Binding of Cu(II) ions to peptides studied by fluorescence spectroscopy and isothermal titration calorimetry

Design, Synthesis, and Target Identification of Novel Phenylalanine Derivatives by Drug Affinity Responsive Target Stability (DARTS) in Xanthomonas oryzae pv Oryzae

The increasing resistance displayed by plant phytopathogenic bacteria to conventional pesticides has heightened the urgency for the exploration of novel antibacterial agents possessing distinct modes of action (MOAs). In this study, a series of novel phenylalanine derivatives with the unique structure of acylhydrazone dithioether have been designed and synthesized. Bioassay results demonstrated that most target compounds exhibited excellent in vitro antibacterial activity against Xanthomonas oryzae pv oryzae (Xoo) and Xanthomonas axonopodis pv citri (Xac). Among them, the EC50 values of L3, L4, L6, L21, and L22 against Xoo were 7.4, 9.3, 6.7, 8.9, and 5.1 μg/mL, respectively, superior to that of bismerthiazol (BT) and thiodiazole copper (TC) (41.5 and >100 μg/mL); the EC50 values of L3, L4, L5, L6, L7, L8, L20, L21, and L22 against Xac were 5.6, 2.5, 6.2, 4.1, 4.2, 6.4, 6.3, 3.6, and 5.2 μg/mL, respectively, superior to that of BT and TC (43.3 and >100 μg/mL). An unmodified drug affinity responsive target stability (DARTS) technology was used to investigate the antibacterial MOAs of active compound L22, and the 50S ribosomal protein L2 (RL2) as an unprecedented target protein in Xoo cells was first discovered. The target protein RL2 was then expressed and purified. Furthermore, the in vitro interactions by microscale thermophoresis (Kd = 0.050 μM) and fluorescence titration (Ka = 1.4 × 105 M-1) experiments also demonstrated a strong binding force between compound L22 and RL2. Overall, these results not only facilitate the development of novel antibacterial agents but also establish a reliable method for exploring the targets of bactericides.

Fluorescent dual-mode sensor for the determination of graphene oxide and catechin in environmental or food field

The novel fluorescent sensor is proposed in this work based on the competitive interactions between the known bioactive compounds, riboflavin and catechin, which act as guests, and graphene oxide (GO) material that acts as host. Specifically, this proposal is based on an indicator displacement assay which allows the detection of GO and catechin (fluorescence quenching of riboflavin signal by GO and increase in fluorescence by catechin on the GO-riboflavin system). Three GO structures with different lateral dimensions and thickness were synthesized and tested, being able to be the three differentiated depending on the attenuation capacity of the fluorescent signal that each one possesses. The environmental analytical control of GO is more and more important, being this method sensitive and selective in the presence of other potential interferent substances. On the other hand, the other sensing capacity of the sensor also allows the determination of catechin in food samples based on the formation of riboflavin-GO complex. It is a rapid, simple and non-expensive procedure. Thus, the same 2D nanomaterial (GO) is seen to play a double role in this sensing strategy (analyte and analytical tool for the determination of another compound).

Interface interaction between silica and organic macromolecule conditioned forward osmosis membranes: Insights into quantitative thermodynamics and dynamics

Silica scaling is a rising concern in forward osmosis membrane-based water treatment process. The coexistence of ubiquitous organic macromolecules causes complex silica scaling. The silica scaling mechanism on the surface of the organic conditioned membrane remains unclear. An integrated multi scale thermodynamic and dynamic approach was used in this study to provide in-depth insights into the binding effect at the interface between the silica and the organic conditioned membrane at the molecular level. Sodium alginate (SA) was used as the model polysaccharide, bovine serum albumin (BSA) and lysozyme (LYZ) were chosen as two oppositely charged proteins. The results show that the silica scaling degree of different organic conditioned membranes follows the order LYZ > BSA > SA. The binding strength between silica and organic macromolecules and the membrane surface charge are the major factors governing the degree of silica scaling. Quartz crystal microbalance with dissipation (QCM-D), isothermal titration calorimetry (ITC), and extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) model analyses were conducted to quantify the binding capacity of silica to the organic conditioned membrane. The LYZ conditioned membrane exhibits the highest affinity for silica adsorption, and electrostatic interaction was the main molecular interaction force. This study provides fresh insights into how silica and an organic conditioned membrane interact and induce silica scaling, providing new information on potential mechanisms and control strategies to prevent membrane scaling.

Metal-Peptide Complexes with Antimicrobial Potential for Cotton Fiber Protection

A study of the formation of copper (II) complexes with hemorphin peptide motifs in alkalic water solutions is presented. The effect of the peptide ligand on the complexing properties of the Cu (II) ion was quantified by giving the stoichiometry and stability of the complex compounds in the medium in which they are formed using voltammetric (cyclic) and spectral (UV-Vis and fluorimetric) analytical techniques. The resulting complexes were examined via IR spectroscopy to detect M-N and M-O oscillations and using the EPR approach in solution and in the solid phase to view the coordination and ligand binding regime. The possibility of the synergistic action of copper ions in the antivirus protection processes of cotton fibers coated in the same solvent with the newly obtained complex compounds was also investigated. One of the advantages is the formation of the complexes in an environment where the immobilization takes place, which contributes to increasing the efficiency of the process. The obtained results may serve as an aid for future more detailed biological studies of structure-activity relationships (SARs).

Progress in the Development of Biosensors Based on Peptide-Copper Coordination Interaction

Copper ions, as the active centers of natural enzymes, play an important role in many physiological processes. Copper ion-based catalysts which mimic the activity of enzymes have been widely used in the field of industrial catalysis and sensing devices. As an important class of small biological molecules, peptides have the advantages of easy synthesis, excellent biocompatibility, low toxicity, and good water solubility. The peptide-copper complexes exhibit the characteristics of low molecular weight, high tenability, and unique catalytic and photophysical properties. Biosensors with peptide-copper complexes as the signal probes have promising application prospects in environmental monitoring and biomedical analysis and diagnosis. In this review, we discussed the design and application of fluorescent, colorimetric and electrochemical biosensors based on the peptide-copper coordination interaction.

A novel amphiphilic oligopeptide induced the intrafibrillar mineralisation via interacting with collagen and minerals

Mineralised collagen fibrils constitute the basic building blocks of bone, dentin and cementum. Noncollagenous proteins (NCPs) that are indispensable for collagen biomineralisation are not commercially available, and the mechanism of intrafibrillar mineralisation remains debatable. Herein, synthetic biomimetic molecules are regarded as alternative candidates for NCPs, and more convenient in revealing the mechanism of intrafibrillar mineralisation in vitro. Here, we fabricated a novel amphiphilic oligopeptide imitating a natural NCP. We aimed to investigate the effectiveness of the oligopeptide in intrafibrillar mineralisation and partially reveal the corresponding mechanism in vitro. The effectiveness of the oligopeptide in intrafibrillar mineralisation was characterised from the following aspects: (1) mineral interaction, (2) collagen binding and (3) induction of intrafibrillar mineralisation. Results indicated that the self-assembled oligopeptide could attract calcium ions inducing the formation of amorphous precursors; and bind onto the surface of collagen fibrils. These processes were mainly driven by the electrostatic attraction and hydrogen bonds. The self-assembled oligopeptide induced the intrafibrillar mineralisation of reconstituted collagen fibrils, in which the c-axis of apatite crystallites was roughly parallel to the long axis of the fibrils. The collagen mineralisation was achieved by binding with the self-assembled oligopeptide to increase the pool of mineralization precursors available for intrafibrillar mineralisation. In addition, the self-assembled oligopeptide induced dentin collagen remineralisation and formed a 30 μm-thick remineralised layer within 96 h. Our work sheds light on the fabrication of a novel biomimetic molecule for collagen mineralisation. The results should serve as a reference for understanding the mechanism of intrafibrillar mineralisation.

Revealing the dynamics and energetics of interaction of a cationic biological photosensitizer within a bile salt aggregate

The present investigation reports a detailed characterization of the interaction of a cationic photosensitizer, phenosafranin (PSF) with sodium deoxycholate (NaDC) bile salt aggregates based on spectroscopic and calorimetric techniques. Our explicit spectroscopic results not only establish the occurrence of PSF-NaDC binding interaction, but also reveal marked lowering of micropolarity at the interaction site (E_T(30) = 55.97 kcal mol^-1 in the presence of NaDC as compared to E_T(30) = 63.1 kcal mol^-1 in bulk aqueous buffer). A thorough mathematical analysis of the fluorescence depolarization results based on the two-step and wobbling in cone model yields critical insight into the complex rotational relaxation dynamics of the bound drug. The impartation of motional restriction on the PSF molecules within the bile salt aggregates is evidenced from enhancement of average rotational correlation time from <τ_r> = 136 ps in aqueous buffer to 1.11 ns with added NaDC (8.0 mM). This is further supported from a high value of the generalized order parameter (S = 0.81) as well as the diffusion coefficient (D_w = 1.40 × 10¹² s^-1). Furthermore, our extensive calorimetric investigation unveils the complicated thermodynamics of the interaction process in terms of predominant entropic contribution over the enthalpic part in the lower temperature regime (TΔS = 18.84 ± 1.13 kJ mol^-1, ΔH = -5.82 ± 0.35 kJ mol^-1 at 288 K) with subsequent reversal of the relative contributions with increasing temperature (TΔS = 7.54 ± 0.39 kJ mol^-1, ΔH = - 17.09 ± 0.90 kJ mol^-1 at 318 K). The instrumental role of the hydrophobic effect underlying the PSF-NaDC interaction is characterized by a negative heat capacity change (ΔC_p = -364 J mol^-1 K^-1). An intriguing thermodynamic feature in terms of enthalpy-entropy compensation (with increasing temperature ΔG remains almost constant while ΔH and TΔS vary significantly) aptly corroborates the aforesaid argument and establishes an appreciable hydrophobic contribution to the overall binding energies.

Hg2+ and Cd2+ binding of a bioinspired hexapeptide with two cysteine units constructed as a minimalistic metal ion sensing fluorescent probe

Hg²⁺ and Cd²⁺ complexation of a short hexapeptide, Ac-DCSSCY-NH₂ (DY), was studied by pH-potentiometry, UV and NMR spectroscopy and fluorimetry in aqueous solutions and the Hg²⁺-binding ability of the ligand was also described in an immobilized form, where the peptides were anchored to a hydrophilic resin. Hg²⁺ was demonstrated to form a 1 : 1 complex with the ligand even at pH = 2.0 while Cd²⁺ coordination by the peptide takes place only above pH ∼ 3.5. Both metal ions form bis-ligand complexes by the coordination of four Cys-thiolates at ligand excess above pH ∼ 5.5 (Cd²⁺) and 7.0 (Hg²⁺). Fluorescence studies demonstrated a Hg²⁺ induced concentration-dependent quenching of the Tyr fluorescence until a 1 : 1 Hg²⁺ : DY ratio. The fluorescence emission intensity decreases linearly with the increasing Hg²⁺ concentration in a range of over two orders of magnitude. The fact that this occurs even in the presence of 1.0 eq. of Cd²⁺ per ligand reflects a complete displacement of the latter metal ion by Hg²⁺ from its peptide-bound form. The immobilized peptide was also shown to bind Hg²⁺ very efficiently even from samples at pH = 2.0. However, the existence of lower affinity binding sites was also demonstrated by binding of more than 1.0 eq. of Hg²⁺ per immobilized DY molecule under Hg²⁺-excess conditions. Experiments performed with a mixture of four metal ions, Hg²⁺, Cd²⁺, Zn²⁺ and Ni²⁺, indicate that this molecular probe may potentially be used in Hg²⁺-sensing systems under acidic conditions for the measurement of μM range concentrations.

Copper Binding Induces Nitration of NPY under Nitrative Stress: Complicating the Role of NPY in Alzheimer's Disease

Neuropeptide Y (NPY) is a 36 amino acid peptide that regulates a multitude of physiological functions in the central nervous system and has been shown to be involved in Alzheimer's disease (AD). A change in copper homeostasis is a remarkable feature of AD, and the dysregulation may contribute to toxicity in neural cells. Moreover, it has been shown that copper could interact with many neuropeptides and result in catalyzing the production of reactive oxygen species, which may lead to peptide oxidation. Besides, copper could also catalyze protein tyrosine nitration under oxidative stress, and there are two tyrosine residues playing an important role in NPY. Therefore, it is also likely that copper has an action on NPY and potentially influences its functions through tyrosine nitration. In this paper, the studies of the interaction of copper with NPY and the copper-catalyzed NPY nitration were performed. The electrochemical techniques, UV-vis spectroscopy, mass spectrometry, and fluorescence titration, have been applied to show that copper can interact with NPY to form a Cu-NPY complex with a conditional dissociation constant of 0.021 μmol/L, and the binding promotes the generation of •OH. Dot blotting results reveal that NPY can be nitrated upon binding with copper under nitrative stress. Furthermore, liquid chromatography-mass spectrometry (LC-MS) identify that the tyrosine residues in NPY are all nitrated during the nitration process, which will cause the inactivation of NPY shown by our previous study. This study supports the hypothesis that copper has a close correlation with NPY and implicates the peptide in AD. These data may provide a new insight into understanding the pathology and pathogenesis of AD.

Copper(II) complexation by fragment of central part of FBP28 protein from Mus musculus

Steady-state and time-resolved fluorescence spectroscopy, UV spectrophotometry and isothermal titration calorimetry techniques were used to study the coordinating properties of the 17aa peptide fragment (D17) derived from the central part of the mouse formin binding protein (FBP28 with the PDB code: 1E0L) towards Cu²⁺ ions. All the measurements were run in the 2-(N-morpholino)ethanesulfonic acid buffer (20 mM, pH 6.0). Under experimental conditions the formation of the 1:1 complex of Cu²⁺ ions with D17 is an entropy-driven process. Cu²⁺ ions cause the static fluorescence quenching of the peptide studied through the formation of a non-fluorescent complex. Furthermore, the thermal stability of D17 was discussed based on the results obtained from differential scanning fluorimetry (nanoDSF) data.

NPY binds with heme to form a NPY–heme complex: enhancing peroxidase activity in free heme and promoting NPY nitration and inactivation

NPY binding with heme enhances the peroxidase activity of free heme, resulting in the important tyrosine nitration, which will attenuate its bioactivity.

Probing the binding of Cu(2+) ions to a fragment of the Aβ(1-42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations

Steady-state and time-resolved fluorescence quenching measurements supported by isothermal titration calorimetry (ITC) and molecular dynamics simulations (MD), with the NMR-derived restraints, were used to investigate the interactions of Cu(2+) ions with a fragment of the Aβ(1-42) polypeptide, Aβ(5-16) with the following sequence: Ac-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-NH2, denoted as HZ1. The studies presented in this paper, when compared with our previous results (Makowska et al., Spectrochim. Acta A 153: 451-456), show that the affinity of the peptide to metal ions is conformation-dependent. All the measurements were carried out in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution, pH6.0. The Stern-Volmer equations, along with spectroscopic observations, were used to determine the quenching and binding parameters. The obtained results unequivocally suggest that Cu(2+) ions quench the fluorescence of HZ1 only through a static quenching mechanism, in contrast to the fragment from the N-terminal part of the FPB28 protein, with sequence Ac-Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr- NH2 (D9) and its derivative with a single point mutation: Ac-Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr- NH2 (D9_M), where dynamic quenching occurred. The thermodynamic parameters (ΔITCH, ΔITCS) for the interactions between Cu(2+) ions and the HZ1 peptide were determined from the calorimetric data. The conditional thermodynamic parameters suggest that, under the experimental conditions, the formation of the Cu(2+)-HZ1 complex is both an enthalpy and entropy driven process.

Recognition of diamond with phage display peptides

We show for the first time the identification of diamond-binding peptide motifs for diamond with phage display.