinsic chirality of polypeptides, the promising generation of aqueous circularly polarized luminescence (CPL) based on their self-assembly has been rarely reported due to the weak fluorescence of most polypeptides and the indeterminate self-assembly mechanism. Here, we propose a facile strategy for achieving aqueous CPL based on the self-assembly of simple homopolypeptides modified with a terminal group featuring both twisted intramolecular charge transfer and aggregation-induced emission properties. A morphology-dependent CPL can be observed under different self-assembly conditions by altering the solvents. A nanotoroid-dispersed aqueous solution with detectable CPL can be obtained by using tetrahydrofuran as a good solvent for the self-assembly, which is attributed to the involvement of the terminal group in the chiral environment formed by the homopolypeptide chains. However, such a chiral packing mode cannot be realized in nanorods self-assembled from dioxane, resulting in an inactive CPL phenomenon. Furthermore, CPL signals can be greatly amplified by co-assembly of homopolypeptides with the achiral small molecule derived from the terminal group. This work not only provides a pathway to construct aqueous CPL-active homopolypeptide nanomaterials but also reveals a potential mechanism in the self-assembly for chiral production, transfer, and amplification in polypeptide-based nanostructures.

Influence of Supercritical Carbon Dioxide on the Activity and Conformational Changes of α-Amylase, Lipase, and Peroxidase in the Solid State Using White Wheat Flour as an Example

Green technologies using renewable and alternative sources, including supercritical carbon dioxide (sc-CO2), are becoming a priority for researchers in a variety of fields, including the control of enzyme activity which, among other applications, is extremely important in the food industry. Namely, extending shelf life of e.g., flour could be reached by tuning the present enzymes activity. In this study, the effect of different sc-CO2 conditions such as temperature (35-50 °C), pressure (200 bar and 300 bar), and exposure time (1-6 h) on the inactivation and structural changes of α-amylase, lipase, and horseradish peroxidase (POD) from white wheat flour and native enzymes was investigated. The total protein (TPC) content and residual activities of the enzymes were determined by standard spectrophotometric methods, while the changes in the secondary structures of the enzymes were determined by circular dichroism spectrometry (CD). The present work is therefore concerned for the first time with the study of the stability and structural changes of the enzyme molecules dominant in white wheat flour under sc-CO2 conditions at different pressures and temperatures. In addition, the changes in aggregation or dissociation of the enzyme molecules were investigated based on the changes in particle size distribution and ζ-potential. The results of the activity assays showed a decrease in the activity of native POD and lipase under optimal exposure conditions (6 h and 50 °C; and 1 h and 50 °C) by 22% and 16%, respectively. In contrast, no significant changes were observed in α-amylase activity. Consequently, analysis of the CD spectra of POD and lipase confirmed a significant effect on secondary structure damage (changes in α-helix, β-sheet, and β-turn content), whereas the secondary structure of α-amylase retained its original configuration. Moreover, the changes in particle size distribution and ζ-potential showed a significant effect of sc-CO2 treatment on the aggregation and dissociation of the selected enzymes. The results of this study confirm that sc-CO2 technology can be effectively used as an environmentally friendly technology to control the activity of major flour enzymes by altering their structures.

A supramolecular assembly-based strategy towards the generation and amplification of photon up-conversion and circularly polarized luminescence

For the molecular properties in which energy transfer/migration is determinantal, such as triplet-triplet annihilation-based photon up-conversion (TTAUC), the overall performance is largely affected by the intermolecular distance and relative molecular orientations. In such scenarios, tools that may steer the intermolecular interactions and provide control over molecular organisation in the bulk, become most valuable. Often these non-covalent interactions, found predominantly in supramolecular assemblies, enable pre-programming of the molecular network in the assembled structures. In other words, by employing supramolecular chemistry principles, an arrangement where molecular units are arranged in a desired fashion, very much like a Lego toy, could be achieved. This leads to enhanced energy transfer from one molecule to other. In recent past, chiral luminescent systems have attracted huge attention for producing circularly polarized luminescence (CPL). In such systems, chirality is a necessary requirement. Chirality induction/transfer through supramolecular interactions has been known for a long time. It was realized recently that it may help in the generation and amplification of CPL signals as well. In this review article we have discussed the applicability of self-/co-assembly processes for achieving maximum TTA-UC and CPL in various molecular systems.

DichroPipeline: A suite of online and downloadable tools and resources for protein circular dichroism spectroscopic data analyses, interpretations, and their interoperability with other bioinformatics tools and resources

Circular Dichroism (CD) spectroscopy is a widely-used method for characterizing individual protein structures in solutions, membranes, films and macromolecular complexes, as well as for probing macromolecular interactions, conformational changes associated with binding substrates, and in different functionally-related environments. This paper describes a series of related computational and display tools that have been developed over many years to aid in those characterizations and functional interpretations. The new DichroPipeline described herein links a series of format-compatible data processing, analysis, and display tools to enable users to facilely produce the spectra, which can then be made available in the Protein Circular Dichroism Data Bank (https://pcddb.cryst.bbk.ac.uk/) resource, in which the CD spectral and associated metadata for each entry are linked to other structural and functional data bases including the Protein Data Bank (PDB), and the UniProt sequence data base, amongst others. These tools and resources thus provide the basis for a wide range of traceable structural characterizations of soluble, membrane and intrinsically-disordered proteins.

Unveiling Chiral Perovskite CD Signal Scaling: Discerning Authentic and Counterfeit Signals through Sample-State Analysis

Circular dichroism (CD) spectroscopy is a well-known and powerful technique widely used for distinguishing chiral enantiomers based on their differential absorbance of the right and left circularly polarized light. With the increasing demand for solid-state chiral optics, CD spectroscopy has been extended to elucidate the chirality of solid-state samples beyond the traditional solution state. However, due to the sample preparation differential, the CD spectra of the same compound measured by different researchers may not be mutually consistent. In this study, we employ solution, powder, thin-film, and single-crystal samples to explore the challenges associated with CD measurements and distinguish between genuine and fake signals. Rational fabrication of the solid-state samples can effectively minimize the macroscopic anisotropic nature of the samples and thereby mitigate the influence of linear dichroism (LD) and linear birefringence (LB) effects, which arise from anisotropy-induced differences in the absorbances and refractive indices. The local anisotropic and overall isotropic features of the high-quality thin-film sample achieve an optically isotropic state, which exhibits superior CD signal repeatability at the front and back sides at different angles by rotating the sample along the light path. In addition, sample thickness-induced CD signal overload and absorption saturation pose more severe challenges than the LBLD-induced amplified CD signal but are rarely focused on. The CD signal overload in the deep UV region leads to the presence of fake signals, while absorption saturation results in a complete loss of the CD signal. These findings help obtain accurate CD signals by a well-fabricated optically isotropic sample to avoid LDLB and optimize the sample thickness to avoid fake signals and no signals.

Functional insulin aspart/insulin degludec-based microneedles for promoting postprandial glycemic control

Insulin aspart (IAsp) and insulin degludec (IDeg), as the third generation of insulin, have a faster onset time or a more durable action period, which may simulate the secretion of insulin under physiological conditions. Microneedles (MNs) are transdermal delivery devices that may allow diabetic patients to easily deploy transdermal insulin therapy while considerably reducing injection pain. In this study, we investigated the combination of dissolving MNs with IAsp or IDeg therapy as an alternative to daily multiple insulin injections, aiming to improve glycemic control and patient compliance. Mechanical properties of the MNs, structural stability of insulin encapsulated in the MNs, and transdermal application characteristics were studied to assess the practicality of insulin-loaded MNs for diabetes therapy. In vivo experiments conducted on diabetic rats demonstrated that the IAsp- and IDeg-loaded MNs have comparable blood glucose control abilities to that of subcutaneous injections. In addition, the therapeutic properties of insulin-loaded MNs under diverse dietary conditions and application strategies were further investigated to provide new information to support future clinical trials. Taken together, the proposed MNs have the potential to improve balances between glycemic control, hypoglycemia risk, and convenience, providing patients with simpler regimens. STATEMENT OF SIGNIFICANCE: 1. The fabricated functional insulin-loaded dissolving microneedles closely matched the glucose rise that occurs in response to meals, demonstrating promising alternatives for multiple daily insulin injections. 2. The hypoglycemic properties of insulin microneedles were investigated under diverse dietary conditions and application strategies, yielding new information to support future clinical trials. 3. Molecular dynamics simulations were utilized to study the interactions between the insulin and microneedle matrix materials, providing a strategy for theoretically understanding drug stability as well as the release mechanism of drug-loaded microneedles.

Trinuclear rhenium(I)-based metallocages as anticancer agents towards human cervical cancer cells

The first examples of spherical-shaped trinuclear rhenium(I) organometallic cages displaying cytotoxic, antimetastatic, antiproliferative and DNA-damaging behavior towards a human cervical (HeLa) cancer cell line are reported. The compact design of the metallocages facilitates their interactions with biosystems leading to comparable efficiency to that of the commonly used anticancer drug cisplatin.

Detector of UV light chirality based on a diamond metasurface

Circularly polarized light (CPL) finds diverse applications in fields such as quantum communications, quantum computing, circular dichroism (CD) spectroscopy, polarization imaging, and sensing. However, conventional techniques for detecting CPL face challenges related to equipment miniaturization, system integration, and high-speed operation. In this study, we propose a novel design that addresses these limitations by employing a quarter waveplate constructed from a diamond metasurface, in combination with a linear polarizer crafted from metallic aluminum. The diamond array, with specific dimensions (a = 84 nm, b = 52 nm), effectively transforms left-handed and right-handed circularly polarized light into two orthogonally linearly polarized beams who have a polarization degree of approximately 0.9. The aluminum linear polarizer then selectively permits the transmission of these transformed linearly polarized beams.Our proposed design showcases remarkable circular dichroism performance at a wavelength of 280 nm, concurrently maintaining high transmittance and achieving a substantial extinction ratio of 25. Notably, the design attains an ultraviolet wavelength transmission efficiency surpassing 80%. Moreover, our design incorporates a rotation mechanism that enables the differentiation of linearly polarized light and singly circularly polarized light. In essence, this innovative design introduces a fresh paradigm for ultraviolet circularly polarized light detection, offering invaluable insights and references for applications in polarization detection, imaging, biomedical diagnostics, and circular dichroic spectroscopy.

Individually Tailored Modular "Egg" Hydrogels Capable of Spatiotemporally Controlled Drug Release for Spinal Cord Injury Repair

Controllable drug delivery systems (DDS) can overcome the disadvantages of conventional drug administration processes, such as high dosages or repeated administration. Herein, a smart DDS collagen hydrogel is deployed for spinal cord injury (SCI) repair based on modular designing of "egg" nanoparticles (NPs) that ingeniously accomplish controlled drug release via inducing a signaling cascade in response to external and internal stimuli. The "egg" NPs consist of a three-layered structure: tannic acid/Fe3+ /tetradecanol "eggshell," zeolitic imidazolate framework-8 (ZIF-8) "egg white," and paclitaxel "yolk." Then NPs served as a crosslinking epicenter, blending with collagen solutions to generate functional hydrogels. Remarkably, the "eggshell" efficiently converts near-infrared (NIR) irradiation into heat. Subsequently, tetradecanol can be triggered to disintegrate via heat, exposing the structure of ZIF-8. The Zn-imidazolium ion coordination bond of the "egg white" is susceptible to cleaving at the acidic SCI site, decomposing the skeleton to release paclitaxel on demand. As expected, the paclitaxel release rate upon NIR irradiation increased up to threefold on the seventh day, which matches endogenous neural stem/progenitor cell migration process. Taken together, the collagen hydrogels facilitate the neurogenesis and motor function recovery, demonstrating a revolutionary strategy for spatiotemporally controlled drug release and providing guidelines for the design of DDS.

Hierarchical self-assembly of a reflectin-derived peptide

Reflectins are a family of intrinsically disordered proteins involved in cephalopod camouflage, making them an interesting source for bioinspired optical materials. Understanding reflectin assembly into higher-order structures by standard biophysical methods enables the rational design of new materials, but it is difficult due to their low solubility. To address this challenge, we aim to understand the molecular self-assembly mechanism of reflectin's basic unit-the protopeptide sequence YMDMSGYQ-as a means to understand reflectin's assembly phenomena. Protopeptide self-assembly was triggered by different environmental cues, yielding supramolecular hydrogels, and characterized by experimental and theoretical methods. Protopeptide films were also prepared to assess optical properties. Our results support the hypothesis for the protopeptide aggregation model at an atomistic level, led by hydrophilic and hydrophobic interactions mediated by tyrosine residues. Protopeptide-derived films were optically active, presenting diffuse reflectance in the visible region of the light spectrum. Hence, these results contribute to a better understanding of the protopeptide structural assembly, crucial for the design of peptide- and reflectin-based functional materials.

Structural, kinetic, and thermodynamic aspects of insulin aggregation

Given the significance of protein aggregation in proteinopathies and the development of therapeutic protein pharmaceuticals, revamped interest in assessing and modelling the aggregation kinetics has been observed. Quantitative analysis of aggregation includes data of gradual monomeric depletion followed by the formation of subvisible particles. Kinetic and thermodynamic studies are essential to gain key insights into the aggregation process. Despite being the medical marvel in the world of diabetes, insulin suffers from the challenge of aggregation. Physicochemical stresses are experienced by insulin during industrial formulation, storage, delivery, and transport, considerably impacting product quality, efficacy, and effectiveness. The present review briefly describes the pathways, mathematical kinetic models, and thermodynamics of protein misfolding and aggregation. With a specific focus on insulin, further discussions include the structural heterogeneity and modifications of the intermediates incurred during insulin fibrillation. Finally, different model equations to fit the kinetic data of insulin fibrillation are discussed. We believe that this review will shed light on the conditions that induce structural changes in insulin during the lag phase of fibrillation and will motivate scientists to devise strategies to block the initialization of the aggregation cascade. Subsequent abrogation of insulin fibrillation during bioprocessing will ensure stable and globally accessible insulin for efficient management of diabetes.

Methods for the study of ribonuclease targeting chimeras (RiboTACs)

Recently, a class of heterobifunctional small molecules called ribonuclease targeting chimeras (RiboTACs) have been developed that selectively induce degradation of RNAs in cells. These molecules function by recruiting latent ribonuclease (RNase L), an endoribonuclease involved in the innate immune response, to targeted RNA structures. The RiboTACs must activate RNase L in proximity to the RNA, resulting in cleavage of the RNA and downstream degradation. To develop and validate a new RiboTAC, several steps must be taken. First, small molecule activators that bind to RNase L must be identified. Next, since RNase L is only catalytically active upon ligand-induced homodimerization, the capability of identified small molecules to activate RNase L must be assessed. RNase L-activating small molecules should then be coupled to validated RNA-binding small molecules to construct the active RiboTAC. This RiboTAC can finally be assessed in cells for RNase L-dependent degradation of target RNAs. This chapter will provide several methods that are helpful to develop and assess RiboTACs throughout this process, including recombinant RNase L expression, methods to assess RNase L engagement in vitro such as saturation transfer difference nuclear magnetic resonance (STD NMR), an in vitro assay to assess activation of RNase L, and cellular methods to demonstrate RNase L-dependent cleavage.

New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.

Insights into the Mechanism Underlying the Influence of Glycation with Different Saccharides and Temperatures on the IgG/IgE Binding Ability, Immunodetection, In Vitro Digestibility of Shrimp (Litopenaeus vannamei) Tropomyosin

Tropomyosin (TM) is a heat-stable protein that plays a crucial role as a major pan-allergen in crustacean shellfish. Despite the high thermal stability of the TM structure, its IgG/IgE binding ability, immunodetection, and in vitro digestibility can be negatively influenced by glycation during food processing, and the underlying mechanism remains unclear. In this study, TM was subjected to glycosylation using various sugars and temperatures. The resulting effects on IgG/IgE-binding capacity, immunodetection, and in vitro digestibility were analyzed, meanwhile, the structural alterations and modifications using spectroscopic and LC-MS/MS analysis were determined. Obtained results suggested that the IgG/IgE binding capacity of glycosylated TM, immunodetection recovery, and in vitro digestibility were significantly reduced depending on the degree of glycosylation, with the greatest reduction occurring in Rib-TM. These changes may be attributable to structural alterations and modifications that occur during glycosylation processing, which could mask or shield antigenic epitopes of TM (E3: 61-81, E5b: 142-162, and E5c: 157-183), subsequently reducing the immunodetection recognition and digestive enzyme degradation. Overall, these findings shed light on the detrimental impact of glycation on TMs potential allergenicity and digestibility immunodetection and provide insights into the structural changes and modifications induced by thermal processing.

DichroIDP: a method for analyses of intrinsically disordered proteins using circular dichroism spectroscopy

Intrinsically disordered proteins (IDPs) are comprised of significant numbers of residues that form neither helix, sheet, nor any other canonical type of secondary structure. They play important roles in a broad range of biological processes, such as molecular recognition and signalling, largely due to their chameleon-like ability to change structure from unordered when free in solution to ordered when bound to partner molecules. Circular dichroism (CD) spectroscopy is a widely-used method for characterising protein secondary structures, but analyses of IDPs using CD spectroscopy have suffered because the methods and reference datasets used for the empirical determination of secondary structures do not contain adequate representations of unordered structures. This work describes the creation, validation and testing of a standalone Windows-based application, DichroIDP, and a new reference dataset, IDP175, which is suitable for analyses of proteins containing significant amounts of disordered structure. DichroIDP enables secondary structure determinations of IDPs and proteins containing intrinsically disordered regions.

Circular dichroism assessment of an imidazole antifungal drug with plant based silver nanoparticles: Quantitative and DFT analysis

Circular dichroism (CD) methods have been developed for the analysis of luliconazole (LUC) using plant based silver nanoparticles (P-AgNPs). Cleaner and natural approach have found significant attention in recent times owing to their exceptional physicochemical characteristics. Utilizing FTIR, SEM, and XRD, the produced nanoparticles were analyzed. The produced P-AgNPs were then used to assay LUC in formulation drugs. Four CD methods are developed as zero order and second order derivative methods. Methods I and II are based on a normal CD scan (zero order) that produced calibration range from 2 - 16 μgmL^-1 at 232 nm (positive band) and 299 nm (negative band), respectively. Methods III and IV are the second order derivative methods that are developed at 232 nm (negative band) and at 251 nm (positive band). Density functional theory study was done to comprehend the feasibility of the developed methods and to optimize the structure and energy gap that validated the experimental procedure. The LUC assay methods using the proposed CD approach are simple, sensitive and precise with a limit of detection for methods I, II, III and IV of 0.527, 0.428, 0.250 and 0.30 μgmL^-1 and limit of quantification of 1.75, 1.42, 0.833 and 1.0 μgmL^-1, respectively. For intra- and inter-day precision, the recovery data ranged from 99.48 to 101% and 99.37 to 101%, respectively. The methods were used in dosage forms that produced a relative standard deviation of less than 2% and the true bias (θ_L and θ_U) within ±2%, demonstrating the potential use of the developed methods.

Polylysine-Containing Hydrogel Formulation of Fuzapladib, Inhibitor of Leukocyte-Function Associated Antigen-1 (LFA-1) Activation, for Sustained Release

The aim of the present study was to develop an injectable hydrogel (HG) formulation of fuzapladib sodium (FZP), an animal drug for acute pancreatitis (AP), with the use of polyethyleneoxide (PEO) and polylysine (pLys), a cationic polymer. A mixture of pLys and FZP was added to PEO to prepare an HG formulation, and the formulation was optimized by release test and viscosity measurements. Circular dichroism (CD) and infrared absorption (IR) spectral analyses were applied to clarify the intermolecular interactions between FZP and pLys. The pharmacokinetic behavior of FZP was evaluated after a subcutaneous administration of FZP samples (2.0 mg-FZP/kg) to rats. Although the immediate release of FZP was observed for the HG formulation, the addition of pLys at a 20-fold amount of FZP or higher led to the sustained release of FZP. Considering release behavior, the concentration of pLys was optimized as 100-fold that of FZP in the HG formulation. CD and IR spectroscopic analyses of FZP and/or pLys demonstrated an intermolecular interaction between FZP and pLys, as evidenced by the slight spectral transition. After a subcutaneous administration of HG formulation containing pLys to rats, compared with FZP alone, significant differences were observed in the pharmacokinetic behavior with a decrease of C_max from 2.3 to 0.9 mg/mL and slower elimination kinetics. HG formulation using pLys might be a viable dosage option for FZP for the treatment of AP in animals.

Metal-protein solution interactions investigated using model systems: Thermodynamic and spectroscopic methods

The first-row D-block metal ions are essential for the physiology of living organisms, functioning as cofactors in metalloproteins or structural components for enzymes: almost half of all proteins require metals to perform the biological function. Understanding metal-protein interactions is crucial to unravel the mysteries behind molecular biology, understanding the effects of metal imbalance and toxicity or the diseases due to disorders in metal homeostasis. Metal-protein interactions are dynamic: they are noncovalent and affected by the environment to which the system is exposed. To reach a complete comprehension of the system, different conditions must be considered for the experimental investigation, in order to get information on the species distribution, the ligand coordination modes, complex stoichiometry and geometry. Thinking about the whole environment where a protein acts, investigations are often challenging, and simplifications are required to study in detail the mechanisms of metal interaction. This chapter is intended to help researchers addressing the problem of the complexity of metal-protein interactions, with particular emphasis on the use of peptides as model systems for the metal coordination site. The thermodynamic and spectroscopic methods most widely employed to investigate the interaction between metal ions and peptides in solution are here covered. These include solid-phase peptide synthesis, potentiometric titrations, calorimetry, electrospray ionization mass spectrometry, UV-Vis spectrophotometry, circular dichroism (CD), nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). Additional experimental methods, which can be employed to study metal complexes with peptides, are also briefly mentioned. A case-study is finally reported providing a practical example of the investigation of metal-protein interaction by means of thermodynamic and spectroscopic methods applied to peptide model systems.

Structural and functional analyses of Pcal_0917, an α-glucosidase from hyperthermophilic archaeon Pyrobaculum calidifontis

Genome analysis of Pyrobaculum calidifontis revealed the presence of α-glucosidase (Pcal_0917) gene. Structural analysis affirmed the presence of signature sequences of Type II α-glucosidases in Pcal_0917. We have heterologously expressed the gene and produced recombinant Pcal_0917 in Escherichia coli. Biochemical characteristics of the recombinant enzyme resembled to that of Type I α-glucosidases, instead of Type II. Recombinant Pcal_0917 existed in a tetrameric form in solution and displayed highest activity at 95 °C and pH 6.0, independent of any metal ions. A short heat-treatment at 90 °C resulted in a 35 % increase in enzyme activity. A slight structural shift was observed by CD spectrometry at this temperature. Half-life of the enzyme was >7 h at 90 °C. Pcal_0917 exhibited apparent V_max values of 1190 ± 5 and 3.9 ± 0.1 U/mg against p-nitrophenyl α-D-glucopyranoside and maltose, respectively. To the best of our knowledge, Pcal_0917 displayed the highest ever reported p-nitrophenyl α-D-glucopyranosidase activity among the characterized counterparts. Moreover, Pcal_0917 displayed transglycosylation activity in addition to α-glucosidase activity. Furthermore, in combination with α-amylase, Pcal_0917 was capable of producing glucose syrup from starch with >40 % glucose content. These properties make Pcal_0917 a potential candidate for starch hydrolyzing industry.

Synchrotron Radiation Circular Dichroism Spectroscopy of Oligonucleotides at Millimolar Concentrations

Circular dichroism spectroscopy of nucleic acids has been traditionally performed at sample concentrations orders of magnitude lower than what occur in biological systems. While recent work from us demonstrated the flexibility of an adjustable sample cell that allowed for successful recording of CD spectra of an 18- and a 21-mer double stranded DNA sequences at around 1 mM, sample concentrations beyond 1 mM present a challenge for standard benchtop CD spectrometers. In the present work, the synchrotron radiation circular dichroism (SRCD) spectra were recorded for d(CG)₉ and a mixed 18-mer double stranded DNA at 1, 5, and 10 mM in 100 mM or 4 M NaCl. SRCD of low molecular weight salmon DNA was also measured at a 10 mg/ml concentration. These results represent the first report of CD spectra of DNA samples measured at concentrations comparable to those found in the nucleus. The results suggest that dsDNA maintain very similar structures at concentrations up to 10s of mg/ml, as evident by the very similar CD patterns in this concentration range. Furthermore, the SRCD allowed for the recording of CD patterns of DNA in the far UV region, which is not readily accessible by standard benchtop CD spectropolarimeters. These far UV signals appear to be quite characteristic of DNA structures and are sensitive to sample conditions.

Orthogonal Versatile Interacting Peptide Tags for Imaging Cellular Proteins

Genetic tags are transformative tools for investigating the function, localization, and interactions of cellular proteins. Most studies today are reliant on selective labeling of more than one protein to obtain comprehensive information on a protein's behavior in situ. Some proteins can be analyzed by fusion to a protein tag, such as green fluorescent protein, HaloTag, or SNAP-Tag. Other proteins benefit from labeling via small peptide tags, such as the recently reported versatile interacting peptide (VIP) tags. VIP tags enable observations of protein localization and trafficking with bright fluorophores or nanoparticles. Here, we expand the VIP toolkit by presenting two new tags: TinyVIPER and PunyVIPER. These two tags were designed for use with MiniVIPER for labeling up to three distinct proteins at once in cells. Labeling is mediated by the formation of a high-affinity, biocompatible heterodimeric coiled coil. Each tag was validated by fluorescence microscopy, including observation of transferrin receptor 1 trafficking in live cells. We verified that labeling via each tag is highly specific for one- or two-color imaging. Last, the self-sorting tags were used for simultaneous labeling of three protein targets (i.e., TOMM20, histone 2B, and actin) in fixed cells, highlighting their utility for multicolor microscopy. MiniVIPER, TinyVIPER, and PunyVIPER are small and robust peptide tags for selective labeling of cellular proteins.

Quantum Cascade Laser Based Infrared Spectroscopy: A New Paradigm for Protein Secondary Structure Measurement

Mid-infrared spectroscopy is one of the major analytical techniques employed for measurements of protein structure in solution. Traditional Fourier Transform-Infrared (FT-IR) measurement is limited by its blackbody light source that is inherently spatially incoherent and has low optical power output. This limitation is pronounced when working with proteins in aqueous solutions. Strong absorbance of water in protein amide I region 1600-1700 cm-1 restricts light path length to <10 μm and imposes significant experimental challenges in sample and flow cell handling. Emerging laser spectroscopic techniques use high-power coherent laser as light source that overcomes the limitation in FT-IR measurement. In this study, we employed an innovative infrared spectrometer that uses quantum cascade laser (QCL) as light source. Continuous infrared radiation from this laser source can be swiftly swept within the amide I region (1600-1700 cm-1) and amide II region (1500-1600 cm-1), which makes this technique ideal for protein secondary structure study. Protein solutions as low as 0.5 mg/mL were measured rapidly without any sample preparation. Infrared spectra of model proteins were thus collected, and a chemometric model based on partial least squares regression was developed to quantify α-helix and β-strand motifs in protein secondary structure. The model was applied to measurement of the native secondary structure of commercial therapeutic proteins and bovine serum albumin (BSA) and in thermal degradation studies.

Understanding the pH-dependent interaction of anthocyanin with two food-derived transferrins

The potential binding of cyanidin-3-O-glucoside (C3G) to bovine lactoferrin (BLF) and ovotransferrin (OTF) at pH 3, 5, and 7 was investigated for the first time. Multiple spectroscopic techniques demonstrated pH-dependent alterations in the conformational characteristics of BLF and OTF upon complexation with C3G. Fluorescence quenching assays showed that their highest binding affinity was at pH 7. Hydrophobic interactions and hydrogen bonds were found to be crucial in molecular dynamics simulations but with significantly lower probabilities of formation at pH 3 (p < 0.05). At pH 7, electrostatic attraction can occur for the negatively charged forms of C3G, and the well-maintained native structures of BLF and OTF may be favorable for stabilizing the C3G binding sites. This study sheds light on the stronger interaction of C3G with BLF/OTF at pH 7, which may have implications for future applications such as anthocyanin stabilization or the development of functional food ingredients.