Aromatic Interactions Research Articles

Computational engineering of water-soluble human potassium ion channels through QTY transformation.

Transmembrane potassium ion channels are crucial for ion transport, metabolism, and signaling, and serve as promising targets for anti-cancer therapies. However, their hydrophobic transmembrane nature requires detergents, posing a major bottleneck for experimental handling. In this paper, we present a structural bioinformatics study of six experimentally determined and twelve modeled potassium channel structures, in which hydrophobic amino acids (L, I/V, and F) were systematically replaced with neutral hydrophilic ones (Q, T, and Y), making the proteins more water-soluble. QTY (computationally predicted) and native (experimental and repredicted) variants show remarkable structural similarity (RMSD: ~0.50 Å - ~2.14 Å) despite significant sequence differences. QTY variants, both rigid and refined with MD simulations, maintain comparable to native variants stability, solvent-accessible surface area (SASA), and ionic, aromatic, and van der Waals interactions but differ in the grand average of hydropathy (GRAVY), solubility, and hydrophobic contacts. Overall, our study presents a computational approach for designing hydrophilic potassium ion channels while maintaining the native global structure that could potentially simplify their practical use by eliminating the need for detergents.

Long-Range Proton Channels Constructed via Hierarchical Peptide Self-Assembly.

The quest to understand and mimic proton translocation mechanisms in natural channels has driven the development of peptide-based artificial channels facilitating efficient proton transport across nanometric membranes. It is demonstrated here that hierarchical peptide self-assembly can form micrometers-long proton nanochannels. The fourfold symmetrical peptide design leverages intermolecular aromatic interactions to align self-assembled cyclic peptide nanotubes, creating hydrophilic nanochannels between them. Titratable amino acid sidechains are positioned adjacent to each other within the channels, enabling the formation of hydrogen-bonded chains upon hydration, and facilitating efficient proton transport. Moreover, these chains are enriched with protons and water molecules by interacting with immobile counter ions introduced into the channels, increasing proton flow density and rate. This system maintains proton transfer rates closely resembling those in natural protein channels over micrometer distances. The functional behavior of these inherently recyclable and biocompatible systems opens the door for their exploitation in diverse applications in energy storage and conversion, biomedicine, and bioelectronics.

Structure and Energetics of PET-Hydrolyzing Enzyme Complexes: A Systematic Comparison from Molecular Dynamics Simulations.

Discovered in 2016, the enzyme PETase, secreted by bacterial Ideonella Sakaiensis 201-F6, has an excellent hydrolytic activity toward poly(ethylene terephthalate) (PET) at room temperature, while it decreases at higher temperatures due to the low thermostability. Many variants have been engineered to overcome this limitation, which hinders industrial application. In this work, we systematically compare PETase wild-type (WT) and four mutants (DuraPETase, ThermoPETase, FastPETase, and HotPETase) using standard molecular dynamics (MD) simulations and unbinding free energy calculations. In particular, we analyze the enzymes' structural characteristics and binding to a tetrameric PET chain (PET4) under two temperature conditions: T1─300 K and T2─350 K. Our results indicate that (i) PET4 forms stable complexes with the five enzymes at room temperature (∼300 K) and (ii) most of the interactions are localized close to the active site of the protein, where the W185 and Y87 residues interact with the aromatic rings of the substrate. Specifically, (iii) the W185 side-chain explores different conformations in each variant (a phenomenon known in the literature as "W185 wobbling"). This suggests that the binding pocket retains structural plasticity and flexibility among the variants, facilitating substrate recognition and localization events at moderate temperatures. Moreover, (iv) PET4 establishes aromatic interactions with the catalytic H237 residue, stabilizing the catalytic triad composed of residues S160-H237-D206, and helping the system achieve an effective configuration for the hydrolysis reaction. Conversely, (v) the binding affinity decreases at a higher temperature (∼350 K), retaining moderate interactions only for HotPETase. Finally, (vi) MD simulations of complexes formed with poly(ethylene-2,5-furan dicarboxylate) (PEF) show no persistent interactions, suggesting that these enzymes are not yet optimized for binding this alternative semiaromatic plastic polymer. Our study offers valuable insights into the structural stability of these enzymes and the molecular determinants driving PET binding onto their surfaces, sheds light on the mechanistic steps that precede the onset of hydrolysis, and provides a foundation for future enzyme optimization.

Taste characterization and molecular docking study of novel umami flavor peptides in Yanjin black bone Chicken meat

Five polypeptides with a potential umami taste were isolated and purified from Yanjin black bone chicken. However, the flavor characteristics and umami mechanism have not been clarified. The umami properties of these five peptides were investigated in this work using a range of analytical techniques, computer simulation, and sensory evaluation. HE-10 and TP-7 exhibited the strongest umami flavors. Furthermore, dose-response experiments showed that the umami peptides enhanced umami by generating peptide mineral chelates. Environmental scanning electron microscopy (ESEM) microstructural analyses supported this finding. The molecular docking results indicated that the five polypeptides bind to four critical amino acid residues, namely Glu217, Glu148, Asp216, and His145, of the T1R1/T1R3 receptor. The binding occurred through van der Waals, electrostatic interactions, hydrogen bonding, and hydrophobic interactions. The main surface forces implicated include aromatic interactions, hydrogen bonding, hydrophilicity, and solvent accessibility.

Taxus chinensis (Pilg.) Rehder fruit attenuates aging behaviors and neuroinflammation by inhibiting microglia activation via TLR4/NF-κB/NLRP3 pathway

Ethnopharmacological relevanceAs one of the important by-products of Taxus chinensis (Pilg.) Rehder, its fruit (TCF) has a sweet taste, which is commonly used in folklore to make health care wine reputed for enhancing immune function and promoting anti-aging effects, especially popular in the longevity villages of China for a long history. Evidences had showed that Taxus chinensis fruit contained polysaccharides, flavonoids, amino acids and terpenoids, which all were free of toxic compounds, but its medicinal value has not been fully recognized. Our previous studies have found that TCF extract may reverse many biological events, including oxidative stress, inflammatory response, neuronal apoptosis, etc. by in silico methods, suggesting potential avenues for future pharmaceutical exploration in aging and age-related diseases. Aim of the studyYet, the anti-aging properties of TCF have not been specifically studied, this study aims to fill this gap by investigating the effects of TCF extract (TCFE) in an aging mouse model, particularly focusing on its role in inhibiting microglial activation and elucidating its underlying anti-aging mechanisms. Materials and methodsAn aging mouse model was induced using D-galactose, with interventions involving high, medium, and low doses of TCFE compared to a positive control (2 mg/kg rapamycin combined with 100 mg/kg metformin). The methodology involved evaluating behavioral changes, serum oxidative and antioxidative markers, hypothalamic β-galactosidase activity, expression of the aging-related protein P63, serum inflammatory factors, and the TLR4/NF-κB/NLRP3 inflammatory pathway in hypothalamic tissues. Additionally, to strengthen our in vivo findings, we conducted in vitro experiments on LPS-stimulated BV2 microglial cells. Finally, UPLC-MS/MS for precise component analysis using compound standards, coupled with molecular docking analyses, were employed to discern and elucidate the anti-inflammatory mechanisms of TCF. ResultsIn vivo results revealed TCFE significantly ameliorated behavioral deficits, reduced oxidative stress markers (MDA) and pro-inflammatory cytokines (IL1-β, IL-6, IFNg, TNFα, IL-17), and increased in antioxidants (SOD, T-AOC) and anti-inflammatory factors (IL-10). TCFE also reduced hypothalamic senescence, improved cellular integrity, lowered p63, and inhibited microglia activation and inflammatory pathways (TLR4, NFKB, NLRP3). The overall effect of TCFE was better than that of the positive drug group (rapamycin combined with metformin). In vitro results further revealed that TCFE markedly decreased IL1-β, NFKB, and TLR4 levels in BV2 microglial cells, showing comparable efficacy to a TLR4 classic positive inhibitor C34, supporting its anti-inflammatory role. Through UPLC-MS/MS analysis coupled with compound standards, we identified ten bioactive compounds, including gallocatechin, epigallocatechin, catechin, procyanidin B2, kaempferol, quercetin, rutin, naringin, apigenin, ginkgetin. All these compounds showed strong binding affinity to TLR4, notably procyanidin B2 and rutin, potentially through hydrogen bonds, aromatic cation-π interactions, and hydrophobic interactions, suggesting a molecular basis for their anti-inflammatory action. ConclusionTCFE showed strong anti-aging effects by inhibiting microglia activation and lessening oxidative stress and modulating inflammatory pathways. This research supports TCF's use in anti-aging and sets a base for future drug development in the realms of neuroinflammation and aging.

WDR5 Binding to Histone Serotonylation Is Driven by an Edge-Face Aromatic Interaction with Unexpected Electrostatic Effects.

Histone serotonylation has emerged as a key post-translational modification. WDR5 preferentially binds to serotonylated histone 3 (H3), and this binding event has been associated with tumorigenesis. Herein, we utilize genetic code expansion, structure-activity relationship studies, and computation to study an edge-face aromatic interaction between WDR5 Phe149 and serotonin on H3 that is key to this protein-protein interaction. We find experimentally that this edge-face aromatic interaction is unaffected by modulating the electrostatics of the face component but is weakened by electron-withdrawing substituents on the edge component. Overall, these results elucidate that this interaction is governed by van der Waals forces as well as electrostatics of the edge ring, a result that clarifies discrepancies among previous theoretical models and model system studies of this interaction type. This is the first evaluation of the driving force of an edge-face aromatic interaction at a protein-protein interface and provides a key benchmark for the nature of these understudied interactions that are abundant in the proteome.

Determinants of Unfolding Cooperativity and Binding Are Decoupled in a DNA Binding Domain.

The relative magnitudes of noncovalent stabilization energies or the coupling free energies in folded proteins are anisotropically distributed, uniquely influencing folding and functional behaviors. In this regard, the fructose repressor (FruR) DBD belonging to the LacR repressor family harbors a three-residue insertion─KQY─between the canonical second and third helices. This sequence insertion promotes a strong Tyr-Tyr stacking interaction that is not observed in related homologues. Combining experiments with simulations, we show that the Tyr-Tyr stacking contributes to a decoupled unfolding due to the localization of a large part of the stabilization energy in this specific structural region. This leads to melting temperatures from different probes spanning nearly 10 K, while concomitantly stabilizing a partially structured intermediate state. Disruption of the aromatic stacking interaction via an alanine mutation promotes a molten-globular state whose native ensemble is replete with non-native interactions while displaying enhanced thermodynamic fluctuations and minimal calorimetric cooperativity. Surprisingly, the molten-globular variant of FruR DBD binds to the operator site on DNA with an affinity similar to that of the wild-type but with altered secondary-structure characteristics in the bound state, underscoring the chaperone-like role of DNA through its large negative electrostatic potential. FruR DBD thus appears to be at the verge of disorder as expected of an entropically destabilizing three-residue insertion but is rescued by the aromatic stacking interaction that distinctly dictates the finer details of stability, cooperativity, and binding.

Structural insight into the lead identification of a dual inhibitor of PDE1B and PDE10A: Integrating pharmacophore-based virtual screening, molecular docking, and structure-activity-relationship approaches

Schizophrenia is a chronic neuropsychiatric disorder affecting more than 1% of the world's population. Current antipsychotic treatments show inadequacy in mitigating the negative and cognitive symptoms of schizophrenia. In addition, these medications cause undesirable extrapyramidal side effects. According to the studies, inhibition of phosphodiesterase (PDE) 1B and PDE10A simultaneously can alleviate positive, negative, and cognitive symptoms of schizophrenia. Thus, this study aims to identify new dual inhibitors of PDE1B and PDE10A using ligand-based pharmacophore modelling, virtual screening, and molecular docking studies. Accordingly, the generated pharmacophore models of PDE1B and PDE10A comprised hydrogen bond acceptor, aromatic ring, and hydrophobic features. These features were essential for retrieving the active hits from the Universal Natural Product Database in the virtual screening. Additional filters were subsequently employed to identify potential hits that could be developed into central nervous system-active compounds. Hits meeting all the screening criteria were subjected to docking studies with PDE1B and PDE10A. Among these hits, UNPD167314 exhibited significant binding affinities for the target receptors. It occupied the P-clamp and displayed hydrophobic, aromatic, and hydrogen bond interactions with the active site residues of both receptors, thus selected as a lead compound for the design of potent and selective dual inhibitors. The structural modifications of UNPD167314 resulted in the design of 35 novel inhibitors. Out of 35, four compounds exhibited high and comparable binding affinities for both PDE1B and PDE10A, making them promising candidates for further evaluation and optimisation.

Pyrazole-based N-phenyl pyrazolines: Synthesis, docking, and pharmacological evaluation

A series of methoxy substituted pyrazole based pyrazoline derivatives (4a-j) were synthesized in good to excellent yield from corresponding pyrazole-chalcones (3a-j). All synthesized derivatives were characterized and screened for their in vitro anti-inflammatory, antioxidant, antidiabetic, and antibacterial activities. Among the series, compounds 4f, 4j, 4a, and 4i showed better anti-inflammatory activity as compared to diclofenac sodium. In DPPH free radical scavenging assay, all the compounds were shown excellent activity and moderate to good activity in SO and NO free radical scavenging assay as compared to standard ascorbic acid. Antibacterial screening of synthesized pyrazolines showed that compounds 4f and 4j have significant antibacterial activity. The compounds 4j, 4f, 4h, 4a, and 4c have shown comparable inhibition of alpha-amylase enzyme leading to good antidiabetic activity as compared to standard acarbose. Molecular docking studies suggest that these compounds have strong binding with COX-2 and alpha-amylase enzyme due to significant capability of aromatic and hydrophobic interaction. The outstanding results of reported compounds in all biological screening will pave the way for the design of new drug candidate bearing pyrazole moiety.

Modification of rice protein and its components: Enhanced fibrils formation and improved foaming properties

Plant-derived proteins like rice protein are considered an ideal source for yielding amyloid fibrils due to sustainability and affordability. However, the inherent low solubility of rice protein often restricts its self-assembly capability under common fibrillization protocols. Hence, this study comprehensively investigated the effect of modification on the self-assembly behavior, protein structure and foaming properties of rice protein and its components. The modification facilitated the transformation of α-helix to β-sheet, promoting fibrils formation. All modified proteins, except rice protein, exhibited significantly increased zeta potential values. AFM results revealed that the modified rice protein and globulin fibrils exhibited entangled aggregation behavior, while the glutelin fibril was notably extended, with several micrometers in length. Additionally, modification promoted the aggregation of albumin and prolamin particles to form short and straight fibrils. Amino acid analysis indicated that the content difference of amino acids with different characteristics and the change of aromatic amino acid interaction caused by modification may lead to different self-assembly behavior of the same protein. Furthermore, the foaming capability and stability of most protein fibrils were significantly improved by the modification. These findings provide valuable insights into the regulation of plant-derived protein fibrillation through modification.

The robustness waterproof ionogel based on the phase separation to form soft hard heterostructures and the interaction of cation-π realizes underwater adhesion and sensing

Flexible ionic conductors hold significant promise for advancing the field of soft ion electronics in the future. However, the creation of flexible conductors that possess mechanical robustness, underwater adhesion and underwater motion monitoring remains a challenge. Drawing inspiration from the multiphase hetero structure found in biological connective tissues, such as high modulus fibers and low modulus water-rich matrices, this article proposes a one-pot polymerization in-situ design strategy to create a hydrophobic ionogel with a hetero structure of soft and hard domains. The mechanical robustness, elasticity, and toughness of the ionogel are achieved through a synergistic combination of a strong skeleton in the hard domain and an elastic matrix in the soft domain. Additionally,hydrophobic aromatic rings and quaternary ammonium cation simulated cation-π interactions in mussel foot silk protein. Upon contact with water, the hydrophobic clusters quickly aggregate, facilitating the expulsion of interfacial water and exposing salicylic acid groups and quaternary ammonium cationic groups, leading to outstanding underwater adhesion between the ionogel and various substrates. The resulting hydrophobic ionogel can be utilized in underwater wearable electronic devices for monitoring human movement and physiological information, underwater repair monitoring, and intelligent soft robotics, demonstrating its vast potential in the field of underwater sensors.

Structure-based pharmacophore modeling for precision inhibition of mutant ESR2 in breast cancer: A systematic computational approach.

Breast cancer, a leading cause of female mortality, is closely linked to mutations in estrogen receptor beta (ESR2), particularly in the ligand-binding domain, which contributed to altered signaling pathways and uncontrolled cell growth. This study investigates the molecular and structural aspects of ESR2 mutant proteins to identify shared pharmacophoric regions of ESR2 mutant proteins and potential therapeutic targets aligned within the pharmacophore model. This study was initiated by establishing a common pharmacophore model among three mutant ESR2 proteins (PDB ID: 2FSZ, 7XVZ, and 7XWR). The generated shared feature pharmacophore (SFP) includes four primary binding interactions: Hydrogen bond donors (HBD), hydrogen bond acceptors (HBA), hydrophobic interactions (HPho), and Aromatic interactions (Ar), along with halogen bond donors (XBD) and totalling 11 features (HBD: 2, HBA: 3, HPho: 3, Ar: 2, XBD: 1). By employing an in-house Python script, these 11 features distributed into 336 combinations, which were used as query to isolate a drug library of 41,248 compounds and subjected to virtual screening through the generated SFP. The virtual screening demonstrated 33 hits showing potential pharmacophoric fit scores and low RMSD value. The top four compounds: ZINC94272748, ZINC79046938, ZINC05925939, and ZINC59928516 showed a fit score of more than 86% and satisfied the Lipinski rule of five. These four compounds and a control underwent molecular (XP Glide mode) docking analysis against wild-type ESR2 protein (PDB ID: 1QKM), resulting in binding affinity of -8.26, -5.73, -10.80, and -8.42 kcal/mol, respectively, along with the control -7.2 kcal/mol. Furthermore, the stability of the selected candidates was determined through molecular dynamics (MD) simulations of 200 ns and MM-GBSA analysis. Based on MD simulations and MM-GBSA analysis, our study identified ZINC05925939 as a promising ESR2 inhibitor among the top four hits. However, it is essential to conduct further wet lab evaluation to assess its efficacy.

Chiral inversion induced by aromatic interactions in short peptide assembly

Although hydrophobic interactions provide the main driving force for initial peptide aggregation, their role in regulating suprastructure handedness of higher-order architectures remains largely unknown. We here interrogate the effects of hydrophobic amino acids on handedness at various assembly stages of peptide amphiphiles. Our studies reveal that relative to aliphatic side chains, aromatic side chains set the twisting directions of single β-strands due to their strong steric repulsion to the backbone, and upon packing into multi-stranded β-sheets, the side-chain aromatic interactions between strands form the aromatic ladders with a directional preference. This ordering not only leads to parallel β-sheet arrangements but also induces the chiral flipping over of single β-strands within a β-sheet. In contrast, the lack of orientational hydrophobic interactions in the assembly of aliphatic peptides implies no chiral inversion upon packing into β-sheets. This study opens an avenue to harness peptide aggregates with targeted handedness via aromatic side-chain interactions.

Sequence-specific interactions determine viscoelasticity and aging dynamics of protein condensates.

Biomolecular condensates are viscoelastic materials. Here, we investigate the determinants of sequence-encoded and age-dependent viscoelasticity of condensates formed by the prion-like low-complexity domain of the protein hnRNP A1 and its designed variants. We find that the dominantly viscous forms of the condensates are metastable Maxwell fluids. A Rouse-Zimm model that accounts for the network-like organization of proteins within condensates reproduces the measured viscoelastic moduli. We show that the strengths of aromatic inter-sticker interactions determine sequence-specific amplitudes of elastic and viscous moduli, and the timescales over which elastic properties dominate. These condensates undergo physical ageing on sequence-specific timescales. This is driven by mutations to spacer residues that weaken the metastability of dominantly viscous phases. The ageing of condensates is accompanied by disorder-to-order transitions, leading to the formation of non-fibrillar, beta-sheet-containing, semi-crystalline, elastic, Kelvin-Voigt solids. Our results suggest that sequence grammars, which refer to amino acid identities of stickers versus spacers in prion-like low-complexity domains, have evolved to afford control over metastabilities of dominantly viscous fluid phases of condensates. This selection is likely to render barriers for conversion from metastable fluids to globally stable solids insurmountable on functionally relevant timescales.

Development of a mechanically robust silicon-based cross-linking polymer for the sustainable marine antifouling coatings

Silicone-based fouling release coatings (FRCs) have shown great promise as an environmentally friendly antifouling technology, while inferior mechanical properties and insufficient substrate adhesion have hindered their further application. We focused on enhancing the mechanical robustness of silicone-based coating through the synergistic effects of hydrogen bonding, π-π aromatic interaction and covalent bonding. The resulting silicone-based coating displayed a low surface energy of 23 mJ/m2 and improved mechanical strength and substrate adhesion, offering values up to 6.4 MPa (9.1 times higher) and 2.87 MPa (25.7 times higher), respectively. Additionally, the modified coating demonstrated a tear strength of 9.8 kN/m and mass loss only about 30 mg after enduring 10,000 wear cycles. Alkoxysilane-functionalized polyethylene glycol and quaternary ammonium salt were grafted into the cross-linking structure to make them anchored to the networks and migrated to the surface layer in seawater without releasing. The coating provided 99.1% antibacterial efficiency and effective antidiatom performance (≤ 11.2 cell/mm2). After a 12-month marine field test, the developed film showed only 20% micro bio-fouling compared to 100% fouling coverage on the PDMS surface. By combining improved mechanical properties with antifouling characteristics, this new multifunctional silicone-based FRC exhibits tremendous potential for sustainable marine antifouling coating application.

Modulation of polyaniline memristive device switching voltage by nucleotide-free analogue of vitamin B12

Memristive devices offer essential properties to become a part of the next-generation computing systems based on neuromorphic principles. Organic memristive devices exhibit a unique set of properties which makes them an indispensable choice for specific applications, such as interfacing with biological systems. While the switching rate of organic devices can be easily adjusted over a wide range through various methods, controlling the switching potential is often more challenging, as this parameter is intricately tied to the materials used. Given the limited options in the selection conductive polymers and the complexity of polymer chemical engineering, the most straightforward and accessible approach to modulate switching potentials is by introducing specific molecules into the electrolyte solution. In our study, we show polyaniline (PANI)-based device switching potential control by adding nucleotide-free analogue of vitamin B12, aquacyanocobinamide, to the electrolyte solution. The employed concentrations of this molecule, ranging from 0.2 to 2 mM, enabled organic memristive devices to achieve switching potential decrease for up to 100 mV, thus providing a way to control device properties. This effect is attributed to strong aromatic interactions between PANI phenyl groups and corrin macrocycle of the aquacyanocobinamide molecule, which was supported by ultraviolet-visible spectra analysis.

Comparative Analysis of the Inhibitory Mechanism of Aβ1-42 Aggregation by Diruthenium Complexes.

There is a growing interest in the search for metal-based therapeutics for protein misfolding disorders such as Alzheimer's disease (AD). A novel and largely unexplored class of metallodrugs is constituted by paddlewheel diruthenium complexes, which exhibit unusual water solubility and stability and unique coordination modes to proteins. Here, we investigate the ability of the complexes [Ru2Cl(DPhF)(O2CCH3)3]·H2O (1), [Ru2Cl(DPhF)2(O2CCH3)2]·H2O (2), and K2[Ru2(DPhF)(CO3)3]·3H2O (3) (DPhF- = N,N'-diphenylformamidinate) to interfere with the amyloid aggregation of the Aβ1-42 peptide. These compounds differ in charge and steric hindrance due to the coordination of a different number of bulky ligands. The mechanisms of action of the three complexes were studied by employing a plethora of physicochemical and biophysical techniques as well as cellular assays. All these studies converge on different mechanisms of inhibition of amyloid fibrillation: complexes 1 and 2 show a clear inhibitory effect due to an exchange ligand process in the Ru2 unit aided by aromatic interactions. Complex 3 shows no inhibition of aggregation, probably due to its negative charge in solution. This study demonstrates that slight variations in the ligands surrounding the bimetallic core can modulate the amyloid aggregation inhibition and supports the use of paddlewheel diruthenium complexes as promising therapeutics for Alzheimer's disease.

Folding Kinetics and Volume Variation of the β-Hairpin Peptide Chignolin upon Ultrafast pH-Jumps.

In-depth characterization of fundamental folding steps of small model peptides is crucial for a better understanding of the folding mechanisms of more complex biomacromolecules. We have previously reported on the folding/unfolding kinetics of a model α-helix. Here, we study folding transitions in chignolin (GYDPETGTWG), a short β-hairpin peptide previously used as a model to study conformational changes in β-sheet proteins. Although previously suggested, until now, the role of the Tyr2-Trp9 interaction in the folding mechanism of chignolin was not clear. In the present work, pH-dependent conformational changes of chignolin were characterized by circular dichroism (CD), nuclear magnetic resonance (NMR), ultrafast pH-jump coupled with time-resolved photoacoustic calorimetry (TR-PAC), and molecular dynamics (MD) simulations. Taken together, our results present a comprehensive view of chignolin's folding kinetics upon local pH changes and the role of the Tyr2-Trp9 interaction in the folding process. CD data show that chignolin's β-hairpin formation displays a pH-dependent skew bell-shaped curve, with a maximum close to pH 6, and a large decrease in β-sheet content at alkaline pH. The β-hairpin structure is mainly stabilized by aromatic interactions between Tyr2 and Trp9 and CH-π interactions between Tyr2 and Pro4. Unfolding of chignolin at high pH demonstrates that protonation of Tyr2 is essential for the stability of the β-hairpin. Refolding studies were triggered by laser-induced pH-jumps and detected by TR-PAC. The refolding of chignolin from high pH, mainly due to the protonation of Tyr2, is characterized by a volume expansion (10.4 mL mol-1), independent of peptide concentration, in the microsecond time range (lifetime of 1.15 μs). At high pH, the presence of the deprotonated hydroxyl (tyrosinate) hinders the formation of the aromatic interaction between Tyr2 and Trp9 resulting in a more disorganized and dynamic tridimensional structure of the peptide. This was also confirmed by comparing MD simulations of chignolin under conditions mimicking neutral and high pH.

A Halogen Bonding [2]Rotaxane Shuttle for Chloride-Selective Optical Sensing.

The first example of a [2]rotaxane shuttle capable of selective optical sensing of chloride anions over other halides is reported. The rotaxane was synthesised via a chloride ion template-directed cyclisation of an isophthalamide macrocycle around a multi-station axle containing peripheral naphthalene diimide (NDI) stations and a halogen bonding (XB) bis(iodotriazole) based station. Proton NMR studies indicate the macrocycle resides preferentially at the NDI stations in the free rotaxane, where it is stabilised by aromatic donor-acceptor charge transfer interactions between the axle NDI and macrocycle hydroquinone moieties. Addition of chloride ions in an aqueous-acetone solvent mixture induces macrocycle translocation to the XB anion binding station to facilitate the formation of convergent XB⋅⋅⋅Cl- and hydrogen bonding HB⋅⋅⋅Cl- interactions, which is accompanied by a reduction of the charge-transfer absorption band. Importantly, little to no optical response was induced by addition of bromide or iodide to the rotaxane, indicative of the size discriminative steric inaccessibility of the interlocked cavity to the larger halides, demonstrating the potential of using the mechanical bond effect as a potent strategy and tool in chloride-selective chemo-sensing applications in aqueous containing solvent environments.

Deciphering S100B Allosteric Signaling: The Role of a Peptide Target, TRTK-12, as an Ensemble Modulator.

Allostery is an essential biological phenomenon in which perturbation at one site in a biomolecule elicits a functional response at a distal location(s). It is integral to biological processes, such as cellular signaling, metabolism, and transcription regulation. Understanding allostery is also crucial for rational drug discovery. In this work, we focus on an allosteric S100B protein that belongs to the S100 class of EF-hand Ca2+-binding proteins. The Ca2+-binding affinity of S100B is modulated allosterically by TRTK-12 peptide binding 25 Å away from the Ca2+-binding site. We investigated S100B allostery by carrying out nuclear magnetic resonance (NMR) measurements along with microsecond-long molecular dynamics (MD) simulations on S100B/Ca2+ with/without TRTK-12 at different NaCl salt concentrations. NMR HSQC results show that TRTK-12 reorganizes how S100B/Ca2+ responds to different salt concentrations at both orthosteric and allosteric sites. The MD data suggest that TRTK-12 breaks the dynamic aromatic and hydrogen-bond interactions (not observed in X-ray crystallographic structures) between the hinge/helix and Ca2+-binding EF-hand loop of the two subunits in the homodimeric protein. This triggers rearrangement in the protein network architectures and leads to allosteric communication. Finally, computational studies of S100B at distinct ionic strengths suggest that ligand-bound species are more robust to the changing environment relative to the S100B/Ca2+ complex.