Characterization of the Interactions of Lysozyme with DNA by Surface Plasmon Resonance and Circular Dichroism Spectroscopy

Lysozyme: A Natural Product with Multiple and Useful Antiviral Properties

Lysozyme, especially the one obtained from hen's egg white, continues to show new pharmacological properties. The fact that only a few of these properties can be translated into therapeutic applications is due to the lack of suitable clinical studies. However, this lack cannot hide the evidence that is emerging from scientific research. This review for the first time examines, from a pharmacological point of view, all the relevant studies on the antiviral properties of lysozyme, analyzing its possible mechanism of action and its ability to block viral infections and, in some cases, inhibit viral replication. Lysozyme can interact with nucleic acids and alter their function, but this effect is uncoupled from the catalytic activity that determines its antibacterial activity; it is present in intact lysozyme but is equally potent in a heat-degraded lysozyme or in a nonapeptide isolated by proteolytic digestion. An analysis of the literature shows that lysozyme can be used both as a disinfectant for raw and processed foods and as a drug to combat viral infections in animals and humans. To summarize, it can be said that lysozyme has important antiviral properties, as already suspected in the initial studies conducted over 50 years ago, and it should be explored in suitable clinical studies on humans.

Nonspecific Binding of Adenosine Tripolyphosphate and Tripolyphosphate Modulates the Phase Behavior of Lysozyme

Adenosine tripolyphosphate (ATP) is a small polyvalent anion that has recently been shown to interact with proteins and have a major impact on assembly processes involved in biomolecular condensate formation and protein aggregation. However, the nature of non-specific protein-ATP interactions and their effects on protein solubility are largely unknown. Here, the binding of ATP to the globular model protein is characterized in detail using X-ray crystallography and nuclear magnetic resonance (NMR). Using NMR, we identified six ATP binding sites on the lysozyme surface, with one known high-affinity nucleic acid binding site and five non-specific previously unknown sites with millimolar affinities that also bind tripolyphosphate (TPP). ATP binding occurs primarily through the polyphosphate moiety, which was confirmed by the X-ray structure of the lysozyme-ATP complex. Importantly, ATP binds preferentially to arginine over lysine in non-specific binding sites. ATP and TPP have similar effects on solution-phase protein-protein interactions. At low salt concentrations, ion binding to lysozyme causes precipitation, while at higher salt concentrations, redissolution occurs. The addition of an equimolar concentration of magnesium to ATP does not alter ATP binding affinities but prevents lysozyme precipitation. These findings have important implications for both protein crystallization and cell biology. Crystallization occurs readily in ATP solutions outside the well-established crystallization window. In the context of cell biology, the findings suggest that ATP binds non-specifically to folded proteins in physiological conditions. Based on the nature of the binding sites identified by NMR, we propose several mechanisms for how ATP binding can prevent the aggregation of natively folded proteins.

DNA–Lysozyme Nanoarchitectonics: Quantitative Investigation on Charge Inversion and Compaction

The interaction between DNA and proteins is fundamentally important not only for basic research in biology, but also for potential applications in nanotechnology. In the present study, the complexes formed by λ DNA and lysozyme in a dilute aqueous solution have been investigated using magnetic tweezers (MT), dynamic light scattering (DLS), and atomic force microscopy (AFM). We found that lysozyme induced DNA charge inversion by measuring its electrophoretic mobility by DLS. Lysozyme is very effective at neutralizing the positive charge of DNA, and its critical charge ration to induce charge inversion in solution is only 2.26. We infer that the high efficiency of charge neutralization is due to the highly positively charged (+8 e) and compact structure of lysozyme. When increasing the concentration of lysozymes from 6 ng·µL⁻¹ to 70 ng·µL⁻¹, DNA mobility (at fixed concentration of 2 ng·µL⁻¹) increases from −2.8 to 1.5 (in unit of 10⁻⁴ cm²·V⁻¹·S), implying that the effective charge of DNA switches its sign from negative to positive in the process. The corresponding condensing force increased from 0 pN to its maximal value of about 10.7 pN at concentrations of lysozyme at 25 ng·µL⁻¹, then decreases gradually to 3.8 pN at 200 ng·µL⁻¹. The maximal condensing force occurs at the complete DNA charge neutralization point. The corresponding morphology of DNA–lysozyme complex changes from loosely extensible chains to compact globule, and finally to less compact flower-like structure due to the change of attached lysozyme particles as observed by AFM.

Tear Lipocalin and Lipocalin-Interacting Membrane Receptor

Tear lipocalin is a primate protein that was recognized as a lipocalin from the homology of the primary sequence. The protein is most concentrated in tears and produced by lacrimal glands. Tear lipocalin is also produced in the tongue, pituitary, prostate, and the tracheobronchial tree. Tear lipocalin has been assigned a multitude of functions. The functions of tear lipocalin are inexorably linked to structural characteristics that are often shared by the lipocalin family. These characteristics result in the binding and or transport of a wide range of small hydrophobic molecules. The cavity of tear lipocalin is formed by eight strands (A-H) that are arranged in a β-barrel and are joined by loops between the β-strands. Recently, studies of the solution structure of tear lipocalin have unveiled new structural features such as cation-π interactions, which are extant throughout the lipocalin family. Lipocalin has many unique features that affect ligand specificity. These include a capacious and a flexible cavity with mobile and short overhanging loops. Specific features that confer promiscuity for ligand binding in tear lipocalin will be analyzed. The functions of tear lipocalin include the following: antimicrobial activities, scavenger of toxic and tear disruptive compounds, endonuclease activity, and inhibition of cysteine proteases. In addition, tear lipocalin binds and may modulate lipids in the tears. Such actions support roles as an acceptor for phospholipid transfer protein, heteropolymer formation to alter viscosity, and tear surface interactions. The promiscuous lipid-binding properties of tear lipocalin have created opportunities for its use as a drug carrier. Mutant analogs have been created to bind other molecules such as vascular endothelial growth factor for medicinal use. Tear lipocalin has been touted as a useful biomarker for several diseases including breast cancer, chronic obstructive pulmonary disease, diabetic retinopathy, and keratoconus. The functional possibilities of tear lipocalin dramatically expanded when a putative receptor, lipocalin-interacting membrane receptor was identified. However, opposing studies claim that lipocalin-interacting membrane receptor is not specific for lipocalin. A recent study even suggests a different function for the membrane protein. This controversy will be reviewed in light of gene expression data, which suggest that tear lipocalin has a different tissue distribution than the putative receptor. But the data show lipocalin-interacting membrane receptor is expressed on ocular surface epithelium and that a receptor function here would be rational.

Structures of the germline-specific Deadhead and thioredoxin T proteins from Drosophila melanogaster reveal unique features among thioredoxins

Thioredoxins (Trxs) are ubiquitous enzymes that regulate the redox state in cells. In Drosophila, there are two germline-specific Trxs, Deadhead (Dhd) and thioredoxin T (TrxT), that belong to the lethal(3)malignant brain tumor signature genes and to the 'survival network' of genes that mediate the cellular response to DNA damage. Dhd is a maternal protein required for early embryogenesis that promotes protamine-histone exchange in fertilized eggs and midblastula transition. TrxT is testis-specific and associates with the lampbrush loops of the Y chromosome. Here, the first structures of Dhd and TrxT are presented, unveiling new features of these two thioredoxins. Dhd has positively charged patches on its surface, in contrast to the negatively charged surfaces commonly found in most Trxs. This distinctive charge distribution helps to define initial encounter complexes with DNA/RNA that will lead to final specific interactions with cofactors to promote chromatin remodeling. TrxT contains a C-terminal extension, which is mostly unstructured and highly flexible, that wraps the conserved core through a closed conformation. It is believed that these new structures can guide future work aimed at understanding embryo development and redox homeostasis in Drosophila. Moreover, due to their restricted presence in Schizophora (a section of the true flies), these structures can help in the design of small-molecular binders to modulate native redox homeostasis, thereby providing new applications for the control of plagues that cause human diseases and/or bring about economic losses by damaging crop production.

Reviewing the experimental and mathematical factors involved in tight binding inhibitors Ki values determination: The bi-functional protease inhibitor SmCI as a test model

Different methodologies for determining the dissociation equilibrium constant (K_i) of protein tight binding inhibitors are frequently found in the scientific literature. Taking into account that the K_i value is the main parameter characterizing the inhibition strength, its determination often represents the first step during the characterization of a potential drug. The purpose of this review is to summarize the current information related to tight binding inhibitors K_i values determination and discuss about the importance of different factors as the enzyme concentration, the inhibitor concentration dilution series, the enzyme-inhibitor incubation time and the dose-response data mathematical fitting. For this aim, the bi-functional SmCI protease inhibitor is used as a tool for exemplifying the experimental and mathematical steps performed during tight binding inhibitors K_i values determination. In addition, the natural and the different recombinant forms of SmCI were used to go deeply into the comparison of some mathematic approaches that are frequently used in the literature. Finally, other biochemical techniques that could be potentially used for tight binding inhibitors K_i values determination are also commented.

Lysozyme-Induced Transcriptional Regulation of TNF-α Pathway Genes in Cells of the Monocyte Lineage

Lysozyme is one of the most important anti-bacterial effectors in the innate immune system of animals. Besides its direct antibacterial enzymatic activity, lysozyme displays other biological properties, pointing toward a significant anti-inflammatory effect, many aspects of which are still elusive. Here we investigate the perturbation of gene expression profiles induced by lysozyme in a monocyte cell line in vitro considering a perspective as broad as the whole transcriptome profiling. The results of the RNA-seq experiment show that lysozyme induces transcriptional modulation of the TNF-α/IL-1β pathway genes in U937 monocytes. The analysis of transcriptomic profiles with IPA^® identified a simple but robust molecular network of genes, in which the regulation trends are fully consistent with the anti-inflammatory activity of lysozyme. This study provides the first evidence in support of the anti-inflammatory action of lysozyme on the basis of transcriptomic regulation data resulting from the broad perspective of a whole-transcriptome profiling. Such important effects can be achieved with the supplementation of relatively low concentrations of lysozyme, for a short time of exposure. These new insights allow the potential of lysozyme in pharmacological applications to be better exploited.

Sensitive determination of lysozyme by using a luminescent and colorimetric probe based on the aggregation of gold nanoparticles induced by an anionic ruthenate(II) complex

The negatively charged ruthenate(II) complex [Ru(bpy)(PPh₃)(CN)₃]^- and gold nanoparticles (AuNPs) were used for detecting lysozyme (LYS). The luminescence of the ruthenate(II) complex is quenched by AuNPs, and this induces the aggregation of AuNPs and a color change from red to blue. After addition of lysozyme, the positively charged lysozyme and the negatively charged ruthenate(II) complex bind each other by electrostatic interaction firstly. This prevents AuNPs from aggregation and quenches the emission of the ruthenate(II) complex. Its luminescence and the degree of aggregation of the AuNPs can be used to quantify LYS. The fluorometric calibration plot is linear in the 0.01 to 0.20 μM LYS concentration range, and the calibration plot is linear between 0.02 and 0.20 μM of LYS. The color of the solution can be easily distinguished by bare eyes at 0.08 μM or higher concentration of LYS. The applicability of the method was verified by the correct analysis of LYS in chicken egg white. Graphical abstract Schematic of a luminometric and colorimetric probe based on the induced aggregation of gold nanoparticles by an anionic luminescent ruthenate(II) complex or sensitive lysozyme detection.

Inhibition of Human Immunodeficiency Type 1 Virus (HIV-1) Life Cycle by Different Egg White Lysozymes

Lysozyme is a relatively small enzyme with different biological activities, which is found in tears, saliva, egg white, and human milk. In the study, the anti-HIV-1 activity of lysozymes purified from quail, Meleagris, and hen egg white has been determined. For this end, a time-of-drug-addition assay was performed to identify the target of anti-HIV-1 agents and for determination of probable anti HIV-1 mechanism of the studied lysozyme, the binding affinity of the lysozymes to the human CD4 receptor was studied by molecular docking method. To define structural differences between studied lysozymes, structural motifs of them were predicted by MEME tool. Quail, hen, and Meleagris lysozymes showed potent anti-HIV-1 activity with EC₅₀ of 7.5, 10, and 55 nM, respectively. The time-of-drug-addition study demonstrated that the inhibitory effect of all purified lysozymes is before HIV-1 infection. The frequency and intensity of CD4 expression in PBMCs decreased in the presence of all mentioned lysozymes. Also, the expression level of C-C chemokine receptor type 5 (CCR5) and chemokine receptor type 4 (CXCR4) on CD4+ T cells was not changed in cells treated with these lysozymes. The results of in silico study confirmed that the binding energy of quail lysozyme with CD4 was more than that of other studied lysozymes. The results revealed that these lysozymes restrict HIV-1 attachment to host cell CD4.

Model studies of the effects of intracellular crowding on nucleic acid interactions

Molecular interactions and reactions in living cells occur with high concentrations of background molecules and ions. Many research studies have shown that intracellular molecules have characteristics different from those obtained using simple aqueous solutions. To better understand the behavior of biomolecules in intracellular environments, biophysical experiments were conducted under cell-mimicking conditions in a test tube. It has been shown that the molecular environments at the physiological level of macromolecular crowding, spatial confinement, water activity and dielectric constant, have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The experimental approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model experiments used to evaluate the influences of intracellular environment on nucleic acid interactions.

Inhibition of nuclear factor kappaB proteins-platinated DNA interactions correlates with cytotoxic effectiveness of the platinum complexes

Nuclear DNA is the target responsible for anticancer activity of platinum anticancer drugs. Their activity is mediated by altered signals related to programmed cell death and the activation of various signaling pathways. An example is activation of nuclear factor kappaB (NF-κB). Binding of NF-κB proteins to their consensus sequences in DNA (κB sites) is the key biochemical activity responsible for the biological functions of NF-κB. Using gel-mobility-shift assays and surface plasmon resonance spectroscopy we examined the interactions of NF-κB proteins with oligodeoxyribonucleotide duplexes containing κB site damaged by DNA adducts of three platinum complexes. These complexes markedly differed in their toxic effects in tumor cells and comprised highly cytotoxic trinuclear platinum(II) complex BBR3464, less cytotoxic conventional cisplatin and ineffective transplatin. The results indicate that structurally different DNA adducts of these platinum complexes exhibit a different efficiency to affect the affinity of the platinated DNA (κB sites) to NF-κB proteins. Our results support the hypothesis that structural perturbations induced in DNA by platinum(II) complexes correlate with their higher efficiency to inhibit binding of NF-κB proteins to their κB sites and cytotoxicity as well. However, the full generalization of this hypothesis will require to evaluate a larger series of platinum(II) complexes.

Turn-off–on fluorescence probe based on 3-mercaptopropionic acid-capped CdS quantum dots for selective and sensitive lysozyme detection

The fluorescence of CdS QDs was first quenched by hemoglobin and then restored with the increasing concentration of the lysozyme in a certain range. Therefore, a fluorescence assay for the determination of lysozyme was established.

Challenges of metagenomics and single-cell genomics approaches for exploring cyanobacterial diversity

Cyanobacteria have played a crucial role in the history of early earth and continue to be instrumental in shaping our planet, yet applications of cutting edge technology have not yet been widely used to explore cyanobacterial diversity. To provide adequate background, we briefly review current sequencing technologies and their innovative uses in genomics and metagenomics. Next, we focus on current cell capture technologies and the challenges of using them with cyanobacteria. We illustrate the utility in coupling breakthroughs in DNA amplification with cell capture platforms, with an example of microfluidic isolation and subsequent targeted amplicon sequencing from individual terrestrial thermophilic cyanobacteria. Single cells of thermophilic, unicellular Synechococcus sp. JA-2-3-B'a(2-13) (Syn OS-B') were sorted in a microfluidic device, lysed, and subjected to whole genome amplification by multiple displacement amplification. We amplified regions from specific CRISPR spacer arrays, which are known to be highly diverse, contain semi-palindromic repeats which form secondary structure, and can be difficult to amplify. Cell capture, lysis, and genome amplification on a microfluidic device have been optimized, setting a stage for further investigations of individual cyanobacterial cells isolated directly from natural populations.

An amplified electrochemical aptasensor based on hybridization chain reactions and catalysis of silver nanoclusters

In the present study, based on the mimic oxidase catalytic character of nucleic-acid-stabilized silver nanoclusters (DNA/AgNCs) and hybridization chain reactions for signal amplification, the fabrication of a label-free sensitive "turn-on" electrochemical aptasensor for the amplified determination of lysozyme was demonstrated. First, the designed DNA duplex was modified on the electrode. With the specific binding of the target, lysozyme and its aptamer, the lysozyme-binding DNA sequence was liberated, exposing the induced DNA sequence, which in turn triggered the formation of the supersandwich DNA structure. Because the cytosine-rich sequence was designed ingeniously on the DNA sequence, DNA/AgNCs were formed on the supersandwich DNA structure. The peroxidase-like character of DNA/AgNCs produced detectable electrochemical signals for the lysozyme aptasensor, which showed a satisfying sensitive detection of lysozyme with a low detection limit of 42 pM and a wide linear range of 10(-10) M to 10(-5) M.

Tandem ion exchange fractionation of chicken egg white reveals the presence of proliferative bioactivity

Chicken eggs are recognized for their versatility as a food product and as a model for research in biology and medicine. This study investigated the egg white as a source of bioactive compounds. Egg white was fractionated using tandem ion exchange chromatography (SAX and SCX), and seven fractions were assessed for any associated bioactivity. Four fractions at various protein concentrations were shown to contain proliferative bioactivity that exceeded the FBS control. The most potent fraction (6) was used in an in vitro wound closure assay to demonstrate a positive influence on cell migration and restored scratch wounds more rapidly than the control. LC-MS/MS identified 33 proteins in fraction 6 of egg white, most of which play important roles in cell growth and development, signaling, motility, and proliferation. These candidate bioactives suggest that the egg white contains essential compounds that contribute to the growth of an embryo prior to fertilization.

Multiple biological functions of novel basic proteins isolated from duck egg white: duck basic protein small 1 (dBPS1) and 2 (dBPS2)

Biological functions of duck basic protein small 1 (dBPS(1)) and 2 (dBPS(2)) were investigated by in vitro experiments. Results of agarose gel retardation assay indicated that dBPS(1) and dBPS(2) associate with RNA. Addition of NaCl or urea induced partial dissociation of dBPS(1)/dBPS(2)-RNA complex, implying that electrostatic interaction, hydrophobic interaction, and hydrogen bonds are involved in the association of dBPS(1)/dBPS(2) to RNA. dBPS(1) and dBPS(2) inhibited pancreatic lipase activity with the fifty percent inhibitory concentration (IC(50)) of 250 and 100 μg/mL, respectively. Peptic hydrolysates of dBPS(1) and those of dBPS(2) showed a potent angiotensin I-converting enzyme (ACE) inhibition with an IC(50) of 22.5 and 49.6 mg/L. The most potent ACE-inhibitory peptide was a nanopeptide (EKKGFCAGY) from dBPS(1) and an octapeptide (KYCPKVGY) from dBPS(2). These multiple biological functions of dBPS(1) and dBPS(2) may contribute to reducing the risk of lifestyle diseases.

B cells do not take up bacterial DNA: an essential role for antigen in exposure of DNA to toll-like receptor-9

Murine dendritic cells (DC) and macrophages respond to bacterial CpG DNA through toll-like receptor 9 (TLR9). Although it is frequently assumed that bacterial DNA is a direct stimulus for B cells, published work does not reliably show responses of purified B cells. Here we show that purified splenic B cells did not respond to Escherichia coli DNA with induction of CD86, despite readily responding to single-stranded (ss) phosphodiester CpG oligodeoxynucleotides (ODN). This was due to a combination of weak responses to both long and double-stranded (ds) DNA. B-cell DNA uptake was greatly reduced with increasing DNA length. This contrasts with macrophages where DNA uptake and subsequent responses were enhanced with increasing DNA length. However, when DNA was physically linked to hen egg lysozyme (HEL), HEL-specific B cells showed efficient uptake of DNA, and limited proliferation in response to the HEL-DNA complex. We propose that, in the absence of other signals, B cells have poor uptake and responses to long dsDNA to prevent polyclonal activation. Conversely, when DNA is physically linked to a B-cell receptor (BCR) ligand, its uptake is increased, allowing TLR9-dependent B-cell activation in an antigen-specific manner. We could not generate fragments of E. coli DNA by limited DNaseI digestion that could mimic the stimulatory effect of ss CpG ODN on naïve B cells. We suggest that the frequently studied polyclonal B-cell responses to CpG ODN are relevant to therapeutic applications of phosphorothioate-modified CpG-containing ODN, but not to natural responses to foreign or host dsDNA.

Protection of blue shrimp (Litopenaeus stylirostris) against the White Spot Syndrome Virus (WSSV) when injected with shrimp lysozyme

In this study we found that a blue shrimp (Litopenaeus stylirostris) lysozyme gene (Lslzm) was up-regulated in WSSV-infected shrimp, suggesting that lysozyme is involved in the innate response of shrimp to this virus. Shrimp were intramuscularly injected with Lslzm protein to identify how this recombinant protein protects L. stylirostris from WSSV infection and to determine how this protein influences nonspecific cellular and humoral defense mechanisms. Higher survival rates and a lower viral load (compared with controls) were reported for shrimps that were first injected with the Lslzm protein and then infected with WSSV. In addition, the Lslzm expression level and the immunological parameters (including THC, phagocytic activity, respiratory burst activity, phenoloxidase activity and lysozyme activity) were all significantly higher in the WSSV-infected shrimp treated with the Lslzm protein, compared with the controls. These results indicate that lysozyme is effective at blocking WSSV infection in L. stylirostris and that lysozyme modulates the cellular and humoral defense mechanisms after they are suppressed by the WSSV virus.

Hen egg lysozyme attenuates inflammation and modulates local gene expression in a porcine model of dextran sodium sulfate (DSS)-induced colitis

Inflammatory bowel disease (IBD) is a chronic and recurring inflammation of the gastrointestinal tract, associated with a dysregulation of the mucosal immune system. There is an increasing prevalence of IBD; however, current pharmaceutical treatments are only moderately effective and have been associated with potential long-term toxicity. Lysozyme, a well-known antimicrobial protein found in large quantities in hen egg white, is a promising alternative for the treatment of IBD. A porcine model of dextran sodium sulfate (DSS)-induced colitis was used to examine the effect of hen egg lysozyme (HEL) supplementation on intestinal inflammation. Treatment with DSS resulted in weight loss, severe mucosal and submucosal inflammation, colonic crypt distortion, muscle wall thickening, down-regulation of mucin gene expression, and increased gastric permeability, but these symptoms were attenuated following supplementation with HEL and restored to basal levels observed in untreated control animals. Treatment with HEL also significantly reduced the local expression of pro-inflammatory cytokines TNF-alpha, IL-6, IFN-gamma, IL-8, and IL-17 while increasing the expression of the anti-inflammatory mediators IL-4 and TGF-beta, indicating that HEL may function as a potent anti-inflammatory and immunomodulator. Furthermore, the concomitant increases in TGF-beta and Foxp3 levels suggest that HEL may aid in restoring gut homeostasis by activating regulatory T cells, which are important in the regulation of the mucosal immune system. These results suggest that HEL is a promising novel therapeutic for the treatment of IBD.