Machine learning-based modulation of Ca2+-binding affinity in EFhand proteins and comparative structural insights into site-specific cooperative binding

Ca2+-binding proteins are present in almost all living organisms and different types display different levels of binding affinities for the cation. Here, we applied two new scoring schemes enabling the user to manipulate the binding affinities of such proteins. We specifically designed a unique EF-hand loop capable of binding calcium with high affinity by altering five residues of the loop based on the scoring scheme. We worked on the N-terminal domain of Entamoeba histolytica calcium-binding protein1 (NtEhCaBP1), and used site-directed mutagenesis to incorporate the designed loop sequence into the second EF hand motif of this protein. The binding isotherms calculated using ITC calorimetry showed a ~500-fold greater association constant (Ka) for the mutant. The crystal structure of the mutant was also determined, and displayed more compact Ca2+-coordination spheres in both of its EF loops than did the structure of the wildtype protein, consistent with the greater calcium-binding affinities of the mutant. The NtEhCaBP1 mutant was also shown to form a hexamer rather than just a trimer, and this hexamer formation was attributed to the position of the last helix of the mutant having been changed as a result of the strong calcium coordination. Further dynamic correlation analysis revealed that the mutation in the second EF loop changed the entire residue network of the monomer, resulting in a stronger coordination of Ca2+.

Mechanism of a Disassembly Driven Sensing System Studied by Stopped-Flow Kinetics

<div> Mechanistic studies were carried out on the kinetics for the assembly of a DimerDye (DD12) and the binding of the monomeric DimerDye (DD1) with nicotine in aqueous buffer and artificial saliva. DD12 is non-fluorescent, while monomeric DD1 and DD1-nicotine fluoresce. Binding isotherms were determined from steady-state fluorescence experiments. The report includes measurements of the steady-state fluorescence at pHs 2.2, 6.3 and 12.1, and stopped-flow kinetic data for the homodimerization forming DD12 and DD1-nicotine formation in buffer and artificial saliva. Analysis of the homodimerization kinetics led to the recovery of the association and dissociation rate constants for DD12. These rate constants were used in the global analysis for the coupled kinetics for DD1-nicotine formation, which led to the determination of the association and dissociation rate constants for nicotine binding to DD1.</div>

Mechanism of a Disassembly Driven Sensing System Studied by Stopped-Flow Kinetics

<div> Mechanistic studies were carried out on the kinetics for the assembly of a DimerDye (DD12) and the binding of the monomeric DimerDye (DD1) with nicotine in aqueous buffer and artificial saliva. DD12 is non-fluorescent, while monomeric DD1 and DD1-nicotine fluoresce. Binding isotherms were determined from steady-state fluorescence experiments. The report includes measurements of the steady-state fluorescence at pHs 2.2, 6.3 and 12.1, and stopped-flow kinetic data for the homodimerization forming DD12 and DD1-nicotine formation in buffer and artificial saliva. Analysis of the homodimerization kinetics led to the recovery of the association and dissociation rate constants for DD12. These rate constants were used in the global analysis for the coupled kinetics for DD1-nicotine formation, which led to the determination of the association and dissociation rate constants for nicotine binding to DD1.</div>

Multiphysics and Multiscale Modeling of Coupled Transport of Chloride Ions in Concrete

Chloride ions (Cl−)-induced corrosion is one of the main degradation mechanisms in reinforced concrete (RC) structures. In most situations, the degradation initiates with the transport of Cl− from the surface of the concrete towards the reinforcing steel. The accumulation of Cl− at the steel-concrete interface could initiate reinforcement corrosion once a threshold Cl− concentration is achieved. An accurate numerical model of the Cl− transport in concrete is required to predict the corrosion initiation in RC structures. However, existing numerical models lack a representation of the heterogenous concrete microstructure resulting from the varying environmental conditions and the indirect effect of time dependent temperature and relative humidity (RH) on the water adsorption and Cl− binding isotherms. In this study, a numerical model is developed to study the coupled transport of Cl− with heat, RH and oxygen (O2) into the concrete. The modeling of the concrete microstructure is performed using the Virtual Cement and Concrete Testing Laboratory (VCCTL) code developed by the U.S. National Institute of Standards and Technology (NIST). The concept of equivalent maturation time is utilized to eliminate the limitation of simulating concrete microstructure using VCCTL in specific environmental conditions such as adiabatic. Thus, a time-dependent concrete microstructure, which depends on the hydration reactions coupled with the temperature and RH of the environment, is achieved to study the Cl− transport. Additionally, Cl− binding isotherms, which are a function of the pH of the concrete pore solution, Cl− concentration, and weight fraction of mono-sulfate aluminate (AFm) and calcium-silicate-hydrate (C-S-H), obtained from an experimental study by the same authors are utilized to account for the Cl− binding of cement hydration products. The temperature dependent RH diffusion was considered to account for the transport of Cl− with moisture transport. The temperature and RH diffusion in the concrete domain, composite theory, and Cl− binding and water adsorption isotherms are used in combination, to estimate the ensuing Cl− diffusion field within the concrete. The coupled transport process of heat, RH, Cl−, and O2 is implemented in the Multiphysics Object-Oriented Simulation Environment (MOOSE) developed by the U.S. Idaho National Laboratory (INL). The model was verified and validated using data from multiple experimental studies with different concrete mixture proportions, curing durations, and environmental conditions. Additionally, a sensitivity analysis was performed to identify that the water-to-cement (w/c) ratio, the exposure duration, the boundary conditions: temperature, RH, surface Cl− concentration, Cl− diffusion coefficient in the capillary water, and the critical RH are the important parameters that govern the Cl− transport in RC structures. In a case study, the capabilities of the developed numerical model are demonstrated by studying the complex 2D diffusion of Cl− in a RC beam located in two different climatic regions: warm and humid weather in Galveston, Texas, and cold and dry weather in North Minnesota, Minnesota, subjected to time varying temperature, RH, and surface Cl− concentrations.

Effective and Apparent Diffusion Coefficients of Chloride Ions and Chloride Binding Kinetics Parameters in Mortars: Non-Stationary Diffusion–Reaction Model and the Inverse Problem

A non-equilibrium diffusion–reaction model is proposed to describe chloride transport and binding in cementitious materials. A numerical solution for this non-linear transport with reaction problem is obtained using the finite element method. The effective chloride diffusion coefficients and parameters of the chloride binding are determined using the inverse method based on a diffusion–reaction model and experimentally measured chloride concentrations. The investigations are performed for two significantly different cements: ordinary Portland and blast furnace cements. The results are compared with the classical diffusion model and appropriate apparent diffusion coefficients. The role of chloride binding, with respect to the different binding isotherms applied, in the overall transport of chlorides is discussed, along with the applicability of the two models. The proposed work allows the determination of important parameters that influence the longevity of concrete structures. The developed methodology can be extended to include more ions, electrostatic interactions, and activity coefficients for even more accurate estimation of the longevity.

Allosterically Coupled Multisite Binding of Testosterone to Human Serum Albumin

Human serum albumin (HSA) acts as a carrier for testosterone, other sex hormones, fatty acids, and drugs. However, the dynamics of testosterone’s binding to HSA and the structure of its binding sites remain incompletely understood. Here, we characterize the dynamics of testosterone’s binding to HSA and the stoichiometry and structural location of the binding sites using 2-dimensional nuclear magnetic resonance (2D NMR), fluorescence spectroscopy, 4,4′-dianilino-1,1′-binaphthyl-5,5′-disulfonic acid dipotassium salt partitioning, and equilibrium dialysis, complemented by molecular modeling. 2D NMR studies showed that testosterone competitively displaced 18-[13C]-oleic acid from at least 3 known fatty acid binding sites on HSA that also bind many drugs. Binding isotherms of testosterone’s binding to HSA generated using fluorescence spectroscopy and equilibrium dialysis were nonlinear and the apparent dissociation constant varied with different concentrations of testosterone and HSA. The binding isotherms neither conformed to a linear binding model with 1:1 stoichiometry nor to 2 independent binding sites; the binding isotherms were most consistent with 2 or more allosterically coupled binding sites. Molecular dynamics studies revealed that testosterone’s binding to fatty acid binding site 3 on HSA was associated with conformational changes at site 6, indicating that residues in in these 2 distinct binding sites are allosterically coupled. There are multiple, allosterically coupled binding sites for testosterone on HSA. Testosterone shares these binding sites on HSA with free fatty acids, which could displace testosterone from HSA under various physiological states or disease conditions, affecting its bioavailability.

Delayed Addition of Template Molecules Enhances the Binding Properties of Diclofenac-Imprinted Polymers

It has been reported that in the molecular imprinting technique, the use of preformed oligomers instead of functional monomers increases the stability of the non-covalent interactions with the template molecule, providing a sharp gain in terms of binding properties for the resulting imprinted polymer. Based on this theory, we assumed that the delayed addition of template molecules to a polymerization mixture enhances the binding properties of the resulting polymer. To verify this hypothesis, we imprinted several mixtures of 4-vinylpyridine/ethylene dimethacrylate (1:6 mol/mol) in acetonitrile by adding diclofenac progressively later from the beginning of the polymerization process. After polymerization, the binding isotherms of imprinted and non-imprinted materials were measured in acetonitrile by partition equilibrium experiments. Binding data confirm our hypothesis, as imprinted polymers prepared by delayed addition, with delay times of 5 and 10 min, showed higher binding affinity (Keq = 1.37 × 104 L mol−1 and 1.80 × 104 L mol−1) than the polymer obtained in the presence of template at the beginning (Keq = 5.30 × 103 L mol−1). Similarly, an increase in the imprinting factor measured vs. the non-imprinted polymer in the binding selectivity with respect to mefenamic acid was observed. We believe that the delayed addition approach could be useful in prepar imprinted polymers with higher binding affinity and increased binding selectivity in cases of difficult imprinting polymerization.

Tissue Distribution and Receptor Activation by Somapacitan, a Long Acting Growth Hormone Derivative

Somapacitan is a long-acting, once-weekly, albumin-binding growth hormone (GH) derivative. The reversible albumin-binding properties leads to prolonged circulation half-life. Here, we investigated and compared somapacitan with human GH on downstream receptor signaling in primary hepatocytes and hepatocellular models and using isothermal titration calorimetry to characterize receptor binding of somapacitan in the presence or absence of human serum albumin (HSA). With non-invasive fluorescence imaging we quantitatively visualize and compare the temporal distribution and examine the tissue-specific growth hormone receptor (GHR) activation at distribution sites. We found that signaling kinetics were slightly more rapid and intense for GH compared with somapacitan. Receptor binding isotherms were characterized by a high and a low affinity interaction site with or without HSA. Using in vivo optical imaging we found prolonged systemically biodistribution of somapacitan compared with GH, which correlated with plasma pharmacokinetics. Ex vivo mouse organ analysis revealed that the temporal fluorescent intensity in livers dosed with somapacitan was significantly increased compared with GH-dosed livers and correlated with the degree of downstream GHR activation. Finally, we show that fluorescent-labeled analogs distributed to the hypertrophic zone in the epiphysis of proximal tibia of hypophysectomized rats and that somapacitan and GH activate the GHR signaling in epiphyseal tissues.