Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications

Tetramethrin (TMT) is a commonly used insecticide and has a carcinogenic and neurodegenerative effect on humans. The binding mechanism and toxicological implications of TMT to human serum albumin (HSA) were examined in this study employing a combination of biophysical and computational methods indicating moderate binding affinity and potential hepato and renal toxicity. Fluorescence quenching experiments showed that TMT binds to HSA with a moderate affinity, and the binding process was spontaneous and predominantly enthalpy-driven. Circular dichroism spectroscopy revealed that TMT binding did not induce any significant conformational changes in HSA, resulting in no changes in its alpha-helix content. The binding site and modalities of TMT interactions with HSA as computed by molecular docking and molecular dynamics simulations revealed that it binds to Sudlow site II of HSA via hydrophobic interactions through its dimethylcyclopropane carboxylate methyl propanyl group. The structural dynamics of TMT induce proper fit into the binding site creating increased and stabilizing interactions. Additionally, molecular mechanics-Poisson Boltzmann surface area calculations also indicated that non-polar and van der Waals were found to be the major contributors to the high binding free energy of the complex. Quantum mechanics (QM) revealed the conformational energies of the binding confirmation and the degree of deviation from the global minimum energy conformation of TMT. The results of this study provide a comprehensive understanding of the binding mechanism of TMT with HSA, which is important for evaluating the toxicity of this insecticide in humans.

Integrated spectroscopic and computational analyses unravel the molecular interaction of pesticide azinphos-methyl with bovine beta-lactoglobulin

Organophosphorus are typically hazardous chemicals used in the pharmaceutical, agricultural, and other industries. They pose a serious risk to human life and can be fatal upon direct exposure. Hence, studying the interaction between such compounds with proteins is crucial for environmental, health, and food safety. In this study, we investigated the interaction mechanism between azinphos-methyl (AZM) and β-lactoglobulin (BLG) at pH 7.4 using a combination of biophysical techniques. Intrinsic fluorescence investigations revealed that BLG fluorescence was quenched in the presence of increasing AZM concentrations. The quenching mechanism was identified as static, as evidenced by a decrease in the fluorescence quenching constant (1.25 × 104, 1.18 × 104, and 0.86 × 104 M-1) with an increase in temperatures. Thermodynamic calculations (ΔH > 0; ΔS > 0) affirmed the formation of a complex between AZM and BLG through hydrophobic interactions. The BLG's secondary structure was found to be increased due to AZM interaction. Ultraviolet -visible spectroscopy data showed alterations in BLG conformation in the presence of AZM. Molecular docking highlighted the significant role of hydrophobic interactions involving residues such as Val43, Ile56, Ile71, Val92, Phe105, and Met107 in the binding between BLG and AZM. A docking energy of -6.9 kcal mol-1, and binding affinity of 1.15 × 105 M-1 suggest spontaneous interaction between AZM and BLG with moderate to high affinity. These findings underscore the potential health risks associated with the entry of AZM into the food chain, emphasizing the need for further consideration of its impact on human health.

Drivers of the In-Mouth Interaction between Lupin Protein Isolate and Selected Aroma Compounds: A Proton Transfer Reaction-Mass Spectrometry and Dynamic Time Intensity Analysis

Plant proteins often carry off-notes, necessitating customized aroma addition. In vitro studies revealed protein-aroma binding, limiting release during consumption. This study employs in vivo nose space proton transfer reaction-time-of-flight-mass spectrometry and dynamic sensory evaluation (time intensity) to explore in-mouth interactions. In a lupin protein-based aqueous system, a sensory evaluation of a trained "green" attribute was conducted simultaneously with aroma release of hexanal, nonanal, and 2-nonanone during consumption. Results demonstrated that enlarging aldehyde chains and relocating the keto group reduced maximum perceived intensity (Imax_R) by 71.92 and 72.25%. Protein addition decreased Imax_R by 30.91, 36.84, and 72.41%, indicating protein-aroma interactions. Sensory findings revealed a perceived intensity that was lower upon protein addition. Aroma lingering correlated with aroma compounds' volatility and hydrophobicity, with nonanal exhibiting the longest persistence. In vitro mucin addition increased aroma binding four to 12-fold. Combining PTR-ToF-MS and time intensity elucidated crucial food behavior, i.e., protein-aroma interactions, that are pivotal for food design.

Minimal Determinants for Lifelong Antiviral Antibody Responses in Mice from a Single Exposure to Virus-like Immunogens at Low Doses

The durability of an antibody (Ab) response is highly important for antiviral vaccines. However, due to the complex compositions of natural virions, the molecular determinants of Ab durability from viral infection or inactivated viral vaccines have been incompletely understood. Here we used a reductionist system of liposome-based virus-like structures to examine the durability of Abs from primary immune responses in mice. This system allowed us to independently vary fundamental viral attributes and to do so without additional adjuvants to model natural viruses. We show that a single injection of protein antigens (Ags) orderly displayed on a virion-sized liposome is sufficient to induce a long-lived neutralizing Ab (nAb) response. The introduction of internal nucleic acids dramatically modulates the magnitude of Ab responses without an alteration of the long-term kinetic trends. These Abs are characterized by very slow off-rates of ~0.0005 s-1, which emerged as early as day 5 after injection and these off-rates are comparable to that of affinity-matured monoclonal Abs. A single injection of these structures at doses as low as 100 ng led to lifelong nAb production in mice. Thus, a minimal virus-like immunogen can give rise to potent and long-lasting antiviral Abs in a primary response in mice without live infection. This has important implications for understanding both live viral infection and for optimizing vaccine design.

Structural and Functional Insights into CRF Peptides and Their Receptors

Corticotropin-releasing factor or hormone (CRF or CRH) and the urocortins regulate a plethora of physiological functions and are involved in many pathophysiological processes. CRF and urocortins belong to the family of CRF peptides (CRF family), which includes sauvagine, urotensin, and many synthetic peptide and non-peptide CRF analogs. Several of the CRF analogs have shown considerable therapeutic potential in the treatment of various diseases. The CRF peptide family act by interacting with two types of plasma membrane proteins, type 1 (CRF1R) and type 2 (CRF2R), which belong to subfamily B1 of the family B G-protein-coupled receptors (GPCRs). This work describes the structure of CRF peptides and their receptors and the activation mechanism of the latter, which is compared with that of other GPCRs. It also discusses recent structural information that rationalizes the selective binding of various ligands to the two CRF receptor types and the activation of receptors by different agonists.

Neural correlates of an illusionary sense of agency caused by virtual reality

Sense of agency (SoA) is the sensation that self-actions lead to ensuing perceptual consequences. The prospective mechanism emphasizes that SoA arises from motor prediction and its comparison with actual action outcomes, while the reconstructive mechanism stresses that SoA emerges from retrospective causal processing about the action outcomes. Consistent with the prospective mechanism, motor planning regions were identified by neuroimaging studies using the temporal binding (TB) effect, a behavioral measure often linked to implicit SoA. Yet, TB also occurs during passive observation of another's action, lending support to the reconstructive mechanism, but its neural correlates remain unexplored. Here, we employed virtual reality (VR) to modulate such observation-based SoA and examined it with functional magnetic resonance imaging (fMRI). After manipulating an avatar hand in VR, participants passively observed an avatar's "action" and showed a significant increase in TB. The binding effect was associated with the right angular gyrus and inferior parietal lobule, which are critical nodes for inferential and agency processing. These results suggest that the experience of controlling an avatar may potentiate inferential processing within the right inferior parietal cortex and give rise to the illusionary SoA without voluntary action.

Design, Characterization, and Incorporation of the Alkaline Aluminosilicate Binder in Temperature-Insulating Composites

This paper covers the design of binder formulations and technology for low-energy building materials based on alkaline aluminosilicate binders developed for special uses. The microstructure of the binders was investigated using scanning electron and atomic force microscopy examination techniques. The identification of phase compositions was performed by means of X-ray diffraction. The degree of binding of the alkali metal ions within the binder was determined with the help of chemical analysis of the pore fluid. Structure formation depending upon binder mix design and curing conditions was also studied. Some examples of the manufacture and application of binder-based glues and adhesives, including those developed for heat insulation and fire prevention, are discussed. The advantages of binder-based temperature-insulating composite materials compared with traditionally used materials are highlighted.

In Vitro and In Silico Analysis of the Bindings between Legacy and Novel Per- and Polyfluoroalkyl Substances and Human Serum Albumin

Per- and polyfluoroalkyl substances (PFASs) are emerging contaminants of concern that can enter the human body through a variety of pathways and thereby cause harmful effects. Exposure of pregnant women to PFASs could even affect both the mother and the child. Human serum albumin (HSA) is considered to be the primary transport protein for a variety of substances in body fluids. It can be bound to different contaminants and might result in possible effects on human health. Yet, few studies are available on the binding affinity of legacy PFASs and their novel alternatives to HSA. In this study, the binding mechanisms of HSA to both legacy PFASs and their novel alternatives were investigated using fluorescence spectroscopy, together with further molecular docking. The results show that all the target PFASs were statically quenched against HSA with binding ratios of 1:1. The binding constants of long-chain PFASs and novel alternatives of perfluoroalkanesulfonic acids (PFSAs) were greater than 102, whereas those of short-chain PFASs alternatives and novel alternatives of perfluorocarboxylic acids (PFCAs) were less than 102. In general, the binding affinities of PFCAs on HSA were less than that of PFSAs, while the binding affinities of short-chain PFASs alternatives on HSA were smaller than those of long-chain PFASs and their novel alternatives. Therefore, bindings to HSA could be considered as an important influencing factor for the bioaccumulation of legacy and novel PFASs in the human body.

Co-occurring ripple oscillations facilitate neuronal interactions between cortical locations in humans

How the human cortex integrates ("binds") information encoded by spatially distributed neurons remains largely unknown. One hypothesis suggests that synchronous bursts of high-frequency oscillations ("ripples") contribute to binding by facilitating integration of neuronal firing across different cortical locations. While studies have demonstrated that ripples modulate local activity in the cortex, it is not known whether their co-occurrence coordinates neural firing across larger distances. We tested this hypothesis using local field-potentials and single-unit firing from four 96-channel microelectrode arrays in the supragranular cortex of 3 patients. Neurons in co-rippling locations showed increased short-latency co-firing, prediction of each other's firing, and co-participation in neural assemblies. Effects were similar for putative pyramidal and interneurons, during non-rapid eye movement sleep and waking, in temporal and Rolandic cortices, and at distances up to 16 mm (the longest tested). Increased co-prediction during co-ripples was maintained when firing-rate changes were equated, indicating that it was not secondary to non-oscillatory activation. Co-rippling enhanced prediction was strongly modulated by ripple phase, supporting the most common posited mechanism for binding-by-synchrony. Co-ripple enhanced prediction is reciprocal, synergistic with local upstates, and further enhanced when multiple sites co-ripple, supporting re-entrant facilitation. Together, these results support the hypothesis that trans-cortical co-occurring ripples increase the integration of neuronal firing of neurons in different cortical locations and do so in part through phase-modulation rather than unstructured activation.

A Robust and Efficient FRET-Based Assay for Cannabinoid Receptor Ligands Discovery

The identification of new modulators for Cannabinoid Receptors (CBRs) has garnered significant attention in drug discovery over recent years, owing to their manifold pathophysiological implications. In the context of hit identification, the availability of robust and sensitive high-throughput screening assays is essential to enhance the likelihood of success. In this study, we present the development and validation of a Tag-lite® binding assay designed for screening hCB1/hCB2 binding, employing a dual fluorescent ligand, CELT-335. Representative ligands for CBRs, exhibiting diverse affinity and functional profiles, were utilized as reference compounds to validate the robustness and efficiency of the newly developed Tag-lite® binding assay protocol. The homogeneous format, coupled with the sensitivity and optimal performance of the fluorescent ligand CELT-335, establishes this assay as a viable and reliable method for screening in hit and lead identification campaigns.

Solvent Acts as the Referee in a Match-Up Between Charged and Preorganized Receptors

The prevalence of anion-cation contacts in biomolecular recognition under aqueous conditions suggests that ionic interactions should dominate the binding of anions in solvents across both high and low polarities. Investigations of this idea using titrations in low polarity solvents are impaired by interferences from ion pairing that prevent a clear picture of binding. To address this limitation and test the impact of ion-ion interactions across multiple solvents, we quantified chloride binding to a cationic receptor after accounting for ion pairing. In these studies, we created a chelate receptor using aryl-triazole CH donors and a quinolinium unit that directs its cationic methyl inside the binding pocket. In low-polarity dichloromethane, the 1 : 1 complex (log K1 : 1 ~ 7.3) is more stable than neutral chelates, but fortuitously comparable to a preorganized macrocycle (log K1 : 1 ~ 6.9). Polar acetonitrile and DMSO diminish stabilities of the charged receptor (log K1 : 1 ~ 3.7 and 1.9) but surprisingly 100-fold more than the macrocycle. While both receptors lose stability by dielectric screening of electrostatic stability, the cationic receptor also pays additional costs of organization. Thus even though the charged receptor has stronger binding in apolar solvents, the uncharged receptor has more anion affinity in polar solvents.

Aggregation and cytotoxicity of food additive dye (Azorubine)-albumin adducts: a multi-spectroscopic, microscopic and computational analysis

Protein and peptide misfolding is a central factor in the formation of pathological aggregates and fibrils linked to disorders like Alzheimer's and Parkinson's diseases. Therefore, it's essential to understand how food additives, particularly Azorubine, affect protein structures and their ability to induce aggregation. In this study, human serum albumin (HSA) was used as a model protein to investigate the binding and conformational changes caused by azorubine, a common food and drink colorant. The research revealed that azorubine destabilized the conformation of HSA at both physiological (pH 7.4) and acidic (pH 3.5) conditions. The loss of tryptophan fluorescence in HSA suggested significant structural alterations, particularly around aromatic residues. Far UV-CD analysis demonstrated disruptions in HSA's secondary structure, with a notable reduction in α-helical structures at pH 7.4. At pH 3.5, Azorubine induced even more extensive perturbations, resulting in a random coil conformation at higher azorubine concentrations. The study also investigated aggregation phenomena through turbidity measurements, RLS analysis, and TEM imaging. At pH 3.5, larger insoluble aggregates formed, while at pH 7.4, only conformational changes occurred without aggregate formation. Cytotoxicity assessments on neuroblastoma (SH-SY5Y) cells highlighted the concentration-dependent toxicity of albumin aggregates. Molecular dynamics simulations reaffirmed the stable interaction between azorubine and HSA. This research provides valuable insights into the mechanisms by which azorubine influences protein conformations. To further advance our understanding and contribute to the broader knowledge in this area, several future directions can be considered such as exploring other proteins, studying dose-response relationship, gaining mechanistic insights, biological relevance, toxicity assessment, identifying alternative food colorants, and mitigation strategies to prevent adverse effects of azorubine on serum proteins.Communicated by Ramaswamy H. Sarma.

Virucidal activity of trehalose 6-monolaurate against dengue virus in vitro

Dengue fever is an acute febrile disease caused by dengue virus (DENV) infection. Over the past 60 years, DENV has spread throughout tropical regions and currently affects more than 50% of the world's population; however, there are as of yet no effective anti-DENV drugs for clinical treatment. A number of research teams have investigated derivatives of glycolipids as possible agents for the inhibition of DENV. Our objective in this research was to study the antiviral effects of trehalose 6-caprate (TMC), trehalose 6-monolaurate (TML), and trehalose 6-monooleate (TMO), based on reports that the corresponding glycosyl, trehalose, reduces the transmission of Zika virus (ZIKV). We also sought to elucidate the molecular mechanisms underlying inhibition using the RNA isolation and reverse transcription-quantitative polymerase chain reaction, western blot analysis, median tissue culture infectious dose (TCID50 ) assay, and immunofluorescence assay and immunochemistry staining, in vitro. This is the first study to demonstrate the TML-induced inhibition of DENV serotype 2 (DENV-2) in a dose-dependent manner. The inhibitory effects of TML in the pretreated, cotreated, and full-treated groups were confirmed using time of addition assays. We determined that TML restricted viral binding, entry, replication, and release. We also confirmed the efficacy of TML against three clinical isolates of DENV serotypes 1, 3, and 4 (DENV-1, DENV-3, and DENV-4). The findings obtained in this study identify TML as a promising candidate for the development of drugs to treat DENV infection.

Structural plasticity of omicron BA.5 and BA.2.75 for enhanced ACE-dependent entry into cells

The current study investigated the binding variations among the wilt type, Omicron sub-variants BA.2.75 and BA.5, using protein-protein docking, protein structural graphs (P SG), and molecular simulation methods. HADDOCK predicted docking scores and dissociation constant (KD) revealed tighter binding of these sub-variants in contrast to the WT. Further investigation revealed variations in the hub residues, protein sub-networks, and GlobalMetapath in these variants as compared to the WT. A very unusual dynamic for BA.2.75 and BA.5 was observed, and secondary structure transition can also be witnessed in the loops (44-505). The results show that the flexibility of these three loops is increased by the mutations as an allosteric effect and thus enhances the chances of bonding with the nearby residues to connect and form a stable connection. Furthermore, the additional hydrogen bonding contacts steer the robust binding of these variants in contrast to the wild type. The total binding free energy for the wild type was calculated to be -61.38 kcal/mol, while for BA.2.75 and BA.5 variants the T BE was calculated to be -70.42 kcal/mol and 69.78 kcal/mol, respectively. We observed that the binding of BA.2.75 is steered by the electrostatic interactions while the BA.5 additional contacts are due to the vdW (Van der Waal) energy. From these findings, it can be observed the Spike (S) protein is undergoing structural adjustments to bind efficiently to the hACE2 (human angiotensin-converting enzyme 2) receptor and, in turn, increase entry to the host cells. The current study will aid the development of structure-based drugs against these variants.Communicated by Ramaswamy H. Sarma.

A mechanistic insight into sources of error of visual working memory in multiple sclerosis

Working memory (WM) is one of the most affected cognitive domains in multiple sclerosis (MS), which is mainly studied by the previously established binary model for information storage (slot model). However, recent observations based on the continuous reproduction paradigms have shown that assuming dynamic allocation of WM resources (resource model) instead of the binary hypothesis will give more accurate predictions in WM assessment. Moreover, continuous reproduction paradigms allow for assessing the distribution of error in recalling information, providing new insights into the organization of the WM system. Hence, by utilizing two continuous reproduction paradigms, memory-guided localization (MGL) and analog recall task with sequential presentation, we investigated WM dysfunction in MS. Our results demonstrated an overall increase in recall error and decreased recall precision in MS. While sequential paradigms were better in distinguishing healthy control from relapsing-remitting MS, MGL were more accurate in discriminating MS subtypes (relapsing-remitting from secondary progressive), providing evidence about the underlying mechanisms of WM deficit in progressive states of the disease. Furthermore, computational modeling of the results from the sequential paradigm determined that imprecision in decoding information and swap error (mistakenly reporting the feature of other presented items) was responsible for WM dysfunction in MS. Overall, this study offered a sensitive measure for assessing WM deficit and provided new insight into the organization of the WM system in MS population.

Enhanced antioxidant and cytotoxic activity of ferrocenyl-substituted curcumin via stabilization of promoter c-MYC silencer element

We are reporting a successful attachment of ferrocenyl moiety at the active methylene carbon atom of β-diketone of curcumin via Knoevenagel condensation reaction, to utilize the optimum selectivity toward biological targets. The formation of ferrocenyl curcumin (i.e., Fc-cur) has been confirmed by 1H NMR, 13C NMR, and FT-IR spectra analysis. Further, circular dichroism (CD) spectroscopy, thermal denaturation, absorption, and fluorescence spectroscopy have been used to understand the association of ligand (i.e., Fc-cur) with G-quadruplex. Based on these analysis, the binding mechanism of the ligand i.e., Fc-cur to the parallel and hybrid topology present in different G-quadruplex has been proposed. Further, the binding and modes of the interaction of Fc-cur with Pu27 c-MYC silencer element and H-telo G-quadruplex have unravelled selective and stronger binding via intercalation with the parallel topology of c-MYC G-quadruplex rather than the hybrid topology of H-telo quadruplex. The manifestation of better antioxidant activity of Fc-cur has been demonstrated by showing a stronger radical scavenging capability than pristine curcumin. The cytotoxicity analysis of the proposed ligand i.e., Fc-cur against Vero and HeLa cells have clearly reflected the nontoxicity toward Vero cells and quite effective against the HeLa cells which reduces the cancer cells more effectively than the already reported for curcumin.Communicated by Ramaswamy H. Sarma.

Agency effects on the binding of event elements in episodic memory

Representing events in episodic memory in a coherent manner requires that their constituent elements are bound together. So far, only few moderators of these binding processes have been identified. Here we investigate whether the presence of an agentic element in an event facilitates binding. The results from six experiments provided no evidence for a facilitating effect of agency on the binding of event elements. In addition, binding effects were only found when event elements were presented simultaneously, but not when they were presented sequentially pairwise, contrary to previous findings. The results suggest that the presence of an agentic element in an event does not, or only to a very limited extent, contribute to the formation of coherent memory representations and that additional processes may be required when binding event elements across temporarily divided encoding episodes. These findings add to a growing body of research regarding moderators and processes relevant for the binding of event elements in episodic memory. Explanations of these findings and directions for future research are discussed.

Inhibition, Attentional Control and Binding Abilities in Relation to Dissociative Symptoms Among PTSD Patients

INTRODUCTION

The relationship between dissociation and cognitive abilities remains controversial. Empirical studies have reported positive, negative and non-existent associations between dissociation and cognition. These inconsistent results may be due to the fact that the studies focused mainly on trait dissociation, while dissociation is not stable but transient. After validating the French version of the Clinician Administered Dissociative States Scale (CADSS), the aim of the present study was to evaluate the relationship between state dissociation and cognitive abilities.

METHOD

We recruited 83 patients suffering from post-traumatic stress disorder (PTSD) and assessed them twice. At T1, they performed a neutral Stroop task and a neutral binding task. At T2 (one to three weeks later), after a script-driven dissociative induction, they performed an emotional Stroop task and an emotional binding task. Between the two sessions, they completed questionnaires at home evaluating PTSD severity, trait dissociation and cognitive difficulties. State dissociation was assessed at T1 and T2 using the Clinician-Administered Dissociative States Scale (CADSS).

RESULTS

We found good psychometric properties of the French version of the CADSS. After inducing dissociation, significantly lower attentional performance was found among patients with than without dissociative reactions. We found a significant positive correlation between state dissociation and increased attention and memory difficulties after induction.

CONCLUSION

The French version of the CADSS is a reliable and valid tool to assess state dissociation, which is correlated with attentional difficulties. Attentional training is recommended to help patients control dissociative symptoms.

Serum Albumin Aggregation Facilitated by Cobalt and Chromium Metal Ions

The interaction of serum proteins with cobalt (Co) and chromium (Cr) ions is poorly understood, but it is suspected to result in protein aggregation, which may alter the corrosion process of biomedical CoCr alloys or result in adverse health effects. Here, we study the aggregation ability and mechanism of bovine serum albumin (BSA) induced or accelerated by aqueous Co(II) and Cr(III) ions. The metal salts were selected by chemical speciation modeling, and they did not affect the pH or precipitate under simulated physiological conditions (150 mM NaCl and pH 7.3). The counterion of Cr(III) influenced the binding to BSA only at physiologically irrelevant low ionic strength. This study used a variety of spectroscopic and light scattering methods. It was determined that both metal ions and an equimolar mixture of metal ions have the potential to induce protein aggregation. Melting curves collected by circular dichroism spectroscopy indicate that Co(II) significantly reduced BSA's melting temperature when compared with Cr(III) or an equimolar mixture of Co(II) and Cr(III), both of which increased the melting temperature of BSA. The metal ions in solution preferentially interacted with BSA, resulting in the depletion of metal ions from the surrounding protein-free solution. Finally, this study suggests that the likely mechanism for Co(II)- and Cr(III)-induced BSA aggregation is salt bridging between protein molecules.

Interactionally Embedded Gestalt Principles of Multimodal Human Communication

Natural human interaction requires us to produce and process many different signals, including speech, hand and head gestures, and facial expressions. These communicative signals, which occur in a variety of temporal relations with each other (e.g., parallel or temporally misaligned), must be rapidly processed as a coherent message by the receiver. In this contribution, we introduce the notion of interactionally embedded, affordance-driven gestalt perception as a framework that can explain how this rapid processing of multimodal signals is achieved as efficiently as it is. We discuss empirical evidence showing how basic principles of gestalt perception can explain some aspects of unimodal phenomena such as verbal language processing and visual scene perception but require additional features to explain multimodal human communication. We propose a framework in which high-level gestalt predictions are continuously updated by incoming sensory input, such as unfolding speech and visual signals. We outline the constituent processes that shape high-level gestalt perception and their role in perceiving relevance and prägnanz. Finally, we provide testable predictions that arise from this multimodal interactionally embedded gestalt-perception framework. This review and framework therefore provide a theoretically motivated account of how we may understand the highly complex, multimodal behaviors inherent in natural social interaction.

Structural communication fingerprinting and dynamic investigation of RBD-hACE2 complex from BA.1 × AY.4 recombinant variant (Deltacron) of SARS-CoV-2 to decipher the structural basis for enhanced transmission

The BA.1 × AY.4 recombinant variant (Deltacron) continues to inflict chaos globally due to its rapid transmission and infectivity. To decipher the mechanism of pathogenesis by the BA.1 × AY.4 recombinant variant (Deltacron), a protein coupling, protein structural graphs (PSG), residue communication and all atoms simulation protocols were used. We observed that the bonding network is altered by this variant; engaging new residues that helps to robustly bind. HADDOCK docking score for the wild type has been previously reported to be -111.8 ± 1.5 kcal/mol while the docking score for the Deltacron variant was calculated to be -128.3 ± 2.5 kcal/mol. The protein structural graphs revealed variations in the hub residues, number of nodes, inter and intra residues communities, and path communication perturbation caused by the acquired mutations in the Deltacron-RBD thus alter the binding approach and infectivity. Moreover, the dynamic behaviour reported a highly flexible structure with enhanced residues flexibility particularly by the loops required for interaction with ACE2. It was observed that these mutations have altered the secondary structure of the RBD mostly transited to the loops thus acquired higher flexible dynamics than the native structure during the simulation. The total binding free energy for each of these complexes, that is, WT-RBD and Deltacron-RBD were reported to be -61.38 kcal/mol and -70.47 kcal/mol. Protein's motion revealed a high trace value in the Deltacron variant that clearly depict more structural flexibility. The broad range of phase space covered by the Deltacron variant along PC1 and PC2 suggests that these mutations are important in contributing conformational heterogeneity or flexibility that consequently help the variant to bind more efficiently than the wild type. The current study provides a basis for structure-based drug designing against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Resistance to anti-PD-1/anti-PD-L1: galectin-3 inhibition with GB1211 reverses galectin-3-induced blockade of pembrolizumab and atezolizumab binding to PD-1/PD-L1

Background

Galectin-3 (Gal-3) is a β-galactoside-binding lectin that is highly expressed within the tumor microenvironment of aggressive cancers and has been suggested to predict a poor response to immune checkpoint therapy with the anti-PD-1 monoclonal antibody pembrolizumab. We aimed to assess if the effect of Gal-3 was a result of direct interaction with the immune checkpoint receptor.

Methods

The ability of Gal-3 to interact with the PD-1/PD-L1 complex in the absence and presence of blocking antibodies was assessed in in vitro biochemical and cellular assays as well as in an in vivo syngeneic mouse cancer model.

Results

Gal-3 reduced the binding of the checkpoint inhibitors pembrolizumab (anti-PD-1) and atezolizumab (anti-PD-L1), by potentiating the interaction between the PD-1/PD-L1 complex. In the presence of a highly selective Gal-3 small molecule inhibitor (GB1211) the binding of the anti-PD-1/anti-PD-L1 therapeutics was restored to control levels. This was observed in both a surface plasmon resonance assay measuring protein-protein interactions and via flow cytometry. Combination therapy with GB1211 and an anti-PD-L1 blocking antibody reduced tumor growth in an in vivo syngeneic model and increased the percentage of tumor infiltrating T lymphocytes.

Conclusion

Our study suggests that Gal-3 can potentiate the PD-1/PD-L1 immune axis and potentially contribute to the immunosuppressive signalling mechanisms within the tumor microenvironment. In addition, Gal-3 prevents atezolizumab and pembrolizumab target engagement with their respective immune checkpoint receptors. Reversal of this effect with the clinical candidate GB1211 offers a potential enhancing combination therapeutic with anti-PD-1 and -PD-L1 blocking antibodies.

Binding and Sliding Dynamics of the Hepatitis C Virus Polymerase: Hunting the 3' Terminus

The hepatitis C virus (HCV) nonstructural protein 5B (NS5B) polymerase catalyzes the replication of the (+) single-stranded RNA genome of HCV. In vitro studies have shown that replication can be performed in the absence of a primer. However, the dynamics and mechanism by which NS5B locates the 3'-terminus of the RNA template to initiate de novo synthesis remain elusive. Here, we performed single-molecule fluorescence studies based on protein-induced fluorescence enhancement reporting on NS5B dynamics on a short model RNA substrate. Our results suggest that NS5B exists in a fully open conformation in solution wherefrom it accesses its binding site along RNA and then closes. Our results revealed two NS5B binding modes: an unstable one resulting in rapid dissociation, and a stable one characterized by a larger residence time on the substrate. We associate these bindings to an unproductive and productive orientation, respectively. Addition of extra mono (Na+)- and divalent (Mg2+) ions increases the mobility of NS5B along its RNA substrate. However, only Mg2+ ions induce a decrease in NS5B residence time. Dwell times of residence increase with the length of the single-stranded template, suggesting that NS5B unbinds its substrate by unthreading the template rather than by spontaneous opening.

In vivo and in vitro characterizations of melibiose permease (MelB) conformation-dependent nanobodies reveal sugar-binding mechanisms

Salmonella enterica serovar Typhimurium melibiose permease (MelBSt) is a prototype of the Na+-coupled major facilitator superfamily transporters, which are important for the cellular uptake of molecules including sugars and small drugs. Although the symport mechanisms have been well-studied, mechanisms of substrate binding and translocation remain enigmatic. We have previously determined the sugar-binding site of outward-facing MelBSt by crystallography. To obtain other key kinetic states, here we raised camelid single-domain nanobodies (Nbs) and carried out a screening against the WT MelBSt under 4 ligand conditions. We applied an in vivo cAMP-dependent two-hybrid assay to detect interactions of Nbs with MelBSt and melibiose transport assays to determine the effects on MelBSt functions. We found that all selected Nbs showed partial to complete inhibitions of MelBSt transport activities, confirming their intracellular interactions. A group of Nbs (714, 725, and 733) was purified, and isothermal titration calorimetry measurements showed that their binding affinities were significantly inhibited by the substrate melibiose. When titrating melibiose to the MelBSt/Nb complexes, Nb also inhibited the sugar-binding. However, the Nb733/MelBSt complex retained binding to the coupling cation Na+ and also to the regulatory enzyme EIIAGlc of the glucose-specific phosphoenolpyruvate/sugar phosphotransferase system. Further, EIIAGlc/MelBSt complex also retained binding to Nb733 and formed a stable supercomplex. All data indicated that MelBSt trapped by Nbs retained its physiological functions and the trapped conformation is similar to that bound by the physiological regulator EIIAGlc. Therefore, these conformational Nbs can be useful tools for further structural, functional, and conformational analyses.

Soluble SARS-CoV-2 RBD and human ACE2 peptidase domain produced in Drosophila S2 cells show functions evoking virus-cell interface

The interaction between the receptor-binding domain (RBD) of the spike glycoprotein of SARS-CoV-2 and the peptidase domain of the human angiotensin-converting enzyme 2 (ACE2) allows the first specific contact at the virus-cell interface making it the main target of neutralizing antibodies. Here, we show a unique and cost-effective protocol using Drosophila S2 cells to produce both RBD and soluble human ACE2 peptidase domain (shACE2) as thermostable proteins, purified via Strep-tag with yields >40 mg L-1 in a laboratory scale. Furthermore, we demonstrate its binding with KD values in the lower nanomolar range (independently of Strep-tag removal) and its capability to be blocked by serum antibodies in a competition ELISA with Strep-Tactin-HRP as a proof-of-concept. In addition, we assess the capacity of RBD to bind native dimeric ACE2 overexpressed in human cells and its antigen properties with specific serum antibodies. Finally, for completeness, we analyzed RBD microheterogeneity associated with glycosylation and negative charges, with negligible effect on binding either with antibodies or shACE2. Our system represents an accessible and reliable tool for designing in-house surrogate virus neutralization tests (sVNTs), enabling the rapid characterization of neutralizing humoral responses elicited against vaccines or infection, especially in the absence of facilities to conduct virus neutralization tests. Moreover, our biophysical and biochemical characterization of RBD and shACE2 produced in S2 cells lays the groundwork for adapting to different variants of concern (VOCs) to study humoral responses elicited against different VOCs and vaccine formulations.

Heterodimers Are an Integral Component of Chemokine Signaling Repertoire

Chemokines are a family of signaling proteins that play a crucial role in cell-cell communication, cell migration, and cell trafficking, particularly leukocytes, under both normal and pathological conditions. The oligomerization state of chemokines influences their biological activity. The heterooligomerization occurs when multiple chemokines spatially and temporally co-localize, and it can significantly affect cellular responses. Recently, obligate heterodimers have emerged as tools to investigate the activities and molecular mechanisms of chemokine heterodimers, providing valuable insights into their functional roles. This review focuses on the latest progress in understanding the roles of chemokine heterodimers and their contribution to the functioning of the chemokine network.

A comparison of the binding sites of antibodies and single-domain antibodies

Antibodies are the largest class of biotherapeutics. However, in recent years, single-domain antibodies have gained traction due to their smaller size and comparable binding affinity. Antibodies (Abs) and single-domain antibodies (sdAbs) differ in the structures of their binding sites: most significantly, single-domain antibodies lack a light chain and so have just three CDR loops. Given this inherent structural difference, it is important to understand whether Abs and sdAbs are distinguishable in how they engage a binding partner and thus, whether they are suited to different types of epitopes. In this study, we use non-redundant sequence and structural datasets to compare the paratopes, epitopes and antigen interactions of Abs and sdAbs. We demonstrate that even though sdAbs have smaller paratopes, they target epitopes of equal size to those targeted by Abs. To achieve this, the paratopes of sdAbs contribute more interactions per residue than the paratopes of Abs. Additionally, we find that conserved framework residues are of increased importance in the paratopes of sdAbs, suggesting that they include non-specific interactions to achieve comparable affinity. Furthermore, the epitopes of sdAbs are only marginally less accessible than those of Abs: we posit that this may be explained by differences in the orientation and compaction of sdAb and Ab CDR-H3 loops. Overall, our results have important implications for the engineering and humanization of sdAbs, as well as the selection of the best modality for targeting a particular epitope.

Affinity of Tannins to Cellulose: A Chromatographic Tool for Revealing Structure-Activity Patterns

Food, feed and beverage processing brings tannins into contact with macromolecules, such as proteins and polysaccharides, leading to different chemical and physical interactions. The interactions of tannins with proteins are well known but less is known about the affinity of tannins to polysaccharides. We used bacterial cellulose from nata de coco as a model compound to investigate how tannins and cellulose interact by adsorption measurements using UPLC-DAD. We also explored how the structure of tannins influences these interactions. The model tannins included nine individual structurally different hydrolysable tannins (HTs) and eight well-defined proanthocyanidin (PA) fractions with different monomeric units, mean degree of polymerization and both A- and B-type linkages. Tannins were found to have both strong and weak interactions with bacterial cellulose, depending on the exact structure of the tannin. For HTs, the main structural features affecting the interactions were the structural flexibility of the HT molecule and the number of free galloyl groups. For PAs, prodelphinidins were found to have a higher affinity to cellulose than procyanidins. Similarly to HTs, the presence of free galloyl groups in galloylated PAs and the flexibility of the PA molecule led to a stronger interaction. Adsorption measurements by UPLC-DAD proved to be a sensitive and rapid tool to evaluate the affinity of tannins to cellulose.

Longitudinal Exploration of Binding Ability across Early Childhood: The Differential Contribution of Hits and False Alarms

Childhood is a period of pronounced improvements in children's ability to remember connections between details of an event (i.e. binding ability). However, the mechanisms supporting these changes remain unclear. Prior evidence is mixed, with some proposing that improvements in the ability to identify previous connections (i.e. increases in hits) account for memory changes, whereas other evidence suggests changes are additionally supported by the ability to identify inaccurate connections (i.e. decreases in false alarms). To disentangle the role of each process, we investigated changes in hits and false alarms within the same paradigm. The present study of 200 4-to-8-year-old children (100 female) used a cohort sequential design to assess longitudinal change in binding ability. Developmental trajectories of d', hit, and false alarm rates were examined using latent growth analysis. Findings demonstrated non-linear improvements in children's binding ability from age 4-to-8-years. Improvements were differentially supported by hits and false alarms. Hit rates improved non-linearly from 4-to-8-years, with greater growth from 4-to-6-years. False alarm rates did not significantly change from 4-to-6-years, but significantly decreased from 6-to-8-years. Overall, findings show improvements in binding ability are predominantly supported by increased hit rates between 4-to-6-years and by both increasing hit rates and decreasing false alarms rates between 6-to-8-years. Together, these results suggest that binding development is non-linear and that mechanisms underlying improvements differ across childhood.

Insights into Chemical Structure-Based Modeling for New Sweetener Discovery

The search for novel, natural, high-sweetness, low-calorie sweeteners remains open and challenging. In the present study, the structure-based machine learning modeling and sweetness recognition mechanism were investigated to assist this process. It was found that whether or not a compound was sweet was closely related to molecular connectivity and composition (the number of hydrogen bond acceptors and donors), tpsaEfficiency, structural complexity, and shape (nAtomP and Fsp3). While the relative sweetness of sweet compounds was more determined by the molecular properties (tpsaEfficiency and Log P), structural complexity and composition (nAtomP and ATSm 1). The built machine learning models exhibited very good performance for classifying the sweet/non-sweet compounds and predicting the relative sweetness of the compounds. Moreover, a specific binding pocket was found for sweet compounds, and the sweet compounds mainly interacted with the VFT domain of the T1R2-T1R3 through hydrogen bonds. In addition, the results indicated that among the sweet compounds, those that were sweeter bound to the VFT domain stronger than those that had low sweetness. This study provides very useful information for developing new sweeteners.

Behavioral and neuro-functional consequences of eliminating the KCNQ3 GABA binding site in mice

Voltage-gated potassium (Kv) channels formed by α subunits KCNQ2-5 are important in regulating neuronal excitability. We previously found that GABA directly binds to and activates channels containing KCNQ3, challenging the traditional understanding of inhibitory neurotransmission. To investigate the functional significance and behavioral role of this direct interaction, mice with a mutated KCNQ3 GABA binding site (Kcnq3-W266L) were generated and subjected to behavioral studies. Kcnq3-W266L mice exhibited distinctive behavioral phenotypes, of which reduced nociceptive and stress responses were profound and sex-specific. In female Kcnq3-W266L mice, the phenotype was shifted towards more nociceptive effects, while in male Kcnq3-W266L mice, it was shifted towards the stress response. In addition, female Kcnq3-W266L mice exhibited lower motor activity and reduced working spatial memory. The neuronal activity in the lateral habenula and visual cortex was altered in the female Kcnq3-W266L mice, suggesting that GABAergic activation of KCNQ3 in these regions may play a role in the regulation of the responses. Given the known overlap between the nociceptive and stress brain circuits, our data provide new insights into a sex-dependent role of KCNQ3 in regulating neural circuits involved in nociception and stress, via its GABA binding site. These findings identify new targets for effective treatments for neurological and psychiatric conditions such as pain and anxiety.

Human Hemoglobin and Antipsychotics Clozapine, Ziprasidone and Sertindole: Friends or Foes?

Packed with hemoglobin, an essential protein for oxygen transport, human erythrocytes are a suitable model system for testing the pleiotropic effects of lipophilic drugs. Our study investigated the interaction between antipsychotic drugs clozapine, ziprasidone, sertindole, and human hemoglobin under simulated physiological conditions. Analysis of protein fluorescence quenching at different temperatures and data obtained from the van't Hoff diagram and molecular docking indicate that the interactions are static and that the tetrameric human hemoglobin has one binding site for all drugs in the central cavity near αβ interfaces and is dominantly mediated through hydrophobic forces. The association constants were lower-moderate strength (~10⁴ M^-1), the highest observed for clozapine (2.2 × 10⁴ M^-1 at 25 °C). The clozapine binding showed "friendly" effects: increased α-helical content, a higher melting point, and protein protection from free radical-mediated oxidation. On the other hand, bound ziprasidone and sertindole had a slightly pro-oxidative effect, increasing ferrihemoglobin content, a possible "foe". Since the interaction of proteins with drugs plays a vital role in their pharmacokinetic and pharmacodynamic properties, the physiological significance of the obtained findings is briefly discussed.

Flavone and Hydroxyflavones Are Ligands That Bind the Orphan Nuclear Receptor 4A1 (NR4A1)

It was recently reported that the hydroxyflavones quercetin and kaempferol bind the orphan nuclear receptor 4A1 (NR4A1, Nur77) and act as antagonists in cancer cells and tumors, and they inhibit pro-oncogenic NR4A1-regulated genes and pathways. In this study, we investigated the interactions of flavone, six hydroxyflavones, seven dihydroxyflavones, three trihydroxyflavones, two tetrahydroxyflavones, and one pentahydroxyflavone with the ligand-binding domain (LBD) of NR4A1 using direct-binding fluorescence and an isothermal titration calorimetry (ITC) assays. Flavone and the hydroxyflavones bound NR4A1, and their KD values ranged from 0.36 µM for 3,5,7-trihydroxyflavone (galangin) to 45.8 µM for 3'-hydroxyflavone. KD values determined using ITC and KD values for most (15/20) of the hydroxyflavones were decreased compared to those obtained using the fluorescence assay. The results of binding, transactivation and receptor-ligand modeling assays showed that KD values, transactivation data and docking scores for these compounds are highly variable with respect to the number and position of the hydroxyl groups on the flavone backbone structure, suggesting that hydroxyflavones are selective NR4A1 modulators. Nevertheless, the data show that hydroxyflavone-based neutraceuticals are NR4A1 ligands and that some of these compounds can now be repurposed and used to target sub-populations of patients that overexpress NR4A1.

Omicron Spike Protein Is Vulnerable to Reduction

SARS-CoV-2 virus spike (S) protein is an envelope protein responsible for binding to the ACE2 receptor, driving subsequent entry into host cells. The existence of multiple disulfide bonds in the S protein makes it potentially susceptible to reductive cleavage. Using a tri-part split luciferase-based binding assay, we evaluated the impacts of chemical reduction on S proteins from different virus variants and found that those from the Omicron family are highly vulnerable to reduction. Through manipulation of different Omicron mutations, we found that alterations in the receptor binding module (RBM) are the major determinants of this vulnerability. Specifically we discovered that Omicron mutations facilitate the cleavage of C480-C488 and C379-C432 disulfides, which consequently impairs binding activity and protein stability. The vulnerability of Omicron S proteins suggests a mechanism that can be harnessed to treat specific SARS-CoV-2 strains.

Binding Behavior between Transforming-Growth-Factor-Beta1 and Its Receptor Reconstituted in Biomimetic Membranes

Transforming growth factor β1 (TGF-β1) is critical to cell differentiation, proliferation, and apoptosis. It is important to understand the binding affinity between TGF-β1 and its receptors. In this study, their binding force was measured using an atomic force microscope. Significant adhesion was induced by the interaction between the TGF-β1 immobilized on the tip and its receptor reconstituted in the bilayer. Rupture and adhesive failure occurred at a specific force around 0.4~0.5 nN. The relationship of the force to loading rate was used to estimate the displacement where the rupture occurred. The binding was also monitored in real time with surface plasmon resonance (SPR) and interpreted with kinetics to acquire the rate constant. Using the Langmuir adsorption, the SPR data were analyzed to estimate equilibrium and association constants to be approximately 10⁷ M^-1 and 10⁶ M^-1 s^-1. These results indicated that the natural release of the binding seldom occurred. Furthermore, the degree of binding dissociation, confirmed by the rupture interpretation, supported that the reverse of the binding hardly happened.

Three-Dimensional Structural Insights Have Revealed the Distinct Binding Interactions of Agonists, Partial Agonists, and Antagonists with the µ Opioid Receptor

The United States is experiencing the most profound and devastating opioid crisis in history, with the number of deaths involving opioids, including prescription and illegal opioids, continuing to climb over the past two decades. This severe public health issue is difficult to combat as opioids remain a crucial treatment for pain, and at the same time, they are also highly addictive. Opioids act on the opioid receptor, which in turn activates its downstream signaling pathway that eventually leads to an analgesic effect. Among the four types of opioid receptors, the µ subtype is primarily responsible for the analgesic cascade. This review describes available 3D structures of the µ opioid receptor in the protein data bank and provides structural insights for the binding of agonists and antagonists to the receptor. Comparative analysis on the atomic details of the binding site in these structures was conducted and distinct binding interactions for agonists, partial agonists, and antagonists were observed. The findings in this article deepen our understanding of the ligand binding activity and shed some light on the development of novel opioid analgesics which may improve the risk benefit balance of existing opioids.

Solving the binding problem: Assemblies form when neurons enhance their firing rate-they don't need to oscillate or synchronize

When we look at an image, its features are represented in our visual system in a highly distributed manner, calling for a mechanism that binds them into coherent object representations. There have been different proposals for the neuronal mechanisms that can mediate binding. One hypothesis is that binding is achieved by oscillations that synchronize neurons representing features of the same perceptual object. This view allows separate communication channels between different brain areas. Another hypothesis is that binding of features that are represented in different brain regions occurs when the neurons in these areas that respond to the same object simultaneously enhance their firing rate, which would correspond to directing object-based attention to these features. This review summarizes evidence in favor of and against these two hypotheses, examining the neuronal correlates of binding and assessing the time course of perceptual grouping. I conclude that enhanced neuronal firing rates bind features into coherent object representations, whereas oscillations and synchrony are unrelated to binding.

The binding structure of event elements in episodic memory and the role of animacy

Experienced events consist of several elements which need to be bound together in memory to represent the event in a coherent manner. Given such bindings, the retrieval of one event element should be related to the successful retrieval of another element of the same event, thus leading to a stochastic dependency of the retrieval of event elements. The way in which bindings are structured is not yet clearly established and only few moderators of the binding of event elements have been identified. We present results from three experiments aiming to distinguish between an integrated binding structure, in which event elements are bound into a unitary representation, and a hierarchical binding structure, in which event elements are preferentially bound to specific types of elements. Experiments 2 and 3 were additionally designed to identify animacy, an entity's property of being alive, as a potential moderator of the binding of event elements. We also offer a new approach for modelling dependencies of the retrieval of event elements which mitigates some limitations of previous approaches. Consistent with previous literature, we found dependencies of the retrieval of event elements if all of an event's constituent associations were shown. We found mixed evidence for integrated or hierarchical binding structures but found dependency of the retrieval of event elements to be sensitive to the presence of animacy in an event. The results suggest that binding structures may vary depending on moderators such as animacy or event structure awareness. Theoretical implications and directions for future research are discussed.

NanoB2 to monitor interactions of ligands with membrane proteins by combining nanobodies and NanoBRET

The therapeutic potential of ligands targeting disease-associated membrane proteins is predicted by ligand-receptor binding constants, which can be determined using NanoLuciferase (NanoLuc)-based bioluminescence resonance energy transfer (NanoBRET) methods. However, the broad applicability of these methods is hampered by the restricted availability of fluorescent probes. We describe the use of antibody fragments, like nanobodies, as universal building blocks for fluorescent probes for use in NanoBRET. Our nanobody-NanoBRET (NanoB2) workflow starts with the generation of NanoLuc-tagged receptors and fluorescent nanobodies, enabling homogeneous, real-time monitoring of nanobody-receptor binding. Moreover, NanoB2 facilitates the assessment of receptor binding of unlabeled ligands in competition binding experiments. The broad significance is illustrated by the successful application of NanoB2 to different drug targets (e.g., multiple G protein-coupled receptors [GPCRs] and a receptor tyrosine kinase [RTK]) at distinct therapeutically relevant binding sites (i.e., extracellular and intracellular).

Beyond Antiresorptive Activity: Risedronate-Based Coordination Complexes To Potentially Treat Osteolytic Metastases

Coordination of clinically employed bisphosphonate, risedronate (RISE), to bioactive metals, Ca²⁺, Mg²⁺, and Zn²⁺, allowed the formation of bisphosphonate-based coordination complexes (BPCCs). Three RISE-based BPCCs, RISE-Ca, RISE-Mg, and RISE-Zn, were produced, and their structures were elucidated by single crystal X-ray diffraction. Interestingly, the addition of an auxiliary ligand, etidronic acid (HEDP), resulted in the recrystallized protonated form of the ligand, H-RISE. The pH-dependent structural stability of the RISE-based BPCCs was measured by means of dissolution profiles under neutral and acidic simulated physiological conditions (PBS and FaSSGF, respectively). In comparison to RISE (Actonel), the complexes showed a lower equilibrium solubility (∼70-85% in 18-24 h) in PBS, while a higher equilibrium solubility (∼100% in 3 h) in acidic media. The results point to the capacity to release this BP in a pH-dependent manner from the RISE-based BPCCs. Subsequently, the particle size of RISE-Ca was reduced, from 300 μm to ∼350 d.nm, employing the phase inversion temperature (PIT)-nanoemulsion method, resulting in nano-Ca@RISE. Aggregation measurements of nano-Ca@RISE in 1% fetal bovine serum (FBS):H₂O was monitored after 24, 48, and 72 h to study the particle size longevity in physiological media, showing that the suspended material has the potential to maintain its particle size over time. Furthermore, binding assays were performed to determine the potential binding of nano-Ca@RISE to the bone, where results show higher binding (∼1.7×) for the material to hydroxyapatite (HA, 30%) when compared to RISE (17%) in 1 d. The cytotoxicity effects of nano-Ca@RISE were compared to those of RISE against the human breast cancer MDA-MB-231 and normal osteoblast-like hFOB 1.19 cell lines by dose-response curves and relative cell viability assays in an in vitro setting. The results demonstrate that nano-Ca@RISE significantly decreases the viability of MDA-MB-231 with high specificity, at concentrations ∼2-3× lower than the ones reported employing other third-generation BPs. This is supported by the fact that when normal osteoblast cells (hFOB 1.19), which are part of the tissue microenvironment at metastatic sites, were treated with nano-Ca@RISE no significant decrease in viability was observed. This study expands on the therapeutic potential of RISE beyond its antiresorptive activity through the design of BPCCs, specifically nano-Ca@RISE, that bind to the bone and degrade in a pH-dependent manner under acidic conditions.

Nanoparticle Scanners for the Identification of Key Sequences Involved in the Assembly and Disassembly of β-Amyloid Peptides

The aggregation of β-amyloid peptides (Aβ), implied in the development and progression of Alzheimer's disease, is driven by a complex set of intramolecular and intermolecular interactions involving both hydrophobic and polar residues. The key residues responsible for the forward assembling process may be different from those that should be targeted to disassemble already formed aggregates. Molecularly imprinted nanoparticle (MINP) receptors are reported in this work to strongly and selectively bind specific segments of Aβ₄₀. Combined fluorescence spectroscopy, atomic force microscopy (AFM) imaging, and circular dichroism (CD) spectroscopy indicate that binding residues 21-30 near the loop region is most effective at inhibiting the aggregation of monomeric Aβ₄₀, but residues 11-20 that include the internal β strand closer to the N-terminal represent the best target for disaggregating already formed aggregates in the polymerization phase. Once the aggregation proceeds to the saturation phase, binding residues 1-10 has the largest effect on the disaggregation, likely because of the accessibility of these amino acids relative to others to the MINP receptors.

Atypical histone targets of PHD fingers

Plant homeodomain (PHD) fingers are structurally conserved zinc fingers that selectively bind unmodified or methylated at lysine 4 histone H3 tails. This binding stabilizes transcription factors and chromatin-modifying proteins at specific genomic sites, which is required for vital cellular processes, including gene expression and DNA repair. Several PHD fingers have recently been shown to recognize other regions of H3 or histone H4. In this review, we detail molecular mechanisms and structural features of the non-canonical histone recognition, discuss biological implications of the atypical interactions, highlight therapeutic potential of PHD fingers, and compare inhibition strategies.

Binding objects to their spatiotemporal context: Age gradient and neuropsychological correlates of What-Where-When task performance

A number of recent studies have shown that the ability to accurately recall bound object and spatiotemporal aspects of an experienced event develops gradually in children and is greatly impaired in the elderly, reflecting developmental discontinuities in the integrity of the underlying medial temporal lobe network. Using a novel What-Where-When (WWW) visuospatial reconstruction task, the experiential memory performance of a group of healthy older adults (aged 60-80) was compared to that of a group of younger adults (aged 20-40). Both groups were equated on their general cognitive ability, their executive functioning, and on the presence of depression, anxiety, and stress symptomatology. As hypothesized, the performance of the older adults in the binding task was significantly lower, with younger participants recalling three times the amount of bound object and spatiotemporal triads than their older counterparts. Psychomotor speed was found to be lower in older adults and was the only neuropsychological index to significantly affect success on the WWW binding task. Based on this and other relevant studies, the selective associative memory impairment obtained using a non-verbal What-Where-When paradigm emerges as a marker for the detection of early pre-clinical signs of experiential memory pathology.

Novel Biomaterial-Binding/Osteogenic Bi-Functional Peptide Binds to Silk Fibroin Membranes to Effectively Induce Osteogenesis In Vitro and In Vivo

Peptides can introduce new functions to biomaterials but their immobilization usually relies on inefficient physical adsorption or tedious chemical conjugation. Using the Bombyx mori silk fibroin (SF) membrane (SFm) as a model biomaterial, here, we demonstrate a universal strategy for discovering new peptides that can "stick" to a biomaterial to functionalize it. Specifically, two peptide motifs, one screened by phage display biopanning for binding to the biomaterial (i.e., SF) and another derived from an osteogenic growth factor (i.e., bone morphogenetic protein-2), are fused into a new chimeric peptide that can bind to SFm for more efficient osteogenesis. Theoretical simulations and experimental assays confirm that the chimeric peptide binds to SF with high affinity, facilely achieving its immobilization onto SFm. The peptide enables SFm to effectively induce osteogenic differentiation of human mesenchymal stem cells (MSCs) even without other osteogenic inducers and efficiently stimulate bone regeneration in a subcutaneous rat model in 8 weeks, even without MSC seeding, while not causing inflammatory responses. Since biomaterial-binding peptides can be readily screened using phage display and functional peptides can be generated from growth factors, our work suggests a universal strategy for combining them to seek new peptides for binding and functionalizing biomaterials.

Assessing a computational pipeline to identify binding motifs to the α2β1 integrin

Integrins in the cell surface interact with functional motifs found in the extracellular matrix (ECM) that queue the cell for biological actions such as migration, adhesion, or growth. Multiple fibrous proteins such as collagen or fibronectin compose the ECM. The field of biomechanical engineering often deals with the design of biomaterials compatible with the ECM that will trigger cellular response (e.g., in tissue regeneration). However, there are a relative few number of known integrin binding motifs compared to all the possible peptide epitope sequences available. Computational tools could help identify novel motifs, but have been limited by the challenges in modeling the binding to integrin domains. We revisit a series of traditional and novel computational tools to assess their performance in identifying novel binding motifs for the I-domain of the α2β1 integrin.

Cortical VIP neurons locally control the gain but globally control the coherence of gamma band rhythms

Gamma band synchronization can facilitate local and long-range neural communication. In the primary visual cortex, visual stimulus properties within a specific location determine local synchronization strength, while the match of stimulus properties between distant locations controls long-range synchronization. The neural basis for the differential control of local and global gamma band synchronization is unknown. Combining electrophysiology, optogenetics, and computational modeling, we found that VIP disinhibitory interneurons in mouse cortex linearly scale gamma power locally without changing its stimulus tuning. Conversely, they suppress long-range synchronization when two regions process non-matched stimuli, tuning gamma coherence globally. Modeling shows that like-to-like connectivity across space and specific VIP→SST inhibition capture these opposing effects. VIP neurons thus differentially impact local and global properties of gamma rhythms depending on visual stimulus statistics. They may thereby construct gamma-band filters for spatially extended but continuous image features, such as contours, facilitating the downstream generation of coherent visual percepts.

Residues E53, L55, H59, and G70 of the cellular receptor protein Tva mediate cell binding and entry of the novel subgroup K avian leukosis virus

Subgroup K avian leukosis virus (ALV-K) is a novel subgroup of ALV isolated from Chinese native chickens. As for a retrovirus, the interaction between its envelope protein and cellular receptor is a crucial step in ALV-K infection. Tva, a protein previously determined to be associated with vitamin B₁₂/cobalamin uptake, has been identified as the receptor of ALV-K. However, the molecular mechanism underlying the interaction between Tva and the envelope protein of ALV-K remains unclear. In this study, we identified the C-terminal loop of the LDL-A module of Tva as the minimal functional domain that directly interacts with gp85, the surface component of the ALV-K envelope protein. Further point-mutation analysis revealed that E53, L55, H59, and G70, which are exposed on the surface of Tva and are spatially adjacent, are key residues for the binding of Tva and gp85 and facilitate the entry of ALV-K. Homology modeling analysis indicated that the substitution of these four residues did not significantly impact the Tva structure but impaired the interaction between Tva and gp85 of ALV-K. Importantly, the gene-edited DF-1 cell line with precisely substituted E53, L55, H59, and G70 was completely resistant to ALV-K infection and did not affect vitamin B₁₂/cobalamin uptake. Collectively, these findings not only contribute to a better understanding of the mechanism of ALV-K entry into host cells but also provide an ideal gene-editing target for antiviral study.

Theta Activity Dynamics during Embedded Response Plan Processing in Tourette Syndrome

Gilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder. Because motor signs are the defining feature of GTS, addressing the neurophysiology of motor processes is central to understanding GTS. The integration of voluntary motor processes is subject to so-called "binding problems", i.e., how different aspects of an action are integrated. This was conceptualized in the theory of event coding, in which 'action files' accomplish the integration of motor features. We examined the functional neuroanatomical architecture of EEG theta band activity related to action file processing in GTS patients and healthy controls. Whereas, in keeping with previous data, behavioral performance during action file processing did not differ between GTS and controls, underlying patterns of neural activity were profoundly different. Superior parietal regions (BA7) were predominantly engaged in healthy controls, but superior frontal regions (BA9, BA10) in GTS indicated that the processing of different motor feature codes was central for action file processing in healthy controls, whereas episodic processing was more relevant in GTS. The data suggests a cascade of cognitive branching in fronto-polar areas followed by episodic processing in superior frontal regions in GTS. Patients with GTS accomplish the integration of motor plans via qualitatively different neurophysiological processes.

Molecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives

The implications of surfactant-enzyme/protein interactions in a variety of fields, including biotechnology, cosmetics, paints and pharmaceuticals, have attracted a lot of attention in contemporary studies. Herein, we have employed several in vitro and in silico techniques such as excitation and absorption spectroscopies, circular dichroism and FT-IR spectroscopies, density functional and molecular dynamics simulations to understand the interaction behavior of oxy-diester-based green cationic Gemini surfactants, N1,N1,N14,N14-tetramethyl-2,13-dioxo-N1,N14-dialkyl-3,6,12-tetraoxateradecane-1,14-diaminiumdichloride (abbreviated as Cm-E2O2-Cm, where 'm' stands for alkyl chain length, m = 12 and 14) with one of the main digestive proteins, pepsin. The spectroscopic techniques confirm the static quenching effect of surfactants on pepsin. The calculated physical parameters (Ksv, Kb and ΔG) and their order reveal the distinguished implications for the surfactants' chain lengths. The spontaneity of interaction was also confirmed by negative Gibbs free energy change values. The extrinsic spectroscopic study with pyrene as fluorescence probe, FT-IR and CD techniques indicated a potential conformational change in pepsin induced by the Gemini surfactants. DFT, docking and MD simulations provided the theoretical understanding regarding the quantum mechanical environment, location of binding and stability of the protein-surfactant complexation in energy terms. We believe this study will be a humble addition to our existing knowledge in the field of protein-surfactant interactions.Communicated by Ramaswamy H. Sarma.