Ion-dipole interactions and their functions in proteins

Techniques of incorporation of salty compounds, food matrix, and sodium behaviour and its effect over saltiness perception: an overview

The salty taste is usually associated with the positively charged ion sodium present in sodium chloride. Due to its relevance in the food industry, there have been several studies to determine how this ion behaves in various food matrices, or the use of techniques to improve saltiness perception to reduce the amount necessary for savoury food. Several databases were searched, and it was discovered that sodium can interact with the protein, modifying its mobility, as well as, other components of the food matrix, such as fat, that seem to interfere with saltiness perception, increasing or reducing it. Several techniques were used to identify the interaction between sodium and the food matrix, as well as sensory testing to determine the influence of different modification strategies to enhance the saltiness perception. Due to the multiple factors involved in the salty taste, understanding the effect of the technique to modify saltiness perception, the interaction of the matrix components of the food, and the sodium interaction with those components, can be of use in the developing process of foods with a reduction in the sodium content.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05861-6.

Quantum biochemical analysis of the TtgR regulator and effectors

The recent expansion of multidrug-resistant (MDR) pathogens poses significant challenges in treating healthcare-associated infections. Although antibacterial resistance occurs by numerous mechanisms, active efflux of the drugs is a critical concern. A single species of efflux pump can produce a simultaneous resistance to several drugs. One of the best-studied efflux pumps is the TtgABC: a tripartite resistance-nodulation-division (RND) efflux pump implicated in the intrinsic antibiotic resistance in Pseudomonas putida DOT-T1E. The expression of the TtgABC gene is down-regulated by the HTH-type transcriptional repressor TtgR. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT) within the Molecular Fragmentation with Conjugate Caps (MFCC) approach, we investigate the coupling profiles of the transcriptional regulator TtgR in complex with quercetin (QUE), a natural polyphenolic flavonoid, tetracycline (TAC), and chloramphenicol (CLM), two broad-spectrum antimicrobial agents. Our quantum biochemical computational results show the: [i] convergence radius, [ii] total binding energy, [iii] relevance (energetically) of the ligands regions, and [iv] most relevant amino acids residues of the TtgR-QUE/TAC/CLM complexes, pointing out distinctions and similarities among them. These findings improve the understanding of the binding mechanism of effectors and facilitate the development of new chemicals targeting TtgR, helping in the battle against the rise of resistance to antimicrobial drugs. These advances are crucial in the ongoing fight against rising antimicrobial drug resistance, providing hope for a future where healthcare-associated infections can be more beneficially treated.

Bioinformatics, thermodynamics, and mechanical resistance of the FtsZ-ZipA complex of Escherichia coli supports a highly dynamic protein interaction in the divisome

In most microorganisms, cell division is guided by the divisome, a multiprotein complex that assembles at the equator of the cell and is responsible for the synthesis of new cell wall material. FtsZ, the first protein to assemble into this complex forms protofilaments in the cytosol which are anchored to the inner side of the cytosolic membrane by the proteins ZipA and FtsA. FtsZ protofilaments generate a force that deforms the cytosolic membrane and may contribute to the constriction force that leads to the septation of the cell. It has not been studied yet how the membrane protein anchors respond to this force generated by FtsZ. Here we studied the effect of force in the FtsZ-ZipA interaction. We used SMD and obtained the distance to the transition state of key interacting amino acids and SASA of FtsZ and ZipA through the dissociation. The SMD mechanism was corroborated by ITC, and the thermodynamic parameters ΔG0, ΔH0 and ΔS0 were obtained. Finally, we used force spectroscopy by optical tweezers to determine the lifetime of the interaction and rupture probability and their dependence on force at single molecule level. We also obtained the transition state distance, and free energy of the interaction. With the gathering of structural, thermodynamic, kinetic and force parameters we conclude that interaction between FtsZ and ZipA proteins is consistence with the highly dynamic treadmilling process and at least seven ZipA molecules are required to bind to a FtsZ protofilaments to transduce a significant force.

The Implications of Drug-Polymer Interactions on the Physical Stability of Amorphous Solid Dispersions

Amorphous solid dispersions (ASDs) are a formulation and development strategy that can be used to increase the apparent aqueous solubility of poorly water-soluble drugs. Their implementation, however, can be hindered by destabilization of the amorphous form, as the drug recrystallizes from its metastable state. Factors such as the drug-polymer solubility, miscibility, mobility, and nucleation/crystal growth rates are all known to impact the physical stability of an ASD. Non-covalent interactions (NCI) between the drug and polymer have also been widely reported to influence product shelf-life. In this review, the relationship between thermodynamic/kinetic factors and adhesive NCI is assessed. Various types of NCIs reported to stabilize ASDs are described, and their role in affecting physical stability is examined. Finally, NCIs that have not yet been widely explored in ASD formulations, but may potentially impact their physical stability are also briefly described. This review aims to stimulate further theoretical and practical exploration of various NCIs and their applications in ASD formulations in the future.

pH-dependent self-assembly mechanism of a single repetitive domain from a spider silk protein

Spider silk is self-assembled from full-length silk proteins, and some silk protein fragments can also form silk-like fibers in vitro. However, the mechanism underlying the silk fiber formation is not understood well. In this study, we investigated the fiber formation of a single repetitive domain (RP) from a minor ampullate silk protein (MiSp). Our findings revealed that pH and salt concentration affect not only the stability of MiSp-RP but also its self-assembly into fibers and aggregates. Using nuclear magnetic resonance (NMR) spectroscopy, we solved the three-dimensional (3D) structure of MiSp RP in aqueous solution. On the basis of the structure and mutagenesis, we revealed that charge-dipole interactions are responsible for the pH- and salt-dependent properties of MiSp-RP. Our results indicate that fiber formation is regulated by a delicate balance between intermolecular and intramolecular interactions, rather than by the protein stability alone. These findings have implications for the design of silk proteins for mass production of spider silk.

Advancements in antimicrobial nanoscale materials and self-assembling systems

Antimicrobial resistance is directly responsible for more deaths per year than either HIV/AIDS or malaria and is predicted to incur a cumulative societal financial burden of at least $100 trillion between 2014 and 2050. Already heralded as one of the greatest threats to human health, the onset of the coronavirus pandemic has accelerated the prevalence of antimicrobial resistant bacterial infections due to factors including increased global antibiotic/antimicrobial use. Thus an urgent need for novel therapeutics to combat what some have termed the 'silent pandemic' is evident. This review acts as a repository of research and an overview of the novel therapeutic strategies being developed to overcome antimicrobial resistance, with a focus on self-assembling systems and nanoscale materials. The fundamental mechanisms of action, as well as the key advantages and disadvantages of each system are discussed, and attention is drawn to key examples within each field. As a result, this review provides a guide to the further design and development of antimicrobial systems, and outlines the interdisciplinary techniques required to translate this fundamental research towards the clinic.

IBPred: a sequence-based predictor for identifying ion binding protein in phage

Ion binding proteins (IBPs) can selectively and non-covalently interact with ions. IBPs in phages also play an important role in biological processes. Therefore, accurate identification of IBPs is necessary for understanding their biological functions and molecular mechanisms that involve binding to ions. Since molecular biology experimental methods are still labor-intensive and cost-ineffective in identifying IBPs, it is helpful to develop computational methods to identify IBPs quickly and efficiently. In this work, a random forest (RF)-based model was constructed to quickly identify IBPs. Based on the protein sequence information and residues’ physicochemical properties, the dipeptide composition combined with the physicochemical correlation between two residues were proposed for the extraction of features. A feature selection technique called analysis of variance (ANOVA) was used to exclude redundant information. By comparing with other classified methods, we demonstrated that our method could identify IBPs accurately. Based on the model, a Python package named IBPred was built with the source code which can be accessed at https://github.com/ShishiYuan/IBPred.

Structural basis of ion - substrate coupling in the Na+-dependent dicarboxylate transporter VcINDY

The Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen cooperative mechanism by conformational selection. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's conformational selection mechanism is a result of the sodium-dependent formation of the substrate binding site.

Anionic Species Regulate Chemical Storage in Nanometer Vesicles and Amperometrically Detected Exocytotic Dynamics

Hofmeister effects have often been ignored in living organisms, although they affect the activity and functions of biological molecules. Herein, amperometry has been applied to show that the vesicular content, dynamics of exocytosis and vesicles opening, depend on the anionic species treatment. Compared to 100 μM Cl^- treated chromaffin cells, a similar number of catecholamine molecules is released after chaotropic anions (ClO₄^- and SCN^-) treatment, even though the vesicular catecholamine content significantly increases, suggesting a lower release fraction. In addition, there are opposite effects on the dynamics of vesicles release (shorter duration) and vesicle opening (longer duration) for chaotropic anions treated cells. Our results show anion-dependent vesicle release, vesicle opening, and vesicular content, providing understanding of the pharmacological and pathological processes induced by inorganic ions.

A Fully Biodegradable Ferroelectric Skin Sensor from Edible Porcine Skin Gelatine

High-performance biodegradable electronic devices are being investigated to address the global electronic waste problem. In this work, a fully biodegradable ferroelectric nanogenerator-driven skin sensor with ultrasensitive bimodal sensing capability based on edible porcine skin gelatine is demonstrated. The microstructure and molecular engineering of gelatine induces polarization confinement that gives rise the ferroelectric properties, resulting in a piezoelectric coefficient (d33) of ≈24 pC N-1 and pyroelectric coefficient of ≈13 µC m-2K-1, which are 6 and 11.8 times higher, respectively, than those of the conventional planar gelatine. The ferroelectric gelatine skin sensor has exceptionally high pressure sensitivity (≈41 mV Pa-1) and the lowest detection limit of pressure (≈0.005 Pa) and temperature (≈0.04 K) ever reported for ferroelectric sensors. In proof-of-concept tests, this device is able to sense the spatially resolved pressure, temperature, and surface texture of an unknown object, demonstrating potential for robotic skins and wearable electronics with zero waste footprint.

High sensitivity room temperature sulfur dioxide sensor based on conductive poly(p-phenylene)/ZSM-5 nanocomposite

Recently, there has been growing interests in the development of composite materials as the new alternative gas sensing materials for replacing metal oxide based sensors which require the elevated operating temperature. Herein, we reported the fabrication and testing of new sensing composite materials based on the conductive poly(p-phenylene) (PPP) nanoparticle and zeolites for sulfur dioxide (SO₂) detection at room temperature under the effects of doping, zeolite type, zeolite content, SO₂ concentration as well as interferences and humidity. The relative electrical conductivity response depended critically on the doping agent type, doping ratio, and doping temperature. The addition of porous zeolites into the doped-PPP (dPPP) matrix induced the improvement in selectivity and sensing performances towards SO₂ as it promoted more surface area for SO₂ adsorption and its new synergistic effect with the conductive dPPP, related to the additional conductive polymer doping from the dissolution of the SO₂ in intrazeolitic water as identified and reported here. Among all materials, the dPPP/ZSM-5 composite with perchloric acid (HClO₄) as the doping agent, the doping ratio of 50:1, the doping temperature of 70 °C, and the zeolite content of 30% exhibited the highest relative response of 25.42 towards 500 mg L^-1 SO₂ with good repeatability. This composite provided the SO₂ sensitivity of 0.0483 L mg^-1 with R² of 0.9927 and the limit of detection (LOD) of 5 mg L^-1 as determined from the electrical conductivity signal to noise ratio. The present sensing material is a potential candidate in the practical detection of SO₂ at room temperature.

Dynamic signature of ligand binding over a protein surface

We study the motion of Zn^{2+} in the presence of ubiquitin by all-atom molecular-dynamics simulations. We observe that unlike normal diffusive liquid, metal ions show an exponential tail in the self-van Hove function (self-vHf). Moreover, the metal ions are trapped strongly by acidic residues which form a binding pocket over the protein surface. The exponential tail disappears by mutation of trapping residues, suggesting that the tail appears due to trapped motion of the ions. The mean-squared displacements, however, in all the cases show linear dependence on time. Our model establishes that ligand binding generically results in an exponential tail of self-vHf. The self-vHf may give an approach to find binding pockets over a protein surface.

Cation-specific interactions of protein surface charges in dilute aqueous salt solutions: a combined study using dielectric relaxation spectroscopy and Raman spectroscopy

We exploited glycine as a zwitterionic model system to experimentally probe the cation specific interaction of protein surface charges in dilute (≤0.25 mol L-1) aqueous solutions of four biologically relevant inorganic salts, NaCl, KCl, MgCl2 and CaCl2, via dielectric relaxation spectroscopy (DRS) and Raman spectroscopy. Glycine is the simplest building block of proteins and it exposes the same charged groups (carboxylate and ammonium) to the solvent that dominate the protein-water interface. As a counter ion, we selected Cl- due to its biological importance. For all systems, we performed simultaneous fitting of the real (ε') and imaginary (ε″) parts of the dielectric functions, assuming a multimodal relaxation model, obtained from concentration dependent dielectric measurements at ∼293 K. We observe a reduction of the dielectric amplitude for the glycine relaxation while the corresponding time constant shows only small (<7%) deviations compared to aqueous glycine solutions. We propose that the observed reduction in dielectric amplitude is due to a reduction of the effective dipole moment (µeff) of zwitterionic glycine caused by the interaction of glycine with the ion even at very low (0.05 M) salt concentrations. The interaction between divalent metal ions and zwitterionic glycine is increased compared to the monovalent cation-zwitterion interaction; a finding that is also supported by Raman spectroscopy. Our combined dielectric relaxation and Raman spectroscopic study indicates that ion-glycine interactions are weak and mediated by the solvent. Cation-specificity of protein surface charges is also observed in dilute salt solutions (≤0.25 mol L-1), where electrostatic interactions dominate.

Peptide nanoparticles (PNPs) modified disposable platform for sensitive electrochemical cytosensing of DLD-1 cancer cells

A novel diphenylalaninamid (FFA) based peptide nanoparticles (PNPs) modified pencil graphite electrodes (PGEs) for construction of electrochemical cytosensor was demonstrated for the first time in this study. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images revealed the spherical nanostructure of the synthesized FFA based PNPs while attenuated total reflectance-fourier transform infrared (ATR-FTIR) spectra provided information about the structure and conformation of proteins in their structure. Self-assembly of PNPs on PGE surface and adhesion of DLD-1 cancer cells on this surface was also characterized by electrochemical measurements. PNP/PGEs acted as a sensitive platform for simple and rapid quantification of low concentration of DLD-1 cancer cells in early diagnosis using the electrochemical impedance method (EIS). The offered cytosensor demonstrated outstanding performance for the detection of DLD-1 cells by the EIS method. The impedance of electronic transduction was associated with the amount of the immobilized cells ranging from 2 × 10² to 2.0 × 10⁵ cellsmL^-1 with a limit of detection of 100 cellsmL^-1. The efficient performance of the cytosensor was attributed to the well-defined nanostructure and biocompability of PNPs on the substrate.

Atomic determinants of BK channel activation by polyunsaturated fatty acids

Docosahexaenoic acid (DHA), a polyunsaturated ω-3 fatty acid enriched in oily fish, contributes to better health by affecting multiple targets. Large-conductance Ca²⁺- and voltage-gated Slo1 BK channels are directly activated by nanomolar levels of DHA. We investigated DHA-channel interaction by manipulating both the fatty acid structure and the channel composition through the site-directed incorporation of unnatural amino acids. Electrophysiological measurements show that the para-group of a Tyr residue near the ion conduction pathway has a critical role. To robustly activate the channel, ionization must occur readily by a fatty acid for a good efficacy, and a long nonpolar acyl tail with a Z double bond present at the halfway position for a high affinity. The results suggest that DHA and the channel form an ion-dipole bond to promote opening and demonstrate the channel druggability. DHA, a marine-derived nutraceutical, represents a promising lead compound for rational drug design and discovery.

Highly Dynamic Anion-Quadrupole Networks in Proteins

The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.

Catalytic scaffolds for phosphoryl group transfer

A single genome encodes a large number of phosphoryl hydrolases for the purposes of phosphate recycling, primary and secondary metabolism, signal transduction and regulation, and protection from xenobiotics. Phosphate monoester hydrolysis faces a high kinetic barrier, yet there are multiple solutions to the problem both in terms of catalytic mechanisms and three-dimensional structure of the hydrolases. Recent structural and mechanistic findings highlight the trigonal-bipyramidal nature of the transition state for enzyme promoted phosphate monoester hydrolysis and the evolution and role of inserted loops/domains in governing substrate specificity and promiscuity. Important questions remain as to how electrostatics modulate water networks and critical proton-transfer events. How substrate targeting and catalysis is achieved by the independently evolved catalytic platforms is compared and contrasted in this article.