Binding Kinetics Research Articles

Characterization of squash polysaccharide and the anti-diabetic effect on type 2 diabetic rat revealed by urine metabolomics analysis

The present study reports the structural characteristics of 3 polysaccharide fractions (SPS-F1, SPS-F2 and SPS-F3) isolated and purified from squash. SPS-F1 (molecular weight (Mw) = 12.30 kDa) and SPS-F2 (Mw = 19.40 kDa) were likely to contain HG and RG-I domain of pectic polysaccharide, respectively. SPS-F2 (Mw = 270.4 kDa) was mainly composed of rhamnose, galactose and arabinose. The treatment with SPS decreased body weight gain, glucose and TG levels in type 2 diabetes rats. Besides, 25 differential metabolites were identified based on urinary metabolomics analysis, which are crucial to the anti-diabetic effect of SPS. The regulation of nicotinamide N-oxide, histamine, cis-aconitate, citrate, L-malic acid, 3-(3-hydroxyphenyl) propanoic acid and N-acetyl-L-aspartic acid were mainly associated with energy metabolism, gut microbiota and inflammation. Study of surface plasmon resonance revealed the binding kinetics with galectin-3 (Gal-3) and fibroblast growth factor 2 (FGF2). The KD values of SPS-F2 and SPS-F3 to Gal-3 were 4.97 × 10-3 and 1.48 × 10-3 mol/L, indicating a weak binding affinity. All 3 fractions showed moderate binding to FGF2 and the affinity was SPS-F3 > SPS-F2 > SPS-F1. Thus, the metabolomics and SPR approach were proved to be a promising tool in exploring the anti-diabetes effects of SPS and provided a deep understanding of the mechanisms.

Optimal Humanized Scg3-Neutralizing Antibodies for Anti-Angiogenic Therapy of Diabetic Retinopathy.

Secretogranin III (Scg3) is a diabetic retinopathy (DR)-restricted angiogenic factor identified in preclinical studies as a target for DR therapy. Previously, our group generated and characterized ML49.3, an anti-Scg3 monoclonal antibody (mAb) which we then converted into an EBP2 humanized antibody Fab fragment (hFab) with potential for clinical application. We also generated anti-Scg3 mT4 mAb and related EBP3 hFab. In this study, to identify the preferred hFab for DR therapy, we compared all four antibodies for binding, neutralizing and therapeutic activities in vitro and in vivo. Octet binding kinetics analyses revealed that ML49.3 mAb, EBP2 hFab, mT4 mAb and EBP3 hFab have Scg3-binding affinities of 35, 8.7, 0.859 and 0.116 nM, respectively. Both anti-Scg3 EBP2 and EBP3 hFabs significantly inhibited Scg3-induced proliferation and migration of human umbilical vein endothelial cells in vitro, and alleviated DR vascular leakage and choroidal neovascularization with high efficacy. Paired assays in DR mice revealed that intravitreally injected EBP3 hFab is 26.4% and 10.3% more effective than EBP2 hFab and aflibercept, respectively, for ameliorating DR leakage. In conclusion, this study confirms the markedly improved binding affinities of hFabs compared to mAbs and further identifies EBP3 hFab as the preferred antibody to develop for anti-Scg3 therapy.

Label-free, real-time monitoring of membrane binding events at zeptomolar concentrations using frequency-locked optical microresonators

G-protein coupled receptors help regulate cellular function and communication, and are targets of small molecule drug discovery efforts. Conventional techniques to probe these interactions require labels and large amounts of receptor to achieve satisfactory sensitivity. Here, we use frequency-locked optical microtoroids for label-free characterization of membrane interactions in vitro at zeptomolar concentrations for the kappa opioid receptor and its native agonist dynorphin A 1-13, as well as big dynorphin (dynorphin A and dynorphin B) using a supported biomimetic membrane. The measured affinity of the agonist dynorphin A 1-13 to the κ-opioid receptor was also measured and found to be 3.1 nM. Radioligand assays revealed a dissociation constant in agreement with this value (1.1 nM). The limit of detection for the κOR/DynA 1-13 was calculated as 180 zM. The binding of Cholera Toxin B-monosialotetrahexosyl ganglioside was also monitored in real-time and an equilibrium dissociation constant of 1.53 nM was found. Our biosensing platform provides a method for highly sensitive real-time characterization of membrane embedded protein binding kinetics that is rapid and label-free, for drug discovery and toxin screening among other applications.

The Role of Water Networks in Phosphodiesterase Inhibitor Dissociation and Kinetic Selectivity.

In search of new opportunities to develop Trypanosoma brucei phosphodiesterase B1 (TbrPDEB1) inhibitors that have selectivity over the off-target human PDE4 (hPDE4), different stages of a fragment-growing campaign were studied using a variety of biochemical, structural, thermodynamic, and kinetic binding assays. Remarkable differences in binding kinetics were identified and this kinetic selectivity was explored with computational methods, including molecular dynamics and interaction fingerprint analyses. These studies indicate that a key hydrogen bond between GlnQ.50 and the inhibitors is exposed to a water channel in TbrPDEB1, leading to fast unbinding. This water channel is not present in hPDE4, leading to inhibitors with a longer residence time. The computer-aided drug design protocols were applied to a recently disclosed TbrPDEB1 inhibitor with a different scaffold and our results confirm that shielding this key hydrogen bond through disruption of the water channel represents a viable design strategy to develop more selective inhibitors of TbrPDEB1. Our work shows how computational protocols can be used to understand the contribution of solvent dynamics to inhibitor binding, and our results can be applied in the design of selective inhibitors for homologous PDEs found in related parasites.

Field theory of enzyme-substrate systems with restricted long-range interactions.

Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent -γ. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1-γ) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents -γ on short distances and -(2/3)(2-γ) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate.

A versatile approach to quality control of protein-based receptor layers by reversible, nonspecific staining for multiplex SPRi immunosensing

SPRi protein arrays for rapid, label-free immunodetection offer an attractive approach for high throughput biosensing and analysis of molecular interactions. However, their routine use for quantitative analysis requires adequate reproducibility and homogeneity of receptor assemblies manufactured ex-situ using microdispensing techniques. There is also an emerging need to develop versatile and non-destructive methods for the determination of protein surface density for quality control of the immobilization process. Here, we report on a simple, one-step method of surface proteins visualization by their reversible, non-specific staining with anionic dyes: Ponceau S (PS), Amido Black (AB) or Coomassie Brilliant Blue G (CBB-G). Using rabbit IgG antibody and transferrin as model receptors, we demonstrate the possibility of protein surface density determination in a broad range up to ∼ 3 ng∙mm−2 (for a 2D monolayer) and up to at least 12.5 ng∙mm−2 (for a 3D hydrogel-coated substrate). The ranges of dynamic response for the developed methods cover the typical surface densities required for biosensing and studies of the binding kinetics. It was demonstrated that each of the investigated dyes manifests advantages in specified applications. While CBB-G shows the highest sensitivity of SPRi response, AB requires the gentlest labeling conditions, and PS shows the highest association rate and ease of washing out, even from protein layers of high density. The feasibility of the developed method for the quality control of SPRi microarray was confirmed. The advantages of the new, dye-based, non-specific labeling method over immunolabeling in terms of simplicity of implementation and versatility have also been highlighted.

Methods for monitoring protein-membrane binding. Comparison based on the interactions between amyloidogenic protein human cystatin C and phospholipid liposomes

A cell membrane is an essential cellular component providing protection against the outer environment. It is also a host for proteins and carbohydrates responsible for, e.g. transporter, receptor, or enzymatic functions. In parallel, the membrane may also be implicated in pathological processes leading, e.g. to the oligomerization of amyloid-forming proteins, a hallmark of i.a. Alzheimer's disease. The increasing need for detailed information on mechanisms driving the amyloid formation and the potential role of cell membranes in the process proves the research on protein-membrane interactions biologically relevant. Considering the potential and limitations of the relatively well established and newly developed methods, this study focused on selecting methods that allow a broad and comprehensive description of interactions between amyloidogenic protein human cystatin C and lipid bilayers. In the first step, dot-blot and ELISA tests were selected as techniques allowing fast screening for protein-ligand interactions. Next, surface plasmon resonance, spectral shift, biolayer interferometry, and switchSENSE® technology were used to determine kinetic parameters and binding constants for interactions between human cystatin C and the selected lipid bilayers. Based on the obtained results we have proposed the most promising candidates for monitoring of interactions and determining affinity between amyloidogenic proteins and membrane mimetics.

General quasi-equilibrium multivalent binding model to study diverse and complex drug-receptor interactions of biologics.

Pharmacokinetics and pharmacodynamics of many biologics are influenced by their complex binding to biological receptors. Biologics consist of diverse groups of molecules with different binding kinetics to its receptors including IgG with simple one-to-one drug receptor bindings, bispecific antibody (BsAb) that binds to two different receptors, and antibodies that can bind to six or more identical receptors. As the binding process is typically much faster than elimination (or internalization) and distribution processes, quasi-equilibrium (QE) binding models are commonly used to describe drug-receptor binding kinetics of biologics. However, no general QE modeling framework is available to describe complex binding kinetics for diverse classes of biologics. In this paper, we describe novel approaches of using differential algebraic equations (DAE) to solve three QE multivalent drug-receptor binding (QEMB) models. The first example describes the binding kinetics of three-body equilibria of BsAb that binds to 2 different receptors for trimer formation. The second example models an engineered IgG variant (Multabody) that can bind to 24 identical target receptors. The third example describes an IgG with modified neonatal Fc receptor (FcRn) binding affinity that competes for the same FcRn receptor as endogenous IgG. The model parameter estimates were obtained by fitting the model to all data simultaneously. The models allowed us to study potential roles of cooperative binding on bell-shaped drug exposure-response relationships of BsAb, and concentration-depended distribution of different drug-receptor complexes for Multabody. This DAE-based QEMB model platform can serve as an important tool to better understand complex binding kinetics of diverse classes of biologics.

Different VH3-Binding Protein A Resins Show Comparable VH3-Binding Mediated By product Separation Capabilities Despite Having Varied Dynamic Binding Capacities Towards A VH3 Fab.

Protein A resins have been widely used for product capture during mAb, bispecific antibody (bsAb), and Fc-fusion protein purification. While Protein A ligands mainly bind the Fc region, many of them can also bind the VH3 domain. During mAb/bsAb purification, certain truncated byproducts may contain the same Fc region as the product but fewer numbers of the VH3 domain. In such a scenario, VH3-binding Protein A resins provide a potential means for byproduct separation based on the difference in VH3-binding valency. As the ligands of different VH3-binding Protein A resins are derived from distinct domains of the native Protein A, it would be interesting to know whether they possess comparable capabilities for separating species with the same Fc region but different numbers of VH3 domain. This study aims to explore the potential of different VH3-binding Protein A resins for separating antibody species with the same Fc region but different numbers of VH3 domain. The VH3 Fab was released from a VH3-containing mAb by papain digestion. Post digestion, the released VH3 Fab was purified sequentially using CaptureSelect CH1-XL and MabSelect SuRe affinity chromatography. The purified VH3 Fab was used as the load material to assess the dynamic binding capacity (DBC) of five VH3-binding Protein A resins (i.e., Amshpere A3, Jetted A50, MabCapture C, MabSelect and MabSelect PrismA). The potential of VH3-binding Protein A resins for separating species having the same Fc region but different numbers of VH3 domain was evaluated using an artificial mixture composed of the product and a truncated byproduct, which contained one and zero VH3 domain, respectively (both species contained the same Fc region). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was used to monitor Fab purification and separation of species containing the same Fc region but different numbers of VH3 domain. When loaded with an isolated VH3 Fab, different VH3-binding Protein A resins showed varied DBCs. Nevertheless, when these Protein A resins were used to separate a truncated byproduct, which contained the Fc region only without any VH3 domain, from the product, which included one VH3 domain in addition to the Fc region, they showed comparable capabilities for separating these two species. Although different VH3-binding Protein A resins showed varied DBCs towards a VH3 Fab, they exhibited comparable capabilities for separating species with the same Fc region but different numbers of VH3 domain.

Lignin-based vitrimer containing dynamic borate ester bonds with intrinsic photoconversion and excellent photothermal remoldability

The development of photoresponsive shape memory materials based on the photothermal conversion properties of lignin and the low activation energy of the dynamic covalent borate bond is of great importance. In this paper, a kind of lignin-based vitrimer polymer (LBP) containing dynamic boronic ester bonds was prepared by a “sulfhydryl-epoxy” click reaction and etherification reaction. The results show that the rigid segment EP-EL (lignin-based epoxy resin) and BDB (2,2′-(1,4-phenylene)-bis-[4-mercapto-1,3,2-dioxaneborane]) with benzene ring structure can impart tensile strength (20.8 MPa) to the LBP, while the flexible segment PEG imparts good elongation at break (15 %). The dynamic binding and dissociation exchange mechanism of the boronic ester bonds enables LBP to exhibit thermal remodelling properties (up to 36.2 %) and water-assisted self-healing properties at room temperature (up to 49.0 %). In addition, LBP exhibits excellent thermal and light-responsive shape memory properties due to its own photothermal conversion performance (photothermal conversion efficiency up to 18.2 %) and the dynamic boronic ester bond thermal activation bond exchange mechanism. The insulating properties of LBP make it suitable for use in high temperature protection circuit devices and light-responsive circuit devices. This study provides new insights into the design and application of Vitrimer and photoresponsive shape memory polymers, and also offers a new avenue for high-value utilization of lignin.

Gelatin-based carbon quantum dot-molecularly imprinted polymer: Safe photoluminescent core-shell nano-carrier for the pH-responsive anticancer drug delivery

This study aims to synthesize a core-shell gelatin-based carbon quantum dot-molecularly imprinted polymer (MIP@g-CQD) via the precipitation free-radical polymerization process using methotrexate (MTX) as a model anticancer template. To investigate the efficiency of the prepared photoluminescent MIP@g-CQD as a pH-responsive nano-carrier, MTX was loaded into MIP@g-CQD by soaking in a drug solution and the release behavior of the loaded drug was evaluated in the necessary pH values (7.4, 5). The successful synthesis of materials was characterized using PL, TEM, FE-SEM, DLS, and FT-IR analyses. Interestingly, the created cavities in the core-shell nano-carriers can interact with the MTX molecules effectively, leading to an increase in the loading capacity. According to the obtained results from Langmuir adsorption isotherms, the imprinting factor was calculated (IF = 4.91). Also, the binding kinetics of MTX revealed the creation of particular recognition sites in the core-shell polymeric network. The MTX-loaded MIP@g-CQD displayed a low rate and limited release at the simulated physiological environment (pH 7.4, 37 °C), but it is increased at tumor tissue (pH 5, 41 °C) conditions, which can lead to long-term and sustained release of MTX in the desired target. This property of MIP@g-CQD could avoid the release of MTX in normal physiological conditions, decreasing the possible side effects of MTX drug. Owing to the existence of amide functional groups in the nano-carrier structure and its negatively charged nature, the MTT assay displayed desirable cytotoxicity against the breast cancer cell line (MCF-7) for the MTX-loaded nano-carrier. According to the obtained results, the prepared safe photoluminescent MIP@g-CQD with appropriate pH-responsivity has a high ability to be applied as an anticancer and bio-detection agent.

Advanced Quantification of Receptor-Ligand Interaction Lifetimes via Single-Molecule FRET Microscopy.

Receptor-ligand interactions at cell interfaces initiate signaling cascades essential for cellular communication and effector functions. Specifically, T cell receptor (TCR) interactions with pathogen-derived peptides presented by the major histocompatibility complex (pMHC) molecules on antigen-presenting cells are crucial for T cell activation. The binding duration, or dwell time, of TCR-pMHC interactions correlates with downstream signaling efficacy, with strong agonists exhibiting longer lifetimes compared to weak agonists. Traditional surface plasmon resonance (SPR) methods quantify 3D affinity but lack cellular context and fail to account for factors like membrane fluctuations. In the recent years, single-molecule Förster resonance energy transfer (smFRET) has been applied to measure 2D binding kinetics of TCR-pMHC interactions in a cellular context. Here, we introduce a rigorous mathematical model based on survival analysis to determine exponentially distributed receptor-ligand interaction lifetimes, verified through simulated data. Additionally, we developed a comprehensive analysis pipeline to extract interaction lifetimes from raw microscopy images, demonstrating the model's accuracy and robustness across multiple TCR-pMHC pairs. Our new software suite automates data processing to enhance throughput and reduce bias. This methodology provides a refined tool for investigating T cell activation mechanisms, offering insights into immune response modulation.

Ligand-assisted reprecipitation synthesis of highly luminescent and stable CsPbBr3@SiO2 nanoparticles with formation kinetics analysis

Cesium lead bromide (CsPbBr3) perovskite nanocrystals are becoming a popular alternative to chalcogenide quantum dots because of their bright green fluorescence and high color purity. However, owing to the poor stability caused by their highly ionic nature and the dynamic binding of long-chain capping ligands, their practical applications are limited. Although (3-aminopropyl)triethoxysilane (APTES) is a frequently used insulating material for wrapping CsPbBr3nanocrystals, it often causes surface etching. To address this issue, we introduced oleic acid into the anti-solvent toluene to inhibit the etching effect of APTES using a modified room-temperature ligand-assisted reprecipitation process. We utilized in situ time-dependent photoluminescence measurements to study the formation kinetics of CsPbBr3nanocrystals and determine the optimal ligands ratio. This innovative approach enables precise control over CsPbBr3@SiO2nanoparticles synthesis, yielding uniformly shaped nanocrystals with a silica shell, a consistent size around 10.17 ± 1.6 nm, and enhanced photoluminescence quantum yields ranging from 90% and 100%. The photoluminescence lifetimes of our CsPbBr3@SiO2nanoparticles were significantly prolonged owing to a reduction in non-radiative recombination. This boosts their stability in thermal and polar solvent environments, making them superior candidates for use in photonic devices.

Lithium Recovery from Geologic Brines by Advanced Cation-Exchange Ionomers

As of today a massive restructuring of the energy system is taking place at the global level to curtail the use of fossil fuels and foster the large-scale implementation of renewable sources such as the sun and the wind. This is a crucial stepping stone to minimize the emissions of the greenhouse gases associated with the combustion of fossil fuels, with the ultimate goal to slow down global warming and ensure that the development of humankind could become compatible with the conservation of the natural environment.A major drawback of most renewable sources (e.g., the sun and the wind) is that they are intermittent and non-programmable. Hence, energy storage and distribution technologies are necessary to close the spatial and temporal gaps between the production of energy and its exploitation by end users. In this regard, lithium batteries (LiBs) are becoming one of the most promising tools to profitably use the energy obtained from renewable sources to power to a broad variety of applications, from portable electronics to light-duty (LD) vehicles.After decades of R&D efforts a large-scale rollout of LD vehicles powered by LiBs is currently taking place worldwide. Consequently, the production of massive amounts of LiBs is underway, straining the traditional supply chains of lithium and leading to a huge increase in the cost of this element, now listed by the European Union as a Critical Raw Material [1]. Accordingly, major efforts are dedicated at the global level to identify new and unexploited sources of lithium. In recent years it was acknowledged the potential of geologic brines to supply lithium. Geologic brines are widely available and abundant worldwide. However, an effective and inexpensive technology to selectively extract Li from a brine (that is typically much richer in other cations such as Na+, and Ca2+) is still not available.In this contribution a family of very inexpensive and chemically-stable cation-exchange ionomers is proposed. The physicochemical features of the ionomers are elucidated, with a particular reference to the cation-exchange capacity, the morphology (probed by scanning electron microscopy) and the porosimetric features (investigated by nitrogen physisorption techniques). In a second step it is studied the kinetics of cation binding upon immersing the ionomers into a suitable synthetic brine closely mimicking a natural specimen and including the following cations: Li+, Na+, K+, Ca2+ and Mg2+. The kinetic information is then used in experiments meant to determine the binding features at equilibrium of the various cations present in the synthetic brine to the ionomers.The following binding features of the ionomers are determined: (i) number of distinct binding sites; (ii) number of cations that can be coordinated to each binding site; and (iii) maximum theoretical binding of each cation to the ionomer, with a particular reference to Li+ [2]. The physicochemical properties of the ionomers are finally correlated to the binding parameters, allowing to suggest new strategies to devise enhanced ionomers able to extract selectively and cheaply Li+ from the brines.

Dynamic and large field of view photonic resonator absorption microscopy for ultrasensitive digital resolution detection of nucleic acid and protein biomarkers

In this paper, we describe a biosensing instrument based on our previously developed photonic resonator absorption microscope (PRAM) that incorporates autofocus, digital representation of the gold nanoparticle (AuNP) accumulation, and the ability to gather time-series image sequences of AuNP attachment and detachment from the photonic crystal (PC) surface. The combined capabilities are used to fully automate PRAM image collection during biomolecular assays to enable tiling of PRAM images to provide millimeter-scale field of view. The instrument can also gather PRAM “movies” that enables digital showcasing and dynamic counting AuNPs as they arrive and depart from the PC surface. We utilize the capabilities in the context of two biomolecular assays for detection of protein biomarkers in a conventional AuNP-tagged sandwich format. Utilizing dynamic counting of AuNP attachment and detachment events during the assay we present a detection for microRNA-375 (miRNA-375) down to 1 aM with a 10-min, room temperature, enzyme-free approach, while revealing characteristics of the binding-rate and unbinding-rate of the biomolecular interactions. Our instrument can potentially find broad applications in multiplexed point-of-care diagnostic testing, and as a general-purpose tool for quantitative characterization of biomolecular binding kinetics with single-molecule resolution.

Advances in the structural basis for angiotensin-1 converting enzyme (ACE) inhibitors.

Human somatic angiotensin-converting enzyme (ACE) is a key zinc metallopeptidase that plays a pivotal role in the renin-angiotensin-aldosterone system (RAAS) by regulating blood pressure and electrolyte balance. Inhibition of ACE is a cornerstone in the management of hypertension, cardiovascular diseases, and renal disorders. Recent advances in structural biology techniques have provided invaluable insights into the molecular mechanisms underlying ACE inhibition, facilitating the design and development of more effective therapeutic agents. This review focuses on the latest advancements in elucidating the structural basis for ACE inhibition. High-resolution crystallographic studies of minimally glycosylated individual domains of ACE have revealed intricate molecular details of the ACE catalytic N- and C-domains, and their detailed interactions with clinically relevant and newly designed domain-specific inhibitors. In addition, the recently elucidated structure of the glycosylated form of full-length ACE by cryo-electron microscopy (cryo-EM) has shed light on the mechanism of ACE dimerization and revealed continuous conformational changes which occur prior to ligand binding. In addition to these experimental techniques, computational approaches have also played a pivotal role in elucidating the structural basis for ACE inhibition. Molecular dynamics simulations and computational docking studies have provided atomic details of inhibitor binding kinetics and energetics, facilitating the rational design of novel ACE inhibitors with improved potency and selectivity. Furthermore, computational analysis of the motions observed by cryo-EM allowed the identification of allosteric binding sites on ACE. This affords new opportunities for the development of next-generation allosteric inhibitors with enhanced pharmacological properties. Overall, the insights highlighted in this review could enable the rational design of novel ACE inhibitors with improved efficacy and safety profiles, ultimately leading to better therapeutic outcomes for patients with hypertension and cardiovascular diseases.

Relaxation and Noise-Driven Oscillations in a Model of Mitotic Spindle Dynamics

During cell division, the mitotic spindle moves dynamically through the cell to position the chromosomes and determine the ultimate spatial position of the two daughter cells. These movements have been attributed to the action of cortical force generators which pull on the astral microtubules to position the spindle, as well as pushing events by these same microtubules against the cell cortex and plasma membrane. Attachment and detachment of cortical force generators working antagonistically against centring forces of microtubules have been modelled previously (Grill et al. in Phys Rev Lett 94:108104, 2005) via stochastic simulations and mean-field Fokker–Planck equations (describing random motion of force generators) to predict oscillations of a spindle pole in one spatial dimension. Using systematic asymptotic methods, we reduce the Fokker–Planck system to a set of ordinary differential equations (ODEs), consistent with a set proposed by Grill et al., which can provide accurate predictions of the conditions for the Fokker–Planck system to exhibit oscillations. In the limit of small restoring forces, we derive an algebraic prediction of the amplitude of spindle-pole oscillations and demonstrate the relaxation structure of nonlinear oscillations. We also show how noise-induced oscillations can arise in stochastic simulations for conditions in which the mean-field Fokker–Planck system predicts stability, but for which the period can be estimated directly by the ODE model and the amplitude by a related stochastic differential equation that incorporates random binding kinetics.

Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters.

Rational predictions on binding kinetics parameters of drugs to targets play significant roles in future drug designs. Full conformational samplings of targets are requisite for accurate predictions of binding kinetic parameters. In this review, we mainly focus on the applications of enhanced sampling technologies in calculations of binding kinetics parameters and residence time of drugs. The methods involved in molecular dynamics simulations are applied to not only probe conformational changes of targets but also reveal calculations of residence time that is significant for drug efficiency. For this review, special attention are paid to accelerated molecular dynamics (aMD) and Gaussian aMD (GaMD) simulations that have been adopted to predict the association or disassociation rate constant. We also expect that this review can provide useful information for future drug design.

In-situ synthesis of quaternary alkylammonium ligand capped organic-inorganic hybrid halide perovskite for high pure green luminescence in display application

This study delves into the intricate dynamics of ligand engineering for the synthesis of Methyl Ammonium Lead Bromide (MAPbBr3) nanocrystals (NCs), which exhibit immense potential in optoelectronic and photovoltaic applications. Our focus centres on the role of the quaternary ammonium molecule CTAB as a ligand in stabilizing MAPbBr3 NCs. This also addresses the challenges related to the stability and surface defects of NCs that hinder their commercial viability. Employing a modified ligand-assisted reprecipitation technique (LARP) with a dual solvent system, we optimized the CTAB concentration to 0.05 mmol, resulting in MAPbBr3 NCs with an impressive 88% quantum yield. XPS and FTIR analyses confirm the presence and binding of CTAB on the NC surface. The MAPbBr3-CTAB NCs exhibit higher exciton–phonon binding energy, enhancing their optical properties. Despite an unfavourable geometric fit, CTAB is effective in surface defect passivation due to its binding, solvation, and desorption energy during the dynamic binding process. 2D-DOSY NMR reveals approximately 66% CTAB bound to the NC surface. A comparative study involving MAPbBr3-OA, OLA, and MAPbBr3-CTAB deposited on LEDs demonstrates the superior performance of the latter, achieving a luminous efficiency of 42.18 lm W−1 at 1.2 ml deposition. These findings highlight the efficacy of CTAB in achieving high-purity green luminescence, aligning with BT.2020 display colour standards and paving the way for advanced optoelectronic applications. The successful synthesis and improved performance of MAPbBr3-CTAB NCs underscore their potential as a promising material for future optoelectronic and photovoltaic technologies.

Competitive Binding Kinetics of Methylmercury-Cysteine with Dissolved Organic Matter: Critical Impacts of Thiols on Adsorption and Uptake of Methylmercury by Algae.

Complexes with low-molecular-weight thiols are crucial species of methylmercury (MeHg) excreted by anaerobic Hg-methylating microbes, notably, MeHg-cysteine (MeHg-Cys). As MeHg-Cys diffuses into surface water, it would undergo a ligand exchange process with dissolved organic matter (DOM) under nonsulfidic conditions, inevitably altering MeHg speciation and bioavailability to phytoplankton. In this study, we investigated the competitive binding kinetics between MeHg-Cys and Suwannee River natural organic matter, and their influence on the adsorption and uptake of MeHg by the cyanobacterium, Synechocystis sp. PCC6803. Liquid chromatography-inductively coupled plasma mass spectrometry was employed to monitor the kinetics processes involving competition of DOM with Cys for MeHg binding, which revealed that competitive binding kinetics were dictated by the abundance of thiol moieties in DOM. Thiol concentrations of 0.97 and 49.34 μmol of thiol (g C)-1 resulted in competitive binding rate constant (k values) of 0.30 and 3.47 h-1, respectively. Furthermore, the time-dependent competitive binding of DOM toward MeHg-Cys significantly inhibited MeHg adsorption and uptake by cyanobacteria, an effect that was amplified by an increased thiol abundance in DOM. These findings offer valuable insights into the kinetic characteristics of MeHg's fate and transport, as well as their impact on bioconcentration in aquatic organisms within natural aquatic ecosystems.