Circular Dichroism Techniques: Biomolecular and Nanostructural Analyses- A Review

K1K8: an Hp1404-derived antibacterial peptide

As an alternative class of antimicrobial agents used to overcome drug-resistant infections, antimicrobial peptides (AMPs) have recently gained significant attention. In this study, we designed an improved antimicrobial peptide, K1K8, based on the molecular template of Hp1404. Compared to the wild-type Hp1404, K1K8 showed an improved antibacterial spectrum in vitro, a lower hemolytic activity, and an enhanced serum stability. Importantly, K1K8 also decreased methicillin-resistant Staphylococcus aureus (MRSA) bacterial counts in the wounded region in a mouse skin infection model. Interestingly, K1K8 did not induce bacterial resistance or non-specific immune response reactions. Moreover, the peptide killed bacterial cells mainly by disrupting the bacterial membrane. In summary, K1K8 has the potential to be used as an improved anti-infection agent for topical use, which opens an avenue that potential anti-infection drugs may be designed and developed from the molecular templates of AMPs.

The interaction of human serum albumin with selected lanthanide and actinide ions: Binding affinities, protein unfolding and conformational changes

Human serum albumin (HSA), the most abundant soluble protein in blood plays critical roles in transportation of biomolecules and maintenance of osmotic pressure. In view of increasing applications of lanthanides- and actinides-based materials in nuclear energy, space, industries and medical applications, the risk of exposure with these metal ions is a growing concern for human health. In present study, binding interaction of actinides/lanthanides [thorium: Th(IV), uranium: U(VI), lanthanum: La(III), cerium: Ce(III) and (IV)] with HSA and its structural consequences have been investigated. Ultraviolet-visible, Fourier transform-infrared, Raman, Fluorescence and Circular dichroism spectroscopic techniques were applied to study the site of metal ions interaction, binding affinity determination and the effect of metal ions on protein unfolding and HSA conformation. Results showed that these metal ions interacted with carbonyl (CO..:)/amide(N..-H) groups and induced exposure of aromatic residues of HSA. The fluorescence analysis indicated that the actinide binding altered the microenvironment around Trp214 in the subdomain IIA. Binding affinity of U(VI) to HSA was slightly higher than that of Th(IV). Actinides and Ce(IV) altered the secondary conformation of HSA with a significant decrease of α-helix and an increase of β-sheet, turn and random coil structures, indicating a partial unfolding of HSA. A correlation was observed between metal ion's ability to alter HSA conformation and protein unfolding. Both cationic effects and coordination ability of metal ions seemed to determine the consequences of their interaction with HSA. Present study improves our understanding about the protein interaction of these heavy ions and their impact on its secondary structure. In addition, binding characteristics may have important implications for the development of rational antidote for the medical management of health effects of actinides and lanthanides.

Structural and functional characterization of phosphomimetic mutants of cytochrome c at threonine 28 and serine 47

Protein function is frequently modulated by post-translational modifications of specific residues. Cytochrome c, in particular, is phosphorylated in vivo at threonine 28 and serine 47. However, the effect of such modifications on the physiological functions of cytochrome c - namely, the transfer of electrons in the respiratory electron transport chain and the triggering of programmed cell death - is still unknown. Here we replace each of these two residues by aspartate, in order to mimic phosphorylation, and report the structural and functional changes in the resulting cytochrome c variants. We find that the T28D mutant causes a 30-mV decrease on the midpoint redox potential and lowers the affinity for the distal site of Arabidopsis thaliana cytochrome c1 in complex III. Both the T28D and S47D variants display a higher efficiency as electron donors for the cytochrome c oxidase activity of complex IV. In both protein mutants, the peroxidase activity is significantly higher, which is related to the ability of cytochrome c to leave the mitochondria and reach the cytoplasm. We also find that both mutations at serine 47 (S47D and S47A) impair the ability of cytoplasmic cytochrome c to activate the caspases cascade, which is essential for triggering programmed cell death.

Lipoplexes of dicationic gemini surfactants with DNA: Structural features of DNA compaction and transfection efficiency

The internal structure of DNA lipoplexes with hydroxyethylated alkylammonium gemini surfactants (GS) with high transfection activity was studied by circular dichroism. It was shown that the efficiency of transfection of HEK293T cells with the pEGFP-N1 circular plasmid was different from zero only in the region of existence of chiral supramolecular DNA-GS complexes and reaches a maximum at concentrations at which the spontaneous aggregation of components is observed.

Chiral recognition by fullerenes: CHFClBr enantiomers in the C82cage

Theoretical studies of complexes of the enantiomers of CHFClBr with C₈₂-3 show that the too large guests are stabilized in the C₈₂cage by electrostatic interactions. The sign of v(CH) stretching vibration of S-CHFClBr@C₈₂-3 in the VCD spectrum is reversed as compared to that of the free guest. Spectra of the complexes exhibit differences.

A colorimetric and fluorometric dual-modal DNA logic gate based on the response of a cyanine dye supramolecule to G-quadruplexes

The INHIBIT DNA logic gate with dual-modal outputs based on the response of MTC aggregates to G-quadruplexes.

Interaction Of Calcium Phosphate Nanoparticles With Human Chorionic Gonadotropin Modifies Secondary And Tertiary Protein Structure

Calcium phosphate nanoparticles (CaPNP) have good biocompatibility and bioactivity inside human body. In this study, the interaction between CaPNP and human chorionic gonadotropin (hCG) was analyzed to determine the changes in the protein structure in the presence of CaPNP and the quantity of protein adsorbed on the CaPNP surface. The results showed a significant adsorption of hCG on the CaPNP nanoparticle surface. The optimal fit was achieved using the Sips isotherm equation with a maximum adsorption capacity of 68.23 µg/mg. The thermodynamic parameters, including ∆H° and ∆G°, of the adsorption process are positive, whereas ∆S° is negative. The circular dichroism results of the adsorption of hCG on CaPNP showed the changes in its secondary structure; such changes include the decomposition of α-helix strand and the increase in β-pleated sheet and random coil percentages. Fluorescence study indicated minimal changes in the tertiary structure near the microenvironment of the aromatic amino acids such as tyrosine and phenyl alanine caused by the interaction forces between the CaPNP and hCG protein. The desorption process showed that the quantity of the hCG desorbed significantly increases as temperature increases, which indicates the weak forces between hCG and the surface.

Spin Exchange Interaction in Substituted Copper Phthalocyanine Crystalline Thin Films

The origins of spin exchange in crystalline thin films of Copper Octabutoxy Phthalocyanine (Cu-OBPc) are investigated using Magnetic Circular Dichroism (MCD) spectroscopy. These studies are made possible by a solution deposition technique which produces highly ordered films with macroscopic grain sizes suitable for optical studies. For temperatures lower than 2 K, the contribution of a specific state in the valence band manifold originating from the hybridized lone pair in nitrogen orbitals of the Phthalocyanine ring, bears the Brillouin-like signature of an exchange interaction with the localized d-shell Cu spins. A comprehensive MCD spectral analysis coupled with a molecular field model of a σπ − d exchange analogous to sp-d interactions in Diluted Magnetic Semiconductors (DMS) renders an enhanced Zeeman splitting and a modified g-factor of −4 for the electrons that mediate the interaction. These studies define an experimental tool for identifying electronic states involved in spin-dependent exchange interactions in organic materials.

Binding of glutathione and melatonin to pepsin occurs via different binding mechanisms

Glutathione is a hydrophilic antioxidant and melatonin is a hydrophobic antioxidant, thus, the binding mechanism of the two antioxidants interacting with protease may be different. In this study, binding of glutathione and melatonin to pepsin has been studied using isothermal titration calorimetry (ITC), equilibrium microdialysis, UV-Vis absorption spectroscopy, circular dichroism (CD) spectroscopy, and molecular modeling. Thermodynamic investigations reveal that the binding of glutathione/melatonin to pepsin is driven by favorable enthalpy and unfavorable entropy, and the major driving forces are hydrogen bond and van der Waals force. ITC, equilibrium microdialysis, and molecular modeling reveal that the binding of glutathione to pepsin is characterized by a high number of binding sites. For melatonin, one molecule of melatonin combines with one molecule of pepsin. These results confirm that glutathione/melatonin interact with pepsin through two different binding mechanisms. In addition, the UV-Vis absorption and CD experiments indicate that glutathione and melatonin may induce conformational and microenvironmental changes of pepsin. The conformational changes of pepsin may affect its biological function as protease.

Numerical study of achiral phase-change metamaterials for ultrafast tuning of giant circular conversion dichroism

Control of the polarization of light is highly desirable for detection of material’s chirality since biomolecules have vibrational modes in the optical region. Here, we report an ultrafast tuning of pronounced circular conversion dichroism (CCD) in the mid-infrared (M-IR) region, using an achiral phase change metamaterial (PCMM). Our structure consists of an array of Au squares separated from a continuous Au film by a phase change material (Ge₂Sb₂Te₅) dielectric layer, where the Au square patches occupy the sites of a rectangular lattice. The extrinsically giant 2D chirality appears provided that the rectangular array of the Au squares is illuminated at an oblique incidence, and accomplishes a wide tunable wavelength range between 2664 and 3912 nm in the M-IR regime by switching between the amorphous and crystalline states of the Ge₂Sb₂Te₅. A photothermal model is investigated to study the temporal variation of the temperature of the Ge₂Sb₂Te₅ layer, and shows the advantage of fast transiting the phase of Ge₂Sb₂Te₅ of 3.2 ns under an ultralow incident light intensity of 1.9 μW/μm². Our design is straightforward to fabricate and will be a promising candidate for controlling electromagnetic (EM) wave in the optical region.

Stabilization of Chromobacterium viscosum Lipase (CVL) Against Ultrasound Inactivation by the Pretreatment with Polyethylene Glycol (PEG)

Although ultrasound has been used to accelerate many enzymatic reactions, the low stability of enzymes in such a system still remains a critical issue, limiting its industrial application. Here, we have reported that polyethylene glycol (PEG) pretreatment stabilized Chromobacterium viscosum lipase (CVL) in ultrasound-assisted water-isooctane emulsion. PEGs of different molecular weights and concentrations were used to pretreat CVL, and the pretreated lipase activities for olive oil hydrolysis were investigated at different ultrasonic powers. The best result was attained with PEG400 at 100 mg/ml for a lipase concentration of 0.02 mg/ml and an ultrasonic power of 106 W. The half-life time of PEG400-treated lipase at 106 W was 54 min, a 27-fold higher than that attained using untreated lipase. Circular dichroism (CD) spectra suggested that PEG increased the rigidity of CVL structure, which favored the lipase stability against ultrasound inactivation. These results have important implications for the exploitation of ultrasound in biocatalytic process.

Characterization of the structural and protein recognition properties of hybrid PNA-DNA four-way junctions

The objective of this study is to evaluate the structure and protein recognition properties of hybrid four-way junctions (4WJs) composed of DNA and peptide nucleic acid (PNA) strands. We compare a classic immobile DNA junction, J1, vs. six PNA-DNA junctions, including a number with blunt DNA ends and multiple PNA strands. Circular dichroism (CD) analysis reveals that hybrid 4WJs are composed of helices that possess structures intermediate between A- and B-form DNA, the apparent level of A-form structure correlates with the PNA content. The structure of hybrids that contain one PNA strand is sensitive to Mg(+2). For these constructs, the apparent B-form structure and conformational stability (Tm) increase in high Mg(+2). The blunt-ended junction, b4WJ-PNA3, possesses the highest B-form CD signals and Tm (40.1 °C) values vs. all hybrids and J1. Protein recognition studies are carried out using the recombinant DNA-binding protein, HMGB1b. HMGB1b binds the blunt ended single-PNA hybrids, b4WJ-PNA1 and b4WJ-PNA3, with high affinity. HMGB1b binds the multi-PNA hybrids, 4WJ-PNA1,3 and b4WJ-PNA1,3, but does not form stable protein-nucleic acid complexes. Protein interactions with hybrid 4WJs are influenced by the ratio of A- to B-form helices: hybrids with helices composed of higher levels of B-form structure preferentially associate with HMGB1b.

Gold triple-helix mid-infrared metamaterial by STED-inspired laser lithography

In analogy to wire-grid polarizers for linear polarization, metal-helix metamaterials can act as broadband circular polarizers. This concept has brought circular-polarization capabilities to mid-infrared and terahertz frequencies, which were previously difficult to access. Due to the lack of rotational symmetry, however, single-helix metamaterials exhibit unwanted circular-polarization conversions. Recent theoretical work showed that conversions can be fully eliminated by intertwining N=3 or 4 helices within each unit cell. While direct laser writing in positive-tone photo-resist yielded good results for single-helix metamaterials operating at mid-infrared frequencies, the axial resolution is insufficient for N-helix metamaterials. Here, we use stimulated emission depletion-inspired three-dimensional laser lithography to fabricate such microstructures. We measure all entries of the Jones transmission and reflection matrices and show experimentally that polarization conversions are minimized, in good agreement with theory.

Physicochemical and biological characterization of chitosan-microRNA nanocomplexes for gene delivery to MCF-7 breast cancer cells

Cancer gene therapy requires the design of non-viral vectors that carry genetic material and selectively deliver it with minimal toxicity. Non-viral vectors based on cationic natural polymers can form electrostatic complexes with negatively-charged polynucleotides such as microRNAs (miRNAs). Here we investigated the physicochemical/biophysical properties of chitosan-hsa-miRNA-145 (CS-miRNA) nanocomplexes and the biological responses of MCF-7 breast cancer cells cultured in vitro. Self-assembled CS-miRNA nanocomplexes were produced with a range of (+/-) charge ratios (from 0.6 to 8) using chitosans with various degrees of acetylation and molecular weight. The Z-average particle diameter of the complexes was <200 nm. The surface charge increased with increasing amount of chitosan. We observed that chitosan induces the base-stacking of miRNA in a concentration dependent manner. Surface plasmon resonance spectroscopy shows that complexes formed by low degree of acetylation chitosans are highly stable, regardless of the molecular weight. We found no evidence that these complexes were cytotoxic towards MCF-7 cells. Furthermore, CS-miRNA nanocomplexes with degree of acetylation 12% and 29% were biologically active, showing successful downregulation of target mRNA expression in MCF-7 cells. Our data, therefore, shows that CS-miRNA complexes offer a promising non-viral platform for breast cancer gene therapy.

Mimicking Tyrosine Phosphorylation in Human Cytochrome c by the Evolved tRNA Synthetase Technique

Phosphorylation of tyrosine 48 of cytochrome c is related to a wide range of human diseases due to the pleiotropic role of the heme-protein in cell life and death. However, the structural conformation and physicochemical properties of phosphorylated cytochrome c are difficult to study as its yield from cell extracts is very low and its kinase remains unknown. Herein, we report a high-yielding synthesis of a close mimic of phosphorylated cytochrome c, developed by optimization of the synthesis of the non-canonical amino acid p-carboxymethyl-L-phenylalanine (pCMF) and its efficient site-specific incorporation at position 48. It is noteworthy that the Y48pCMF mutation significantly destabilizes the Fe-Met bond in the ferric form of cytochrome c, thereby lowering the pKa value for the alkaline transition of the heme-protein. This finding reveals the differential ability of the phosphomimic protein to drive certain events. This modified cytochrome c might be an important tool to investigate the role of the natural protein following phosphorylation.

Enzyme stability, thermodynamics and secondary structures of α-amylase as probed by the CD spectroscopy

An amylase of a thermophilic bacterium, Bacillus sp. TSSC-3 (GenBank Number, EU710557) isolated from the Tulsi Shyam hot spring reservoir (Gujarat, India) was purified to the homogeneity in a single step on phenyl sepharose 6FF. The molecular weight of the enzyme was 25kD, while the temperature and pH optima for the enzyme catalysis were 80°C and 7, respectively. The purified enzyme was highly thermostable with broad pH stability and displayed remarkable resistance against surfactants, chelators, urea, guanidine HCl and various solvents as well. The stability and changes in the secondary structure of the enzyme under various extreme conditions were determined by the circular dichroism (CD) spectroscopy. The stability trends and the changes in the α-helices and β-sheets were analyzed by Mean Residual Ellipticity (MRE) and K2D3. The CD data confirmed the structural stability of the enzyme under various harsh conditions, yet it indicated reduced α-helix content and increased β-sheets upon denaturation. The thermodynamic parameters; deactivation rate constant, half-life, changes in entropy, enthalpy, activation energy and Gibb's free energy indicated that the enzyme-substrate reactions were highly stable. The overall profile of the enzyme: high thermostability, alkalitolerance, calcium independent nature, dextrose equivalent values and resistance against chemical denaturants, solvents and surfactants suggest its commercial applications.

Engineering of a disulfide loop instead of a Zn binding loop restores the anti-proliferative, anti-angiogenic and anti-tumor activities of the N-terminal fragment of endostatin: Mechanistic and therapeutic insights

Although considerable effort has been devoted to understanding the molecular mechanism of endostatin's anti-cancer activity, the role of its Zn bound N-terminal loop has not been completely clarified. To investigate whether Zn binding or the N-terminal loop is involved in the anti-cancer properties of endostatin, we compared the structure and biological activity of a native Zn binding endostatin peptide (ES-Zn) with three variants: a Zn free variant (ES), a variant containing both a Zn binding site and a disulfide bond (ES-SSZn), and a variant including a disulfide loop but incapable of Zn binding (ES-SS). Spectroscopic studies indicated that ES-Zn and ES-SS consist of random coil and β structures, whereas ES-SSZn and ES fold into random coils. Theoretical analysis proposed that ES-Zn and ES-SS have a similar binding site to αVβ3 integrin. The anti-proliferative activity of endostatin was retained by all peptides except ES, and the in vitro anti-angiogenic property was preserved in ES-Zn and ES-SS. Remarkably, breast tumor growth and CD31 activity were inhibited more effectively by ES-SS than by ES-Zn. Therefore, a correlation exists between the N-terminal loop and anti-cancer properties of endostatin fragment and a disulfide loop may be more promising than a Zn binding loop for inhibiting tumor growth.

Tuning of giant 2D-chiroptical response using achiral metasurface integrated with graphene

Tuning the chiroptical response of a molecule is crucial for detecting the material's chirality. Here, we demonstrate a pronounced circular conversion dichroism (CCD) by using an achiral metasurface (AMS) which is composed of a rectangular reflectarray of Au squares separated from a continuous Au film by a dielectric interlayer. This extrinsically 2D chirality originates from the mutual orientation between the AMS and oblique incident wave. The AMS is further incorporated with graphene to tune the CCD spectra in the mid-infrared (MIR) region by electrically modulating the graphene's Fermi level. This approach offers a high fabrication tolerance and will be a promising candidate for controlling electromagnetic (EM) waves in the MIR region from 1500 to 3000 nm.

Studies on the binding of fulvic acid with transferrin by spectroscopic analysis

Transferrin has shown potential in the delivery of anticancer drugs into primarily proliferating cancer cells that over-express transferrin receptors. Fulvic acid has a wide range of biological and pharmacological activities which caused widespread concerns, the interaction of fulvic acid with human serum transferrin (Tf) has great significance for gaining a deeper insight about anticancer activities of fulvic acid. In this study, the mechanism of interaction between fulvic acid and Tf, has been investigated by using fluorescence quenching, thermodynamics, synchronous fluorescence and circular dichroism (CD) under physiological condition. Our results have shown that fulvic acid binds to Tf and form a new complex, and the calculated apparent association constants are 5.04×10(8) M(-1), 5.48×10(7) M(-1), 7.38×10(6) M(-1) from the fluorescence quenching at 288 K, 298 K, and 310 K. The thermodynamic parameters indicate that hydrogen bonding and weak van der Waals are involved in the interaction between fulvic acid and Tf. The binding of fulvic acid to Tf causes the α-helix structure content of the protein to reduce, and resulting that peptide chains of Tf become more stretched. Our results have indicated a mechanism of the interaction between fulvic acid and Tf, which may provide information for possible design of methods to deliver drug molecules via transferrin to target tissues and cells effectively.

Characterization of the interaction between resmethrin and calf thymus DNA in vitro

Resmethrin preferentially binds to the G–C rich region of the ctDNA groove, and the UV-vis spectral matrix is decomposed by MCR-ALS.

An IDB-containing low molecular weight short peptide as an efficient DNA cleavage reagent

We present poly(aspartic acid) grafting bis-amine conjugates as artificial nucleases, which can effectively induce double-strand DNA cleavage.

Groove binding interaction between daphnetin and calf thymus DNA

The binding characteristics of daphnetin with calf thymus DNA (ctDNA) were investigated by multispectroscopic and chemometric approaches coupled with DNA viscosity measurements, melting studies and molecular docking technique. The expanded UV-vis spectral data matrix was processed by multivariate curve resolution-alternating least-squares method to obtain the concentration profiles of the components (daphnetin, ctDNA and daphnetin-ctDNA complex) to quantitatively monitor the daphnetin-ctDNA interaction. The groove mode of daphnetin binding to ctDNA was concluded by little change in melting temperature, viscosity of ctDNA and iodide quenching effect as well as increase in single-stranded DNA quenching effect. Moreover, the quantitative data for the competitive binding between daphnetin and Hoechst 33258 for ctDNA obtained by resolving the three-way synchronous fluorescence spectra data using parallel factor analysis modeling further supported the groove binding. The molecular docking visualized the results of the Fourier transform infrared analysis that the adenine and thymine bases in the minor groove of ctDNA were the main binding sites for daphnetin, and the circular dichroism spectra showed that the groove binding of daphnetin to ctDNA led to the conformational change in ctDNA from B-form to A-form. This study revealed the interaction mechanism of daphnetin with ctDNA.

Extrinsic 2D chirality: giant circular conversion dichroism from a metal-dielectric-metal square array

Giant chiroptical responses routinely occur in three dimensional chiral metamaterials (MMs), but their resonance elements with complex subwavelength chiral shapes are challenging to fabricate in the optical region. Here, we propose a new paradigm for obtaining strong circular conversion dichroism (CCD) based on extrinsic 2D chirality in multilayer achiral MMs, showing that giant chiroptical response can be alternatively attained without complex structures. Our structure consists of an array of thin Au squares separated from a continuous Au film by a GaAs dielectric layer, where the Au squares occupy the sites of a rectangular lattice. This structure gives rise to a pronounced extrinsically 2D-chiral effect (CCD) in the mid-infrared (M-IR) region under an oblique incidence, where the 2D-chiral effect is due to the mutual orientation of the Au squares array and the incident light propagation direction; the large magnitude of CCD due to the large difference between left-to-left and right-to-right circularly polarized reflectance conversion efficiencies.

New insights into the structure and mode of action of Mo-CBP3, an antifungal chitin-binding protein of Moringa oleifera seeds

Mo-CBP3 is a chitin-binding protein purified from Moringa oleifera Lam. seeds that displays inhibitory activity against phytopathogenic fungi. This study investigated the structural properties and the antifungal mode of action of this protein. To this end, circular dichroism spectroscopy, antifungal assays, measurements of the production of reactive oxygen species and microscopic analyses were utilized. Mo-CBP3 is composed of 30.3% α-helices, 16.3% β-sheets, 22.3% turns and 30.4% unordered forms. The Mo-CBP3 structure is highly stable and retains its antifungal activity regardless of temperature and pH. Fusarium solani was used as a model organism for studying the mechanisms by which this protein acts as an antifungal agent. Mo-CBP3 significantly inhibited spore germination and mycelial growth at 0.05 mg.mL-1. Mo-CBP3 has both fungistatic and fungicidal effects, depending on the concentration used. Binding of Mo-CBP3 to the fungal cell surface is achieved, at least in part, via electrostatic interactions, as salt was able to reduce its inhibitory effect. Mo-CBP3 induced the production of ROS and caused disorganization of both the cytoplasm and the plasma membrane in F. solani cells. Based on its high stability and specific toxicity, with broad-spectrum efficacy against important phytopathogenic fungi at low inhibitory concentrations but not to human cells, Mo-CBP3 has great potential for the development of new antifungal drugs or transgenic crops with enhanced resistance to phytopathogens.

Spectral properties and thermal stability of AS1411 G-quadruplex

G-quadruplexes are supramolecular structures of G-rich nucleic acid, formed by non-canonical base pairing in the presence of specific environmental inducers. These structures have been vastly considered in diagnostic and therapeutic applications. However, detailed information on structure, optical properties and thermal stability of G-quadruplex potent oligonucleotides is scarce. Herein, optical properties and thermodynamic stability of AS1411 quadruplex is reported for various concentrations of potassium and lead ions. Circular dichroism showed that AS1411 ss-DNA folds into parallel conformation in the presence of metal ions and molecular crowding condition. UV-vis spectroscopy indicated formation of quadruplex and fluorescent spectroscopy revealed intercalation of PicoGreen in its structure, with enhancement of emission intensity upon increment of metal ion concentration. This investigation also proposes high-throughput and reliable analysis of AS1411 quadruplex's thermal stability by real-time PCR technique, which can be further applied for other quadruplex structures.

Synthesis, characterization, DNA binding, cleavage activity and cytotoxicity of copper(II) complexes

Three new mononuclear copper(II) complexes, [Cu(L2)](2+) (1), [Cu(acac)(L)](+) (2), and [Cu(acac-Cl)(L)](+) (3) (L = 2-(4-pyridine)oxazo[4,5-f]1,10-phenanthroline (4-PDOP); acac = acetylacetone; acac-Cl = 3-chloroacetylacetone), have been synthesized and characterized by elemental analysis, high resolution mass spectrometry (Q-TOF), and IR spectroscopy. Two of the complexes were structurally characterized by single-crystal X-ray diffraction techniques. Their interactions with DNA were studied by UV-vis absorption and emission spectra, viscosity, thermal melting, DNA unwinding assay and CD spectroscopy. The nucleolytic cleavage activity of the compounds was carried out on double stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment in the presence and absence of an oxidant (H2O2). Active oxygen intermediates such as hydroxyl radicals and hydrogen peroxide generated in the presence of L and complexes 1-3 may act as active species for the DNA scission. The cytotoxicity of the complexes against HepG2 cancer cells was also studied.

An ALS-mutant TDP-43 neurotoxic peptide adopts an anti-parallel β-structure and induces TDP-43 redistribution

TDP-43 proteinopathies are clinically and genetically heterogeneous diseases that had been considered distinct from classical amyloid diseases. Here, we provide evidence for the structural similarity between TDP-43 peptides and other amyloid proteins. Atomic force microscopy and electron microscopy examination of peptides spanning a previously defined amyloidogenic fragment revealed a minimal core region that forms amyloid fibrils similar to the TDP-43 fibrils detected in FTLD-TDP brain tissues. An ALS-mutant A315E amyloidogenic TDP-43 peptide is capable of cross-seeding other TDP-43 peptides and an amyloid-β peptide. Sequential Nuclear Overhauser Effects and double-quantum-filtered correlation spectroscopy in nuclear magnetic resonance (NMR) analyses of the A315E-mutant TDP-43 peptide indicate that it adopts an anti-parallel β conformation. When added to cell cultures, the amyloidogenic TDP-43 peptides induce TDP-43 redistribution from the nucleus to the cytoplasm. Neuronal cultures in compartmentalized microfluidic-chambers demonstrate that the TDP-43 peptides can be taken up by axons and induce axonotoxicity and neuronal death, thus recapitulating key neuropathological features of TDP-43 proteinopathies. Importantly, a single amino acid change in the amyloidogenic TDP-43 peptide that disrupts fibril formation also eliminates neurotoxicity, supporting that amyloidogenesis is critical for TDP-43 neurotoxicity.

Recognition of bacterial lipopolysaccharide using bacteriophage-adhesin-coated long-period gratings

In this paper we present a new type of highly sensitive label-free sensor based on long-period gratings (LPG) coated with T4 bacteriophage (phage) adhesin. The adhesin (gp37) binds Escherichia coli B (E. coli B) by recognizing its bacterial lipopolysaccharide (LPS). The LPG biofunctionalization methodology is based on coating LPG surface with nickel ions capable of gp37 histidine tag reversible binding. For the first time recombinant adhesive phage protein has been used as a receptor molecule in biosensing scheme. The specificity of LPS binding by adhesin has been tested with LPG-based device and confirmed using Western blot, Enzyme-Linked Immunosorbent Assay (ELISA) and BIACORE methods. The LPG-based sensor can measure bacterial contamination in real time and with a high accuracy. We show that T4 phage adhesin binds E. coli B LPS in its native or denatured form. The binding is highly specific and irreversible. The applied procedure allows for obtaining reusable biosensors.

Unnatural amino acid mutagenesis reveals dimerization as a negative regulatory mechanism of VHR's phosphatase activity

Vaccinia H1-related (VHR) phosphatase is a dual specificity phosphatase that is required for cell-cycle progression and plays a role in cell growth of certain cancers. Therefore, it represents a potential drug target. VHR is structurally and biochemically well characterized, yet its regulatory principles are still poorly understood. Understanding its regulation is important, not only to comprehend VHR's biological mechanisms and roles but also to determine its potential and druggability as a target in cancer. Here, we investigated the functional role of the unique "variable insert" region in VHR by selectively introducing the photo-cross-linkable amino acid para-benzoylphenylalanine (pBPA) using the amber suppression method. This approach led to the discovery of VHR dimerization, which was further confirmed using traditional chemical cross-linkers. Phe68 in VHR was discovered as a residue involved in the dimerization. We demonstrate that VHR can dimerize inside cells, and that VHR catalytic activity is reduced upon dimerization. Our results suggest that dimerization could occlude the active site of VHR, thereby blocking its accessibility to substrates. These findings indicate that the previously unknown transient self-association of VHR acts as a means for the negative regulation of its catalytic activity.

Techniques for physicochemical characterization of nanomaterials

Advances in nanotechnology have opened up a new era of diagnosis, prevention and treatment of diseases and traumatic injuries. Nanomaterials, including those with potential for clinical applications, possess novel physicochemical properties that have an impact on their physiological interactions, from the molecular level to the systemic level. There is a lack of standardized methodologies or regulatory protocols for detection or characterization of nanomaterials. This review summarizes the techniques that are commonly used to study the size, shape, surface properties, composition, purity and stability of nanomaterials, along with their advantages and disadvantages. At present there are no FDA guidelines that have been developed specifically for nanomaterial based formulations for diagnostic or therapeutic use. There is an urgent need for standardized protocols and procedures for the characterization of nanoparticles, especially those that are intended for use as theranostics.

Synthesis, characterization, and biological activity of poly(arginine)-derived cancer-targeting peptides in HepG2 liver cancer cells

The solid-phase synthesis, structural characterization, and biological evaluation of a small library of cancer-targeting peptides have been determined in HepG2 hepatoblastoma cells. These peptides are based on the highly specific Pep42 motif, which has been shown to target the glucose-regulated protein 78 receptors overexpressed and exclusively localized on the cell surface of tumors. In this study, Pep42 was designed to contain varying lengths (3-12) of poly(arginine) sequences to assess their influence on peptide structure and biology. Peptides were effectively synthesized by 9-fluorenylmethoxycarbonyl-based solid-phase peptide synthesis, in which the use of a poly(ethylene glycol) resin provided good yields (14-46%) and crude purities >95% as analyzed by liquid chromatography-mass spectrometry. Peptide structure and biophysical properties were investigated using circular dichroism spectroscopy. Interestingly, peptides displayed secondary structures that were contingent on solvent and length of the poly(arginine) sequences. Peptides exhibited helical and turn conformations, while retaining significant thermal stability. Structure-activity relationship studies conducted by flow cytometry and confocal microscopy revealed that the poly(arginine) derived Pep42 sequences maintained glucose-regulated protein 78 binding on HepG2 cells while exhibiting cell translocation activity that was contingent on the length of the poly(arginine) strand. In single dose (0.15 mM) and dose-response (0-1.5 mM) cell viability assays, peptides were found to be nontoxic in human HepG2 liver cancer cells, illustrating their potential as safe cancer-targeting delivery agents.

Hp1404, a new antimicrobial peptide from the scorpion Heterometrus petersii

Antimicrobial peptides have attracted much interest as a novel class of antibiotics against a variety of microbes including antibiotics resistant strains. In this study, a new cationic antimicrobial peptide Hp1404 was identified from the scorpion Heterometrus petersii, which is an amphipathic α-helical peptide and has a specific inhibitory activity against gram-positive bacteria including methicillin-resistant Staphylococcus aureus. Hp1404 can penetrate the membrane of S. aureus at low concentration, and disrupts the cellular membrane directly at super high concentration. S. aureus does not develop drug resistance after multiple treatments with Hp1404 at sub MIC concentration, which is possibly associated with the antibacterial mechanism of the peptide. In addition, Hp1404 has low toxicity to both mammalian cells (HC₅₀  =  226.6 µg/mL and CC₅₀ > 100 µg/mL) and balb-c mice (Non-toxicity at 80 mg/Kg by intraperitoneal injection and LD₅₀  =  89.8 mg/Kg by intravenous injection). Interestingly, Hp1404 can improve the survival rate of the MRSA infected balb-c mice in the peritonitis model. Taken together, Hp1404 may have potential applications as an antibacterial agent.

Effect of ultrasound on the activity and conformation of α-amylase, papain and pepsin

The effect of ultrasound on the activity of α-amylase, papain and pepsin was investigated and the mechanism of the effect was explored by determining their conformational changes. With the irradiation of power ultrasound, the activity of α-amylase and papain was inhibited, while the activity of pepsin was activated. According to the analysis of circular dichroism, Fourier transform infrared and fluorescence spectroscopy, the πo → π(∗) amide transitions and secondary structural components, especially β-sheet, of these three enzymes were significantly influenced by ultrasound. The tryptophan fluorescence intensity of the three enzymes was also observed to be affected by sonication. Furthermore, it was found that the pepsin molecule might gradually be resistant to prolonged ultrasonic treatment and recover from the ultrasound-induced damage to its original structure. The results suggested that the activity of α-amylase, papain and pepsin could be modified by ultrasonic treatment mainly due to the variation of their secondary and tertiary structures.

Comparison between the behavior of different hydrophobic peptides allowing membrane anchoring of proteins

Membrane binding of proteins such as short chain dehydrogenase reductases or tail-anchored proteins relies on their N- and/or C-terminal hydrophobic transmembrane segment. In this review, we propose guidelines to characterize such hydrophobic peptide segments using spectroscopic and biophysical measurements. The secondary structure content of the C-terminal peptides of retinol dehydrogenase 8, RGS9-1 anchor protein, lecithin retinol acyl transferase, and of the N-terminal peptide of retinol dehydrogenase 11 has been deduced by prediction tools from their primary sequence as well as by using infrared or circular dichroism analyses. Depending on the solvent and the solubilization method, significant structural differences were observed, often involving α-helices. The helical structure of these peptides was found to be consistent with their presumed membrane binding. Langmuir monolayers have been used as membrane models to study lipid-peptide interactions. The values of maximum insertion pressure obtained for all peptides using a monolayer of 1,2-dioleoyl-sn-glycero-3-phospho-ethanolamine (DOPE) are larger than the estimated lateral pressure of membranes, thus suggesting that they bind membranes. Polarization modulation infrared reflection absorption spectroscopy has been used to determine the structure and orientation of these peptides in the absence and in the presence of a DOPE monolayer. This lipid induced an increase or a decrease in the organization of the peptide secondary structure. Further measurements are necessary using other lipids to better understand the membrane interactions of these peptides.