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Herein, a novel N-(4-(tert-butyl)-phenyl)-2-chloroacetamide functionalized thiacalix[4]arene architecture, viz TCAN2PA has been synthesized and the sensing behaviour towards metal ions was explored. The probe, TCAN2PA displayed a “Turn-ON” fluorescence response towards Hg(II) ions in acetonitrile over a series of competing common metal ions. A bathochromic shift in absorption band along with a significant “Turn-ON” fluorescence behaviour of TCAN2PA was observed upon interaction with Hg(II) ions. The lower rim modification of thiacalixarene with N-(4-(tert-butyl)-phenyl)-2-chloroacetamide actively contributes toward the fluorescence property due to the presence of strong electron-donating aryl amido substituent. Fluorescence titration experiments were conducted to find out the limit of detection and to understand binding stoichiometry as well. The electron transfer interactions between the electron-rich TCAN2PA host with Hg(II) ions have been postulated which is also supported by computational modelling insights.

Vanadium haloperoxidases play an important catalytic role in the natural production of antibiotics which are difficult to make in the laboratory. Understanding the catalytic mechanism of these enzymes will aid in the production of artificial enzymes useful in bioengineering the synthesis of drugs and useful chemicals. However, the catalytic mechanism remains not fully understood yet. In this paper, we investigate one of the key steps of the catalytic mechanism using QM/MM. Our investigation reveals a new N-halohistidyl intermediate in the catalytic cycle of vanadium chloroperoxidase (VCPO). This new intermediate, in turn, can explain the known inhibition of the enzyme by substrate under acidic conditions (pH[Formula: see text]4). Additionally, we examine the possibility of replacing V in VCPO by Nb or Ta using QM modeling. We report the new result that the Gibbs free energy barriers of several steps of the catalytic cycle are lower in the case of artificial enzymes, incorporating NbO[Formula: see text] or TaO[Formula: see text] instead of VO[Formula: see text]. Our results suggest that these new artificial enzymes may catalyze the oxidation of halide faster than the natural enzyme.

Five hybrid tetrapeptides, each consisting a central dipeptide segment of α-amino acid residues flanked by two aromatic γ-amino acid residues, are found to fold into well-defined β-hairpin conformations as shown by NMR, computational study, and X-ray structures. The turn loop of this β-hairpin motif accommodates different two-residue α-amino acid sequences from the highly flexible Gly-Gly, to the more restricted d -Pro-Gly. The presence of α-amino acid side chains enhances the stabilities of the β-hairpins with the exception of d -Pro-Gly-which results in destabilization. Based on this hairpin/turn motif, a variety of different dipeptide sequences of α-amino acids which rarely occur in β-turns can be introduced and presented as two-residue loops.

Two novel fluorescent probes namely 3-(2,4-dinitrophenoxy)-2-(4-(diphenylamino)phenyl)-4H-chromen-4-one (P1) and 3-(2,4-dinitrophenoxy)-2-(pyren-1-yl)-4H-chromen-4-one (P2) were designed and synthesized here. The probes (P1 and P2) were found to be highly selective and sensitive towards hydrogen sulfide (H2S) in presence of wide range of anions. The new probes (P1 and P2) were fully characterized by analytical, NMR spectroscopy (1H and 13C) and ESI mass spectrometry. The sensing capability of chemodosimeters (P1 and P2) towards H2S was confirmed by fluorescence studies. The ‘turn-on’ fluorescence was used to calculate detection limit of probes (LOD) which were found to be 2.4 and 1.2 μM for P1 and P2 respectively. Moreover, the probes were tested for their cytotoxicity against HeLa cells using MTT assay and found to be non-cytotoxic in nature and hence the probes P1 and P2 were successfully utilized to visualize H2S in living cells.

In this work we report on new heteroleptic coordination compounds [Pb2(LI)2](NO3)2∙2MeOH (1), [Pb2(LII)2](NO3)2 (2), [Pb2(LIII)2](NO3)2∙MeOH∙H2O (3) and [Pb2(LIII)2(H2O)](NCS)2 (4), which were obtained through self-assembling of 2-(amino(pyridin-2-yl)methylene)hydrazine-1-carbothioamide (HLI), 2-(amino(pyrazin-2-yl)methylene)hydrazine-1-carbothioamide (HLII) or 2-(amino(pyridin-2-yl)methylene)-N-methylhydrazine-1-carbothioamide (HLIII) with Pb(NO3)2 or a mixture of Pb(ClO4)2 and KNCS, respectively. In all the obtained complexes the lead(II) cation is N,N',S-chelated by the tridentate pincer type monodeprotonated ligand LI–III. In addition to the thiosemicarbazone chelation, the sulfur atom in each structure acts as bridging to connect two [Pb(LI–III)]+ units to form a dinuclear dimeric species having a centrosymmetric geometry, so that the ligands are directed either at different, in 1 and 2, or the same, in 3 and 4, side of the coplanar Pb2S2 core. In the latter structures two metal centers are additionally linked with each other through the oxygen atom of the bridging water molecule. The dimeric units in 1–4 are further linked through the Pb–N tetrel bonds, yielding 1D supramolecular polymeric chains, which, in turn, are interlinked though a myriad of other intermolecular noncovalent inetaractions, including tetrel bonds, hydrogen bonds and π-stacking. Counterions (NO3– and NCS–) as well as co-crystallized solvent molecules (MeOH and H2O) are also responsible in further stabilization of the overall crystal packing of the obtained complexes as a source of either tetrel and/or hydrogen bonds. The observation of the recurrent tetrel bonds in compounds 1–4 has been rationalized using DFT calculations and molecular electrostatic potential (MEP) surface plots. Moreover, coordination bonds (covalent character) and tetrel bonds (noncovalent character) between the complexes and their conterions (and water moelcule) have been differentiated using the quantum theory of «atoms-in-molecules» (QTAIM) and the noncovalent interaction index (NCI index) computational methods.

The alkylating as well as alkoxylating behavior of dialkyl sulfites are well presented in the literature. In the present work dialkyl sulphites behavior has been investigated towards EOSIN Y (tetrabrominated fluorescein). The products of the reactions (dialkylated eosin Y) reveal that alkylation takes place at the both active sites (at hydroxyl and carboxyl functionalities) in a single step through sulphur-centred Arbuzov type rearrangement. Density functional theory (DFT) has been used as a tool to analyze the role of the halogen groups present at the periphery of the xanthene moiety in alkylation at hydroxyl and carboxy positions of EOSIN Y. Furthermore, in photo-physical study, it was observed that compound C acts as a superoxide sensor specifically with the detection limit 63μM. Its anti-microbial activity was checked against the E. coli and S-aureus using the agar well diffusion assay and, it was observed that it could be used as better antimicrobial agent.

Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) is one of the most widely used powerful explosives. The direct and selective detection of HMX, without the requirement of specialized equipment, remains a great challenge due to its extremely low volatility, unfavorable reduction potential and lack of aromatic rings. Here, we report the first chemical probe of direct identification of HMX at ppb sensitivity based on a designed metal-organic cage (MOC). The cage features two unsaturated dicopper units and four electron donating amino groups inside the cavity, providing multiple binding sites to selectively enhance host-guest events. It was found that compared to other explosive molecules the capture of HMX inside the cavity would strongly modulate the emissive behavior of the host cage, resulting in highly induced fluorescence “turn-on” (160 folds). Based on the density functional theory (DFT) simulation, the mutual fit of both size and binding sites between host and guest leads to the synergistic effects that perturb the ligand-to-metal charge-transfer (LMCT) process, which is probably the origin of such selective HMX-induced turn-on behavior.

The polymorphs of 2ClChMe-4 in Form I (ribbon-like crystal) and Form II (block-like crystal) were prepared, and they exhibited curling/flipping and expansion upon heating on account of single-crystal-to-single-crystal transformations. The irreversible phase transformations occurred separately at 53.2 °C and 57.8 °C for the crystals in Form I and Form II, during which the molecular conformation of 2ClChMe-4 changed and the molecules slipped along the (100) plane. Movement at the molecular level resulted in changes of cell parameters, which in turn led to macroscopic motions of the crystals upon heating. Additionally, the ribbon-like crystals of 2ClChMe-4 showed photo-induced bending driven by [2+2] cycloaddition. Accordingly, an actuator showing reversible bending behavior was fabricated triggered by light and heat successively. Like biomimetic self-actuators, such multi-stimuli mechanical responsive molecular crystals might have potential applications in soft robots, artificial muscles and microfluidic systems.

A dual-functional sensor based on a two-dimensional metal–organic framework (MOF), namely, {[Cd(BBZB)(2,6-NDC)]·CH3OH}n (JXUST-6, BBZB = 4,7-bis(1H-benzimidazole-1-yl)-2,1,3-benzothiadiazole and 2,...

The CIDE domain was initially identified in apoptotic nucleases and now forms a highly conserved family with diverse functions ranging from cell death to lipid metabolism. Based on structural determination of the DREP3 domain, it is suggested that the head-to-tail helical filament structure might be a unified mechanism of CIDE-domain assembly and represents a critical higher-order scaffolding structure that is important for the function of CIDE-domain-containing proteins in DNA fragmentation and lipid-droplet fusion., The cell-death-inducing DFF45-like effector (CIDE) domain is a protein-interaction module comprising ∼80 amino acids and was initially identified in several apoptotic nucleases and their regulators. CIDE-domain-containing proteins were subsequently identified among proteins involved in lipid metabolism. Given the involvement of CIDE-domain-containing proteins in cell death and lipid homeostasis, their structure and function have been intensively studied. Here, the head-to-tail helical filament structure of the CIDE domain of DNA fragmentation factor-related protein 3 (DREP3) is presented. The helical filament structure was formed by opposing positively and negatively charged interfaces of the domain and was assembled depending on protein and salt concentrations. Although conserved filament structures are observed in CIDE family members, the structure elucidated in this study and its comparison with previous structures indicated that the size and the number of molecules used in one turn vary. These findings suggest that this charged-surface-based head-to-tail helical filament structure represents a unified mechanism of CIDE-domain assembly and provides insight into the function of various forms of the filament structure of the CIDE domain in higher-order assembly for apoptotic DNA fragmentation and control of lipid-droplet size.

The structure of an ornithine (Orn)-free Gramicidin S (GS) analogue, cyclo(Val-Nle-Leu-D-Phe-Pro)2 (NGS), was studied. Its circular dichroism (CD) spectrum showed that NGS has a structure similar to GS, though the value of [θ] indicated smaller β-turn and sheet populations. This is probably because the Nle side chain could not form intramolecular hydrogen bonds stabilizing the sheet structure. The chemical shift perturbation of αH and JNH-αH were similar in GS and NGS. Three independent NGS molecules formed intramolecular β-sheet structures in crystal. The turn structures of D-Phe-Pro moieties were classed as type II' β-turns, but one part was unclassed. The molecules were arranged in a twisting manner, which resulted in the formation of a helical sheet. Similar structural characteristics were observed previously in a Leu-type, Orn-free GS analogue and in GS trifluoroacetic acid salt.

Synthetic β-hairpin antimicrobial peptides (AMPs) offer a useful source for the development of novel antimicrobial agents. β-hairpin peptides generally consist of two side strands bridged by a reverse turn. In literature, most studies focused on the modifications of the side strands to manipulate the stability and activity of β-hairpin peptides, and much less is known about the impact of the turn region. By designing a series of de novo β-hairpin peptides with identical side strands but varied turns, we demonstrated that mutations of only 2 to 4 amino acids at the turn region could impart a wide range of antimicrobial profiles among synthetic β-hairpin AMPs. BTT2–4 and BTT6 displayed selective potency against Gram-negative bacteria, with minimum inhibitory concentrations (MICs) of 4–8 µM. In contrast, BTT1 exhibited broad-spectrum activity, with MICs of 4–8 µM against both Gram-positive and Gram-negative strains. Additionally, BTT1 was potent against methicillin-resistant Staphylococcus aureus (MRSA) and colistin-resistant Enterobacterales. The antimicrobial potency of BTT1 persisted after 14 days of serial passage. Mechanistic studies revealed that interactions between lipopolysaccharide (LPS) and the peptides were critical to their membranolytic activity against the bacterial inner membrane. Aside from folding stability, we observed that a degree of conformational flexibility was required for disruptive membrane interactions. Statement of significance By examining the significance of the turn region of β-hairpin peptides, we present valuable knowledge to the design toolkit of novel antimicrobial peptides as alternative therapeutics to overcome antibiotic resistance. Our de novo designed synthetic peptides displayed selective activity against Gram-negative bacteria and potent activity against clinically relevant antibiotic-resistant strains (e.g. colistin-resistant Enterobacterales and methicillin-resistant Staphylococcus aureus). The bactericidal activity of our peptides was shown to be robust in the presence of proteolytic trypsin and saline, conditions that could suppress peptide activity. Our peptides were also determined to be non-cytotoxic against a human cell line.

Hydrogen sulfide and biothiol molecules such as Cys and GSH acted important roles in many physiological processes. To simultaneously detect and distinguish them was quite necessary by a suitable fluorescent probe. A novel chemosensor 4-(4-(benzo[d]thiazol-2-yl)-2-methoxyphenoxy)-7-nitrobenzo[c][1,2,5]oxadiazole (BMNO) was designed to detect H2S/Cys/GSH using the combination of nitrobenzofurazan (NBD) and benzothiazole fluorophores linked by a facile ether bond. The probe BMNO was developed for simultaneous identification of H2S, Cys and GSH. Noticeably, the color changes (from colorless to light purple, light orange and light yellow) of probe BMNO solutions for sensing H2S, Cys and GSH could be observed by naked eyes, respectively. The probe BMNO exhibited high selectivity and sensitivity for H2S, Cys and GSH showing distinct optical signal with detection limit as low as 0.15 μM, 0.03 μM and 0.14 μM, respectively. The sensing mechanism was clarified by spectrum analysis and some controlled experiments. In addition, these outstanding properties of probe BMNO enabled its practical applications in detection H2S in beer, and in cell imaging for Cys and GSH as well.

We study the Reconstruction-of-the-Measure Problem (ROMP) for commuting 2-variable weighted shifts $$W_{(\alpha ,\beta )}$$ , when the initial data are given as the Berger measure of the restriction of $$W_{(\alpha ,\beta )}$$ to a canonical invariant subspace, together with the marginal measures for the 0–th row and 0–th column in the weight diagram for $$W_{(\alpha ,\beta )}$$ . We prove that the natural necessary conditions are indeed sufficient. When the initial data correspond to a soluble problem, we give a concrete formula for the Berger measure of $$W_{(\alpha ,\beta )}$$ . Our strategy is to build on previous results for back-step extensions and one-step extensions. A key new theorem allows us to solve ROMP for two-step extensions. This, in turn, leads to a solution of ROMP for arbitrary canonical invariant subspaces of $$\ell ^2({\mathbb {Z}}_+^2)$$ .

Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule doublets (MTDs). Using electron microscopy, we determined high-resolution structures of Tetrahymena thermophila OAD arrays bound to MTDs in two different states. OAD preferentially binds to MTD protofilaments with a pattern resembling the native tracks for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. We propose that OADs in an array sequentially hydrolyze ATP to slide the MTDs. ATP hydrolysis in turn relaxes the TTH interfaces to effect free nucleotide cycles of downstream OADs. These findings lead to a model explaining how conformational changes in the axoneme produce coordinated action of dyneins., Outer-arm dyneins (OADs) assemble in large arrays on the ciliary axoneme to drive rhythmic beating. Cryo-EM structures of microtubule-bound Tetrahymena thermophila OAD arrays reveal details of this complex assembly and suggest a model for its mechanism of coordinated action.

N,N-Diacetylimido protection of 2-aminoglycosides is an elegant strategy but has had limited applications due to unexpected side reactions in glycosylation. We found that high acid concentrations could diminish the side reactions. We observed intermolecular hydrogen bonding among alcohols and acids could disrupt. Assuming that intermolecular hydrogen bonding accelerates the formation of 1,2-orthoamides and disrupting intermolecular hydrogen bonds could turn to the desired glycosylation, we successfully employed sulfenyl triflate pre-activation in the glycosylation of a broad scope of alcohol acceptors, as well as in a one-pot synthesis of a protected human milk oligosaccharide, lacto-N-neotetraose.

The fluorescent turn-on detection of metal ions is highly desirable for public health and environmental security. Herein, we report a rationally designed fluorescent probe (1) for the detection of Cu2+ synthesized by integrating 2-hydrazinylbenzothiazole with 3-acetyl-7-hydroxycoumarin. The probe alone is non-fluorescent due to the isomerization of C=N in the excited state. The addition of Cu2+ can cause a delayed fluorescence enhancement. A comparative study of 1 and its analogues indicated that the turn-on fluorescence response was thanks to the sulfur atom coordinating to Cu2+. The response delay of 1 in sensing Cu2+ was ascribed to the gradual transition from N-coordination to S-coordination (N and S in thiazole moiety). The proposed new function of S-donor would provide a new approach for the turn-on fluorescence sensation of Cu2+.

We investigate the possibility of describing protein response effects on a chromophore excitation by means of subsystem time-dependent density-functional theory (sTDDFT) in combination with a many-body expansion (MBE) approach. While sTDDFT is in principle intrinsically able to include such contributions, addressing cofactor excitations in protein models or entire proteins with full environment-response treatments is currently out of reach. Taking different model structures of the green fluorescent protein (GFP) and bovine rhodopsin as examples, we demonstrate that an embedded-MBE approach based on sTDDFT in its simplest version leads to a good agreement of the predicted protein response effect already at second order. To reproduce reference response effects from nonsubsystem TDDFT calculations quantitatively (error ≤ 5%), however, a third- or even fourth-order MBE may be required. For the latter case, we explore a selective inclusion of fourth-order terms that drastically reduces the computational burden. In addition, we demonstrate how this sTDDFT-MBE treatment can be utilized as an analysis tool to identify residues with dominant response contributions. This, in turn, can be employed to arrive at smaller structural models for light-absorbing proteins, which still feature all of the main characteristics in terms of photoresponse properties.

Although β-hairpins are widespread in proteins, there is still no universal tool to coax any small peptide to adopt a β-hairpin conformation, regardless of sequence. Here, we report that δ-linked γ(R)-methyl-ornithine ((δ)MeOrn) provides an improved β-turn template for inducing a β-hairpin conformation in peptides. We have developed a synthesis of protected (δ)MeOrn as a building block suitable for use in Fmoc-based solid-phase peptide synthesis. The synthesis begins with l-leucine and affords gram quantities of the N(α)-Boc-N(δ)-Fmoc-γ(R)-methyl-ornithine building block. X-ray crystallography confirms that the (δ)MeOrn turn unit adopts a folded structure in a macrocyclic β-hairpin peptide. CD and NMR spectroscopic experiments allow comparison of the (δ)MeOrn turn template to the δ-linked ornithine ((δ)Orn) turn template that our laboratory has previously introduced and also to the popular d-Pro-Gly turn template. Collectively, these studies demonstrate that the folding of the (δ)MeOrn turn template is substantially better than that of (δ)Orn and is comparable to d-Pro-Gly.

We examine the effects of fusing two benzofurans to s-indacene (indacenodibenzofurans, IDBFs) and dicyclopenta[b,g]naphthalene (indenoindenodibenzofurans, IIDBFs) to control the strong antiaromaticity and diradical character of these core units. Synthesis via 3-functionalized benzofuran yields syn-IDBF and syn-IIDBF. syn-IDBF possesses a high degree of paratropicity, exceeding that of the parent hydrocarbon, which in turn results in strong diradical character for syn-IIDBF. In the case of the anti-isomers, synthesized via 2-substituted benzofurans, these effects are decreased; however, both derivatives undergo an unexpected ring-opening reaction during the final dearomatization step. All the results are compared to the benzothiophene-fused analogues and show that the increased electronegativity of oxygen in the syn-fused derivatives leads to enhancement of the antiaromatic core causing greater paratropicity. For syn-IIDBF increased diradical character results from rearomati-zation of the core naphthalene unit in order to relieve this paratropicity.

The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA–protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein’s hydration shell via soft interactions that, in turn, tune protein–ligand binding dynamics and affinity.

This work is devoted to investigations of the influence of O-H···Se(-) hydrogen bonds on the electronic shells of selenolate R-Se(-) fragment (R═CH3 ). The geometric, energetic and nuclear magnetic resonance (NMR) spectral parameters for various conformers of CH3 Se(-)⋯(H2 O)n clusters with n = 0-6 were calculated at CCSD/aug-cc-pVDZ level of theory. For selenolate anion CH3 Se(-) solvation free energy was calculated, and for water media it is equal to -71.41 kcal/mol. For O-H···Se(-) hydrogen bonds the proportionality coefficients between QTAIM parameters at (3; -1) bond critical point and the strength of an individual hydrogen bond ∆E were proposed. It was shown, that despite a relative weakness of O-H···Se(-) hydrogen bonds, the outer electronic shell of the selenium atom changes significantly upon formation of each hydrogen bond. This, in turn, cause the dramatic change of NMR parameters of selenium nuclei.

Structural changes at the active site of an enzyme induced by binding to a substrate molecule can result in enhanced activity in biological systems. Herein, we report that the new hybrid ultramicroporous material sql‐SIFSIX‐bpe‐Zn exhibits an induced fit binding mechanism when exposed to acetylene, C2H2. The resulting phase change affords exceptionally strong C2H2 binding that in turn enables highly selective C2H2/C2H4 and C2H2/CO2 separation demonstrated by dynamic breakthrough experiments. sql‐SIFSIX‐bpe‐Zn was observed to exhibit at least four phases: as‐synthesised (α); activated (β); and C2H2 induced phases (β′ and γ). sql‐SIFSIX‐bpe‐Zn‐β exhibited strong affinity for C2H2 at ambient conditions as demonstrated by benchmark isosteric heat of adsorption (Q st) of 67.5 kJ mol−1 validated through in situ pressure gradient differential scanning calorimetry (PG‐DSC). Further, in situ characterisation and DFT calculations provide insight into the mechanism of the C2H2 induced fit transformation, binding positions and the nature of host‐guest and guest‐guest interactions., We introduce the new flexible physisorbent sql‐SIFSIX‐bpe‐Zn and reveal that it exhibits an induced fit structural change that results in extraordinary affinity for C2H2 that in turn enables high selectivity for separation of C2H2 over C2H4 and CO2.

In this work, a novel fluorescent probe CBO was synthesized for detecting Fe2+ using the natural monoterpenketone camphor as the starting material. The probe CBO displayed turn-on fluorescence to Fe2+ accompanied by the solution change from colorless to green. As expected, there was an excellent linear relationship between the fluorescence intensity of probe CBO and the concentration of Fe2+ (0–20 μM), and the detection limit was as low as 1.56×10−8 M. In particular, CBO could selectively sense Fe2+ more than other analytes (Fe3+ included) through the N-oxide strategy, and quickly responded to Fe2+ (60 s) over a wide pH (4–14) range. Additionally, based on the rapid fluorescence response of CBO to Fe2+, a simple test strip-based detector was designed for boosting practical applicability. The probe CBO had been successfully applied to the fluorescence imaging of Fe2+ in onion cells and living zebrafish. The probe CBO was a powerful tool of detecting Fe2+ level in organisms, which was of significance to understand the role of Fe2+ in Fe2+-related physical processes and diseases.

The effect of melatonin and/or cholesterol on the structural properties of a model lipid bilayer prepared from 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) has been investigated both experimentally and via molecular dynamics (MD) simulations. Neutron reflectometry experiments performed with single supported membranes revealed changes in lipid bilayer thickness upon the introduction of additional components. While the presence of cholesterol led to an increase in membrane thickness, the opposite effect was observed in the case of melatonin. The results obtained are in a good agreement with MD simulations which provided further information on the organization of components within the systems examined, indicating a mechanism underlying the membranes’ thickness changes due to cholesterol and melatonin that had been observed experimentally. Cholesterol and melatonin preferentially accumulate in different membrane regions, presumably affecting the conformation of lipid hydrophobic moieties differently, and in turn having distinct impacts on the structure of the entire membrane. Our findings may be relevant for understanding the effects of age-related changes in cholesterol and melatonin concentrations, including those in the brains of individuals with Alzheimer’s disease.

A simple and sensitive method was developed to determine biothiols in both sulfhydryl (–SH) and disulfide (S–S) forms using a fluorometric sensor composed of citrate–stabilized gold nanoparticles (...

Estimating the binding energies of small molecules to RNA could help uncover their molecular recognition characteristics and be used to rationally design RNA-targeting chemical probes. Here, we leveraged the ability of the fragment molecular orbital (FMO) method to provide detailed pairwise energetic information to examine the interactions between the aptamer domain of the flavin mononucleotide (FMN)-responsive riboswitch and small-molecule ligands. After developing an efficient protocol for executing high-level FMO calculations on RNA-ligand complexes, we applied our protocol to nine FMN-aptamer-ligand complexes. We then used the results to identify "hot-spots" within the aptamer and decomposed pairwise interactions between the hot-spot residues and the ligands. Interestingly, we found that several of these hot-spot residues interact with the ligands via atypical CH···O hydrogen bonds and anion-π contacts, as well as (face-to-edge) T-shaped π-π interactions. We envision that our results should pave the way for the wider and more prominent use of FMO calculations to study structure-energy relationships in diverse RNA-ligand systems, which in turn may provide a basis for dissecting the molecular recognition characteristics of RNAs.

We studied the stability and folding and unfolding kinetics of the tryptophan zipper, containing different double thioamide subsitutions. Conformation change was triggered by photoisomerization of an integrated AMPP photoswitch in the turn region of the hairpin, and transient spectra were recorded in the deep UV and the mid-IR, covering the time window of the (un)folding transition from picoseconds to tens of microseconds. Thio-substitution of inward-pointing backbone carbonyls was found to strongly destabilize the β-hairpin structures, whereas molecules with two outward pointing thio-carbonyls showed similar or enhanced stability with respect to the unsubstituted sequence, which we attribute to stronger interstrand hydrogen bonding. Thiolation of the two Trp residues closest to the turn can even prevent the opening of the hairpin after cis-trans isomerization of the switch. The circular dichroism due to the two thioamide ππ* transitions is spectrally well-separated from the aromatic tryptophan signal. It changes upon photoswitching, reflecting a local change in coupling and geometry.

An efficient iodine-mediated method is developed for the synthesis of functionalized 2-(methylthio)-4H-chromen-4-ones by intramolecular cyclization of easily accessible 1-(2-benzyloxy-aryl)-3,3-bis-methylsulfanyl-propenones. The synthesized chromen-4-ones turn out to be a key precursor for various kinds of chemical reactions. Mechanistically, we observed that iodine-mediated intramolecular cyclization of ketene dithioacetal proceeded through a radical pathway. 3-Halo-2-(methylthio)-4H-chromen-4-ones were achieved via various two- or one-pot halogenation approaches.

We propose a novel approach to stably immobilize gold nanoparticles (AuNPs) on a plastic substrate and demonstrate that the modified substrate is also capable of immobilizing biomolecules. To immobilize citrate-capped AuNPs, an acrylic substrate was simply dip-coated in a functional polymer solution to decorate the outermost surface with amino groups. Electrostatic interactions between AuNPs and the amino groups immobilized the AuNPs with a high density. The AuNP-modified acrylic substrate was transparent with a red tint. A heat treatment promoted the formation of amide bonds between carboxy groups on the AuNPs and amino groups on the substrate surface. These covalent bonds stabilized the immobilized AuNPs and the resulting substrate was resistant to washing with acid and thiol-containing solutions. The surface density of AuNPs was controlled by the surface density of amino groups on the substrate surface, which was in turn controlled by the dip-coating in the functional polymer solution. We attempted to immobilize functional biomolecules on the AuNPs-functionalized plastic surface by two different approaches. An enzyme (horseradish peroxidase) was successfully immobilized on the AuNPs through amide formation and 5 '-thiolated DNA was also immobilized on the AuNPs through S-Au interactions. These chemistries allow for simultaneous immobilization of two different kinds of biomolecules on a plastic substrate without loss of their functional properties.

Because the authors continue to note instances in the scientific literature of failure to use the correct receptor binding site concentration for determining binding constants, herein we discuss the fundamental concepts that need to be considered to determine correct binding constants or conversely calculate accurate reactant concentrations with known equilibrium constants. We also show the derivation and analytical solutions of the cubic and quartic equations that give the exact free ligand concentration in bivalent and trivalent receptor systems at equilibrium as a function of the macroscopic equilibrium dissociation constants and the total concentrations of ligand and multivalent protein. These equations and solutions strongly reemphasize the critical dependency of deriving the correct concentrations of bound or free ligand and multivalent protein on the choice of the correct concentration basis for the multivalent protein, which is in turn dependent upon the type of equilibrium constant used. These results demonstrate the importance of choosing the proper multivalent protein concentration for the determination of either valid microscopic or valid macroscopic equilibrium dissociation constants from binding isotherms of ligand-multivalent protein complexes.

During the final step of the bacteriophage infection cycle, the cytoplasmic membrane of host cells is disrupted by small membrane proteins called holins. The function of holins in cell lysis is carried out by forming a highly ordered structure called lethal lesion, in which the accumulation of holins in the cytoplasmic membrane leads to the sudden opening of a hole in the middle of this oligomer. Previous studies showed that dimerization of holins is a necessary step to induce their higher order assembly. However, the molecular mechanism underlying the holin-mediated lesion formation is not well understood. In order to elucidate the functions of holin, we first computationally constructed a structural model for our testing system: the holin S105 from bacteriophage lambda. All atom molecular dynamic simulations were further applied to refine its structure and study its dynamics as well as interaction in lipid bilayer. Additional simulations on association between two holins provide supportive evidence to the argument that the C-terminal region of holin plays a critical role in regulating the dimerization. In detail, we found that the adhesion of specific nonpolar residues in transmembrane domain 3 (TMD3) in a polar environment serves as the driven force of dimerization. Our study therefore brings insights to the design of binding interfaces between holins, which can be potentially used to modulate the dynamics of lesion formation.

The kinetic and thermodynamic stabilities of G-quadruplex structures have been extensively studied. In contrast, systematic investigations of the volumetric properties of G-quadruplexes determining their pressure stability are still relatively scarce. The G-rich strand from the promoter region of the c-MYC oncogene (G-strand) is known to adopt a range of conformational states including the duplex, G-quadruplex, and coil states depending on the presence of the complementary C-rich strand (C-strand) and solution conditions. In this work, we report changes in volume, ΔV, and adiabatic compressibility, ΔKS, accompanying interconversions of G-strand between the G-quadruplex, duplex, and coil conformations in the presence and absence of C-strand. We rationalize these volumetric characteristics in terms of the hydration and intrinsic properties of the DNA in each of the sampled conformational states. We further use our volumetric results in conjunction with the reported data on changes in expansibility, ΔE, and heat capacity, ΔCP, associated with G-quadruplex-to-coil transitions to construct the pressure-temperature phase diagram describing the stability of the G-quadruplex. The phase diagram is elliptic in shape, resembling the classical elliptic phase diagram of a globular protein, and is distinct from the phase diagram for duplex DNA. The observed similarity of the pressure-temperature phase diagrams of G-quadruplexes and globular proteins stems from their shared structural and hydration features that, in turn, result in the similarity of their volumetric properties. To the best of our knowledge, this is the first pressure-temperature stability diagram reported for a G-quadruplex.

Essential oils (EOs) are natural antibiotic chemicals for food preservation; however, their use is challenging due to low solubility and high volatility. In this study, hybrid protein particles with hydrophobic interiors and colloidal stability were designed to carry hydrophobic eugenol with enhanced storage and thermal stability. Stable self-emulsified delivery systems (SEDSs) were facilitated by simply mixing eugenol with wheat proteins (WPs) and soy proteins (SPs) at pH 12 prior to neutralization. This strategy enabled protein co-folding that permitted the entrapment of eugenol with a high entrapment capacity of ca. 500 mg/g protein. Control over the SP/WP ratios contributed to tunable microstructural conformations, which in turn modulated the stability of SEDSs with prominent bacteriostatic properties against fungi when applied to rice cakes during long-term storage. These results underline the feasibility of properly utilizing EOs by binary protein structures, where the antibacterial properties of EOs could be manipulated coherently.

Perezone is a naturally occurring hydroxyquinone that has been deeply studied from different chemical aspects, such as therapeutics, electrochemistry, physical-chemical properties, or synthetic approaches that turn it an attractive template for new semisynthetic derivatives with a wide range of purposes. Herein, we describe a facile synthetic pathway to obtain new perezone derivatives by the addition of a pyrrole moiety that can be used for ion recognition. Compounds 2-4 showed the capability to interact with several anions and M2+ cations as separate events that result in colorimetric changes. Moreover, the compounds can behave as heteroditopic receptors. Besides, a previous interaction between fluoride ions and perezone derivatives triggered a successful recognition of M2+ ions, remarking Ni2+ as the most interesting phenomenon. These results project the compounds as potential colorimetric receptors for nickel ions in complex solutions.

The ability of B atoms on two different molecules to engage with one another in a noncovalent diboron bond is studied by ab initio calculations. Due to electron donation from its substituents, the trivalent B atom of BYZ2 (Z=CO, N2 , and CNH; Y=H and F) has the ability to in turn donate charge to the B of a BX3 molecule (X=H, F, and CH3 ), thus forming a B⋅⋅⋅B diboron bond. These bonds are of two different strengths and character. BH(CO)2 and BH(CNH)2 , and their fluorosubstituted analogues BF(CO)2 and BF(CNH)2 , engage in a typical noncovalent bond with B(CH3 )3 and BF3 , with interaction energies in the 3-8 kcal/mol range. Certain other combinations result in a much stronger diboron bond, in the 26-44 kcal/mol range, and with a high degree of covalent character. Bonds of this type occur when BH3 is added to BH(CO)2 , BH(CNH)2 , BH(N2 )2 , and BF(CO)2 , or in the complexes of BH(N2 )2 with B(CH3 )3 and BF3 . The weaker noncovalent bonds are held together by roughly equal electrostatic and dispersion components, complemented by smaller polarization energy, while polarization is primarily responsible for the stronger ones.