Protein-nanoparticle interactions and a new insight.

The study of protein-nanoparticle interactions provides knowledge about the bio-reactivity of nanoparticles, and creates a database of nanoparticles for applications in nanomedicine, nanodiagnosis, and nanotherapy. The problem arises when nanoparticles come in contact with physiological fluids such as plasma or serum, wherein they interact with the proteins (or other biomolecules). This interaction leads to the coating of proteins on the nanoparticle surface, mostly due to the electrostatic interaction, called 'corona'. These proteins are usually partially unfolded. The protein corona can deter nanoparticles from their targeted functionalities, such as drug/DNA delivery at the site and fluorescence tagging of diseased tissues. The protein corona also has many repercussions on cellular intake, inflammation, accumulation, degradation, and clearance of the nanoparticles from the body depending on the exposed part of the proteins. Hence, the protein-nanoparticle interaction and the configuration of the bound-proteins on the nanosurface need thorough investigation and understanding. Several techniques such as DLS and zeta potential measurement, UV-vis spectroscopy, fluorescence spectroscopy, circular dichroism, FTIR, and DSC provide valuable information in the protein-nanoparticle interaction study. Besides, theoretical simulations also provide additional understanding. Despite a lot of research publications, the fundamental question remained unresolved. Can we aim for the application of functional nanoparticles in medicine? A new insight, given by us, in this article assumes a reasonable solution to this crucial question.

Structural insights into SARS-CoV-2 proteins.

The unprecedented scale of the ongoing COVID-19 pandemic has catalyzed an intense effort of the global scientific community to unravel different aspects of the disease in a short time. One of the crucial aspects of these developments is the determination of more than three hundred experimental structures of SARS-CoV-2 proteins in the last few months. These include structures of viral non-structural, structural, and accessory proteins and their complexes determined by either X-ray diffraction or cryo-electron microscopy. These structures elucidate the intricate working of different components of the viral machinery at the atomic level during different steps of the viral life cycle, including attachment to the host cell, viral genome replication and transcription, and genome packaging and assembly of the virion. Some of these proteins are also potential targets for drug development against the disease. In this review, we discuss important structural features of different SARS-CoV-2 proteins with their function, and their potential as a target for therapeutic interventions.

Role of surface charges on interaction of rod-shaped magnetic hydroxyapatite nanoparticles with protein.

Magnetic hydroxyapatite (MHAp) exhibits excellent biocompatibility, making it an ideal candidate as a biomaterial. Recent investigations have shown that the combined effect of magnetite and hydroxyapatite nanostructures provide efficient means for diagnostic and therapeutic applications which can be controlled with an external magnetic field. For these applications an important aspect to be considered is the interaction of the MHAp nanoparticles (NPs) with biomolecules such as protein (P) and the subsequent biological response. The present study involves synthesis and characterization of Fe doped MHAp NPs, surface functionalized with tri-lithium citrate and cetyl pyridinium chloride having Li+ and Cl- as counterions, respectively. The electrostatic interaction of the MHAp NPs (with and without surface functionalization) with proteins such as Hen egg white lysozyme and Pepsin A were investigated to study the P-NP interactions. The crystalline structure and compositions of these NPs were characterized using X-ray diffraction. The size and aspect ratio were measured using transmission electron microscopy. The P-NP interaction was characterized by Dynamic light scattering, Zeta-potential measurements, UV-vis absorption and fluorescence emission spectroscopies. The conformational changes of the protein secondary structures were investigated by circular dichroism spectroscopy. The functionality of the protein after interaction with surface modified MHAp NPs were studied using activity assays.

drFrnE Represents a Hitherto Unknown Class of Eubacterial Cytoplasmic Disulfide Oxido-Reductases.

AIMS: Living cells employ thioredoxin and glutaredoxin disulfide oxido-reductases to protect thiol groups in intracellular proteins. FrnE protein of Deinococcus radiodurans (drFrnE) is a disulfide oxido-reductase that is induced in response to Cd2+ exposure and is involved in cadmium and radiation tolerance. The aim of this study is to probe structure, function, and cellular localization of FrnE class of proteins. RESULTS: Here, we show drFrnE as a novel cytoplasmic oxido-reductase that could be functional in eubacteria under conditions where thioredoxin/glutaredoxin systems are inhibited or absent. Crystal structure analysis of drFrnE reveals thioredoxin fold with an alpha helical insertion domain and a unique, flexible, and functionally important C-terminal tail. The C-tail harbors a novel 239-CX4C-244 motif that interacts with the active site 22-CXXC-25 motif. Crystal structures with different active site redox states, including mixed disulfide (Cys22-Cys244), are reported here. The biochemical data show that 239-CX4C-244 motif channels electrons to the active site cysteines. drFrnE is more stable in the oxidized form, compared with the reduced form, supporting its role as a disulfide reductase. Using bioinformatics analysis and fluorescence microscopy, we show cytoplasmic localization of drFrnE. We have found "true" orthologs of drFrnE in several eubacterial phyla and, interestingly, all these groups apparently lack a functional glutaredoxin system. Innovation and Conclusion: We show that drFrnE represents a new class of hitherto unknown intracellular oxido-reductases that are abundantly present in eubacteria. Unlike other well-known oxido-reductases, FrnE harbors an additional dithiol motif that acts as a conduit to channel electrons to the active site during catalytic turnover. Antioxid. Redox Signal. 28, 296-310.

Unfolding and inactivation of proteins by counterions in protein-nanoparticles interaction.

In this work, the structure and activity of proteins; such as, hen egg lysozyme (HEWL) and calf intestine alkaline phosphatase (CIAP); have been investigated after incubation with surface coated iron oxide nanoparticles (IONPs) in water. IONPs were coated with counterions bound charge-ligands and were named as the charge-ligand counterions iron oxide nanoparticles (CLC-IONPs). The coating was done with tri-lithium citrate (TLC) and tri-potassium citrate (TKC) to have negative surface charge of CLC-IONPs and Li(+) and K(+), respectively, as counterions. To have positive surface charge, IONPs were coated with cetylpyridinium chloride (CPC) and cetylpyridinium iodide (CPI) having Cl(-) and I(-), respectively, as counterions. The secondary structure of proteins was measured using far ultraviolet circular dichroism (CD) spectroscopy which showed that both proteins were irreversibly unfolded after incubation with CLC-IONPs. The unfolded proteins were seen to be functionally inactive, as confirmed through their activity assays, i.e., HEWL with Escherichia coli (E. coli) and CIAP with para-nitrophenyl phosphate (pNPP). Additionally, we have observed that monomeric hemoglobin (Hb) from radio-resistant insect Chironomus ramosus (ChHb) was also partially unfolded upon interaction with CLC-IONPs. This work clearly shows the role of counterions in protein inactivation via protein-nanoparticles interaction and, therefore, CLC-IONPs could be used for therapeutic purpose.

Differential sensitivity of Chironomus and human hemoglobin to gamma radiation.

Chironomus ramosus is known to tolerate high doses of gamma radiation exposure. Larvae of this insect possess more than 95% of hemoglobin (Hb) in its circulatory hemolymph. This is a comparative study to see effect of gamma radiation on Hb of Chironomus and humans, two evolutionarily diverse organisms one having extracellular and the other intracellular Hb respectively. Stability and integrity of Chironomus and human Hb to gamma radiation was compared using biophysical techniques like Dynamic Light Scattering (DLS), UV-visible spectroscopy, fluorescence spectrometry and CD spectroscopy after exposure of whole larvae, larval hemolymph, human peripheral blood, purified Chironomus and human Hb. Sequence- and structure-based bioinformatics methods were used to analyze the sequence and structural similarities or differences in the heme pockets of respective Hbs. Resistivity of Chironomus Hb to gamma radiation is remarkably higher than human Hb. Human Hb exhibited loss of heme iron at a relatively low dose of gamma radiation exposure as compared to Chironomus Hb. Unlike human Hb, the heme pocket of Chironomus Hb is rich in aromatic amino acids. Higher hydophobicity around heme pocket confers stability of Chironomus Hb compared to human Hb. Previously reported gamma radiation tolerance of Chironomus can be largely attributed to its evolutionarily ancient form of extracellular Hb as evident from the present study.

Purification, crystallization and preliminary crystallographic investigation of FrnE, a disulfide oxidoreductase from Deinococcus radiodurans.

In prokaryotes, Dsb proteins catalyze the formation of native disulfide bonds through an oxidative folding pathway and are part of the cell machinery that protects proteins from oxidative stress. Deinococcus radiodurans is an extremophile which shows unparalleled resistance to ionizing radiation and oxidative stress. It has a strong mechanism to protect its proteome from oxidative damage. The genome of Deinococcus shows the presence of FrnE, a Dsb protein homologue that potentially provides the bacterium with oxidative stress tolerance. Here, crystallization and preliminary X-ray crystallographic analysis of FrnE from D. radiodurans are reported. Diffraction-quality single crystals were obtained using the hanging-drop vapour-diffusion method with reservoir solution consisting of 100 mM sodium acetate pH 5.0, 10% PEG 8000, 15-20% glycerol. Diffraction data were collected on an Agilent SuperNova system using a microfocus sealed-tube X-ray source. The crystal diffracted to 1.8 Šresolution at 100 K. The space group of the crystal was found to be P21221, with unit-cell parameters a=47.91, b=62.94, c=86.75 Å, α=ß=γ=90°. Based on Matthews coefficient analysis, one monomer per asymmetric unit is present in the crystal, with a solvent content of approximately 45%.

Protein nanoparticle electrostatic interaction: size dependent counterions induced conformational change of hen egg white lysozyme.

In our earlier paper (Ghosh et al., 2013), we have shown that (i) the positively charged hen egg white lysozyme (HEWL), dispersed in water, binds electrostatically with the negatively functionalized iron oxide nanoparticles (IONPs), and (ii) the Na(+) counterions, associated with functionalized IONPs, diffuse into bound proteins and irreversibly unfold them. Having this information, we have extended our investigation and report here the effect of the size and the charge of alkaline metal counterions on the conformational modification of HEWL. In order to obtain a negative functional 'shell' on IONPs and the counterions of different size and charge we have functionalized IONPs with different derivatives of citrate, namely, tri-lithium citrate (TLC, Li3C6H5O7), tri-sodium citrate (TSC, Na3C6H5O7), tri-potassium citrate (TKC, K3C6H5O7) and tri-magnesium citrate (TMC, Mg3C12H10O14). The size of counterions varies as Mg(2+)

Rheology of Indian Honey: Effect of Temperature and Gamma Radiation.

Honey brands commonly available in Indian market were characterized for their rheological and thermal properties. Viscosity of all the honey samples belonging to different commercial brands was found to decrease with increase in temperature (5-40°C) and their sensitivity towards temperature varied significantly as explained by calculating activation energy based on Arrhenius model and ranged from 54.0 to 89.0 kJ/mol. However, shear rate was not found to alter the viscosity of honey indicating their Newtonian character and the shear stress varied linearly with shear rate for all honey samples. Honey is known to contain pathogenic microbial spores and in our earlier study gamma radiation was found to be effective in achieving microbial decontamination of honey. The effect of gamma radiation (5-15 kGy) on rheological properties of honey was assessed, and it was found to remain unchanged upon radiation treatment. The glass transition temperatures (T g ) of these honey analyzed by differential scanning calorimetry varied from -44.1 to -54.1°C and remained unchanged upon gamma radiation treatment. The results provide information about some key physical properties of commercial Indian honey. Radiation treatment which is useful for ensuring microbial safety of honey does not alter these properties.

Counter ion induced irreversible denaturation of hen egg white lysozyme upon electrostatic interaction with iron oxide nanoparticles: a predicted model.

The effects of electrostatic interaction between the hen egg white lysozyme (HEWL) and the functionalized iron oxide nanoparticles (IONPs) have been investigated using several techniques, e.g., CD, DSC, ζ-potential, UV-visible spectroscopy, DLS, TEM. Nanoparticles (IONPs) were functionalized with three hydrophilic ligands, viz., poly(ethylene glycol) (PEG), trisodium citrate (TSC) and sodium triphosphate (STP); where both TSC and STP contain Na(+) counter ions. It has been observed that the secondary structure of HEWL was not affected by PEG functionalized IONPs, but was partially and almost completely perturbed by TSC and STP functionalized IONPs, respectively. The perturbation of the secondary structure was irreversible. We have predicted an interaction model to explain the origin of perturbation of HEWL structure. We have also investigated the stability of nanoparticles dispersions after interaction with HEWL and used the DLVO theory to explain results.

NMR insights into folding and self-association of Plasmodium falciparum P2.

The eukaryotic 60S-ribosomal stalk is composed of acidic ribosomal proteins (P1 and P2) and neutral protein P0, which are thought to be associated as a pentameric structure, [2P1, 2P2, P0]. Plasmodium falciparum P2 (PfP2) appears to play additional non-ribosomal functions associated with its tendency for homo-oligomerization. Recombinant bacterially expressed PfP2 protein also undergoes self-association, as shown by SDS-PAGE analysis and light scattering studies. Secondary structure prediction algorithms predict the native PfP2 protein to be largely helical and this is corroborated by circular dichroism investigation. The (1)H-(15)N HSQC spectrum of native P2 showed only 43 cross peaks compared to the expected 138. The observed peaks were found to belong to the C-terminal region, suggesting that this segment is flexible and solvent exposed. In 9 M urea denaturing conditions the chain exhibited mostly non-native ß structural propensity. (15)N Relaxation data for the denatured state indicated substantial variation in ms-µs time scale motion along the chain. Average area buried upon folding (AABUF) calculations on the monomer enabled identification of hydrophobic patches along the sequence. Interestingly, the segments of slower motion in the denatured state coincided with these hydrophobic patches, suggesting that in the denatured state the monomeric chain undergoes transient hydrophobic collapse. The implications of these results for the folding mechanism and self-association of PfP2 are discussed.

Lecithin-based novel cationic nanocarriers (LeciPlex) I: fabrication, characterization and evaluation.

AIMS: In the present investigation, the feasibility of fabricating novel self-assembled cationic nanocarriers (LeciPlex) containing cetyltrimethylammonium bromide (CTAB) or didodecyldimethylammonium bromide (DDAB) and soybean lecithin using pharmaceutically acceptable biocompatible solvents such as 2-Pyrrolidone (Soluphor P) and diethyleneglycol monoethyl ether (Transcutol) was established. MATERIALS & METHODS: The interaction between DDAB/CTAB and soybean lecithin in the nanocarriers was confirmed by differential scanning calorimetry and in vitro antimicrobial studies. The positive charge on the nanocarriers was confirmed by zeta potential analysis. RESULTS: Transmission electron microscopy analysis could not reveal sufficient information regarding the internal structure of the nanocarriers, whereas cryotransmission electron microscopy studies indicated that these novel nanocarriers have unilamellar structure. Small-angle neutron scattering studies confirmed interaction of cationic surfactant (DDAB) and lecithin in the nanocarriers and confirmed the presence of unilamellar nanostructures. CONCLUSION: Various hydrophobic drugs could be encapsulated in the CTAB/DDAB-based lecithin nanocarriers (CTAB-LeciPlex or DDAB-LeciPlex) irrespective of their difference in log p-values. In vitro antimicrobial studies on triclosan-loaded LeciPlex confirmed entrapment of triclosan in the nanocarriers. The ability of CTAB-LeciPlex and DDAB-LeciPlex to condense plasmid DNA was established using agarose gel electrophoresis. DDAB-LeciPlex could successfully transfect pDNA in HEK-293 cells indicating potential in gene delivery.

Immunological effects and membrane interactions of chitosan nanoparticles.

The objective of this study was to investigate the in vitro and in vivo effects of blank chitosan nanoparticles on various molecular markers such as nitric oxide (NO) production, IL-6 gene expression, and lymphocyte proliferation involved in the wound healing process. In addition, the membrane effects of chitosan nanoparticles were evaluated using phospholipid vesicles as a model membrane. Peripheral blood mononuclear cells (PBMC) were treated with blank chitosan nanoparticles, and the effect on NO production, IL-6 gene expression, and lymphocyte proliferation was evaluated. It was observed that IL-6 gene expression was not induced at any of the doses used; however, a statistically significant dose-dependent increase in NO production was observed at doses above 68.18 microg/mL equivalent to chitosan. Furthermore, chitosan nanoparticles showed a statistically significant and dose-dependent lymphocyte proliferation as compared to the control (P < 0.05). It was observed that blank chitosan nanoparticles resulted in strong membrane perturbation when evaluated by differential scanning calorimetry studies. The in vivo effects of the blank chitosan nanoparticles were evaluated using a wound healing model. Blank chitosan nanoparticles showed significantly higher NO production in vivo as compared to the control. Overall, the study clearly indicates the immunoactivating nature of chitosan nanoparticles and their strong membrane interactive potential.

Interaction of propyl paraben with dipalmitoyl phosphatidylcholine bilayer: a differential scanning calorimetry and nuclear magnetic resonance study.

The influence of the preservative, propyl paraben (PPB) on the biophysical properties of dipalmitoyl phosphatidyl choline (DPPC) vesicles, both in multilamellar vesicle (MLV) and unilamellar vesicle (ULV) forms, has been studied using DSC and ((1)H and (31)P) NMR. The mechanism by which PPB interacts with DPPC bilayers was found to be independent of the morphological organization of the lipid bilayer. Incorporation of PPB in DPPC vesicles causes a significant depression in the transition temperature and enthalpy of both the pre-transition (PT) and the gel to liquid crystalline transition. The presence of the PPB also reduces the co-operativity of these transitions. However, at high PPB concentration the PT disappears. DSC and NMR findings indicate that: (i) PPB is bound strongly to the lipid bilayer leading to increased headgroup fluidity due to reduced headgroup-headgroup interaction and (ii) the PPB molecules are intercalated between the DPPC polar headgroups with its alkyl chain penetrate into the co-operative region. MLV incorporated with high PPB concentration shows additional transitions whose intensity increases with increasing PPB concentration. This phase segregation observed could probably be due to co-existence of PPB-rich and PPB-poor phospholipid domains within the bilayers. The effect of inclusion of cholesterol in the PPB-free and PPB-doped DPPC dispersion was also studied. Equilibration studies suggest that PPB molecules are very strongly bound and remain intercalated between the polar headgroup for prolonged time.

Effect of propyl paraben on the dipalmitoyl phosphatidic acid vesicles.

The effect of the preservative propyl paraben (PPB) on the phase transition and dynamics of dipalmitoyl phosphatidic acid (DPPA)-buffer (pH 7.4/9.3) vesicles has been studied using DSC and ((1)H and (31)P) NMR. These investigations were carried out with DPPA dispersion in both multilamellar vesicular (MLV) and unilamellar vesicular (ULV) forms. DSC results indicate that the mechanism by which PPB interact with the DPPA vesicles is similar in MLV and ULV and is independent of pH of the buffer used to form the dispersion. However, for a given concentration of PPB, the perturbation in DPPA bilayer is more when the dispersion is prepared in buffer pH 7.4. PPB affected both the thermotropic phase transition and the molecular mobility of the DPPA membrane. In the presence of PPB, the gel to liquid crystalline phase transition temperature (T(m)) of the DPPA vesicles decreases hence increases membrane fluidity due to reduced headgroup-headgroup interaction. For all concentrations, the PPB molecules seem to get intercalated between the polar groups of the phospholipids with its alkyl chain penetrating into the co-operative region. At high PPB concentration, additional transitions are observed whose intensity increases with increasing PPB concentration. The large enthalpy values obtained at high PPB concentration suggest that presence of PPB makes the DPPA bilayer more ordered (rigid). The interesting finding obtained with MLV is that the stable gel phase of DPPA-buffer (pH 9.3/7.4) system in the presence of high PPB concentration becomes a metastable gel phase, this metastable gel phase on equilibration at 25 degrees C or when cooled to -20 degrees C transforms to a stable crystalline phase(s). The intensity of this new phase(s) increases with increasing PPB concentration. However, the transition temperatures of these new phases are not significantly changed with increasing PPB concentration. The effect of inclusion of cholesterol in the PPB-free and PPB-doped DPPA dispersion was also studied.

Nuclear magnetic resonance and thermal studies on the interaction between salicylic acid and model membranes.

DSC and (1H and 31P) NMR measurements are used to investigate the perturbation caused by the keratolytic drug, salicylic acid (SA) on the physicochemical properties of the model membranes. Model membranes (in unilamellar vesicular (ULV) form) in the present studies are prepared with the phospholipids, dipalmitoyl phosphatidylcholine (DPPC), dipalmitoyl phosphatidylethanolamine (DPPE), dipalmitoyl phosphatidic acid (DPPA) and mixed lipid DPPC-DPPE (with weight ratio, 2.5:2.2). These lipids have the same acyl (dipalmitoyl) chains but differed in the headgroup. The molar ratio of the drug to lipid (lipid mixture), is in the range 0 to 0.4. The DSC and NMR results suggest that the lipid head groups have a pivotal role in controlling (i) the behavior of the membranes and (ii) their interactions with SA. In the presence of SA, the main phase transition temperature of (a) DPPE membrane decreases, (b) DPPA membrane increases and (c) DPPC and DPPC-DPPE membranes are not significantly changed. The drug increases the transition enthalpy (i.e., acyl chain order) in DPPC, DPPA and DPPC-DPPE membranes. However, the presence of the drug in DPPC membrane formed using water (instead of buffer), shows a decrease in the transition temperature and enthalpy. In all the systems studied, the drug molecules seem to be located in the interfacial region neighboring the glycerol backbone or polar headgroup. However, in DPPC-water system, the drug seems to penetrate the acyl chain region also.

Salicylic acid-induced effects in the mixed-lipid (dipalmitoyl phosphatidylcholine-dipalmitoyl phosphatidylethanolamine) model membrane.

The effect of the keratolytic drug salicylic acid (SA) on the thermotropic properties and fluidity of the mixed lipid membrane dipalmitoyl phosphatidylcholine (DPPC)-dipalmitoyl phosphatidylethanolamine (DPPE) had been studied using DSC, (1H and 31P) NMR, SAXS, and dynamic light scattering. The membrane was in multilamellar vesicular (MLV) and unilamellar vesicular (ULV) form with SA/(DPPC+DPPE) molar ratios, R(m), in the range from 0 to 0.5. It was found that the mechanism of interaction of SA with the lipid mixture exhibited similar patterns in both ULV and MLV. Both the NMR and DSC studies indicated that the drug molecules were probably localized in the lipid-water interfacial region neighboring the lipid headgroups or the glycerol moiety. The presence of the drug increased the fluidity of the membrane and the acyl chain order. However, studies on MLV showed that the presence of the drug in high concentration (R(m)0.2), caused destabilization of the DPPC-DPPE mixture, as indicated by the appearance of two endothermic transitions. DSC studies indicated that prolonged equilibration of the membrane led to reduced interaction between the lipid headgroups and the SA molecules. This reduced interaction could be due to the sequestering of the drug molecules into the lipid-water interfacial region, out of proximity to the polar headgroup or glycerol moiety. Effect of inclusion of cholesterol in the membrane systems was also studied.