Apparent Kd Values Research Articles

Specificity and mechanism of TonB-dependent ferric catecholate uptake by Fiu.

We studied the Escherichia coli outer membrane protein Fiu, a presumed transporter of monomeric ferric catecholates, by introducing Cys residues in its surface loops and modifying them with fluorescein maleimide (FM). Fiu-FM bound iron complexes of the tricatecholate siderophore enterobactin (FeEnt) and glucosylated enterobactin (FeGEnt), their dicatecholate degradation product Fe(DHBS)2 (FeEnt*), the monocatecholates dihydroxybenzoic acid (FeDHBA) and dihydroxybenzoyl serine (FeDHBS), and the siderophore antibiotics cefiderocol (FDC) and MB-1. Unlike high-affinity ligand-gated porins (LGPs), Fiu-FM had only micromolar affinity for iron complexes. Its apparent KD values for FeDHBS, FeDHBA, FeEnt*, FeEnt, FeGEnt, FeFDC, and FeMB-1 were 0.1, 0.7, 0.7, 1.0, 0.3, 0.4, and 4 μM, respectively. Despite its broad binding abilities, the transport repertoires of E. coli Fiu, as well as those of Cir and FepA, were less broad. Fiu only transported FeEnt*. Cir transported FeEnt* and FeDHBS (weakly); FepA transported FeEnt, FeEnt*, and FeDHBA. Both Cir and FepA bound FeGEnt, albeit with lower affinity. Related transporters of Acinetobacter baumannii (PiuA, PirA, BauA) had similarly moderate affinity and broad specificity for di- or monomeric ferric catecholates. Both microbiological and radioisotopic experiments showed Fiu's exclusive transport of FeEnt*, rather than ferric monocatecholate compounds. Molecular docking and molecular dynamics simulations predicted three binding sites for FeEnt*in the external vestibule of Fiu, and a fourth site deeper in its interior. Alanine scanning mutagenesis in the outermost sites (1a, 1b, and 2) decreased FeEnt* binding affinity as much as 20-fold and reduced or eliminated FeEnt* uptake. Finally, the molecular dynamics simulations suggested a pathway of FeEnt* movement through Fiu that may generally describe the process of metal transport by TonB-dependent receptors.

Competitive aptamer switch for modulating ligand binding affinity

Aptamers are short, single-stranded DNA or RNA molecules that selectively bind to a target molecule. Aptamer-complement duplex (ACD) is often used to design molecular switches capable of producing a detectable signal or triggering a structural change upon aptamer binding to a target. However, such aptamer switch generally faces an increased dissociation constant (Kd) due to the energy barrier of the complementary duplex. We reported a competitive hybridization mechanism to modulate the binding affinity of an ACD to a target adenosine. Using the computation-guided design, we calculated the aptamer folding energy for the duplex length from 11-nt to 15-nt, and experimentally measured increased apparent Kd values resulted from these extended duplexes. Using a set of strands to compete with the ACD hybridization, it reduced the aptamer folding energy to facilitate aptamer switches with decreased apparent Kd values ranging from over 400 μM without a competing strand to ∼30 μM with a competing strand. This competitive aptamer switch was also found sensitive to single-nucleotide mutations of a competing strand. Our work provides an approach to modulate the binding affinity and the sensitivity of aptamer-complement duplexes, which could be useful in the nucleic acids-based sensing and nanomedicine.

A Phenylboronic Acid-Based Transition State Analogue Yields Nanomolar Inhibition of Mandelate Racemase.

Mandelate racemase (MR) catalyzes the Mg2+-dependent interconversion of (R)- and (S)-mandelate by stabilizing the altered substrate in the transition state (TS) by ∼26 kcal/mol. The enzyme has been employed as a model to explore the limits to which the free energy of TS stabilization may be captured by TS analogues to effect strong binding. Herein, we determined the thermodynamic parameters accompanying binding of a series of bromo-, chloro-, and fluoro-substituted phenylboronic acids (PBAs) by MR and found that binding was predominately driven by favorable entropy changes. 3,4-Dichloro-PBA was discovered to be the most potent inhibitor yet identified for MR, binding with a Kdapp value of 11 ± 2 nM and exceeding the binding of the substrate by ∼72,000-fold. The ΔCp value accompanying binding (-488 ± 18 cal·mol-1 K-1) suggested that dispersion forces contribute significantly to the binding. The pH-dependence of the inhibition revealed that MR preferentially binds the anionic, tetrahedral form of 3,4-dichloro-PBA with a pH-independent Ki value of 5.7 ± 0.5 nM, which was consistent with the observed upfield shift of the 11B NMR signal. The linear free energy relationship between log(kcat/Km) and log(1/Ki) for wild-type and 11 MR variants binding 3,4-dichloro-PBA had a slope of 0.8 ± 0.2, indicating that MR recognizes the inhibitor as an analogue of the TS. Hence, halogen substitution may be utilized to capture additional free energy of TS stabilization arising from dispersion forces to enhance the binding of boronic acid inhibitors by MR.

Functional characterization of SGLT1 using SSM-based electrophysiology: Kinetics of sugar binding and translocation.

Beside the ongoing efforts to determine structural information, detailed functional studies on transporters are essential to entirely understand the underlying transport mechanisms. We recently found that solid supported membrane-based electrophysiology (SSME) enables the measurement of both sugar binding and transport in the Na+/sugar cotransporter SGLT1 (Bazzone et al, 2022a). Here, we continued with a detailed kinetic characterization of SGLT1 using SSME, determining KM and KD app for different sugars, kobs values for sugar-induced conformational transitions and the effects of Na+, Li+, H+ and Cl- on sugar binding and transport. We found that the sugar-induced pre-steady-state (PSS) charge translocation varies with the bound ion (Na+, Li+, H+ or Cl-), but not with the sugar species, indicating that the conformational state upon sugar binding depends on the ion. Rate constants for the sugar-induced conformational transitions upon binding to the Na+-bound carrier range from 208s-1 for D-glucose to 95s-1 for 3-OMG. In the absence of Na+, rate constants are decreased, but all sugars bind to the empty carrier. From the steady-state transport current, we found a sequence for sugar specificity (Vmax/KM): D-glucose > MDG > D-galactose > 3-OMG > D-xylose. While KM differs 160-fold across tested substrates and plays a major role in substrate specificity, Vmax only varies by a factor of 1.9. Interestingly, D-glucose has the lowest Vmax across all tested substrates, indicating a rate limiting step in the sugar translocation pathway following the fast sugar-induced electrogenic conformational transition. SGLT1 specificity for D-glucose is achieved by optimizing two ratios: the sugar affinity of the empty carrier for D-glucose is similarly low as for all tested sugars (KD,K app = 210mM). Affinity for D-glucose increases 14-fold (KD,Na app = 15mM) in the presence of sodium as a result of cooperativity. Apparent affinity for D-glucose during transport increases 8-fold (KM = 1.9mM) compared to KD,Na app due to optimized kinetics. In contrast, KM and KD app values for 3-OMG and D-xylose are of similar magnitude. Based on our findings we propose an 11-state kinetic model, introducing a random binding order and intermediate states corresponding to the electrogenic transitions detected via SSME upon substrate binding.

Calmodulin binds FGF12A to regulate Nav1.5 channel inactivation.

Activation and inactivation gating of the Nav1.5 voltage-gated ion channel is responsible for the rapid depolarization of the cardiac action potential (AP) and regulates its duration. Altered inactivation kinetics can lead to AP prolongation and potentiate arrhythmia. Th Nav1.5 C-terminal domain (CTD) is known to modulate inactivation. In addition, there are multiple accessory proteins that bind the CTD are CaM and FGF12A. CaM has been linked to a possible Ca2+ modulation of the Nav1.5 as Ca2+ ions typically do not interact directly with the channel. However, the combined interaction on channel inactivation between CaM and FGF12A has also not been determined. We employed the use of cut-open voltage clamping to record the current traces. FRET imaging was used to assess binding affinity between FGF12A and CaM with apparent KD values. The addition of FGF12A to the CTD induces shifts in the activation's voltage dependence (+10.0 ±1.9 SEM mV, p<0.05) and removing CaM with the IQ/AA mutation on Nav1.5 leads to a depolarizing shift in inactivation (+19.5 ±2.1 SEM mV, p<0.01). We have shown that the addition of FGF12A to a channel lacking CaM (IQ/AA) will have a depolarizing shift in the steady state inactivation (+15.5 ±2.6 SEM mV, p<0.01). Furthermore, we have shown that a binding domain for CaM on the FGF12A protein itself requires the presence of Ca2+ ions to associate by measuring increase in the apparent KD value determined through FRET imaging. By removing this CaM binding domain from FGF12A we see a reduction in the recovery from inactivation and a hyperpolarizing shift in the voltage dependence of inactivaiton (−10.0 ±2.8 mV SEM, p<0.0005). The shift in inactivation based upon the presence of CaM could indicate an interaction between Ca2+ ions and the Nav1.5 channel.

Reductionist insights into how chaperone charge influences RNA folding.

Non-coding RNAs are composed of modular secondary and tertiary structural units that themselves must form complex 3D structures for the entire RNA to fold and perform its biological function. However, the high density of negative charges associated with the phosphate backbone gives rise to substantial amounts of electrostatic repulsion, contributing to the large energetic barrier between unfolded and folded states. RNA folding chaperones (RFCs) are proteins that help lower this energy barrier by transiently interacting with RNA. Recent work has shown that some RFCs can function as macromolecular counterions for their RNA clients, thereby screening backbone electrostatic repulsion. However, the fundamental principles associated with how RFCs assist folding is largely unexplored. Here, we reduce RFCs to their smallest cationic constituents and then systematically “re-build” RFCs from these components (e.g., NH4+→ Lys→ polyK10→ RFC). We use single-molecule FRET to determine how these counterions influence both the relative population abundance and mean FRET efficiency of the folded and unfolded states of small model RNAs. From these studies, we have begun to determine aspects of RFCs that contribute to chaperoning RNA folding, such as net cationic charge and charge distribution. Here, we show that cationic amino acids (e.g., Lys and Arg) bind to RNA with apparent Kd values (appKd) on the order of 100 mM, which are comparable to those associated with their characteristic functional groups (e.g., ammonium and guanidinium). Further, increasing the net cationic charge of a counterion systematically decreases the appKd over several orders of magnitude. We also show a correlation between the decrease in appKd and a decrease in the folding free energy barrier. We then compare our observations of these polypeptide chaperones to the behavior of known RFCs (e.g., protamine, H1, and HCV nucleocapsid protein) with the small model RNAs.

Specific S100 Proteins Bind Tumor Necrosis Factor and Inhibit Its Activity.

Tumor necrosis factor (TNF) inhibitors (anti-TNFs) represent a cornerstone of the treatment of various immune-mediated inflammatory diseases and are among the most commercially successful therapeutic agents. Knowledge of TNF binding partners is critical for identification of the factors able to affect clinical efficacy of the anti-TNFs. Here, we report that among eighteen representatives of the multifunctional S100 protein family, only S100A11, S100A12 and S100A13 interact with the soluble form of TNF (sTNF) in vitro. The lowest equilibrium dissociation constants (Kd) for the complexes with monomeric sTNF determined using surface plasmon resonance spectroscopy range from 2 nM to 28 nM. The apparent Kd values for the complexes of multimeric sTNF with S100A11/A12 estimated from fluorimetric titrations are 0.1-0.3 µM. S100A12/A13 suppress the cytotoxic activity of sTNF against Huh-7 cells, as evidenced by the MTT assay. Structural modeling indicates that the sTNF-S100 interactions may interfere with the sTNF recognition by the therapeutic anti-TNFs. Bioinformatics analysis reveals dysregulation of TNF and S100A11/A12/A13 in numerous disorders. Overall, we have shown a novel potential regulatory role of the extracellular forms of specific S100 proteins that may affect the efficacy of anti-TNF treatment in various diseases.

Determination of Anti-drug Antibody Affinity in Clinical Study Samples Provides a Tool for Evaluation of Immune Response Maturation

Characterization of clinical anti-drug antibody (ADA) responses to biotherapeutics can be important to understanding the consequences of immunogenicity. ADA are expected to be polyclonal, with composition and affinities that evolve over time. Measuring ADA binding affinity can be complicated by the polyclonal nature of response, residual drug in sample, and low ADA levels. We developed a novel workflow to determine the apparent ADA affinity (KD) against a monoclonal antibody biotherapeutic, PF-06480605. An affinity capture elution pre-treatment step was used to isolate ADA and remove residual drug interference from samples. Solution-phase equilibrium incubation was performed using drug and sample ADA as variable and fixed binding interactants, respectively. Unbound ADA concentration was measured using a Singulex Erenna ligand-binding assay (LBA) method. Apparent ADA KD values were calculated using a custom R Shiny algorithm. KD values determined for ADA positive samples showed good correlation with other immunogenicity parameters, including titers and neutralizing antibody (NAb) activity with a general increase in affinity over time, indicative of a maturing immune response. Time of onset of high affinity responses (KD < 100 pM) varied between patients, ranging from 16 to 24 weeks. Antibody responses appeared monophasic at earlier time points, trending towards a biphasic response with a variable transition time and general increase in proportion of high affinity ADA over time. Herein, we provide a novel, sensitive bioanalytical method to determine the KD of ADA in clinical samples. The observed decrease in ADA KD is consistent with evidence of a maturing immune response.Graphical

Radiosynthesis and Preclinical Evaluation of an 18F-Labeled Triazolopyridopyrazine-Based Inhibitor for Neuroimaging of the Phosphodiesterase 2A (PDE2A).

The cyclic nucleotide phosphodiesterase 2A is an intracellular enzyme which hydrolyzes the secondary messengers cAMP and cGMP and therefore plays an important role in signaling cascades. A high expression in distinct brain areas as well as in cancer cells makes PDE2A an interesting therapeutic and diagnostic target for neurodegenerative and neuropsychiatric diseases as well as for cancer. Aiming at specific imaging of this enzyme in the brain with positron emission tomography (PET), a new triazolopyridopyrazine-based derivative (11) was identified as a potent PDE2A inhibitor (IC50, PDE2A = 1.99 nM; IC50, PDE10A ~2000 nM) and has been radiofluorinated for biological evaluation. In vitro autoradiographic studies revealed that [18F]11 binds with high affinity and excellent specificity towards PDE2A in the rat brain. For the PDE2A-rich region nucleus caudate and putamen an apparent KD value of 0.24 nM and an apparent Bmax value of 16 pmol/mg protein were estimated. In vivo PET-MR studies in rats showed a moderate brain uptake of [18F]11 with a highest standardized uptake value (SUV) of 0.97. However, no considerable enrichment in PDE2A-specific regions in comparison to a reference region was detectable (SUVcaudate putamen = 0.51 vs. SUVcerebellum = 0.40 at 15 min p.i.). Furthermore, metabolism studies revealed a considerable uptake of radiometabolites of [18F]11 in the brain (66% parent fraction at 30 min p.i.). Altogether, despite the low specificity and the blood–brain barrier crossing of radiometabolites observed in vivo, [18F]11 is a valuable imaging probe for the in vitro investigation of PDE2A in the brain and has potential as a lead compound for further development of a PDE2A-specific PET ligand for neuroimaging.

Silica adsorption tag derived from the silica polycondensation protein glassin for the immobilization of soluble proteins

Glassin is a water-soluble protein from the siliceous skeleton of a marine sponge that adsorbs tightly to silica at pH 7.0-9.0 and accelerates silica particle formation from silicic acid. Glassin comprises three distinct domains: a His and Asp-rich (HD) domain, a Pro-rich (P) domain, and a His and Thr-rich (HT) domain. Here, we investigated the roles of these three domains in silica adsorption by using glutathione S-transferase (GST) fused with glassin or with each domain. GST fused with the HD domain exhibited tight adsorption, equivalent to that of GST fused with the full-length glassin sequence at values above 7.0. The apparent Kd values for the binding of full-length glassin and HD to fumed silica at pH 7.0 were 20.8 and 22.7nM, respectively, indicating that this domain greatly contributes to the silica adsorption ability of glassin. In addition, no internal cleavage was observed in the HD domain, whereas GST fused with the full-length glassin sequence exhibited internal cleavage. The HD domain adsorbed on silica did not dissociate even at pH 6.0. Given these findings, we concluded that the HD domain has potential as a tag for the immobilization of soluble proteins.

Generation of synthetic antibody fragments with optimal complementarity determining region lengths for Notch-1 recognition.

Synthetic antibodies have been engineered against a wide variety of antigens with desirable biophysical, biochemical, and pharmacological properties. Here, we describe the generation and characterization of synthetic antigen-binding fragments (Fabs) against Notch-1. Three single-framework synthetic Fab libraries, named S, F, and modified-F, were screened against the recombinant human Notch-1 extracellular domain using phage display. These libraries were built on a modified trastuzumab framework, containing two or four diversified complementarity-determining regions (CDRs) and different CDR diversity designs. In total, 12 Notch-1 Fabs were generated with 10 different CDRH3 lengths. These Fabs possessed a high affinity for Notch-1 (sub-nM to mid-nM KDapp values) and exhibited different binding profiles (mono-, bi-or tri-specific) toward Notch/Jagged receptors. Importantly, we showed that screening focused diversity libraries, implementing next-generation sequencing approaches, and fine-tuning the CDR length diversity provided improved binding solutions for Notch-1 recognition. These findings have implications for antibody library design and antibody phage display.

The interaction of spongistatin 1 with tubulin

A tritiated derivative of the sponge-derived natural product spongistatin 1 was prepared, and its interactions with tubulin were examined. [3H]Spongistatin 1 was found to bind rapidly to tubulin at a single site (the low specific activity of the [3H]spongistatin 1, 0.75 Ci/mmol, prevented our defining an association rate), and the inability of spongistatin 1 to cause an aberrant assembly reaction was confirmed. Spongistatin 1 bound to tubulin very tightly, and we could detect no significant dissociation reaction from tubulin. The tubulin-[3H]spongistatin 1 complex did dissociate in 8 M urea, so there was no evidence for covalent bond formation. Apparent KD values were obtained by Scatchard analysis of binding data and by Hummel-Dreyer chromatography (3.5 and 1.1 μM, respectively). The effects of a large cohort of vinca domain drugs on the binding of [3H]spongistatin 1 to tubulin were evaluated. Compounds that did not cause aberrant assembly reactions (halichondrin B, eribulin, maytansine, and rhizoxin) caused little inhibition of [3H]spongistatin 1 binding. Little inhibition also occurred with the peptides dolastatin 15, its active pentapeptide derivative, vitilevuamide, or diazonamide A, nor with the vinca alkaloid vinblastine. Strong inhibition was observed with dolastatin 10, hemiasterlin, and cryptophycin 1, all of which cause aberrant assembly reactions that might actually mask the spongistatin 1 binding site. Spongistatin 5 was found to be a competitive inhibitor of [3H]spongistatin 1 binding, with an apparent Ki of 2.2 μM. We propose that the strong picomolar cytotoxicity of spongistatin 1 probably derives from its extremely tight binding to tubulin.

IgM anti-ACE2 autoantibodies in severe COVID-19 activate complement and perturb vascular endothelial function.

BackgroundSome clinical features of severe COVID-19 represent blood vessel damage induced by activation of host immune responses initiated by the coronavirus SARS-CoV-2. We hypothesized autoantibodies against angiotensin-converting enzyme 2 (ACE2), the SARS-CoV-2 receptor expressed on vascular endothelium, are generated during COVID-19 and are of mechanistic importance.MethodsIn an opportunity sample of 118 COVID-19 inpatients, autoantibodies recognizing ACE2 were detected by ELISA. Binding properties of anti-ACE2 IgM were analyzed via biolayer interferometry. Effects of anti-ACE2 IgM on complement activation and endothelial function were demonstrated in a tissue-engineered pulmonary microvessel model.ResultsAnti-ACE2 IgM (not IgG) autoantibodies were associated with severe COVID-19 and found in 18/66 (27.2%) patients with severe disease compared with 2/52 (3.8%) of patients with moderate disease (OR 9.38, 95% CI 2.38–42.0; P = 0.0009). Anti-ACE2 IgM autoantibodies were rare (2/50) in non-COVID-19 ventilated patients with acute respiratory distress syndrome. Unexpectedly, ACE2-reactive IgM autoantibodies in COVID-19 did not undergo class-switching to IgG and had apparent KD values of 5.6–21.7 nM, indicating they are T cell independent. Anti-ACE2 IgMs activated complement and initiated complement-binding and functional changes in endothelial cells in microvessels, suggesting they contribute to the angiocentric pathology of COVID-19.ConclusionWe identify anti-ACE2 IgM as a mechanism-based biomarker strongly associated with severe clinical outcomes in SARS-CoV-2 infection, which has therapeutic implications.FUNDINGBill & Melinda Gates Foundation, Gates Philanthropy Partners, Donald B. and Dorothy L. Stabler Foundation, and Jerome L. Greene Foundation; NIH R01 AR073208, R01 AR069569, Institutional Research and Academic Career Development Award (5K12GM123914-03), National Heart, Lung, and Blood Institute R21HL145216, and Division of Intramural Research, National Institute of Allergy and Infectious Diseases; National Science Foundation Graduate Research Fellowship (DGE1746891)

Riding a VeSPha in the classroom: A Versatile Simulation tool for effective didactic illustration of Pharmacodynamic concepts

A solid mastery of Pharmacodynamics concepts is a cornerstone of effective pharmacology education. Understanding the meaning and appropriate use of pharmacodynamics terms such as potency, affinity, intrinsic efficacy, or receptor reserve is extremely valuable but challenging for most trainees. The onus, therefore, is on the educators to devise effective strategies and tools to facilitate the acquisition of this critical competency.When approaching pharmacodynamics, the ability of learners to explore the influence of driving parameters on the magnitude and position of concentration response curves is a powerful way to visualize and make concrete the basic concepts of pharmacodynamics. To this end, I have developed VeSPha, a Versatile Simulation tool for Pharmacodynamics based on a rapid equilibrium generalization of Furchgott’s views on agonism. Through multiple sliders, the user can vary the parameters of the system, such as the concentrations of orthosteric and allosteric ligands, their respective affinities, the allosteric coupling constant, the intrinsic efficacies of each of the receptor species, the total number of receptors and the sensitivity of the system to the stimulus. A graph panel allows the display of the resulting response curves as a function of the concentration of ligand as well as orthosteric and allosteric ligand occupancy curves. Dropdown lines with corresponding EC50 as well as apparent Kd values for each ligand are also displayed. VeSPha also includes bar graphs as well as an intuitive graphic representation of the model displaying the values of the parameters, the distribution of the receptor species at the chosen state, the total stimulus as well as the resulting responses.The tool allows easy exploration of a wide gamut of possibilities that illustrate basic concepts of affinity, intrinsic efficacy, partial agonism, constitutive activity, inverse agonism, competitive antagonism, as well as allosteric modulation of both affinity and efficacy in any combination. The tool is implemented as an easy‐to‐use Excel file. This allows for flexible standalone use and for straightforward embedding into PowerPoint presentations for real‐time illustrations during lectures. The tool also readily generates simulated data including sampling errors for composing realistic, internally consistent assessment items such as quiz, problem set and exam questions.Implementation of this didactic tool is straightforward and effective in the author’s experience across a wide range of learners spanning from undergraduates, Master’s, Ph.D. M.D. Pharm D and DDS students. The tool, including a tutorial video can be made available to the Pharmacology teaching community upon request and an online version is under development.

High Mannose-Specific Aptamers for Broad-Spectrum Virus Inhibition and Cancer Targeting

High Mannose-Specific Aptamers for Broad-Spectrum Virus Inhibition and Cancer Targeting

Rosmarinic Acid and Sodium Citrate Have a Synergistic Bacteriostatic Effect against Vibrio Species by Inhibiting Iron Uptake.

Background: New strategies are needed to combat multidrug-resistant bacteria. The restriction of iron uptake by bacteria is a promising way to inhibit their growth. We aimed to suppress the growth of Vibrio bacterial species by inhibiting their ferric ion-binding protein (FbpA) using food components. Methods: Twenty spices were selected for the screening of FbpA inhibitors. The candidate was applied to antibacterial tests, and the mechanism was further studied. Results: An active compound, rosmarinic acid (RA), was screened out. RA binds competitively and more tightly than Fe3+ to VmFbpA, the FbpA from V. metschnikovii, with apparent KD values of 8 μM vs. 17 μM. Moreover, RA can inhibit the growth of V. metschnikovii to one-third of the control at 1000 μM. Interestingly, sodium citrate (SC) enhances the growth inhibition effect of RA, although SC only does not inhibit the growth. The combination of RA/SC completely inhibits the growth of not only V. metschnikovii at 100/100 μM but also the vibriosis-causative pathogens V. vulnificus and V. parahaemolyticus, at 100/100 and 1000/100 μM, respectively. However, RA/SC does not affect the growth of Escherichia coli. Conclusions: RA/SC is a potential bacteriostatic agent against Vibrio species while causing little damage to indigenous gastrointestinal bacteria.

Effects of organic matter complexation on partitioning of transition metals into calcite: Cave-analogue crystal growth experiments

We highlight the potential for first row transition metals to carry paleohydrological signals in speleothems, and argue that these metals constitute valuable proxies for climate reconstructions. Metal availability to speleothems is hypothesised to be restricted by organic complexation, which strongly limits the free ion activity of transition metals (Co2+, Ni2+ and Cu2+) in dripwater, thereby creating a kinetic overprint on metal concentrations and isotope ratios in speleothem calcite.This study presents the results of the first cave-analogue experiments of transition metal partitioning into calcite in the absence and presence of organic ligands. The Geological Microclimate (GeoMic) system establishes homeostatic control of air temperature and atmospheric pCO2 (set to 20 ± 0.1 °C and 1000 ± 10 ppm, respectively), and regulates relative humidity to cave-analogue levels (>90%). Calcite was precipitated from flowing aqueous films on inclined glass plates to assess the effect of prior calcite precipitation (PCP) on metal partitioning. We report speleothem-specific inorganic Kd values for Co, Ni and Cu of ∼4, 1, and 44, respectively. Pronounced PCP effects were observed in Co and Cu in the inorganic experiments, leading to strong reduction in Cu/Ca and Co/Ca, whereas Ni/Ca molar ratios remained constant.Introduction of the organic chelating ligand nitrilotriacetic acid (NTA) overturned the behaviour of all three metals, leading to stable solution Cu/Ca ratios and progressive enrichment of Co/Ca and Ni/Ca ratios as PCP progressed and apparent Kd values <1 for all three metals. This result is confirmed in a Cu-fulvic acid experiment. We show that in the presence of organic ligands with stability constants close to those observed in natural systems, the partitioning of transition metals into calcite is dependent on the fluid residence time and the stability of the metal–ligand complexes. Therefore, drip rate should be the first-order control on transition metal concentrations in stalagmites: opening the way to a novel and potentially quantitative paleohydrological proxy.

An Arrhythmic Mutation E7K Facilitates TRPM4 Channel Activation via Enhanced PIP2 Interaction.

A Ca2+-activated monovalent cation-selective TRPM4 channel is abundantly expressed in the heart. Recently, a single gain-of-function mutation identified in the distal N-terminus of the human TRPM4 channel (Glu5 to Lys5; E7K) was found to be arrhythmogenic because of enhanced cell membrane expression. In this study, we conducted detailed analyses of this mutant channel from more functional aspects, in comparison with its wild type (WT). In an expression system, intracellular application of a short soluble PIP2 (diC8PIP2) restored the single-channel activities of both WT and E7K, which had quickly faded after membrane excision. The potency (Kd) of diC8PIP2 for this recovery was stronger in E7K than its WT (1.44 vs. 2.40 μM). FRET-based PIP2 measurements combined with the Danio rerio voltage-sensing phosphatase (DrVSP) and patch clamping revealed that lowering the endogenous PIP2 level by DrVSP activation reduced the TRPM4 channel activity. This effect was less prominent in E7K than its WT (apparent Kd values estimated from DrVSP-mediated PIP2 depletion: 0.97 and 1.06 μM, respectively), being associated with the differential PIP2-mediated modulation of voltage dependence. Moreover, intracellular perfusion of short N-terminal polypeptides containing either the ‘WT’ or ‘E7K’ sequences respectively attenuated the TRPM4 channel activation at whole-cell and single-channel levels, but in both configurations, the E7K polypeptide exerted greater inhibitory effects. These results collectively suggest that N-terminal interaction with endogenous PIP2 is essential for the TRPM4 channel to function, the extent of which may be abnormally strengthened by the E7K mutation through modulating voltage-dependent activation. The altered PIP2 interaction may account for the arrhythmogenic potential of this mutation.

Designed leucine-rich repeat proteins bind two muramyl dipeptide ligands.

Designed protein receptors hold diagnostic and therapeutic promise. We now report the design of five consensus leucine-rich repeat proteins (CLRR4-8) based on the LRR domain of nucleotide-binding oligomerization domain (NOD)-like receptors involved in the innate immune system. The CLRRs bind muramyl dipeptide (MDP), a bacterial cell wall component, with micromolar affinity. The overall Kd app values ranged from 1.0 to 57 μM as measured by fluorescence quenching experiments. Biphasic fluorescence quenching curves were observed in all CLRRs, with higher affinity Kd1 values ranging from 0.04 to 4.5 μM, and lower affinity Kd2 values ranging from 3.1 to 227 μM. These biphasic binding curves, along with the docking studies of MDP binding to CLRR4, suggest that at least two MDPs bind to each protein. Previously, only single MDP binding was reported. This high-capacity binding of MDP promises small, soluble, stable CLRR scaffolds as candidates for the future design of pathogen biosensors.

Conformational Structural Alteration of NCS1 Protein Through Pb2+and Mn2+ Association

NCS1 (Frequenin) is a member of neuronal calcium sensor (NCS) family. This globular protein contains four EF-hand motifs and an amino-terminal myristylation sequence. Pb2+has been widely viewed as a health concern for its anthropogenic toxicity. It has been observed that Pb2+ modulates interactions between calcium-binding protein calmodulin (CaM) and its binding partners through binding in the EF-hands of CaM and it may play a significant role in Pb2+-induced neurotoxicity. Mn is a highly abundant metal in nature which has been found in human brain and associated with the several diseases like multiple sclerosis, Alzheimer's and Parkinson's disease and is considered as potential toxic element. Previous studies from our group showed Pb2+ and Cd2+ binding to DREAM protein that can contribute to Pb2+/Cd2+ induced neurotoxicity. Here we showed that Pb2+ binds to EF-hands in apo-NCS1with a high affinity (Kd = 7.0±1.5 nM) whereas Cd2+ did not show any binding with NCS1. For the first time we investigated the Mn2+ association to NCS1 protein. This cation binds with an apparent equilibrium dissociation constant of 340±67 µM. Pb2+ and Mn2+binding trigger secondary and tertiary structural rearrangements of NCS1 that are analogous to those observed for Ca2+ association. In addition, Pb2+ as well as Mn2+ promote NCS1 interaction with hydrophobic molecule 1,8-ANS. Interestingly,Ca2+NCS1:1,8-ANS complex exhibits a co-operative binding of Pb2+ with Kd = 103±23 µM whereas Mn2+ showed apparent Kd value 924±185 µM with Ca2+NCS1:1,8-ANS complex. These results suggest allosteric interactions between the 1,8-ANS binding site and Pb2+ binding EF-hands. Data provided here points towards ability of EF-hands in NCS-1 to interact with various metals and a possible role of NCS1 in Pb2+/Mn2+ neurotoxicity.