Binding Site Model Research Articles

Exploring the Impact of Protein Chain Selection in Binding Energy Calculations with DFT.

Calculation of binding free energies between a protein and a ligand are highly desired for computer-aided drug design. Here we approximate the binding energies of ABL1, an enzyme which is the target for drugs used in the treatment of chronic myeloid leukaemia, with minimal models and density functional theory (DFT). Starting from the crystal structures of protein-drug complexes, we estimated the binding free energies having used all available individual molecules (protein chains) within each structure, not only a single one as commonly used, in order to see if the choice of the protein chain is important in such calculations. Differences were observed between chains in the same file. Energy decomposition analysis (EDA) revealed that the most important factors for binding were exchange, repulsion and electrostatics. The desolvation term varied dramatically between the inhibitors (between 4.2 and 92.3 kcal/mol). All functionals showed similar patterns in the EDA and in discriminating between the ligands. Non-covalent interactions (NCI) analysis was used to further explain the differences between protein chains and functionals. Overall, it is shown that small minimal models of a drug binding site can be useful to infer on the suitability of an initial crystal structure for further analysis such as EDA.

Intermediate Formation via Proton Release during the Photoassembly of the Water-Oxidizing Mn4CaO5 Cluster in Photosystem II.

The early stages of the photoassembly of the water-oxidizing Mn4CaO5 cluster in spinach photosystem II (PSII) were monitored using rapid-scan time-resolved Fourier transform infrared (FTIR) spectroscopy. Carboxylate stretching and the amide I bands, which appeared upon the flash-induced oxidation of a Mn2+ ion, changed their features during the subsequent dark rearrangement process, indicating the relocation of the Mn3+ ion concomitant with protein conformational changes. Monitoring the isotope-edited FTIR signals of a Mes buffer estimated that nearly two protons are released upon the Mn2+ oxidation. Quantum chemical calculations for models of the Mn binding site suggested that the proton of a water ligand is transferred to D1-H332 through a hydrogen bond upon the Mn3+ formation and then released to the bulk as the Mn3+ shifts to bind to this histidine. Another Mn2+ ion may be inserted to form a binuclear Mn3+Mn2+ complex, whose structure was calculated to be stabilized by a μ-hydroxo bridge hydrogen-bonded with deprotonated D1-H337. Nearly one additional proton can thus be released from this histidine, assuming that it is mostly protonated before illumination. Alternatively, a proton could be released by further insertion of Ca2+, forming a Mn3+Mn2+Ca2+ complex with another hydroxo ligand connecting Ca2+ to the Mn3+Mn2+ complex.

Flexible and Disposable Hafnium Nitride Extended Gates Fabricated by Low-Temperature High-Power Impulse Magnetron Sputtering.

To obtain a high-performance extended gate field-effect transistor for pH detection, hafnium nitride (HfN) was first fabricated on an indium tin oxide on polyethylene terephthalate (ITO/PET) substrate using a high-power impulse magnetron sputter system (HiPIMS) in this study. It can be easily applied in biomedical diagnostic and environmental monitoring applications with the advantages of flexible, disposable, cost-effective, and reliable components. Various duty cycle conditions in HiPIMSs were designed to investigate the corresponding sensing performance and material properties including surface morphology and composition. As the duty cycle increased, the grain size of HfN increased. Additionally, X-ray photoelectron spectroscopy (XPS) analysis illustrated the presence of HfOxNy on the deposited HfN surface. Both behaviors could result in a better pH sensing performance based on the theory of the site-binding model. Subsequently, HfN with a 15% duty cycle exhibited excellent pH sensitivity and linearity, with values of 59.3 mV/pH and 99.8%, respectively; its hysteresis width and drift coefficient were -1 mV and 0.5 mV/h, respectively. Furthermore, this pH-sensing performance remained stable even after 2000 repeated bending cycles. These results indicate the potential and feasibility of this HiPIMS-deposited HfN for future wearable chemical applications.

The Self-Assembly of Cationic Metal Complexes on Gold Nanoparticle Surface.

This work aims to study the interaction between cationic metal complexes (M z +) and gold nanoparticles (AuNPs z- ). The M z + complexes were chosen from previous works described in the literature and were synthesized as defined. For example, they are as follows: 1 = [RuCl(dppb)(bipy)(py)](PF6); 2 = [RuCl(dppb)(bipy)(vpy)](PF6); 3 = [RuCl(dppb)(bipy)(mepy)](PF6); 4 = [RuCl(dppb)(bipy)(tbpy)](PF6); 5 = [RuCl2(dppb)(bipy)](PF6); 6 = [Fe(bipy)3]Cl2; 7 = [Ru(bipy)3](PF6)2; 8 = [TPyP{RuCl(dppb)(bipy)}4](PF6)4; and 9 = [RuCl(p-cymene)(Diipmp)](PF6). The interactions between M z + and AuNPs z- were carried out using conductometry and UV-vis spectroscopy. These experiments allowed determination of kinetic parameters, revealing three different steps in the interaction process: induction time, flocculation, and agglomeration. The self-assembly between M z + and AuNPs z- was investigated using three different models of binding site, namely, Langmuir or direct plot, Benesi-Hildebrand, and Scatchard. These models provide the fraction of total binding sites occupied (θ), the formation constant (K f), which is dependent on the temperature and geometric structure of each group of M z +, and the Gibbs free energy of reaction (ΔG r ), which was negative for each pair of M z + and AuNPs z- , revealing a spontaneous agglomeration process. The Hill coefficient (n) was 1 for almost all complexes, indicating that agglomeration is an independent process, except for 5, where n = 2, suggesting a positive propensity to bind onto the AuNPs z- surface. The models have confirmed a noncovalent interaction between these species. The relative error in site binding does not show any variation with changes in the temperature, but a fine-tuning of the n value to 1.00 was observed with the increase of the temperature. Finally, the reduction reaction of the 4-nitrophenolate anion (4-NP-) by NaBH4 catalyzed by AuNPs z- was used in the presence of M z + as an evaluation test to show how the M z + species will disturb the 4-NP- binding site on the surface of gold nanoparticles.

The apo-acyl coenzyme A binding protein of Leishmania major forms a unique ‘AXXA’ motif mediated dimer

Acyl-Coenzyme A binding domain containing proteins (ACBDs) are ubiquitous in nearly all eukaryotes. They can exist as a free protein, or a domain of a large, multidomain, multifunctional protein. Besides modularity, ACBDs also display multiplicity. The same organism may have multiple ACBDs, differing in sequence and organization. By virtue of this diversity, ACBDs perform functions ranging from transport, synthesis, trafficking, signal transduction, transcription, and gene regulation. In plants and some microorganisms, these ACBDs are designated ACBPs (acyl-CoA binding proteins). The simplest ACBD/ACBP is a small, ∼10 kDa, soluble protein, comprising the acyl-CoA binding (ACB) domain. Most of these small ACBDs exist as monomers, while a few show a tendency to oligomerize. In sync with those studies, we report the crystal structure of two ACBDs from Leishmania major, named ACBP103, and ACBP96 based on the number of residues present. Interestingly, ACBP103 crystallized as a monomer and a dimer under different crystallization conditions. Careful examination of the dimer disclosed an exposed ‘AXXA’ motif in the helix I of the two ACBP103 monomers, aligned in a head-to-tail arrangement in the dimer. Glutaraldehyde cross-linking studies confirm that apo-ACBP103 can self-associate in solution. Isothermal titration calorimetry studies further show that ACBP103 can bind ligands ranging from C8 – to C20-CoA, and the data could be best fit to a ‘two sets of sites’/sequential binding site model. Taken together, our studies show that Leishmania major ACBP103 can self-associate in the apo-form through a unique dimerization motif, an interaction that may play an important role in its function.

Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins.

High binding affinity and selectivity of metal ions are essential to the function of metalloproteins. Thus, understanding the factors that determine these binding characteristics is of major interest for both fundamental mechanistic investigations and guiding of the design of novel metalloproteins. In this work, we perform QM cluster model calculations and quantum mechanics/molecular mechanics (QM/MM) free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and its mutant. While a nonpolarizable MM model (CHARMM36) does not lead to the correct experimental trend, treatment of the metal binding site with the DFTB3 model in a QM/MM framework leads to relative binding free energies (ΔΔGbind) comparable with experimental data. For the wild-type (WT) protein, the calculated ΔΔGbind is ∼6.6 kcal/mol in comparison with the experimental value of 5.6 kcal/mol. The good agreement highlights the value of a QM description of the metal binding site and supports the role of electronic polarization and charge transfer to metal binding selectivity. For the D51A/E101D/F102W mutant, different binding site models lead to considerable variations in computed binding affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant coordination number for the mutant, the calculated relative binding affinity is ∼4.8 kcal/mol, in fair agreement with the experimental value of 1.6 kcal/mol. The WT protein is observed to feature a flexible binding site that accommodates a range of coordination numbers for Ca2+, which is essential to the high binding selectivity for Ca2+ over Mg2+. In the mutant, the E101D mutation reduces the flexibility of the binding site and limits the dominant coordination number of Ca2+ to be seven, thereby leading to reduced binding selectivity against Mg2+. Our results highlight that the binding selectivity of metal ions depends on both the structural and dynamical properties of the protein binding site.

A closer look at amyloid ligands, and what they tell us about protein aggregates.

The accumulation of amyloid fibrils is characteristic of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease. Detecting these fibrils with fluorescent or radiolabelled ligands is one strategy for diagnosing and better understanding these diseases. A vast number of amyloid-binding ligands have been reported in the literature as a result. To obtain a better understanding of how amyloid ligands bind, we have compiled a database of 3457 experimental dissociation constants for 2076 unique amyloid-binding ligands. These ligands target Aβ, tau, or αSyn fibrils, as well as relevant biological samples including AD brain homogenates. From this database significant variation in the reported dissociation constants of ligands was found, possibly due to differences in the morphology of the fibrils being studied. Ligands were also found to bind to Aβ(1-40) and Aβ(1-42) fibrils with similar affinities, whereas a greater difference was found for binding to Aβ and tau or αSyn fibrils. Next, the binding of ligands to fibrils was shown to be largely limited by the hydrophobic effect. Some Aβ ligands do not fit into this hydrophobicity-limited model, suggesting that polar interactions can play an important role when binding to this target. Finally several binding site models were outlined for amyloid fibrils that describe what ligands target what binding sites. These models provide a foundation for interpreting and designing site-specific binding assays.

Charge dynamics of amino acids fingerprints and the effect of density on FinFET-based Electrolyte-gated sensor

This work presents the charge dynamics and the effect of the density of amino acids on a sensing surface with the help of analytical modelling. We have implemented an in-house simulator incorporating the Gouy-Chapman-Stern and Site-Binding model to capture the perturbations in the proton affinity of reactive sites with the variation of amino acid density over a sensing surface. The results of the models are explained for Alanine, Glutamic Acid and Histidine with their α-carboxylic terminal immobilized on the sensor surface. The results show that an increase in amino acid density on the sensing surface over a certain limit deviates the fingerprints of the proton affinity away from the affinity of the reactive sites of individual amino acids. The effect of different electrolyte concentrations on steric hindrance is also captured for Alanine and Glutamic Acid. Finally, we used a junctionless FinFET to model unique signatures of amino acids down to a single molecule.

Hierarchical Model of Weak Polyelectrolytes with Ionization and Conformation Consistency

Conventional models of weak polyelectrolytes are formulated in terms of either an average degree of ionization or a rigid polymer conformation. While the decoupling of segment-level ionization and polymer structure simplifies the theoretical procedure and is beneficial from a computational perspective, it misses intrachain correlations (i.e., interactions beyond adjacent monomers) that are important for systems at a low polymer concentration with strong electrostatic interactions. In this work, we propose a hierarchical method that incorporates the liquid-state theories with the site-binding model to account for the effects of the local ionic environment on both inter- and intrachain correlations. A wormlike-chain model is introduced to describe the coupling of polymer conformation and monomeric ionization with the long-range electrostatic interactions accounted for by using the Gibbs–Bogoliubov variational principle. Through an extensive comparison of the theoretical predictions with experimental titration curves for poly(acrylic acid) in different alkali chloride solutions, we demonstrate that the hierarchical model is able to quantify the charging behavior of weak polyelectrolytes over a broad range of solution conditions.

Rational Loading of Linear Multi-Site Receptors with Functional Lanthanide Containers: The Missing Link between Oligomers and Polymers.

Although metal-containing organic polymers are becoming essential for modern applications in lighting, catalysis, and electronic devices, very little is known about their controlled metallic loading, which mainly limits their design to empirical mixing followed by characterization and often hampers rational developments. Focusing on the appealing optical and magnetic properties of 4f-block cations, the host-guest reactions leading to linear lanthanidopolymers already display some unexpected dependence of the binding-site affinities on the length of the organic polymer backbone: a drift usually, and erroneously, assigned to intersite cooperativity. Taking advantage of the parameters obtained for the stepwise thermodynamic loading of a series of rigid linear multi-tridentate organic receptors with increasing length, N = 1 (monomer L1), N = 2 (dimer L2), and N = 3 (trimer L3), with [Ln(hfa)3] containers in solution (Ln = trivalent lanthanide cations, hfa- = 1,1,1,5,5,5-hexafluoro-pentane-2,4-dione anion), it is demonstrated here that the site-binding model, based on the Potts-Ising approach, successfully predicts the binding properties of the novel soluble polymer P2N made up of nine successive binding units . An in-depth examination of the photophysical properties of these lanthanidopolymers shows impressive UV→vis downshifting quantum yields for the europium-based red luminescence, which can be modulated by the length of the polymeric chain.

Docking cholesterol to integral membrane proteins with Rosetta.

Lipid molecules such as cholesterol interact with the surface of integral membrane proteins (IMP) in a mode different from drug-like molecules in a protein binding pocket. These differences are due to the lipid molecule's shape, the membrane's hydrophobic environment, and the lipid's orientation in the membrane. We can use the recent increase in experimental structures in complex with cholesterol to understand protein-cholesterol interactions. We developed the RosettaCholesterol protocol consisting of (1) a prediction phase using an energy grid to sample and score native-like binding poses and (2) a specificity filter to calculate the likelihood that a cholesterol interaction site may be specific. We used a multi-pronged benchmark (self-dock, flip-dock, cross-dock, and global-dock) of protein-cholesterol complexes to validate our method. RosettaCholesterol improved sampling and scoring of native poses over the standard RosettaLigand baseline method in 91% of cases and performs better regardless of benchmark complexity. On the β2AR, our method found one likely-specific site, which is described in the literature. The RosettaCholesterol protocol quantifies cholesterol binding site specificity. Our approach provides a starting point for high-throughput modeling and prediction of cholesterol binding sites for further experimental validation.

Advanced investigation of a putative adsorption process of nine non key food odorants (non-KFOs) on the broadly tuned human olfactory receptor OR2W1: Statistical physics modeling and molecular docking study

In the present paper, statistical physics formalism was used to understand the olfactory perception via the investigation of dose-olfactory response curves of a putative adsorption process of nine non key food odorants (non-KFOs) on the broadly tuned human olfactory receptor OR2W1, in order to quantitative characterize the interactions between the nine studied non-KFOs, i. e., furfuryl sulfide, furfuryl disulfide, benzyl methyl disulfide, furfuryl methyl disulfide, benzyl methyl sulfide, 1-phenylethanethiol, benzyl mercaptan, furfuryl methyl sulfide and 3-phenylpropanol molecules and OR2W1 binding sites at a molecular level. Two advanced adsorption models have been proposed: the advanced monolayer monoenergy model (monolayer model with identical and independent olfactory receptor binding sites) (Model 1) and the advanced monolayer model with two independent types of olfactory receptor binding sites (Model 2). It was concluded that the monolayer monoenergy model was selected as the most adequate model to fit the experimental dose-olfactory response curves tabulated in literature. Actually, the numerical values of the three fitted physico-chemical parameters (RM1, n and C1) were obtained by a non-linear regression. Indeed, modeling results suggested that the number of docked non-KFOs per OR2W1 binding site n values (1.24 < n < 1.94) was always superior to 1, which indicated the non-parallel orientation of the studied odorants on the olfactory receptor and the multi-molecular adsorption mechanism. The estimated molar adsorption energy ΔEa values (ranged from 6.07 to 12.16 kJ/mol) for the nine olfactory systems confirmed the physical the exothermic characters of the adsorption process since ΔEa values were lower than 40 kJ/mol and positive. Furthermore, these estimated parameters were applied to characterize stereographically and energetically the interaction between the nine non-KFOs and OR2W1 through the determination of the human receptor binding site size distributions (RSDs) and the adsorption energy distributions (AEDs), which were spread out from 0.25 to 6.50 nm and from 0 to 22.50 kJ/mol, respectively. The docking computation between these nine non-KFOs and OR2W1 proved that the estimated binding affinities were belonged to the adsorption energies spectrum in general and the specific adsorption energy band or the molecular vibration modes limited spectrum (between 2.50 kJ/mol and 17 kJ/mol) (approximate olfactory band).

Multi‐tracer comparison in Alzheimer’s disease, Corticobasal Degeneration and Progressive Supranuclear Palsy brains

AbstractBackgroundRecent CryoEM studies in tauopathies clearly bought forward one more time the complexity of these pathologies, and showed that it goes beyond the tau isoforms. Tau PET tracers play an important role in the understanding of this aspect. We have observed in post‐mortem brain tissue from Alzheimer’s disease (AD) patients that the second‐generation of tau PET tracers 3H‐PI2620, 3H‐MK6240, 3H‐RO948, all show similar regional distribution, but also comparable binding affinities to multiple binding sites in AD brain large hemispherical tissue section autoradiography and homogenates. In vitro autoradiography can mirror the in vivo binding pattern of PET tracers and be useful in pre‐clinical validations. The aim of this study was to perform a comparative multi‐tracer study in AD, PSP, CBD and control brains with several second generation tau‐tracers to obtain a deeper insight into tau spatial distribution and discriminative power of tau tracers in degenerative proteinopathies. We also want to study how the binding of the tracers correlate with other pathological hallmarks such as amyloid‐β and reactive astrogliosis.Methodswe performed radioligand binding assays in brain homogenates, in small tissue sections and large frozen hemispherical brain sections autoradiography using tau PET tracers (3H‐PI2620, 3H‐MK6240, 3H‐RO948, and 3H‐JNJ067) in comparison to reactive astrogliosis PET tracers (3H‐BU99008 and 3H‐Deprenyl) and amyloid tracer (3H‐PIB).ResultsIn ongoing studies, 3H‐PI2620, 3H‐MK6240 and 3H‐RO948 clearly followed a two binding sites model in AD brains. 3H‐PI2620 bound to two binding sites in the frontal cortex of both AD and CBD but to one site in PSP brains, but in similar high affinity range in the three pathologies. 3H‐RO948 and 3H‐MK6240 showed low binding in comparison to 3H‐PI2620 in CBD and PSP.ConclusionTau PET tracers showed similar affinities to multiple binding sites and similar regional distribution in AD brains. 3H‐MK6240 and 3H‐RO948 displayed selectivity for AD brains, while 3H‐PI2620 also showed similar binding affinity for CBD and PSP brains. Ongoing studies with several PET tracers targeting different pathological hallmarks will increase possible discriminative properties and provide new knowledge on the spatial distribution of tau and its correlation with other biomarkers in different tauopathies.

Fully Symmetric Cyclodextrin Polycarboxylates: How to Determine Reliable Protonation Constants from NMR Titration Data.

Acid-base properties of cyclodextrins (CDs), persubstituted at C-6 by 3-mercaptopropionic acid, sualphadex (Suα-CD), subetadex (Suβ-CD) and sugammadex (Suγ-CD, the antidote of neuromuscular blocking steroids) were studied by 1H NMR-pH titrations. For each CD, the severe overlap in protonation steps prevented the calculation of macroscopic pKa values using the standard data fitting model. Considering the full symmetry of polycarboxylate structures, we reduced the number of unknown NMR parameters in the "Q-fitting" or the novel "equidistant macroscopic" evaluation approaches. These models already provided pKa values, but some of them proved to be physically unrealistic, deceptively suggesting cooperativity in carboxylate protonations. The latter problem could be circumvented by adapting the microscopic site-binding (cluster expansion) model by Borkovec, which applies pairwise interactivity parameters to quantify the mutual basicity-decreasing effect of carboxylate protonations. Surprisingly, only a single averaged interactivity parameter could be calculated reliably besides the carboxylate 'core' microconstant for each CD derivative. The speciation of protonation isomers hence could not be resolved, but the optimized microscopic basicity parameters could be converted to the following sets of macroscopic pKa values: 3.84, 4.35, 4.81, 5.31, 5.78, 6.28 for Suα-CD; 3.82, 4.31, 4.73, 5.18, 5.64, 6.06, 6.54 for Suβ-CD and 3.83, 4.28, 4.65, 5.03, 5.43, 5.81, 6.18, 6.64 for Suγ-CD. The pH-dependent charge of these compounds can now be accurately calculated, in support of designing new analytical methods to exploit their charge-dependent molecular recognition such as in cyclodextrin-aided chiral capillary electrophoresis.

On the Binding Mechanisms of Calcium Ions to Polycarboxylates: Effects of Molecular Weight, Side Chain, and Backbone Chemistry.

We experimentally determined the characteristics and Langmuir parameters of the binding of calcium ions to different polycarboxylates. By using potentiometric titrations and isothermal titration calorimetry, the effects of side chain chemistry, pH value, and chain length were systematically investigated using the linear polymers poly(aspartic acid), poly(glutamic acid), and poly(acrylic acid). We demonstrate that for polymers with high polymerization degrees, the binding process is governed by higher-order effects, such as the change of apparent pKa of carboxyl groups, and contributions arising from the whole polymer chain while the chemistry of the monomer unit constituting the polymer plays a subordinate role. In addition, primary binding sites need to be present in the polymer, thus rendering the abundance and sequential arrangement of protonated and deprotonated groups important. The detection of higher-order effects contradicts the assumptions posed by the Langmuir model of noninteracting binding sites and puts a question mark on whether ion binding to polycarboxylates can be described using solely a Langmuir binding model. No single uniform mechanism fits all investigated systems, and the whole polymer chain, including terminal groups, needs to be considered for the interpretation of binding data. Therefore, one needs to be careful when explaining ion binding to polymers solely based on studies on monomers or oligomers.

Kinetic characterization of SPR-based biomarker assays enables quality control, calibration free measurements and robust optimization for clinical application

ABSTRACT: Biomarker measurements are essential for the early diagnosis of complex diseases. However, many current biomarker assays lack sensitivity and multiplexing capacity, work in a narrow detection range and importantly lack real time quality control opportunities, which hampers clinical translation. In this paper, we demonstrate a toolbox to kinetically characterize a biomarker measurement assay using Surface Plasmon Resonance imaging (SPRi) with ample opportunities for real time quality control by exploiting quantitative descriptions of the various biomolecular interactions. We show an accurate prediction of SPRi measurements at both low and high concentrations of various analytes with deviations <5% between actual measurements and predicted measurement. The biphasic binding sites model was accurate for fitting the experimental curves and enables optimal detection of heterophilic antibodies, cross-reactivity, spotting irregularities and/or other confounders. The toolbox can also be used to create a (simulated) calibration curve, enabling calibration-free measurements with good recovery, it allows for easy assay optimizations, and could help bridge the gap to bring new biomarker assays to the clinic.

Molecular basis of Toxoplasma gondii oryzalin resistance from a novel α-tubulin binding site model

Oryzalin (ORY) is a dinitroaniline derivative that inhibits the microtubule polymerization in plants and parasitic protozoa by selectively binding to the α-tubulin subunit. This herbicidal agent exhibits good antiprotozoal activity against major human parasites, such as Toxoplasma gondii (toxoplasmosis), Leishmania mexicana (leishmaniasis), and Plasmodium falciparum (malaria). Previous chemical mutagenesis assays on T. gondii α-tubulin (TgAT) have identified key mutations that lead to ORY resistance. Herein, we employed alchemical free energy methods and molecular dynamics simulations to determine if the ORY resistance mutations either decrease the TgAT's affinity of the compound or increase the protein stability. Our results here suggest that L136F and V202F mutations significantly decrease the affinity of ORY to TgAT, while T239I and V252L mutations diminish TgAT's flexibility. On the other hand, protein stability predictors determined that R243S mutation reduces TgAT stability due to the loss of its salt bridge interaction with E27. Interestingly, molecular dynamics simulations confirm that the loss of this key interaction leads to ORY binding site closure. Our study provides a better insight into the TgAT-ORY interaction, further supporting our recently proposed ORY-binding site.

Noise analysis of MoTe2-based dual-cavity MOSFET as a pH sensor

Field-effect transistor (FET) pH sensors have been studied for a long time because of their low cost, sound sensitivity, and high operational speed. Recently, transition metal dichalcogenides (TMD) materials such as MoTe2, MoS2, among others, have emerged as promising channel materials for developing energy-efficient electronic devices. TMD-based sensors have shown excellent results because of the high surface area–volume ratio and better bio-specific interaction. This paper proposes and analyzes a MoTe2 channel–based dual-cavity (DC) accumulation metal oxide semiconductor field effect transistor (MOSFET) as a pH sensor. For a comprehensive study, a pH-FET noise model has been considered to investigate the amount of noise associated with the proposed FET under various ionic concentrations and device dimensions. The electrolytic semiconductor has been modeled based on ion dynamics for the simulation study. A site-binding model has been incorporated to capture the surface charge density fluctuations at the interface of electrolyte and gate oxide for different pH values. The effect of gate length scaling on the device performance is studied to comprehend its scalability. With this MoTe2-based DC accumulation MOSFET sensor, a peak threshold sensitivity of 77 mV pH−1 has been achieved. To provide a comparative performance analysis of the proposed work, a benchmarking figure is included and a detailed fabrication methodology is also presented in this paper. All simulations are performed with an experimentally calibrated setup in SILVACO Technology Computer Aided Design (TCAD).

In vivo competition assays between Vip3 proteins confirm the occurrence of shared binding sites in Spodoptera littoralis

Due to their different specificity, the use of Vip3 proteins from Bacillus thuringiensis in combination with the conventionally used Cry proteins in crop protection is being essential to counteract the appearance of insect resistance. Therefore, understanding the mode of action of Vip3 proteins is crucial for their better application, with special interest on the binding to membrane receptors as the main step for specificity. Derived from in vitro heterologous competition binding assays using 125I-Vip3A and other Vip3 proteins as competitors, it has been shown that Vip3 proteins share receptors in Spodoptera frugiperda and Spodoptera exigua brush border membrane vesicles (BBMV). In this study, using 125I-Vip3Aa, we have first extended the in vitro competition binding site model of Vip3 proteins to Spodoptera littoralis. With the aim to understand the relevance (in terms of toxicity) of the binding to the midgut sites observed in vitro on the insecticidal activity of these proteins, we have performed in vivo competition assays with S. littoralis larvae, using disabled mutant (non-toxic) Vip3 proteins as competitors for blocking the toxicity of Vip3Aa and Vip3Af. The results of the in vivo competition assays confirm the occurrence of shared binding sites among Vip3 proteins and help understand the functional role of the shared binding sites as revealed in vitro.

Comparison of in vitro and in vivo binding site competition of Bacillus thuringiensis Cry1 proteins in two important maize pests.

Binding site models, derived from in vitro competition binding studies, have been widely used for predicting potential cross-resistance among insecticidal proteins from Bacillus thuringiensis. However, because discrepancies have been found between binding data and observed cross-resistance patterns in some insect species, new tools are required to study the functional relevance of the shared binding sites. Here, an in vivo approach has been applied to the competition studies to establish the functional relevance of shared binding sites as determined by in vitro competition assays. Using Cry disabled proteins as competitors in mixed protein overlay assays, we assessed the preference of Cry1Ab, Cry1Fa, and Cry1A.105 proteins for shared binding sites in vivo in two important corn pests, Ostrinia nubilalis and Spodoptera frugiperda. This study shows that in vivo and in vitro binding site competition assays can provide useful information to better ascertain whether different Cry proteins share binding sites and, consequently, whether cross-resistance due to binding site alteration can occur. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.