Membrane structure and internalization dynamics of human Flower isoforms hFWE3 and hFWE4 indicate a conserved endocytic role for hFWE4.

Human Flower (hFWE) isoforms hFWE1-4 are putative transmembrane (TM) proteins that reportedly mediate fitness comparisons during cell competition through extracellular display of their C-terminal tails. Isoform topology, subcellular localization, and duration of plasma membrane presentation are essential to this function. However, disagreement persists regarding the structure of orthologous fly and mouse FWEs, and experimental evidence for hFWE isoform subcellular localization or membrane structure is lacking. Here, we used AlphaFold2 and subsequent molecular dynamics-based structural predictions to construct epitope-tagged hFWE3 and hFWE4, the most abundant human isoforms, for experimental determination of their structure and internalization dynamics. We demonstrate that hFWE3 resides in the membrane of the endoplasmic reticulum (ER), while hFWE4 partially colocalizes with Rab4-, Rab5-, and Rab11-positive vesicles as well as with the plasma membrane. An array of imaging techniques revealed that hFWE4 positions both N- and C-terminal tails and a loop between second and third TM segments within the cytosol, while small (4-12aa) loops between the first and second and the third and fourth TM segments are either exposed to the extracellular space or within the lumen of cytoplasmic vesicles. Similarly, we found hFWE3 positions both N- and C-terminal tails in the cytosol, while a short loop between TM domains extends into the ER lumen. Finally, we demonstrate that hFWE4 exists only transiently at the cell surface and is rapidly internalized in an AP-2- and dynamin-1-dependent manner. Collectively, these data are consistent with a conserved role for hFWE4 in endocytic processes.

The Development of CDC25A-Derived Phosphoseryl Peptides That Bind 14-3-3ε with High Affinities.

Overexpression of the 14-3-3ε protein is associated with suppression of apoptosis in cutaneous squamous cell carcinoma (cSCC). This antiapoptotic activity of 14-3-3ε is dependent on its binding to CDC25A; thus, inhibiting 14-3-3ε - CDC25A interaction is an attractive therapeutic approach to promote apoptosis in cSCC. In this regard, designing peptide inhibitors of 14-3-3ε - CDC25A interactions is of great interest. This work reports the rational design of peptide analogs of pS, a CDC25A-derived peptide that has been shown to inhibit 14-3-3ε-CDC25A interaction and promote apoptosis in cSCC with micromolar IC50. We designed new peptide analogs in silico by shortening the parent pS peptide from 14 to 9 amino acid residues; then, based on binding motifs of 14-3-3 proteins, we introduced modifications in the pS(174-182) peptide. We studied the binding of the peptides using conventional molecular dynamics (MD) and steered MD simulations, as well as biophysical methods. Our results showed that shortening the pS peptide from 14 to 9 amino acids reduced the affinity of the peptide. However, substituting Gln176 with either Phe or Tyr amino acids rescued the binding of the peptide. The optimized peptides obtained in this work can be candidates for inhibition of 14-3-3ε - CDC25A interactions in cSCC.

Probing Intermolecular Interactions within the Amyloid ß Trimer Using a Tethered Polymer Nanoarray.

Amyloid oligomers are considered the most neurotoxic species of amyloid aggregates. Spontaneous assembly of amyloids into aggregates is recognized as a major molecular mechanism behind Alzheimer's disease and other neurodegenerative disorders involving protein aggregation. Characterization of such oligomers is extremely challenging but complicated by their transient nature. Previously, we introduced a flexible nanoarray (FNA) method enabling us to probe dimers assembled by the amyloid ß (14-23) [Aß (14-23)] peptide. The study presented herein modifies and enhances this approach to assemble and probe trimers of Aß (14-23). A metal-free click chemistry approach was used, in which dibenzocyclooctyne (DBCO) groups were incorporated at selected sites within the FNA template to click Aß (14-23) monomers at their terminal azide groups. Atomic force microscopy (AFM) force spectroscopy was employed to characterize the assemblies. The force measurement data demonstrate that the dissociation of the trimer undergoes a stepwise pattern, in which the first monomer dissociates at the rupture force ∼48 ± 2.4 pN. The remaining dimer ruptures at the second step at a slightly larger rupture force (∼53 ± 3.2 pN). The assembled trimer was found to be quite dynamic, and transient species of this inherently dynamic process were identified.

Single-molecule probing of amyloid nano-ensembles using the polymer nanoarray approach.

Soluble amyloid-beta (Aß) oligomers are the prime causative agents of cognitive deficits during early stages of Alzheimer's disease (AD). The transient nature of the oligomers makes them difficult to characterize by traditional techniques, suggesting that advanced approaches are necessary. Previously developed fluorescence-based tethered approach for probing intermolecular interactions (TAPIN) and AFM-based single-molecule force spectroscopy are capable of probing dimers of Aß peptides. In this paper, a novel polymer nanoarray approach to probe trimers and tetramers formed by the Aß(14-23) segment of Aß protein at the single-molecule level is applied. By using this approach combined with TAPIN and AFM force spectroscopy, the impact of pH on the assembly of these oligomers was characterized. Experimental results reveal that pH affects the oligomer assembly process. At neutral pH, trimers and tetramers assemble into structures with a similar stability, while at acidic conditions (pH 3.7), the oligomers adopt a set of structures with different lifetimes and strengths. Models for the assembly of Aß(14-23) trimers and tetramers based on the results obtained is proposed.

A concentration dependent auto-relay-recognition by the same analyte: a dual fluorescence switch-on by hydrogen sulfide via Michael addition followed by reduction and staining for bio-activity.

H2S is shown, for the first time, to play an extraordinary dual role due to its nucleophilicity and reducing property with our single chemosensor, PND [4-(piperidin-1-yl) naphthalene-1,2-dione]. The initial nucleophilic attack via Michael addition (a lower concentration of H2S, blue fluorescence) is followed by the reduction of the 1,2-diketo functionality (a higher concentration of H2S, green fluorescence). This chemosensor, which also shows biological response, is remarkably effective in sensing the same analyte (H2S) at its different concentrations in a relay pathway via a fluorescence "off-on-on" mechanism, and this is also supported by DFT calculation and Cyclic voltammograms.

Rapid detection of hydrazine in a naphthol-fused chromenyl loop and its effectiveness in human lung cancer cells: tuning remarkable selectivity via the reaction altered pathway supported by theoretical studies.

Our designed and synthesized chemosensor naphthalene based chromenyl derivative (NAC) [1-(3-hydroxy-3 methyl-3H-benzo[f]chromen-2-yl) ethanone] has been used for fast (<30 s, DL = 0.22 ppb) and selective detection of N2H4 by a new way via the chromenyl ring opening followed by the pyrazole ring formation giving a strong blue fluorescence. The DFT study and the real application in different water samples along with the dipstick method in low cost devices have also been performed here. Human lung cancer cells (NCI-H460) have been used for hydrazinolysis of the NAC in vivo system for detection by the appearance of blue fluorescence and also for the MTT assay showing its remarkable cancer sensitivity.

Elucidating the mechanism of interaction between peptides and inorganic surfaces.

Understanding the mechanism of interaction between peptides and inorganic materials is of high importance for the development of new composite materials. Here, we combined an experimental approach along with molecular simulations in order to gain insights into this binding process. Using single molecule force spectroscopy by atomic force microscopy and molecular simulations we studied the binding of a peptide towards an inorganic substrate. By performing alanine scan we examined the propensity of each amino acid in the peptide sequence to bind the substrate (mica). Our results indicate that this binding is not controlled by the specific sequence of the peptide, but rather by its conformational freedom in solution versus its freedom when it is in proximity to the substrate. When the conformational freedom of the peptide is identical in both environments, the peptide will not adhere to the substrate. However, when the conformational freedom is reduced, i.e., when the peptide is in close proximity to the substrate, binding will occur. These results shed light on the interaction between peptides and inorganic materials.

Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma.

14-3-3ε is involved in various types of malignancies by increasing cell proliferation, promoting cell invasion, or inhibiting apoptosis. In cutaneous squamous cell carcinoma (cSCC), 14-3-3ε is overexpressed and mislocalized from the nucleus to the cytoplasm where it interacts with the cell division cycle 25 A (CDC25A) and suppresses apoptosis. Hence, inhibition of the 14-3-3ε-CDC25A interaction is an attractive target for promoting apoptosis in cSCC. In this work, we optimized the structure of our previously designed inhibitor of the 14-3-3ε-CDC25A interaction, pT, a phosphopeptide fragment corresponding to one of the two binding regions of CDC25A to 14-3-3ε. Starting from pT, we developed peptide analogs that bind 14-3-3ε with nanomolar affinities. Peptide analogs were designed by shortening the pT peptide and introducing modifications at position 510 of the pT(502-510) analog. Both molecular dynamics (MD) simulations and biophysical methods were used to determine peptide binding to 14-3-3ε. Shortening the pT peptide from 14 to 9 amino acid residues resulted in a peptide (pT(502-510)) that binds 14-3-3ε with a KD value of 45.2 nM. Gly to Phe substitution in position 510 of pT(502-510) led to further improvement in affinity (KD: 22.0 nM) of the peptide for 14-3-3ε. Our results suggest that the designed peptide analogs are potential candidates for inhibiting 14-3-3ε-CDC25A interactions in cSCC cells and thus inducing their apoptosis.

Development of a fluorescent scaffold by utilizing quercetin template for selective detection of Hg2+: Experimental and theoretical studies along with live cell imaging.

Quercetin is an important antioxidant with high bioactivity and it has been used as SARS-CoV-2 inhibitor significantly. Quercetin, one of the most abundant flavonoids in nature, has been in the spot of numerous experimental and theoretical studies in the past decade due to its great biological and medicinal importance. But there have been limited instances of employing quercetin and its derivatives as a fluorescent framework for specific detection of various cations and anions in the chemosensing field. Therefore, we have developed a novel chemosensor based on quercetin coupled benzyl ethers (QBE) for selective detection of Hg2+ with "naked-eye" colorimetric and "turn-on" fluorometric response. Initially QBE itself exhibited very weak fluorescence with low quantum yield (Φ = 0.009) due to operating photoinduced electron transfer (PET) and inhibition of excited state intramolecular proton transfer (ESIPT) as well as intramolecular charge transfer (ICT) within the molecule. But in presence of Hg2+, QBE showed a sharp increase in fluorescence intensity by 18-fold at wavelength 444 nm with high quantum yield (Φ = 0.159) for the chelation-enhanced fluorescence (CHEF) with coordination of Hg2+, which hampers PET within the molecule. The strong binding affinity of QBE towards Hg2+ has been proved by lower detection limit at 8.47 µM and high binding constant value as 2 × 104 M-1. The binding mechanism has been verified by DFT study, Cyclic voltammograms and Jobs plot analysis. For the practical application, the binding selectivity of QBE with Hg2+ has been capitalized in physiological medium to detect intracellular Hg2+ levels in living plant tissue by using green gram seeds. Thus, employing QBE as a fluorescent chemosensor for the specific identification of Hg2+ will pave the way for a novel approach to simplifying the creation of various chemosensors based on quercetin backbone for the precise detection of various biologically significant analytes.

Ratiometric and absolute water-soluble fluorescent tripodal zinc sensor and its application in killing human lung cancer cells.

A new "naked-eye" and ratiometric fluorescent zinc sensor (TAQ) of carboxamidoquinoline with 2-chloro-N-(quinol-8-yl)-acetamide as a receptor was designed and synthesized. The sensor shows good water solubility and high selectivity for sensing; about a 15-fold increase in fluorescence quantum yield and a 100 nm red-shift of fluorescence emission upon binding Zn²âº in aqueous HEPES buffer solution are observed. The human lung cancer cell line (A549) activity is also demonstrated.

Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma.

14-3-3ε is involved in various types of malignancies by increasing cell proliferation, promoting cell invasion or inhibiting apoptosis. In cutaneous squamous cell carcinoma (cSCC), 14-3-3ε is over expressed and mislocalized from the nucleus to the cytoplasm where it interacts with the cell division cycle 25 A (CDC25A) and suppresses apoptosis. Hence inhibition of the 14-3-3ε - CDC25A interaction is an attractive target for promoting apoptosis in cSCC. In this work, we optimized the structure of our previously designed inhibitor of 14-3-3ε - CDC25A interaction, pT, a phosphopeptide fragment corresponding to one of the two binding regions of CDC25A to 14-3-3ε. Starting from pT, we developed peptide analogs that bind 14-3-3ε with nanomolar affinities. Peptide analogs were designed by shortening the pT peptide, and introducing modifications at position 510 of the pT(502-510) analog. Both molecular dynamics (MD) simulations and biophysical methods were used to determine peptides binding to 14-3-3ε. Shortening the pT peptide from 14 to 9 amino acid residues resulted in a peptide (pT(502-510)) that binds 14-3-3ε with a KD value of 45.2 nM. Gly to Phe substitution in position 510 of pT(502-510) led to further improvement in affinity (KD: 22.0 nM) of the peptide for 14-3-3ε. Our results suggest that the designed peptide analogs are potential candidates for inhibiting 14-3-3ε -CDC25A interactions in cSCC cells; thus, inducing their apoptosis.

Dual-mode chemosensor for the fluorescence detection of zinc and hypochlorite on a fluorescein backbone and its cell-imaging applications.

Fluorescein coupled with 3-(aminomethyl)-4,6-dimethylpyridin-2(1H)-one (FAD) was synthesized for the selective recognition of Zn2+ over other interfering metal ions in acetonitrile/aqueous buffer (1 : 1). Interestingly, there was a significant fluorescence enhancement of FAD in association with Zn2+ at 426 nm by strong chelation-induced fluorescence enhancement (CHEF) without interrupting the cyclic spirolactam ring. A binding stoichiometric ratio of 1 : 2 for the ligand FAD with metal Zn2+ was proven by a Jobs plot. However, the cyclic spirolactam ring was opened by hypochlorite (OCl-) as well as oxidative cleavage of the imine bond, which resulted in the emission enhancement of the wavelength at 520 nm. The binding constant and detection limit of FAD towards Zn2+ were determined to be 1 × 104 M-1 and 1.79 µM, respectively, and the detection limit for OCl- was determined as 2.24 µM. We introduced here a dual-mode chemosensor FAD having both the reactive functionalities for the simultaneous detection of Zn2+ and OCl- by employing a metal coordination (Zn2+) and analytes (OCl-) induced chemodosimetric approach, respectively. Furthermore, for the practical application, we studied the fluorescence imaging inside HeLa cells by using FAD, which demonstrated it can be very useful as a selective and sensitive fluorescent probe for zinc.

Fabrication of hollow self-assembled peptide microvesicles and transition from sphere-to-rod structure.

This paper presents the construction of hollow peptide microspheres and the mechanism of transition of microspheres to rod-like vesicles at low concentration. The tripeptides Boc-Phe-Maba-Phe-OMe 1 and Boc-Phe-Maba-Tyr-OMe 2, each of them containing a rigid m-aminobenzoic acid (Maba) template at the central position, forms microspheres at a concentration of 1.6 mM in methanol. At low concentration, these vesicular structures are fused through neck formation, and this leads to sphere-to-rod transition of vesicles. Sizes of these microspheres increase with increasing concentration. We have successfully characterized this transition by fluorescence spectroscopy, DLS, and electron microscopic study. The scanning electron microscopy clearly shows that these spheres are hollow. One important property of these microvesicular structures is the encapsulation of a potent anticonvulsant and mood stabilizing drug carbamazepine, which holds future promise to use these microvesicles as delivery vehicles.

An amyloid-like fibril-forming supramolecular cross-ß-structure of a model peptide: a crystallographic insight.

The peptide Boc-Val-Phe-OMe 1 bearing sequence similarity with the central hydrophobic cluster (CHC) of Alzheimer's Aß(18-19) peptide self-assembles to produce amyloid-like straight unbranched fibrils as examined by atomic force microscopy and Congo red assay. Single crystal X-ray diffraction offers the atomic level structure of the supramolecular parallel ß-sheet aggregation and antiparallel separation between layers (cross-ß-structure).

AFM Probing of Amyloid-Beta 42 Dimers and Trimers.

Elucidating the molecular mechanisms in the development of such a devastating neurodegenerative disorder as Alzheimer's disease (AD) is currently one of the major challenges of molecular medicine. Evidence strongly suggests that the development of AD is due to the accumulation of amyloid ß (Aß) oligomers; therefore, understanding the molecular mechanisms defining the conversion of physiologically important monomers of Aß proteins into neurotoxic oligomeric species is the key for the development of treatments and preventions of AD. However, these oligomers are unstable and unavailable for structural, physical, and chemical studies. We have recently developed a novel flexible nano array (FNA)-oligomer scaffold approach in which monomers tethered inside a flexible template can assemble spontaneously into oligomers with sizes defined by the number of tethered monomers. The FNA approach was tested on short decamer Aß(14-23) peptides which were assembled into dimers and trimers. In this paper, we have extended our FNA technique for assembling full-length Aß42 dimers. The FNA scaffold enabling the self-assembly of Aß42 dimers from tethered monomeric species has been designed and the assembly of the dimers has been validated by AFM force spectroscopy experiments. Two major parameters of the force spectroscopy probing, the rupture forces and the rupture profiles, were obtained to prove the assembly of Aß42 dimers. In addition, the FNA-Aß42 dimers were used to probe Aß42 trimers in the force spectroscopy experiments with the use of AFM tips functionalized with FNA-Aß42 dimers and the surface with immobilized Aß42 monomers. We found that the binding force for the Aß42 trimer is higher than the dimer (75 ± 7 pN vs. 60 ± 3 pN) and the rupture pattern corresponds to a cooperative dissociation of the trimer. The rupture profiles for the dissociation of the Aß42 dimers and trimers are proposed. Prospects for further extension of the FNA-based approach for probing of higher order oligomers of Aß42 proteins are discussed.

Force clamp approach for characterization of nano-assembly in amyloid beta 42 dimer.

Amyloid ß (Aß) oligomers are formed at the early stages of the amyloidogenesis process and exhibit neurotoxicity. Development of oligomer specific therapeutics requires a detailed understanding of oligomerization processes. Amyloid oligomers exist transiently and single-molecule approaches are capable of characterizing such species. In this paper, we describe the application of an AFM based force clamp approach for probing of Aß42 dimers. Aß42 monomers were tethered to the AFM tip and surface and the dimers are formed during the approaching the tip to the surface. AFM force clamp experiments were performed at different force clamps. They revealed two types of transient states for dissociating Aß42 dimers. The analysis showed that these states have distinct lifetimes of 188 ± 52 milliseconds (type 1, short lived) and 317 ± 67 milliseconds (type 2, long lived). Type 1 state prevails over type 2 state as the value of the applied force increases. The rupture lengths analysis led to the models of the dimer dissociation pathways that are proposed.

Bis(2,1,3-benzoselenadiazole-κN)dichloridozinc(II).

In the title complex, [ZnCl(2)(C(6)H(4)N(2)Se)(2)], the Zn(II) center is tetra-coordinated by a Cl(2)N(2) donor set in a distorted tetrahedral geometry. Some of the distortion from the ideal tetrahedral geometry might be ascribed to two agostic Z⋯H interactions The two 2,1,3-benzoselenadiazole ligands are each essentially planar and form a dihedral angle of 35.06 (9)°. An interesting feature of the crystal packing is the observation of short intermolecular contacts between Se and Se, Se and N, and N and N atoms. These arise as a result of three-center bridging of adjacent molecules into chains along the b axis. The crystal structure is stablilized by π-π inter-actions [minimum centroid-centroid distance = 3.5694 (18) Å].

2-Iodo-N-(6-methyl-2-pyrid-yl)benzamide.

The asymmetric unit of the title compound, C(13)H(11)IN(2)O, comprises two crystallographically independent mol-ecules. The dihedral angles between the ring planes are 53.56 (9) and 72.14 (19)° in the two molecules. Pairs of inter-molecular N-H⋯N hydrogen bonds and I⋯O inter-actions link neighbouring mol-ecules into two different pairs of dimers, those involving N-H⋯N interactions having R(2) (2)(8) ring motifs. Short inter-molecular I⋯O [3.1458 (15) Å] and I⋯N [3.4834 (16) Å] contacts are present. The crystal structure is further stabilized by inter-molecular C-H⋯π inter-actions [3.565 (2) and 3.629 (2) Å].

3,5-Dichloro-6-methyl-pyridin-2-amine.

In the title compound, C(6)H(6)Cl(2)N(2), intra-molecular N-H⋯Cl and C-H⋯Cl contacts generate five-membered rings, producing S(5) ring motifs. Pairs of inter-molecular N-H⋯N hydrogen bonds link neighbouring mol-ecules into dimers with R(2) (2)(8) ring motifs. In the crystal structure, these dimers are connected by N-H⋯Cl inter-actions and are packed into columns.

Polymer Nanoarray Approach for the Characterization of Biomolecular Interactions.

Pair-wise interactions at the single-molecule level can be done with nanoprobing techniques, such as AFM force spectroscopy, optical tweezers, and magnetic tweezers. These techniques can be used to probe interactions between well-characterized assemblies of biomolecules, such as monomer-dimer, dimer-dimer, and trimer-monomer. An important step of these techniques is the proper assembly of dimers, trimers, and higher oligomers to enable the interactions to be probed. We have developed a novel approach in which a defined number of peptides are assembled along a flexible polymeric molecule that serves as a linear matrix, termed as flexible nanoarray (FNA). The construct is synthesized with the use of phosphoramidite chemistry (PA), in which non-nucleoside PA spacers and standard oligonucleotide synthesis are used to grow the polymeric chain with the desired length. The reactive sites are incorporated during FNA synthesis. As a result, the FNA polymer contains a set of predesigned reactive sites to which the peptides are covalently conjugated. We describe the protocol for the synthesis of FNA and the application of this methodology to measure the molecular interactions between amyloid peptides of monomer-monomer, monomer-dimer, and dimer-dimer.