Phosphorylation‐Responsive Membrane Transport of Peptides

Phosphorylation and dephosphorylation of peptides by kinases and phosphatases is essential for signal transduction in biological systems, and many diseases involve abnormal activities of these enzymes. Herein, we introduce amphiphilic calixarenes as key components for supramolecular, phosphorylation‐responsive membrane transport systems. Dye‐efflux experiments with liposomes demonstrated that calixarenes are highly active counterion activators for established cell‐penetrating peptides, with EC₅₀ values in the low nanomolar range. We have now found that they can even activate membrane transport of short peptide substrates for kinases involved in signal transduction, whereas the respective phosphorylated products are much less efficiently transported. This allows regulation of membrane transport activity by protein kinase A (PKA) and protein kinase C (PKC), as well as monitoring of their activity in a label‐free kinase assay.     

Quantitation of protein orientation in flow-oriented unilamellar liposomes by linear dichroism

The linear dichroism of the visible wavelength transitions of retinal have been used to analyse linear dichroism spectra to determine the orientation of aromatic and peptide structural motifs of Bacteriorhodopsin incorporated into unilamellar soy bean liposomes. The results are consistent with the available X-ray data. This proves that visible light absorbing chromophores can be used to analyse linear dichroism data to give the orientation of membrane proteins in membrane mimicking environments. The work has been extended by screening a wide range of hydrophobic molecules with high extinction coefficients in transitions above 300 nm to find molecules that could be used as independent probes of liposome orientation for experiments involving proteins incorporated into liposomes. Three probes were found to have potential for future work: bis-(1,3-dibutylbarbituric acid)pentamethine oxonol (DiBAC₄), retinol and rhodamine B. All three can be used to determine the orientation of the porphyrin of cytochrome c, the aromatic residues of gramicidin and the helices of both proteins. The orientation parameter, S, for the liposomes varied from batch to batch of unilamellar liposomes prepared by extruding through a 100 nm membrane. The value and variation in S was 0.030 ± 0.010. Repeat experiments with the same batch of liposomes showed less variation. Film LD data were measured for DiBAC₄ and rhodamine B to determine the polarisations of their long wavelength transitions.     

Ratiometric Fluorescent Nanosensors for Copper(II) Based on Bis(rhodamine)‐Derived PMOs with J‐Type Aggregates

By using pentyl‐linked bis(rhodamine)‐derived tetra‐siloxane (PRh‐Si₄) as the organosilica precursor, highly ordered PRh‐bridged periodic mesoporous organosilicas (PRhPMOs) were prepared. When excited at λ=500 nm, the PRhPMO suspension that contained metal ions showed two separate emission peaks at λ=550 and 623 nm. The first peak, located at λ=550 nm, was due to ring‐opening of the spiro structure in the rhodamine moiety and the second, located at λ=623 nm, originated from fluorescent aggregates of the PRh units embedded in the silica framework of the PRhPMO. By using the different intensity ratios of the two fluorescence signals (FI_550/623), PRhPMOs could be used as turn‐ON type fluorescent ratiometric chemosensors for Cu²⁺. Furthermore, based on the single‐exciton theory, it was deduced that the fluorescent aggregates formed were of the J‐type and had a coplanar configuration. Consequently, PRhPMOs display a longer fluorescence lifetime and greater fluorescent quantum yield than the respective monomers dissolved in solution, which is consistent with the experimental results.     

A pH optical and fluorescent sensor based on rhodamine modified on activated cellulose paper

A rhodamine‐based colorimetric and fluorescent pH chemosensor ( RhA ) was designed and synthesized via a coupling reaction between rhodamine ethylenediamine and succinic anhydride. RhA showed excellent pH response in aqueous solutions. In addition, common cations (Na⁺, K⁺, Ag⁺, Mg²⁺, Ca²⁺, Pb²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, Hg²⁺, Al³⁺, Cr³⁺, Fe³⁺, Au³⁺, Pt²⁺, and Ru²⁺) did not interfere with the pH response. As it has the potential to be used as a portable pH sensor, RhA was immobilized on activated cellulose paper using N,N'‐dicyclohexylcarbodiimide (DCC) and N,N'‐dimethylpyridin‐4‐amine (DMAP) as the coupling reagent to obtain a composite pH sensor ( CP‐RhA ). CP‐RhA was characterized by ATR‐FTIR, UV–vis, and fluorescence spectroscopy, and by scanning electron microscopy (SEM). CP‐RhA showed a rapid response in the pH range 1–8 through color and fluorescence changes. DFT calculations showed a blue‐shifted spectrum in the protonated form compared to the neutral form. Moreover, the pH sensor paper could be reused by dipping in NaOH. Thus, our work demonstrates the potential of the rhodamine dye composite for visualizing pH changes in real systems.     

Directional Potassium Transport through a Unimolecular Peptide Channel

Three unimolecular peptide channels have been designed and prepared by using the β‐helical conformation of gramicidin A (gA). The new peptides bear one to three NH₃⁺ groups at the N‐end and one to three CO₂^? groups at the C‐end. These zwitterionic peptides were inserted into lipid bilayers in an orientation‐selective manner. Conductance experiments on planar lipid bilayers showed that this orientation bias could lead to observable directional K⁺ transport under multi‐channel conditions. This directional transport behavior can further cause the generation of a current across a planar bilayer without applying a voltage. More importantly, in vesicles with identical external and internal KCl concentrations, the channels can pump K⁺ across the lipid bilayer and cause a membrane potential.     

A new rhodamine B-based lysosomal pH fluorescent indicator

We designed and synthesized a new pH fluorescent probe, RCE, based on structural changes of rhodamine dye at different pH values. The probe exhibits high selectivity, high sensitivity and quick response to acidic pH, as well as low cytotoxicity, excellent photostability, reversibility and cell membrane permeability. Fluorescence intensity at 584 nm was increased more than 150-fold within pH range 7.51–3.53. This probe has pK_a value 4.71, which is valuable for studying acidic organelles. Because of its long absorption and emission wavelengths, RCE can avoid associated cell damage. The probe can selectively stain lysosomes and monitor lysosomal pH changes in living cells.     

The Antiproliferative and Apoptotic Effect of a Novel Synthesized S-Triazine Dipeptide Series,and Toxicity Screening in Zebrafish Embryos

Several derivatives containing morpholine/piperidine, anilines, and dipeptides as pending moieties were prepared using s-triazine as a scaffold. These compounds were evaluated for their anticancer activity against two human breast cancer cell lines (MCF-7 and MDA-MB-231), a colon cancer cell line (HCT-116), and a non-tumorigenic cell line (HEK 293). Tamoxifen was used as a reference. Animal toxicity tests were carried out in zebrafish embryos. Most of these compounds showed a higher activity against breast cancer than colon cancer. Compound 3a—which contains morpholine, aniline, and glycylglycinate methyl ester—showed a high level of cytotoxicity against MCF-7 cells with IC₅₀ values of less than 1 µM. This compound showed a much lower level of toxicity against the non-tumorigenic HEK-293 cell line, and in the in vivo studies using zebrafish embryos. Furthermore, it induced cell cycle arrest at the G2/M phase, and apoptosis in MCF-7 cells. On the basis of our results, 3a emerges as a potential candidate for further development as a therapeutic drug to treat hormone receptor-positive breast cancer.     

Quantitative Monitoring and Visualization of Hydrogen Sulfide In Vivo Using a Luminescent Probe Based on a Ruthenium(II) Complex

Development of novel bioanalytical methods for monitoring of H₂S is key toward understanding the physiological and pathological functions of this gasotransmitter in live organisms. A ruthenium(II)‐complex‐based luminescence probe, Ru‐MDB (MDB: 4’‐methyl‐[2,2’‐bipyridine]‐4‐yl)methyl 2‐((2,4‐dinitrophenyl)thio)benzoate), was developed by introducing a new H₂S responsive masking moiety to a red‐emitting Ru^II luminophore. Cleavage of this masking group by a H₂S‐triggered reaction leads to a luminescence “off–on” response. The long‐lived emissions of Ru‐MDB and its reaction product with H₂S allowed quantitative detection of H₂S in autofluorescence‐rich human sera and adult zebrafish organs using the time‐gated luminescence mode. Ru‐MDB exhibits red emission, a large Stokes shift, high specificity and sensitivity for H₂S detection, and low cytotoxicity, which enables imaging and flow cytometry analysis of lysosomal H₂S generation in live inflamed cells under drug stimulation. Monitoring of H₂S in live Daphnia magna, zebrafish embryos, adult zebrafish, and mice, was conducted by in vivo imaging using Ru‐MDB as a probe.     

Deformylated Gramicidin A and Its Derivatives Showing High Antimicrobial Activity and Low Hemolytic Toxicity

Gramicidin A is a natural peptide, which shows high antimicrobial activity to Gram‐positive bacteria. However, the hemolytic toxicity prevents its therapeutic usage. We demonstrated that by simply removing the formyl group at the N terminus, the hemolytic toxicity of the peptide could be obviously decreased. The deformylated gramicidin A ( 1 ) could efficiently insert into the lipid bilayer to form transmembrane channels. The peptide can also selectively insert into the membrane of Gram‐positive bacteria but not that of erythrocytes, leading to its high antimicrobial activity and very low hemolytic toxicity. The derivation of 1 could be achieved by decoration at the terminal NH₂ group, which also produced peptides showing high activity and low hemolytic toxicity. This derivation method provided us with an efficient strategy to build a library for future activity and cytotoxicity screening in vitro and in vivo.     

New Fluorinated Rhodamines for Optical Microscopy and Nanoscopy

New photostable rhodamine dyes represented by the compounds 1 a – r and 3 – 5 are proposed as efficient fluorescent markers with unique combination of structural features. Unlike rhodamines with monoalkylated nitrogen atoms, N′,N‐bis(2,2,2‐trifluoroethyl) derivatives 1 e , 1 i , 1 j , 3 ‐H and 5 were found to undergo sulfonation of the xanthene fragment at the positions 4′ and 5′. Two fluorine atoms were introduced into the positions 2′ and 7′ of the 3′,6′‐diaminoxanthene fragment in compounds 1 a – d , 1 i – l and 1 m – r . The new rhodamine dyes may be excited with λ=488 or 514 nm light; most of them emit light at λ=512–554 nm (compounds 1 q and 1r at λ=576 and 589 nm in methanol, respectively) and have high fluorescence quantum yields in solution (up to 98 %), relatively long excited‐state lifetimes (>3 ns) and are resistant against photobleaching, especially at high laser intensities, as is usually applied in confocal microscopy. Sulfonation of the xanthene fragment with 30 % SO₃ in H₂SO₄ is compatible with the secondary amide bond (rhodamine‐CON(Me)CH₂CH₂COOH) formed with MeNHCH₂CH₂COOCH₃ to providing the sterically unhindered carboxylic group required for further (bio)conjugation reactions. After creating the amino reactive sites, the modified derivatives may be used as fluorescent markers and labels for (bio)molecules in optical microscopy and nanoscopy with very‐high light intensities. Further, the new rhodamine dyes are able to pass the plasma membrane of living cells, introducing them as potential labels for recent live‐cell‐tag approaches. We exemplify the excellent performance of the fluorinated rhodamines in optical microscopy by fluorescence correlation spectroscopy (FCS) and stimulated emission depletion (STED) nanoscopy experiments.     

Synthesis,chemical reactivity,and photophysical properties of 2′,7′ phenylated rhodamine dyes

While exploring water soluble rhodamine based fluorescent polymeric systems for biological imaging applications we came across new rhodamine derivatives that possess interesting optical properties. We report the synthesis of three different 2′,7′-diphenylated rhodamine derivatives (1–3) with distinct photophysical properties. The three rhodamine derivatives differ by the number of methyl groups present on the nitrogens and their absorption maxima are red-shifted on increased methylation. We observed an unusual inertness of these compounds toward traditional DCC–DMAP esterification conditions, which we attribute to the ease of lactonization in the presence of even minute amounts of the nucleophile/base DMAP (pK_a = 9.2). Synthesis of acrylate esters was successfully accomplished using MSNT (1-(Mesitylene-2-sulfonyl)-3-nitro-1,2,4-triazole) coupling conditions using a much milder nucleophile/base, for example, N-methyl imidazole (pK_a = 6.95).     

Enantiomeric Cyclic Peptides with Different Caco‐2 Permeability Suggest Carrier‐Mediated Transport

Recently, oral absorption of cyclic hexapeptides was improved by N‐methylation of their backbone amides. However, the number and position of N‐methylations or of solvent exposed NHs did not correlate to intestinal permeability, measured in a Caco‐2 model. In this study, we investigate enantiomeric pairs of three polar and two lipophilic peptides to demonstrate the participation of carrier‐mediated transporters. As expected, all the enantiomeric peptides exhibited identical lipophilicity (logD_7.4) and passive transcellular permeability determined by the parallel artificial membrane permeability assay (PAMPA). However, the enantiomeric polar peptides exhibited different Caco‐2 permeability (P_app) in both directions a–b and b–a. The same trend was observed for one of the lipophilic peptide, whereas the second lipophilic enantiomer pair showed identical Caco‐2 permeability (within the errors). These findings provide the first evidence for the involvement of carrier‐mediated transport for peptides, especially for those of polar nature.     

The ion transfer of the basic dye rhodamine B across the liquid-liquid interface of two immiscible solvents

The ion transfer of the basic dye rhodamine B at the interface between water and nitrobenzene, water and 1, 2-dichloroethane, as well as water and nitrobenzene - chlorobenzene mixtures has been studied by cyclic voltammetry and chronopotentiometry with linear current scanning. A transfer mechanism of rhodamine B is proposed in terms of its electrochemical behavior, dissociation and distribution equilibria, and is ascribed as diffusion-controlled reversible process of rhodamine B. The experimental data obtained for the relationship between interracial half-wave potential Δ^W_oφ° and pH are in agreement with the theoretical equation based on the mechanism, and the standard interfacial potential differences Δ^W_oφ° and standard Gibbs energies Δ^W_oG° are calculated by extrapolation. The effect of the nature of solvent on the transfer behavior and the stability of the interface have been discussed.     

Global proteomic analysis of lysine acetylation in zebrafish (Danio rerio) embryos

Lysine acetylation is an important post‐translational modification (PTM). Since the development of MS‐based proteomics technology, important roles of lysine acetylation beyond histones have focused on chromatin remodeling during the cell cycle and regulation of nuclear transport, metabolism, and translation. Zebrafish (Danio rerio) is a widely used vertebrate model in genetics and biologic studies. Although studies in several mammalian species have been performed, the mechanism of lysine acetylation in D. rerio embryos is incompletely understood. Here, we investigated the global acetylome in D. rerio embryos by using an MS‐based proteomics approach. We identified 351 acetylated peptides and 377 nonredundant acetylation sites on 189 lysine‐acetylated proteins in 5‐day postfertilization (hpf) embryos of D. rerio. Among lysine‐acetylated peptides, 40.2% indicated three motifs: (ac)KxxxK, (ac)KxxxxK, and Lx(ac)K. Of 190 acetylated proteins, 81 (42.6%) were mainly distributed in the cytoplasm. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that lysine acetylation in D. rerio was enriched in metabolic pathways. Additionally, 17 of 30 acetylated ribosomal proteins were evolutionarily conserved between zebrafish and humans. Our results indicate that acetyllysine might have regulatory effects on ribosomal proteins involved in protein biosynthesis.     

Efficient Access to Enantiopure γ4‐Amino Acids with Proteinogenic Side‐Chains and Structural Investigation of γ4‐Asn and γ4‐Ser in Hybrid Peptide Helices

Hybrid peptides composed of α‐ and β‐amino acids have recently emerged as new class of peptide foldamers. Comparatively, γ‐ and hybrid γ‐peptides composed of γ⁴‐amino acids are less studied than their β‐counterparts. However, recent investigations reveal that γ⁴‐amino acids have a higher propensity to fold into ordered helical structures. As amino acid side‐chain functional groups play a crucial role in the biological context, the objective of this study was to investigate efficient synthesis of γ⁴‐residues with functional proteinogenic side‐chains and their structural analysis in hybrid‐peptide sequences. Here, the efficient and enantiopure synthesis of various N‐ and C‐terminal free‐γ⁴‐residues, starting from the benzyl esters (COOBzl) of N‐Cbz‐protected (E)‐α,β‐unsaturated γ‐amino acids through multiple hydrogenolysis and double‐bond reduction in a single‐pot catalytic hydrogenation is reported. The crystal conformations of eight unprotected γ⁴‐amino acids (γ⁴‐Val, γ⁴‐Leu, γ⁴‐Ile, γ⁴‐Thr(OtBu), γ⁴‐Tyr, γ⁴‐Asp(OtBu), γ⁴‐Glu(OtBu), and γ‐Aib) reveals that these amino acids adopted a helix favoring gauche conformations along the central C^γ? C^β bond. To study the behavior of γ⁴‐residues with functional side chains in peptide sequences, two short hybrid γ‐peptides P1 (Ac‐Aib‐γ⁴‐Asn‐Aib‐γ⁴‐Leu‐Aib‐γ⁴‐Leu‐CONH₂) and P2 (Ac‐Aib‐γ⁴‐Ser‐Aib‐γ⁴‐Val‐Aib‐γ⁴‐Val‐CONH₂) were designed, synthesized on solid phase, and their 12‐helical conformation in single crystals were studied. Remarkably, the γ⁴‐Asn residue in P1 facilitates the tetrameric helical aggregations through interhelical H bonding between the side‐chain amide groups. Furthermore, the hydroxyl side‐chain of γ⁴‐Ser in P2 is involved in the interhelical H bonding with the backbone amide group. In addition, the analysis of 87 γ⁴‐residues in peptide single‐crystals reveal that the γ⁴‐residues in 12‐helices are more ordered as compared with the 10/12‐ and 12/14‐helices.     

Design and Synthesis of Nucleoproline Amino Acids for the Straightforward Preparation of Chiral and Conformationally Constrained Nucleopeptides

A straightforward synthesis of orthogonally protected nucleoproline (Nup) amino acids and their coupling to oligomers are described. A key step is the attachment of alkynylated nucleobases to Fmoc‐protected 4‐azidoproline (Fmoc‐Azp‐OH) by a Cu‐catalyzed 1,3‐dipolar cycloaddition (‘click reaction’). The developed protocol allows preparation of the nucleoprolines in scales of >30 g. Solid‐phase peptide synthesis proved to be straightforward with these Nup amino acids. The resulting oligonucleoproline peptides adopt defined helices, are very well H₂O soluble, and show comparable cell‐penetrating properties as recently reported α‐nucleoalanine peptides.     

A new and sensitive resonance-scattering method for determination of trace nitrite in water with rhodamine 6G

In the medium HCl–KI–rhodamine dye, NO₂^– reacts with excess I^– to form I₃^– and the I₃^– and rhodamine dye combine to form an association particle which gives three resonance-scattering (RS) peaks at 320 nm, 400 nm, and 595 nm. In systems containing rhodamine 6G (Rh6G), rhodamine B (RhB), rhodamine S (RhS), and butyl rhodamine B (BRhB) the resonance scattering intensity at 400 nm is proportional to nitrite concentrations in the range 2.3–276 ng mL^–1, 9.2–184 ng mL^–1, 9.2–184 ng mL^–1, and 9.2–92 ng mL^–1, respectively. Because of the high sensitivity, wide linear range, and good stability of the Rh6G system, it has been used for determination of nitrite in water samples, with satisfactory results. The spectral results have been used to verify that the formation of (Rh6G·I₃)_n association particles and their interface with the system are main factors that cause the RS enhancement.     

Clickable functionalization of liposomes with the gH625 peptide from Herpes simplex virus type I for intracellular drug delivery

Liposomes externally modified with the nineteen residues gH625 peptide, previously identified as a membrane‐perturbing domain in the gH glycoprotein of Herpes simplex virus type I, have been prepared in order to improve the intracellular uptake of an encapsulated drug. An easy and versatile synthetic strategy, based on click chemistry, has been used to bind, in a controlled way, several copies of the hydrophobic gH625 peptide on the external surface of 1,2‐dioleoyl‐sn‐glycero‐3‐phosphocholine (DOPG)‐based liposomes. Electron paramagnetic resonance studies, on liposomes derivatized with gH625 peptides, which are modified with the 2,2,6,6‐tetramethylpiperidine‐1‐oxyl‐4‐amino‐4‐carboxylic acid (TOAC) spin label in several peptide positions, confirm the positioning of the coupled peptides on the liposome external surface, whereas dynamic light scattering measurements indicate an increase of the diameter of the liposomes of approximately 30 % after peptide introduction. Liposomes have been loaded with the cytotoxic drug doxorubicin and their ability to penetrate inside cells has been evaluated by confocal microscopy experiments. Results suggest that liposomes functionalized with gH625 may act as promising intracellular targeting carriers for efficient delivery of drugs, such as chemotherapeutic agents, into tumor cells.     

Conformational Dynamics of Sensory Rhodopsin II in Nanolipoprotein and Styrene–Maleic Acid Lipid Particles

Styrene–maleic acid lipid particles (SMALPs) provide stable water‐soluble nanocontainers for lipid‐encased membrane proteins. Possible effects of the SMA‐stabilized lipid environment on the interaction dynamics between functionally coupled membrane proteins remain to be elucidated. The photoreceptor sensory rhodopsin II, NpSRII and its cognate transducer, NpHtrII, of Natronomonas pharaonis form a transmembrane complex, NpSRII₂/NpHtrII₂ that plays a key role in negative phototaxis and provides a unique model system to study the light‐induced transfer of a conformational signal between two integral membrane proteins. Photon absorption induces transient structural changes in NpSRII comprising an outward movement of helix F that cause further conformational alterations in NpHtrII. We applied site‐directed spin labeling and time‐resolved optical and EPR spectroscopy to compare the conformational dynamics of NpSRII₂/NpHtrII₂ reconstituted in SMALPs with that of nanolipoprotein particle and liposome preparations. NpSRII and NpSRII₂/NpHtrII₂ show similar photocycles in liposomes and nanolipoprotein particles. An accelerated decay of the M photointermediate found for SMALPs can be explained by a high local proton concentration provided by the carboxylic groups of the SMA polymer. Light‐induced large‐scale conformational changes of NpSRII₂/NpHtrII₂ observed in liposomes and nanolipoprotein particles are affected in SMALPs, indicating restrictions of the protein's conformational freedom.