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1.
Int J Mol Sci ; 25(9)2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38732131

ABSTRACT

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.


Subject(s)
14-3-3 Proteins , Molecular Dynamics Simulation , Protein Binding , cdc25 Phosphatases , cdc25 Phosphatases/metabolism , cdc25 Phosphatases/chemistry , cdc25 Phosphatases/antagonists & inhibitors , 14-3-3 Proteins/metabolism , 14-3-3 Proteins/chemistry , Humans , Peptides/chemistry , Peptides/metabolism , Amino Acid Sequence
2.
Spectrochim Acta A Mol Biomol Spectrosc ; 315: 124249, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38603957

ABSTRACT

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.


Subject(s)
Fluorescent Dyes , Mercury , Quercetin , Spectrometry, Fluorescence , Quercetin/analysis , Mercury/analysis , Fluorescent Dyes/chemistry , Humans , Spectrometry, Fluorescence/methods , Limit of Detection
3.
ACS Omega ; 9(2): 2719-2729, 2024 Jan 16.
Article in English | MEDLINE | ID: mdl-38250398

ABSTRACT

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.

4.
bioRxiv ; 2023 Oct 03.
Article in English | MEDLINE | ID: mdl-37873379

ABSTRACT

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.

5.
J Biol Chem ; 299(8): 104945, 2023 08.
Article in English | MEDLINE | ID: mdl-37348560

ABSTRACT

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.


Subject(s)
Endoplasmic Reticulum , Models, Molecular , Humans , Cell Membrane/metabolism , Cell Membrane/ultrastructure , Endocytosis , Endoplasmic Reticulum/metabolism , Membrane Proteins/metabolism , Membrane Proteins/ultrastructure , Protein Isoforms/genetics , Protein Isoforms/metabolism , Protein Isoforms/ultrastructure , Cytoplasmic Vesicles/metabolism , Cytoplasmic Vesicles/ultrastructure , Molecular Dynamics Simulation , Protein Structure, Tertiary , Clathrin/metabolism , HEK293 Cells
6.
Anal Methods ; 14(28): 2739-2744, 2022 07 21.
Article in English | MEDLINE | ID: mdl-35775440

ABSTRACT

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.


Subject(s)
Hypochlorous Acid , Zinc , Flavin-Adenine Dinucleotide , Fluorescein , HeLa Cells , Humans , Spectrometry, Fluorescence , Zinc/chemistry
7.
Front Mol Biosci ; 7: 69, 2020.
Article in English | MEDLINE | ID: mdl-32391380

ABSTRACT

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.

8.
Nanoscale ; 11(25): 12259-12265, 2019 Jul 07.
Article in English | MEDLINE | ID: mdl-31210224

ABSTRACT

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.


Subject(s)
Amyloid beta-Peptides/chemistry , Peptide Fragments/chemistry , Protein Multimerization , Amyloid beta-Peptides/ultrastructure , Humans , Microscopy, Atomic Force , Peptide Fragments/ultrastructure
9.
Bioconjug Chem ; 29(8): 2755-2762, 2018 08 15.
Article in English | MEDLINE | ID: mdl-29975836

ABSTRACT

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.


Subject(s)
Amyloid beta-Peptides/chemistry , Biopolymers/chemistry , Nanotechnology , Alzheimer Disease/metabolism , Amyloid beta-Peptides/metabolism , Click Chemistry , Humans , Microscopy, Atomic Force
10.
Methods Mol Biol ; 1814: 63-74, 2018.
Article in English | MEDLINE | ID: mdl-29956227

ABSTRACT

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.


Subject(s)
Amyloid beta-Peptides/metabolism , Nanotechnology/methods , Polymers/chemistry , Azides/chemistry , Click Chemistry , Peptides/chemistry , Protein Multimerization
11.
Phys Chem Chem Phys ; 19(25): 16387-16394, 2017 Jun 28.
Article in English | MEDLINE | ID: mdl-28621364

ABSTRACT

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.


Subject(s)
Amyloid beta-Peptides/chemistry , Polymers/chemistry , Alzheimer Disease/metabolism , Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Dimerization , Humans , Hydrogen-Ion Concentration , Microscopy, Atomic Force , Nanotechnology , Protein Array Analysis , Protein Multimerization , Surface Properties
12.
Sci Rep ; 7(1): 2344, 2017 05 24.
Article in English | MEDLINE | ID: mdl-28539626

ABSTRACT

Structural investigations have revealed that ß hairpin structures are common features in amyloid fibrils, suggesting that these motifs play an important role in amyloid assembly. To test this hypothesis, we characterized the effect of the hairpin fold on the aggregation process using a model ß hairpin structure, consisting of two Aß(14-23) monomers connected by a turn forming YNGK peptide. AFM studies of the assembled aggregates revealed that the hairpin forms spherical structures whereas linear Aß(14-23) monomers form fibrils. Additionally, an equimolar mixture of the monomer and the hairpin assembles into non-fibrillar aggregates, demonstrating that the hairpin fold dramatically changes the morphology of assembled amyloid aggregates. To understand the molecular mechanism underlying the role of the hairpin fold on amyloid assembly, we performed single-molecule probing experiments to measure interactions between hairpin and monomer and two hairpin complexes. The studies reveal that the stability of hairpin-monomer complexes is much higher than hairpin-hairpin complexes. Molecular dynamics simulations revealed a novel intercalated complex for the hairpin and monomer and Monte Carlo modeling further demonstrated that such nano-assemblies have elevated stability compared with stability of the dimer formed by Aß(14-23) hairpin. The role of such folding on the amyloid assembly is also discussed.


Subject(s)
Amyloid beta-Peptides/chemistry , Nanostructures/chemistry , Peptide Fragments/chemistry , Protein Folding , Protein Structure, Secondary , Algorithms , Amino Acid Sequence , Amyloid/chemistry , Microscopy, Atomic Force , Molecular Dynamics Simulation , Monte Carlo Method , Protein Aggregation, Pathological , Protein Multimerization , Protein Stability , Thermodynamics
13.
Sci Rep ; 7: 45592, 2017 03 30.
Article in English | MEDLINE | ID: mdl-28358113

ABSTRACT

A limitation of the amyloid hypothesis in explaining the development of neurodegenerative diseases is that the level of amyloidogenic polypeptide in vivo is below the critical concentration required to form the aggregates observed in post-mortem brains. We discovered a novel, on-surface aggregation pathway of amyloidogenic polypeptide that eliminates this long-standing controversy. We applied atomic force microscope (AFM) to demonstrate directly that on-surface aggregation takes place at a concentration at which no aggregation in solution is observed. The experiments were performed with the full-size Aß protein (Aß42), a decapeptide Aß(14-23) and α-synuclein; all three systems demonstrate a dramatic preference of the on-surface aggregation pathway compared to the aggregation in the bulk solution. Time-lapse AFM imaging, in solution, show that over time, oligomers increase in size and number and release in solution, suggesting that assembled aggregates can serve as nuclei for aggregation in bulk solution. Computational modeling performed with the all-atom MD simulations for Aß(14-23) peptide shows that surface interactions induce conformational transitions of the monomer, which facilitate interactions with another monomer that undergoes conformational changes stabilizing the dimer assembly. Our findings suggest that interactions of amyloidogenic polypeptides with cellular surfaces play a major role in determining disease onset.


Subject(s)
Amyloid beta-Peptides/metabolism , Protein Aggregation, Pathological/metabolism , Amyloid beta-Peptides/chemistry , Microscopy, Atomic Force , Molecular Dynamics Simulation , Signal Transduction , Surface Properties , alpha-Synuclein/metabolism
14.
J Nat Sci ; 2(4)2016.
Article in English | MEDLINE | ID: mdl-27722203

ABSTRACT

Probing of biomolecular complexes by single-molecule force spectroscopy (SMFS) methods including AFM requires proper and suitable coupling methods for immobilization of biomolecules onto the AFM tip and the surface. The use of flexible tethers for the coupling process has dual advantages. First, they allow the specific immobilization of interacting molecules, and second, their flexibility facilitates the proper orientation of the interacting partners. Recently, we developed an approach termed Flexible Nano Array (FNA) in which interacting partners are located on the same polymeric FNA molecule separated by a flexible segment with a defined length. In this paper, we modified the FNA tether approach by incorporating click chemistry with non-metal modification. FNA was synthesized using DNA synthesis chemistry, in which phosphoramidite (PA) spacers containing six ethylene glycol units were used instead of nucleoside triphosphates. During the synthesis, two T modifiers conjugated to two dibenzocyclooctyl (DBCO) residues were incorporated at selected positions within the FNA. The DBCO functionality allows for coupling azide labeled biomolecules via click chemistry. Amyloid peptide Aß(14-23) terminated with azide was incorporated into the FNA and the reaction was controlled with mass-spectrometry. Assembly of tethered Aß(14-23) peptides into dimers was characterized by AFM force spectroscopy experiments in which the AFM tip functionalized with FNA terminated with biotin probed a streptavidin-coated mica surface. The formation of the peptide dimer was verified with force spectroscopy that showed the appearance of a specific fingerprint for dimer dissociation followed by a rupture event for the biotin-streptavidin link. The developed approach is capable of multiple probing events to allow the collection of a large set of data for a quantitative analysis of the force spectroscopy events.

15.
Org Biomol Chem ; 14(2): 570-576, 2016 Jan 14.
Article in English | MEDLINE | ID: mdl-26510406

ABSTRACT

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.


Subject(s)
Fluorescence , Fluorescent Dyes/chemistry , Hydrogen Sulfide/chemistry , Naphthalenes/chemistry , Electrochemical Techniques , Oxidation-Reduction , Quantum Theory
16.
Article in English | MEDLINE | ID: mdl-28239686

ABSTRACT

Self-assembly and aggregation of amyloid peptides, such as Aß(1-40) and Aß(1-42), lead to the development of Alzheimer disease and similar neurodegenerative disorders associated with protein aggregation. The structures of large aggregates, specifically fibrils, are well characterized. However, our understanding about the structure of oligomeric forms of amyloids is incomplete and needs to be expanded, particularly given the finding that oligomeric rather than fibrillar amyloid morphologies are neurotoxic. This lack of knowledge is primarily due to the existence of transient oligomeric forms that require the use of non-traditional approaches capable of probing transiently existing amyloid forms. We have recently developed the Single-Molecule Force Spectroscopy (SMFS) approach enabling us to probe dimeric forms of amyloids. These studies suggest that the assembly of amyloid proteins into dimers leads to extremely stabilized amyloids in non-native, misfolded states [1]. Herein, we applied the SMFS approach to probe amyloid trimers. We used the Aß(14-23) segment of Aß42 protein that is responsible for full-size protein aggregation. The dimerization of this peptide was recently characterized [2]. The dimeric form of Aß (14-23) was assembled by the use of a tandem Aß(14-23)-YNGK-Aß(14-23), in which the YNGK motif between the two Aß(14-23) monomers makes a ß turn to form a hairpin loop with an antiparallel arrangement of Aß(14-23) monomers[3]. The Aß(14-23) monomer was tethered to the AFM tip, and trimers were formed by approaching the tip to the mica surface on which the Aß(14-23)-YNGK-Aß(14-23) dimer was immobilized via a polyethylene glycol tether. We identified trimers by rupture forces that were considerably larger than those for dimers. Models for the trimer assembly process are discussed.

17.
Sci Rep ; 5: 16365, 2015 Nov 10.
Article in English | MEDLINE | ID: mdl-26553508

ABSTRACT

Natural helical structures have inspired the formation of well-ordered peptide-based chiral nanostructures in vitro. These structures have drawn much attention owing to their diverse applications in the area of asymmetric catalysts, chiral photonic materials, and nanoplasmonics. The self-assembly of two enantiomeric fluorinated aromatic dipeptides into ordered chiral fibrillar nanostructures upon sonication is described. These fibrils form organogels. Our results clearly indicate that fluorine-fluorine interactions play an important role in self-assembly. Circular dichroism analysis revealed that both peptides (peptides 1 and 2), containing two fluorines, depicted opposite cotton effects in their monomeric form compared with their aggregated form. This shows that supramolecular chirality inversion took place during the stimuli-responsive self-aggregation process. Conversely, peptide 3, containing one fluorine, did not exhibit chirality inversion in sonication-induced organogelation. Therefore, our results clearly indicate that fluorination plays an important role in the organogelation process of these aromatic dipeptides. Our findings may have broad implications regarding the design of chiral nanostructures for possible applications such as chiroptical switches, asymmetric catalysis, and chiral recognitions.

18.
Phys Chem Chem Phys ; 17(23): 15305-15, 2015 Jun 21.
Article in English | MEDLINE | ID: mdl-25995084

ABSTRACT

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.

19.
Org Biomol Chem ; 13(7): 2134-9, 2015 Feb 21.
Article in English | MEDLINE | ID: mdl-25530298

ABSTRACT

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.


Subject(s)
Chromones/chemistry , Hydrazines/analysis , Lung Neoplasms/chemistry , Naphthols/chemistry , Quantum Theory , Chromones/chemical synthesis , Humans , Lung Neoplasms/pathology , Molecular Structure , Spectrometry, Fluorescence
20.
Chem Commun (Camb) ; 50(76): 11154-7, 2014 Oct 04.
Article in English | MEDLINE | ID: mdl-25110984

ABSTRACT

This communication describes the self-assembly of a tripeptide into a functional coating that resists biofouling. Using this peptide-based coating we were able to prevent protein adsorption and interrupt biofilm formation. This coating can be applied on numerous substrates and therefore can serve in applications related to health care, marine and water treatment.


Subject(s)
Biofouling/prevention & control , Oligopeptides/chemistry , Adsorption/drug effects , Biofilms/drug effects , Biofilms/growth & development , Molecular Conformation , Oligopeptides/pharmacology , Particle Size , Surface Properties/drug effects
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