Cooperativity in Binding Processes: New Insights from Phenomenological Modeling

Temperature-dependent Spike-ACE2 interaction of Omicron subvariants is associated with viral transmission

The continued evolution of severe acute respiratory syndrome 2 (SARS-CoV-2) requires persistent monitoring of its subvariants. Omicron subvariants are responsible for the vast majority of SARS-CoV-2 infections worldwide, with XBB and BA.2.86 sublineages representing more than 90% of circulating strains as of January 2024. To better understand parameters involved in viral transmission, we characterized the functional properties of Spike glycoproteins from BA.2.75, CH.1.1, DV.7.1, BA.4/5, BQ.1.1, XBB, XBB.1, XBB.1.16, XBB.1.5, FD.1.1, EG.5.1, HK.3, BA.2.86 and JN.1. We tested their capacity to evade plasma-mediated recognition and neutralization, binding to angiotensin-converting enzyme 2 (ACE2), their susceptibility to cold inactivation, Spike processing, as well as the impact of temperature on Spike-ACE2 interaction. We found that compared to the early wild-type (D614G) strain, most Omicron subvariants' Spike glycoproteins evolved to escape recognition and neutralization by plasma from individuals who received a fifth dose of bivalent (BA.1 or BA.4/5) mRNA vaccine and improve ACE2 binding, particularly at low temperatures. Moreover, BA.2.86 had the best affinity for ACE2 at all temperatures tested. We found that Omicron subvariants' Spike processing is associated with their susceptibility to cold inactivation. Intriguingly, we found that Spike-ACE2 binding at low temperature was significantly associated with growth rates of Omicron subvariants in humans. Overall, we report that Spikes from newly emerged Omicron subvariants are relatively more stable and resistant to plasma-mediated neutralization, present improved affinity for ACE2 which is associated, particularly at low temperatures, with their growth rates.IMPORTANCEThe persistent evolution of SARS-CoV-2 gave rise to a wide range of variants harboring new mutations in their Spike glycoproteins. Several factors have been associated with viral transmission and fitness such as plasma-neutralization escape and ACE2 interaction. To better understand whether additional factors could be of importance in SARS-CoV-2 variants' transmission, we characterize the functional properties of Spike glycoproteins from several Omicron subvariants. We found that the Spike glycoprotein of Omicron subvariants presents an improved escape from plasma-mediated recognition and neutralization, Spike processing, and ACE2 binding which was further improved at low temperature. Intriguingly, Spike-ACE2 interaction at low temperature is strongly associated with viral growth rate, as such, low temperatures could represent another parameter affecting viral transmission.

Molecular glues and induced proximity: An evolution of tools and discovery

Small molecule molecular glues can nucleate protein complexes and rewire interactomes. Molecular glues are widely used as probes for understanding functional proximity at a systems level, and the potential to instigate event-driven pharmacology has motivated their application as therapeutics. Despite advantages such as cell permeability and the potential for low off-target activity, glues are still rare when compared to canonical inhibitors in therapeutic development. Their often simple structure and specific ability to reshape protein-protein interactions pose several challenges for widespread, designer applications. Molecular glue discovery and design campaigns can find inspiration from the fields of synthetic biology and biophysics to mine chemical libraries for glue-like molecules.

Salvianolic acid B inhibits thrombosis and directly blocks the thrombin catalytic site

Background

Salvianolic acid B (SAB) is a major component of Salvia miltiorrhiza root (Danshen), widely used in East/Southeast Asia for centuries to treat cardiovascular diseases. Danshen depside salt, 85% of which is made up of SAB, is approved in China to treat chronic angina. Although clinical observations suggest that Danshen extracts inhibited arterial and venous thrombosis, the exact mechanism has not been adequately elucidated.

Objective

To delineate the antithrombotic mechanisms of SAB.

Methods

We applied platelet aggregation and coagulation assays, perfusion chambers, and intravital microscopy models. The inhibition kinetics and binding affinity of SAB to thrombin are measured by thrombin enzymatic assays, intrinsic fluorescence spectrophotometry, and isothermal titration calorimetry. We used molecular in silico docking models to predict the interactions of SAB with thrombin.

Results

SAB dose-dependently inhibited platelet activation and aggregation induced by thrombin. SAB also reduced platelet aggregation induced by adenosine diphosphate and collagen. SAB attenuated blood coagulation by modifying fibrin network structures and significantly decreased thrombus formation in mouse cremaster arterioles and perfusion chambers. The direct SAB-thrombin interaction was confirmed by enzymatic assays, intrinsic fluorescence spectrophotometry, and isothermal titration calorimetry. Interestingly, SAB shares key structural similarities with the trisubstituted benzimidazole class of thrombin inhibitors, such as dabigatran. Molecular docking models predicted the binding of SAB to the thrombin active site.

Conclusion

Our data established SAB as the first herb-derived direct thrombin catalytic site inhibitor, suppressing thrombosis through both thrombin-dependent and thrombin-independent pathways. Purified SAB may be a cost-effective agent for treating arterial and deep vein thrombosis.

On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface

In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.

Binding equations for the lipid composition dependence of peripheral membrane-binding proteins

The specific recognition of peripheral membrane-binding proteins for their target membranes is mediated by a complex constellation of various lipid contacts. Despite the inherent complexities of the heterogeneous protein-membrane interface, the binding dependence of such proteins is, surprisingly, often reliably described by simple models such as the Langmuir Adsorption Isotherm or the Hill equation. However, these models were not developed to describe associations with two-dimensional, highly concentrated heterogeneous ligands such as lipid membranes. In particular, these models fail to capture the dependence on the lipid composition, a significant determinant of binding that distinguishes target from non-target membranes. In this work, we present a model that describes the dependence of peripheral proteins on lipid composition through an analytic expression for their association. The resulting membrane-binding equation retains the features of these simple models but completely describes the binding dependence on multiple relevant variables in addition to the lipid composition, such as protein and vesicle concentration. Implicit in this lipid composition dependence is a new form of membrane-based cooperativity that significantly differs from traditional solution-based cooperativity. We introduce the Membrane-Hill number as a measure of this cooperativity and describe its unique properties. We illustrate the utility and interpretational power of our model by analyzing previously published data on two peripheral proteins that associate with phosphatidylserine-containing membranes: The transmembrane immunoglobulin and mucin domain-containing protein 3 (TIM3) that employs calcium in its association, and milk fat globulin epidermal growth factor VIII (MFG-E8) which is completely insensitive to calcium. We also provide binding equations for systems that exhibit more complexity in their membrane-binding.

Differences in Relevant Physicochemical Properties Correlate with Synergistic Activity of Antimicrobial Peptides

With the urgent need for new medical approaches due to increased bacterial resistance to antibiotics, antimicrobial peptides (AMPs) have been considered as potential treatments for infections. Experiments indicate that combinations of several types of AMPs might be even more effective at inhibiting bacterial growth with reduced toxicity and a lower likelihood of inducing bacterial resistance. The molecular mechanisms of AMP-AMP synergistic antimicrobial activity, however, remain not well understood. Here, we present a theoretical approach that allows us to relate the physicochemical properties of AMPs and their antimicrobial cooperativity. It utilizes correlation and bioinformatics analysis. A concept of physicochemical similarity is introduced, and it is found that less similar AMPs with respect to certain physicochemical properties lead to greater synergy because of their complementary antibacterial actions. The analysis of correlations between the similarity and the antimicrobial properties allows us to effectively separate synergistic from nonsynergistic AMP pairs. Our theoretical approach can be used for the rational design of more effective AMP combinations for specific bacterial targets, for clarifying the mechanisms of bacterial elimination, and for a better understanding of cooperativity phenomena in biological systems.

Uncovering allostery and regulation in SORCIN through molecular dynamics simulations

Soluble resistance-related calcium-binding protein or Sorcin is an allosteric, calcium-binding Penta-EF hand (PEF) family protein implicated in multi-drug resistant cancers. Sorcin is known to bind chemotherapeutic molecules such as Doxorubicin. This study uses in-silico molecular dynamics simulations to explore the dynamics and allosteric behavior of Sorcin in the context of Ca2+ uptake and Doxorubicin binding. The results show that Ca2+ binding induces large, but reversible conformational changes in the Sorcin structure which manifest as rigid body reorientations that preserve the local secondary structure. A reciprocal allosteric handshake centered around the EF5 hand is found to be key in Sorcin dimer formation and stabilization. Binding of Doxorubicin results in rearrangement of allosteric communities which disrupts long-range allosteric information transfer from the N-terminal domain to the middle lobe. However, this binding does not result in secondary structure destabilization. Sorcin does not appear to have a distinct Ca2+ activated mode of Doxorubicin binding.Communicated by Ramaswamy H. Sarma.

Understanding protein-nanoparticle interactions leading to protein corona formation: In vitro - in vivo correlation study

Nanoparticles (NPs) in contact with biological fluids form a biomolecular corona through interactions with proteins, lipids, and sugars, acquiring new physicochemical properties. This work explores the interaction between selected proteins (hemoglobin and fetuin-A) that may alter NP circulation time and NPs of different surface charges (neutral, positive, and negative). The interaction with key proteins albumin and transferrin, the two of the most abundant proteins in plasma was also studied. Binding affinity was investigated using quartz crystal microbalance and fluorescence quenching, while circular dichroism assessed potential conformational changes. The data obtained from in vitro experiments were compared to in vivo protein corona data. The results indicate that electrostatic interactions primarily drive protein-NP interactions, and higher binding affinity does not necessarily translate into more significant structural changes. In vitro and single protein-NP studies provide valuable insights that can be correlated with in vivo observations, opening exciting possibilities for future protein corona studies.

Cooperative Rheological State-Switching of Enzymatically-Driven Composites of Circular DNA And Dextran

Polymer topology, which plays a principal role in the rheology of polymeric fluids, and non-equilibrium materials, which exhibit time-varying rheological properties, are topics of intense investigation. Here, composites of circular DNA and dextran are pushed out-of-equilibrium via enzymatic digestion of DNA rings to linear fragments. These time-resolved rheology measurements reveal discrete state-switching, with composites undergoing abrupt transitions between dissipative and elastic-like states. The gating time and lifetime of the elastic-like states, and the magnitude and sharpness of the transitions, are surprisingly decorrelated from digestion rates and non-monotonically depend on the DNA fraction. These results are modeled using sigmoidal two-state functions to show that bulk state-switching can arise from continuous molecular-level activity due to the necessity for cooperative percolation of entanglements to support macroscopic stresses. This platform, coupling the tunability of topological composites with the power of enzymatic reactions, may be leveraged for diverse material applications from wound-healing to self-repairing infrastructure.

Load sharing between synergistic muscles characterized by a ligand-binding approach and elastography

The skeletal muscle contraction is determined by cross-bridge formation between the myosin heads and the actin active sites. When the muscle contracts, it shortens, increasing its longitudinal shear elastic modulus ([Formula: see text]). Structurally, skeletal muscle can be considered analogous to the molecular receptors that form receptor-ligand complexes and exhibit specific ligand-binding dynamics. In this context, this work aims to apply elastography and the ligand-binding framework to approach the possible intrinsic mechanisms behind muscle synergism. Based on the short-range stiffness principle and the acoustic-elasticity theory, we define the coefficient [Formula: see text], which is directly related to the fraction saturation of molecular receptors and links the relative longitudinal deformation of the muscle to its [Formula: see text]. We show that such a coefficient can be obtained directly from [Formula: see text] estimates, thus calculating it for the biceps brachii, brachioradialis, and brachialis muscles during isometric elbow flexion torque (τ) ramps. The resulting [Formula: see text] curves were analyzed by conventional characterization methods of receptor-ligand systems to study the dynamical behavior of each muscle. The results showed that, depending on muscle, [Formula: see text] exhibits typical ligand-binding dynamics during joint torque production. Therefore, the above indicates that these different behaviors describe the longitudinal shortening pattern of each muscle during load sharing. As a plausible interpretation, we suggested that this could be related to the binding kinetics of the cross-bridges during their synergistic action as torque increases. Likewise, it shows that elastography could be useful to assess contractile processes at different scales related to the change in the mechanical properties of skeletal muscle.

Amphiphilic perylene diimide-based fluorescent hemispherical aggregates as probes for metal ions

The self-assembly behaviour of a newly synthesized amphiphilic core-positioned thioester appended with carboxylic acid functionalized perylene diimide derivative is studied in different organic solvents. Fluorescent J-type hemispherical aggregates are formed in THF solution. The effect of added metal ions on these fluorescent aggregates is evaluated using spectroscopic techniques, where we found these probes bind selectively to Fe³⁺ and Ba²⁺ ions. Two equivalents of Fe³⁺ ions bind cooperatively to one equivalent of perylene diimide derivative in the hemispherical aggregates with a binding constant of 1.4×10⁷ M^-1 and the limit of detection (LOD) was calculated to be 8.66×10^-6 M. The positive cooperative binding effect of Fe³⁺ ions towards hemispherical aggregates equipped with perylene diimide derivatives leads to supramolecular polymerization. Ba²⁺ ions showed selectivity and sensitivity towards the fluorescent aggregates in THF by quenching the fluorescence intensity completely. The linear Stern-Volmer plot with a Stern-Volmer constant value of 502.6 M^-1 signifies the heavy atom effect of Ba²⁺ ions, leading to fluorescence quenching. The morphological transformation of the fluorescent J-type hemispherical aggregates in the presence of Fe³⁺ and Ba²⁺ was studied in detail using electron microscopy.

Diversity in Notch ligand-receptor signaling interactions

The Notch signaling pathway uses families of ligands and receptors to transmit signals to nearby cells. These components are expressed in diverse combinations in different cell types, interact in a many-to-many fashion, both within the same cell (in cis) and between cells (in trans), and their interactions are modulated by Fringe glycosyltransferases. A fundamental question is how the strength of Notch signaling depends on which pathway components are expressed, at what levels, and in which cells. Here, we used a quantitative, bottom-up, cell-based approach to systematically characterize trans-activation, cis-inhibition, and cis-activation signaling efficiencies across a range of ligand and Fringe expression levels in two mammalian cell types. Each ligand (Dll1, Dll4, Jag1, and Jag2) and receptor variant (Notch1 and Notch2) analyzed here exhibited a unique profile of interactions, Fringe-dependence, and signaling outcomes. All four ligands were able to bind receptors in cis and in trans, and all ligands trans-activated both receptors except for Jag1, which failed to activate Notch1. Cis-interactions were predominantly inhibitory, with the exception of the Dll1- and Dll4-Notch2 pairs, which exhibited cis-activation stronger than trans-activation. Lfng strengthened Delta-mediated trans-activation and weakened Jagged-mediated trans-activation for both receptors. Finally, cis-ligands showed diverse cis-inhibition strengths, which depended on the identity of the trans-ligand as well as the receptor. The map of receptor-ligand-Fringe interaction outcomes revealed here should help guide rational perturbation and control of the Notch pathway.

Cooperativity in regulation of membrane protein function: phenomenological analysis of the effects of pH and phospholipids

Interaction between membrane proteins and ligands plays a key role in governing a wide spectrum of cellular processes. These interactions can provide a cooperative-type regulation of protein function. A wide variety of proteins, including enzymes, channels, transporters, and receptors, displays cooperative behavior in their interactions with ligands. Moreover, the ligands involved encompass a vast diversity and include specific molecules or ions that bind to specific binding sites. In this review, our particular focus is on the interaction between integral membrane proteins and ligands that can present multiple "binding sites", such as protons or membrane phospholipids. The study of the interaction that protons or lipids have with membrane proteins often presents challenges for classical mechanistic modeling approaches. In this regard, we show that, like Hill's pioneering work on hemoglobin regulation, phenomenological modeling constitutes a powerful tool for capturing essential features of these systems.

Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders

Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate dim light melatonin onset (established indicator of circadian rhythm sleep disorders) measurement requires lengthy assays, and antibody affinities alterations, especially in patients with circadian rhythm disorders whose melatonin salivary levels vary significantly, making antibodies detection mostly inadequate. In contrast, aptamers with their numerous advantages (e.g., target selectivity, structural flexibility in tuning binding affinities, small size, etc.) can become preferable biorecognition molecules for salivary melatonin detection with high sensitivity and specificity. This study thoroughly characterizes the structural property and binding mechanism of a single-stranded DNA aptamer full sequence (MLT-C-1) and its truncated versions (MLT-A-2, MLT-A-4) to decipher its optimal characteristics for saliva melatonin detection. We use circular dichroism spectroscopy to determine aptamers' conformational changes under different ionic strengths and showed that aptamers display a hairpin loop structure where few base pairs in the stem play a significant role in melatonin binding and formation of aptamer stabilized structure. Through microscale thermophoresis, aptamers demonstrated a high binding affinity in saliva samples (MLT-C-1F K_d = 12.5 ± 1.7 nM; MLT-A-4F K_d = 11.2 ± 1.6 nM; MLT-A-2F K_d = 2.4 ± 2.8 nM; limit-of-detection achieved in pM, highest sensitivity attained for MLT-A-2F aptamer with the lowest detection limit of 1.35 pM). Our data suggest that aptamers are promising as biorecognition molecules and provide the baseline parameters for the development of an aptamer-based point-of-care diagnostic system for melatonin detection and accurate profiling of its fluctuations in saliva.

A Novel and Functionally Diverse Class of Acetylcholine-Gated Ion Channels

Fast cholinergic neurotransmission is mediated by acetylcholine-gated ion channels; in particular, excitatory nicotinic acetylcholine receptors play well established roles in virtually all nervous systems. Acetylcholine-gated inhibitory channels have also been identified in some invertebrate phyla, yet their roles in the nervous system are less well understood. We report the existence of multiple new inhibitory ion channels with diverse ligand activation properties in Caenorhabditis elegans We identify three channels, LGC-40, LGC-57, and LGC-58, whose primary ligand is choline rather than acetylcholine, as well as the first evidence of a truly polymodal channel, LGC-39, which is activated by both cholinergic and aminergic ligands. Using our new ligand-receptor pairs we uncover the surprising extent to which single neurons in the hermaphrodite nervous system express both excitatory and inhibitory channels, not only for acetylcholine but also for the other major neurotransmitters. The results presented in this study offer new insight into the potential evolutionary benefit of a vast and diverse repertoire of ligand-gated ion channels to generate complexity in an anatomically compact nervous system.SIGNIFICANCE STATEMENT Here we describe the diversity of cholinergic signaling in the nematode Caenorhabditis elegans We identify and characterize a novel family of ligand-gated ion channels and show that they are preferentially gated by choline rather than acetylcholine and expressed broadly in the nervous system. Interestingly, we also identify one channel gated by chemically diverse ligands including acetylcholine and aminergic ligands. By using our new knowledge of these ligand-gated ion channels, we built a model to predict the synaptic polarity in the C. elegans connectome. This model can be used for generating hypotheses on neural circuit function.

A Hill Equation for Solid Specific Heat Capacity Calculation

The Hill Equation and Hill Coefficient have been used extensively in biochemistry for the description of noncovalent binding. Previously, the Hill Coefficient was correlated with the Gibbs free energy, which suggests that the Hill Equation might be extensible to covalent binding phenomena. To evaluate this possibility, the Hill Equation was compared to the Debye Model and Einstein Solid in the calculation of heat capacity for 53 covalent solids, which included stainless steels and refractory ceramics. Hill Equation specific heat predictions showed a standard error of 0.37 J/(mole⋅Kelvin), whereas errors from the Debye Model and Einstein Solid were higher at 0.45 J/(mole⋅Kelvin) and 0.81 J/(mole⋅Kelvin), respectively. Furthermore, the Hill Equation is computationally efficient, a feature that can accelerate industrial chemical process simulation(s). Given its speed, simplicity, and accuracy, the Hill Equation likely offers an alternative means of specific heat calculation in chemical process models.

The archaeal glutamate transporter homologue GltPh shows heterogeneous substrate binding

Integral membrane glutamate transporters couple the concentrative substrate transport to ion gradients. There is a wealth of structural and mechanistic information about this protein family. Recent studies of an archaeal homologue, GltPh, revealed transport rate heterogeneity, which is inconsistent with simple kinetic models; however, its structural and mechanistic determinants remain undefined. Here, we demonstrate that in a mutant GltPh, which exclusively populates the outward-facing state, at least two substates coexist in slow equilibrium, binding the substrate with different apparent affinities. Wild type GltPh shows similar binding properties, and modulation of the substate equilibrium correlates with transport rates. The low-affinity substate of the mutant is transient following substrate binding. Consistently, cryo-EM on samples frozen within seconds after substrate addition reveals the presence of structural classes with perturbed helical packing of the extracellular half of the transport domain in regions adjacent to the binding site. By contrast, an equilibrated structure does not show such classes. The structure at 2.2-Å resolution details a pattern of waters in the intracellular half of the domain and resolves classes with subtle differences in the substrate-binding site. We hypothesize that the rigid cytoplasmic half of the domain mediates substrate and ion recognition and coupling, whereas the extracellular labile half sets the affinity and dynamic properties.

Spectroscopic study of L-DOPA and dopamine binding on novel gold nanoparticles towards more efficient drug-delivery system for Parkinson's disease

Nano-drug delivery systems may potentially overcome current challenges in the treatment of Parkinson's disease (PD) by enabling targeted delivery and more efficient blood-brain penetration ability. This study investigates novel gold nanoparticles (AuNPs) to be used as delivery systems for L-DOPA and dopamine by considering their binding capabilities in the presence and absence of a model protein, bovine serum albumin (BSA). Four different AuNPs were prepared by surface functionalization with polyethylene glycol (PEG), 1-adamantylamine (Ad), 1-adamantylglycine (AdGly), and peptidoglycan monomer (PGM). Fluorescence and UV-Vis measurements demonstrated the strongest binding affinity and L-DOPA/dopamine loading efficiency for PGM-functionalized AuNPs with negligible impact of the serum protein presence. Thermodynamic analysis revealed a spontaneous binding process between L-DOPA or dopamine and AuNPs that predominantly occurred through van der Waals interactions/hydrogen bonds or electrostatic interactions. These results represent PGM-functionalized AuNPs as the most efficient at L-DOPA and dopamine binding with a potential to become a drug-delivery system for neurodegenerative diseases. Detailed investigation of L-DOPA/dopamine interactions with different AuNPs was described here for the first time. Moreover, this study highlights a cost- and time-effective methodology for evaluating drug binding to nanomaterials.

Determinants of Ligand Specificity and Functional Plasticity in Type I Interferon Signaling

The Type I Interferon family of cytokines all act through the same cell surface receptor and induce phosphorylation of the same subset of response regulators of the STAT family. Despite their shared receptor, different Type I Interferons have different functions during immune response to infection. In particular, they differ in the potency of their induced anti-viral and anti-proliferative responses in target cells. It remains not fully understood how these functional differences can arise in a ligand-specific manner both at the level of STAT phosphorylation and the downstream function. We use a minimal computational model of Type I Interferon signaling, focusing on Interferon-α and Interferon-β. We validate the model with quantitative experimental data to identify the key determinants of specificity and functional plasticity in Type I Interferon signaling. We investigate different mechanisms of signal discrimination, and how multiple system components such as binding affinity, receptor expression levels and their variability, receptor internalization, short-term negative feedback by SOCS1 protein, and differential receptor expression play together to ensure ligand specificity on the level of STAT phosphorylation. Based on these results, we propose phenomenological functional mappings from STAT activation to downstream anti-viral and anti-proliferative activity to investigate differential signal processing steps downstream of STAT phosphorylation. We find that the negative feedback by the protein USP18, which enhances differences in signaling between Interferons via ligand-dependent refractoriness, can give rise to functional plasticity in Interferon-α and Interferon-β signaling, and explore other factors that control functional plasticity. Beyond Type I Interferon signaling, our results have a broad applicability to questions of signaling specificity and functional plasticity in signaling systems with multiple ligands acting through a bottleneck of a small number of shared receptors.

Cooperativity between the orthosteric and allosteric ligand binding sites of RORγt

RORγt is a nuclear receptor associated with several diseases. Various synthetic ligands have been developed that target the canonical orthosteric or a second, allosteric pocket of RORγt. We show that orthosteric and allosteric ligands can simultaneously bind to RORγt and that their potency is positively influenced by the other ligand, a phenomenon called cooperative dual ligand binding. The mechanism behind cooperative binding in proteins is poorly understood, primarily due to the lack of structural data. We solved 12 crystal structures of RORγt, simultaneously bound to various orthosteric and allosteric ligands. In combination with molecular dynamics, we reveal a mechanism responsible for the cooperative binding behavior. Our comprehensive structural studies provide unique insights into how cooperative binding occurs in proteins.

Cooperative ligand binding is an important phenomenon in biological systems where ligand binding influences the binding of another ligand at an alternative site of the protein via an intramolecular network of interactions. The underlying mechanisms behind cooperative binding remain poorly understood, primarily due to the lack of structural data of these ternary complexes. Using time-resolved fluorescence resonance energy transfer (TR-FRET) studies, we show that cooperative ligand binding occurs for RORγt, a nuclear receptor associated with the pathogenesis of autoimmune diseases. To provide the crucial structural insights, we solved 12 crystal structures of RORγt simultaneously bound to various orthosteric and allosteric ligands. The presence of the orthosteric ligand induces a clamping motion of the allosteric pocket via helices 4 to 5. Additional molecular dynamics simulations revealed the unusual mechanism behind this clamping motion, with Ala355 shifting between helix 4 and 5. The orthosteric RORγt agonists regulate the conformation of Ala355, thereby stabilizing the conformation of the allosteric pocket and cooperatively enhancing the affinity of the allosteric inverse agonists.

Double-side microcantilevers as a key to understand the adsorption mechanisms and kinetics of chemical warfare agents on vertically-aligned TiO2 nanotubes

Microgravimetric sensor platforms with physico- or chemo-selective interfaces offer promising sensing properties. They are widely used to detect chemical warfare agents (CWAs). However, a comprehensive insight into adsorption mechanisms and interactions between low concentrations of these adsorbates and low-mass adsorbents is still lacking. In this study, we report a complete and detailed analytical method to model the adsorption processes of low traces of vapor-phase DiMethyl MethylPhosphonate (DMMP), a conventional simulant of CWAs, on a double-side nanostructured microcantilever coated with vertically-aligned titanium dioxide nanotubes (TiO₂-NTs). We find that the geometrical configuration of NTs plays an important role in the diffusion regimes of molecules during the adsorption. This study shines light on the adsorption and kinetic mechanisms of low-traces DMMP offering opportunities to have a better insight of the adsorption of CWAs on complex nanostructures and to improve microcantilever sensors.

Babesia Bovis Ligand-Receptor Interaction: AMA-1 Contains Small Regions Governing Bovine Erythrocyte Binding

Apical membrane antigen 1 is a microneme protein which plays an indispensable role during Apicomplexa parasite invasion. The detailed mechanism of AMA-1 molecular interaction with its receptor on bovine erythrocytes has not been completely defined in Babesia bovis. This study was focused on identifying the minimum B. bovis AMA-1-derived regions governing specific and high-affinity binding to its target cells. Different approaches were used for detecting ama-1 locus genetic variability and natural selection signatures. The binding properties of twelve highly conserved 20-residue-long peptides were evaluated using a sensitive and specific binding assay based on radio-iodination. B. bovis AMA-1 ectodomain structure was modelled and refined using molecular modelling software. NetMHCIIpan software was used for calculating B- and T-cell epitopes. The B. bovis ama-1 gene had regions under functional constraint, having the highest negative selective pressure intensity in the Domain I encoding region. Interestingly, B. bovis AMA-1-DI (¹⁰⁰YMQKFDIPRNHGSGIYVDLG¹¹⁹ and ¹²⁰GYESVGSKSYRMPVGKCPVV¹³⁹) and DII (³⁰²CPMHPVRDAIFGKWSGGSCV³²¹)-derived peptides had high specificity interaction with erythrocytes and bound to a chymotrypsin and neuraminidase-treatment sensitive receptor. DI-derived peptides appear to be exposed on the protein’s surface and contain predicted B- and T-cell epitopes. These findings provide data (for the first-time) concerning B. bovis AMA-1 functional subunits which are important for establishing receptor-ligand interactions which could be used in synthetic vaccine development.

Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism

The ATP-binding DNA aptamer is often used as a model system for developing new aptamer-based biosensor methods. This aptamer follows a structure-switching binding mechanism and is unusual in that it binds two copies of its ligand. We have used isothermal titration calorimetry methods to study the binding of ATP, ADP, AMP and adenosine to the ATP-binding aptamer. Using both individual and global fitting methods, we show that this aptamer follows a positive cooperative binding mechanism. We have determined the binding affinity and thermodynamics for both ligand-binding sites. By separating the ligand-binding sites by an additional four base pairs, we engineered a variant of this aptamer that binds two adenosine ligands in an independent manner. Together with NMR and thermal stability experiments, these data indicate that the ATP-binding DNA aptamer follows a population-shift binding mechanism that is the source of the positive binding cooperativity by the aptamer.

Water Soluble Host–Guest Chemistry Involving Aromatic N-Oxides and Sulfonateresorcinarene

Resorcinarenes decorated with sulfonate groups are anionic in nature and water soluble with a hydrophobic electron-rich interior cavity. These receptors are shown to bind zwitterionic aromatic mono-N-oxides and cationic di-N-oxide salts with varying spacer lengths. Titration data fit a 1:1 binding isotherm for the mono-N-oxides and 2:1 binding isotherm for the di-N-oxides. The first binding constants for the di-N-oxides (K1: 104 M−1) are higher compared to the neutral mono-N-oxide (K: 103 M−1) due to enhanced electrostatic attraction from a receptor with an electron-rich internal cavity and cationic and electron deficient N-oxides. The interaction parameter α reveals positive cooperativity for the di-N-oxide with a four-carbon spacer and negative cooperativity for the di-N-oxides that have spacers with more four carbons. This is attributed to shape complementarity between the host and the guest.

Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins

Severe acute respiratory syndrome virus 2 (SARS-CoV-2) is responsible for the current global coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The viral entry of SARS-CoV-2 depends on an interaction between the receptor-binding domain of its trimeric spike glycoprotein and the human angiotensin-converting enzyme 2 (ACE2) receptor. A better understanding of the spike/ACE2 interaction is still required to design anti-SARS-CoV-2 therapeutics. Here, we investigated the degree of cooperativity of ACE2 within both the SARS-CoV-2 and the closely related SARS-CoV-1 membrane-bound S glycoproteins. We show that there exist differential inter-protomer conformational transitions between both spike trimers. Interestingly, the SARS-CoV-2 spike exhibits a positive cooperativity for monomeric soluble ACE2 binding when compared to the SARS-CoV-1 spike, which might have more structural restraints. Our findings can be of importance in the development of therapeutics that block the spike/ACE2 interaction.

Graphene oxide integrated silicon photonics for detection of vapour phase volatile organic compounds

The optical response of a graphene oxide integrated silicon micro-ring resonator (GOMRR) to a range of vapour phase Volatile Organic Compounds (VOCs) is reported. The response of the GOMRR to all but one (hexane) of the VOCs tested is significantly higher than that of the uncoated (control) silicon MRR, for the same vapour flow rate. An iterative Finite Difference Eigenmode (FDE) simulation reveals that the sensitivity of the GO integrated device (in terms of RIU/nm) is enhanced by a factor of ~2, which is coupled with a lower limit of detection. Critically, the simulations reveal that the strength of the optical response is determined by molecular specific changes in the local refractive index probed by the evanescent field of the guided optical mode in the device. Analytical modelling of the experimental data, based on Hill-Langmuir adsorption characteristics, suggests that these changes in the local refractive index are determined by the degree of molecular cooperativity, which is enhanced for molecules with a polarity that is high, relative to their kinetic diameter. We believe this reflects a molecular dependent capillary condensation within the graphene oxide interlayers, which, when combined with highly sensitive optical detection, provides a potential route for discriminating between different vapour phase VOCs.

Discriminating between negative cooperativity and ligand binding to independent sites using pre-equilibrium properties of binding curves

Negative cooperativity is a phenomenon in which the binding of a first ligand or substrate molecule decreases the rate of subsequent binding. This definition is not exclusive to ligand-receptor binding, it holds whenever two or more molecules undergo two successive binding events. Negative cooperativity turns the binding curve more graded and cannot be distinguished from two independent and different binding events based on equilibrium measurements only. The need of kinetic data for this purpose was already reported. Here, we study the binding response as a function of the amount of ligand, at different times, from very early times since ligand is added and until equilibrium is reached. Over those binding curves measured at different times, we compute the dynamic range: the fold change required in input to elicit a change from 10 to 90% of maximum output, finding that it evolves in time differently and controlled by different parameters in the two situations that are identical in equilibrium. Deciphering which is the microscopic model that leads to a given binding curve adds understanding on the molecular mechanisms at play, and thus, is a valuable tool. The methods developed in this article were tested both with simulated and experimental data, showing to be robust to noise and experimental constraints.

When two successive events occur, it may make sense to know if they affect somehow each other, particularly if the properties of the second event are modified by the occurrence of the first one. Two scenarios lead to the same overall outcome: first, the two events are identical but they interfere with each other, and second, the two events are independent but non identical. The interference caused in the first scenario produces the same result as having a second event with different properties. Now, let’s name these events as bindings, the interference as negative cooperativity, and the non-identical events as independent binding. In this work we focus on the dynamic process by which the two scenarios produce the same result. We selected a relevant but not characterized before property of the binding process, called its dynamic range, and found it behaves differently in these two scenarios and controlled by different parameters of interest. Based on this feature, we developed and algorithm to distinguish between negative cooperativity and independent binding based on the time evolution of the dynamic range. This tool allows to discover the microscopic model behind the data and may be useful in other similar problems in cell signaling.

Green synthesis of graphitic nanobiochar for the removal of emerging contaminants in aqueous media

This study reports the preparation of nanobiochar (NBC) via top-down approach of bioenergy waste-derived dendro biochar through mechanised grinding in order to assess its capacity to remove emerging contaminants, such as antibiotics, agrochemicals, and potentially toxic elements from aqueous media. Preconditioned biochar was disc milled in ethanol media, and the resulting colloidal biochar was dispersed in water to obtain the NBC fraction by centrifugation. Adsorption edge and isotherm experiments were carried out at pH 3 to 8 and NBC dosages of 0.5 g/L for oxytetracycline (OTC), glyphosate (GL), hexavalent chromium (CrVI), and cadmium (CdII). NBC was characterised by scanning electron microscopy, X-ray photoelectron spectroscopy, Brunauer-Emmett-Teller surface area, and Fourier transform infrared spectroscopy, which demonstrated the flakey and graphitic nature of the NBC particles with a surface area of 28 m²/g and the presence of different functional groups, such as OH, CO, NH, and CH₃. The best pH for OTC and Cd(II) was 9, whereas the best pH levels for GL and Cr(VI) were 7 and 4, respectively. Isotherms depicted a positive cooperative adsorption mechanism by providing the best fit to the Hills equation, with high removal capacities for four contaminants. Dendro NBC showed the best performance, demonstrated by the high partition coefficient for the removal of OTC, GL, Cr(VI), and Cd(II) over various types of adsorbents. The overall results indicated that graphitic NBC produced by mechanical grinding of dendro biochar is a promising material for the removal of OTC, GL, Cr(VI), and Cd(II) from aqueous media.

Halloysite nanoclay supported adsorptive removal of oxytetracycline antibiotic from aqueous media

Halloysite nanoclay was utilized to retain aqueous oxytetracycline (OTC) which is extensively used in the veterinary industry. The micro-structure and functionality of the nanoclay were characterized through spectroscopic techniques before and after adsorption. The OTC removal experiments were performed at different pH conditions (pH 3.0-9.0), ionic strengths (0.001, 0.01, 0.1 M NaNO₃) and contact time (up to 32 h) at an initial 25 mg/L OTC concentration with 1.0 g/L halloysite. Oxytetracycline adsorption was pH dependent, and the best pH was observed in the range of pH 3.5-5.5 at a 0.001 M ionic strength. At pH 3.5, the maximum OTC adsorption amount was 21 mg/g which translated to 68% removal of the initial OTC loading. Positively charged inner lumen and negatively charged outer lumen of the tubular halloysite structure led to form inner-sphere complexes with the anionic and cationic forms of OTC, respectively. A rapid adsorption of OTC was observed in the kinetic study where 62% OTC was adsorbed in 90 min.. Pseudo-second order equation obeyed by the kinetic data indicated that the adsorption was governed by chemisorption, whereas Hill isotherm equation was the most fitted with a maximum adsorption capacity of 52.4 mg/g indicating a cooperative adsorption phenomenon.

Mutation of two key aspartate residues alters stoichiometry of the NhaB Na+/H+ exchanger from Klebsiella pneumoniae

Bacterial NhaB Na⁺/H⁺ exchangers belonging to the Ion Transporter superfamily are poorly characterized in contrast to Na⁺/H⁺ exchangers of the Cation Proton Antiporter superfamily which have NhaA from Escherichia coli as a prominent member. For a more detailed understanding of the intricacies of the exchanger’s transport mechanism, mutational studies are essential. Therefore, we mutated two protonatable residues present in the putative transmembrane region of NhaB from Klebsiella pneumoniae (KpNhaB), which could serve as substrate binding sites, Asp146 and Asp404, to either glutamate or alanine and analyzed transport function and stability of the mutants using electrophysiological and fluorimetric techniques. While mutation of either Asp residue to Glu only had slight to moderate effects on the transport activity of the exchanger, the mutations D404A and D146A, in particular, had more profound effects on the transport function. Furthermore, a double mutant, D146A/D404A, exhibited a remarkable behavior at alkaline pH, where recorded electrical currents changed polarity, showing steady-state transport with a stoichiometry of H⁺:Na⁺ < 1, as opposed to the H⁺:Na⁺ > 1 stoichiometry of the WT. Thus, we showed that Asp146 and Asp404 are part of the substrate binding site(s) of KpNhaB and engineered a Na⁺/H⁺ exchanger with a variable stoichiometry.

Sorptive removal of toluene and m-xylene by municipal solid waste biochar: Simultaneous municipal solid waste management and remediation of volatile organic compounds

The remediation of volatile organic compounds (VOCs) from aqueous solution using Municipal solid waste biochar (MSW-BC) has been evaluated. Municipal solid waste was pyrolyzed in an onsite pyrolyzer around 450 ^°C with a holding time of 30 min for the production of biochar (BC). Physiochemical properties of BC were assessed based on X-Ray Fluorescence (XRF) and Fourier transform infra-red (FTIR) analysis. Adsorption capacities for the VOCs (m-xylene and toluene) were examined by batch sorption experiments. Analysis indicated high loading of m-xylene and toluene in landfill leachates from different dump sites. The FTIR analysis corroborates with the Boehm titration data whereas XRF data demonstrated negligible amounts of trace metals in MSW-BC to be a potential sorbent. Adsorption isotherm exhibited properties of both Langmuir and Freundlich which is indicative of a non-ideal monolayer adsorption process taking place. Langmuir adsorption capacities were high as 850 and 550 μg/g for toluene and m-xylene respectively. The conversion of MSW to a value added product provided a feasible means of solid waste management. The produced MSW-BC was an economical adsorbent which demonstrated a strong ability for removing VOCs. Hence, MSW-BC can be used as a landfill cover or a permeable reactive barrier material to treat MSW leachate. Thus, the conversion of MSW to BC becomes an environmentally friendly and economical means of solid waste remediation.

Cooperativity in proton sensing by PIP aquaporins

One of the most intriguing properties of plasma membrane intrinsic protein (PIP) aquaporins (AQPs) is their ability to modulate water transport by sensing different levels of intracellular pH through the assembly of homo- and heterotetrameric molecular species in the plasma membrane. In this work, using a phenomenological modeling approach, we demonstrate that cooperativity in PIP biological response cannot be directly attributed to a cooperative proton binding, as it is usually considered, since it could also be the consequence of a cooperative conformation transition between open and closed states of the channel. Moreover, our results show that, when mixed populations of homo- and heterotetrameric PIP channels are coexpressed in the plasma membrane of the same cell, the observed decrease in the degree of positive cooperativity would result from the simultaneous presence of molecular species with different levels of proton sensing. Indeed, the random mixing between different PIP paralogues as subunits in a single tetramer, plus the possibility of mixed populations of homo- and heterotetrameric PIP channels widen the spectrum of cooperative responses of a cell membrane. Our approach offers a deep understanding of cooperative transport of AQP channels, as members of a multiprotein family where the relevant proton binding sites of each member have not been clearly elucidated yet.

Cooperative RNA Recognition by a Viral Transcription Antiterminator

RNA transcription of mononegavirales decreases gradually from the 3' leader promoter toward the 5' end of the genome, due to a decay in polymerase processivity. In the respiratory syncytial virus and metapneumovirus, the M_2-1 protein ensures transcription anti-termination. Despite being a homotetramer, respiratory syncytial virus M_2-1 binds two molecules of RNA of 13mer or longer per tetramer, and temperature-sensitive secondary structure in the RNA ligand is unfolded by stoichiometric interaction with M_2-1. Fine quantitative analysis shows positive cooperativity, indicative of conformational asymmetry in the tetramer. RNA binds to M_2-1 through a fast bimolecular association followed by slow rearrangements corresponding to an induced-fit mechanism, providing a sequential description of the time events of cooperativity. The first binding event of half of the RNA molecule to one of the sites increases the affinity of the second binding event on the adjacent contacting protomer by 15-fold, product of increased effective concentration caused by the entropic link. This mechanism allows for high-affinity binding with an otherwise relaxed sequence specificity, and instead suggests a yet undefined structural recognition signature in the RNA for modulating gene transcription. This work provides a basis for an essential event for understanding transcription antitermination in pneumoviruses and its counterpart Ebola virus VP30.

Counterion-Release Entropy Governs the Inhibition of Serum Proteins by Polyelectrolyte Drugs

Dendritic polyelectrolytes constitute high potential drugs and carrier systems for biomedical purposes. Still, their biomolecular interaction modes, in particular those determining the binding affinity to proteins, have not been rationalized. We study the interaction of the drug candidate dendritic polyglycerol sulfate (dPGS) with serum proteins using isothermal titration calorimetry (ITC) interpreted and complemented with molecular computer simulations. Lysozyme is first studied as a well-defined model protein to verify theoretical concepts, which are then applied to the important cell adhesion protein family of selectins. We demonstrate that the driving force of the strong complexation, leading to a distinct protein corona, originates mainly from the release of only a few condensed counterions from the dPGS upon binding. The binding constant shows a surprisingly weak dependence on dPGS size (and bare charge) which can be understood by colloidal charge-renormalization effects and by the fact that the magnitude of the dominating counterion-release mechanism almost exclusively depends on the interfacial charge structure of the protein-specific binding patch. Our findings explain the high selectivity of P- and L-selectins over E-selectin for dPGS to act as a highly anti-inflammatory drug. The entire analysis demonstrates that the interaction of proteins with charged polymeric drugs can be predicted by simulations with unprecedented accuracy. Thus, our results open new perspectives for the rational design of charged polymeric drugs and carrier systems.

An aptamer-based biosensor for detection of doxorubicin by electrochemical impedance spectroscopy

An aptamer-based biosensor was developed for the detection of doxorubicin using electrochemical impedance spectroscopy. Doxorubicin and its 14-dehydroxylated version daunorubicin are anthracyclines often used in cancer treatment. Due to their mutagenic and cardiotoxic effects, detection in groundwater is desirable. We developed a biosensor using the daunorubicin-binding aptamer as biological recognition element. The aptamer was successfully co-immobilized with mercaptohexanol on gold and a density of 1.3*10¹³ ± 2.4*10¹² aptamer molecules per cm² was achieved. The binding of doxorubicin to the immobilized aptamer was detected by electrochemical impedance spectroscopy. The principle is based on the inhibition of electron transfer between electrode and ferro-/ferricyanide in solution caused by the binding of doxorubicin to the immobilized aptamer. A linear relationship between the charge transfer resistance (R _ct ) and the doxorubicin concentration was obtained over the range of 31 nM to 125 nM doxorubicin, with an apparent binding constant of 64 nM and a detection limit of 28 nM. With the advantages of high sensitivity, selectivity, and simple sensor construction, this method shows a high potential of impedimetric aptasensors in environmental monitoring. Graphical abstract Measurement chamber and immobilization principle for the detection of doxorubicin by electrochemical impedance spectroscopy.

A measure to quantify the degree of cooperativity in overall titration curves

In the framework of the grand canonical ensemble, different definitions of cooperativity commonly used in the context of ligand binding are not equivalent. A unifying definition is the existence of non-real roots of the binding polynomial. Using this qualitative criterion, an open question is how to quantify the degree of cooperativity. In this work, we introduce a theoretical measure to quantify the degree of cooperativity of a titriation curve. Its definition is based on a minimal energy approach mapping a given binding polynomial to the minimal interaction energy which is required to generate it. We show that the degree of cooperativity can be calculated easily, if the molecule under consideration is assumed to consist of energetically identical binding sites. Moreover, the property of sub-multiplicativity allows us to determine upper bounds for the degree of cooperativity in asymmetric systems. The approach is consistent with the qualitative definition of cooperativity based on the existence of non-real roots of the binding polynomial, and thus helps to put the concept of cooperativity on a solid theoretical ground. It connects macro- and microstates, but takes here also into account that an infinite number of different molecules can cause the same macroscopic ligand binding behavior, which means that the underlying microsystem cannot be uniquely identified based on the titration curve only.

PIP Water Transport and Its pH Dependence Are Regulated by Tetramer Stoichiometry

Many plasma membrane channels form oligomeric assemblies, and heterooligomerization has been described as a distinctive feature of some protein families. In the particular case of plant plasma membrane aquaporins (PIPs), PIP1 and PIP2 monomers interact to form heterotetramers. However, the biological properties of the different heterotetrameric configurations formed by PIP1 and PIP2 subunits have not been addressed yet. Upon coexpression of tandem PIP2-PIP1 dimers in Xenopus oocytes, we can address, for the first time to our knowledge, the functional properties of single heterotetrameric species having 2:2 stoichiometry. We have also coexpressed PIP2-PIP1 dimers with PIP1 and PIP2 monomers to experimentally investigate the localization and biological activity of each tetrameric assembly. Our results show that PIP2-PIP1 heterotetramers can assemble with 3:1, 1:3, or 2:2 stoichiometry, depending on PIP1 and PIP2 relative expression in the cell. All PIP2-PIP1 heterotetrameric species localize at the plasma membrane and present the same water transport capacity. Furthermore, the contribution of any heterotetrameric assembly to the total water transport through the plasma membrane doubles the contribution of PIP2 homotetramers. Our results also indicate that plasma membrane water transport can be modulated by the coexistence of different tetrameric species and by intracellular pH. Moreover, all the tetrameric species present similar cooperativity behavior for proton sensing. These findings throw light on the functional properties of PIP tetramers, showing that they have flexible stoichiometry dependent on the quantity of PIP1 and PIP2 molecules available. This represents, to our knowledge, a novel regulatory mechanism to adjust water transport across the plasma membrane.