Detailed Scrutiny of the Anion Receptor Pocket in Subdomain IIA of Serum Proteins toward Individual Response to Specific Ligands: HSA-Pocket Resembles Flexible Biological Slide-Wrench Unlike BSA

Present study reveals that the subdomain IIA cavity of two homologous serum albumins (HSA, BSA) has inherent mutual structural and functional deviations which render noticeable difference in behavior toward specific ligands. The major drug binding site (subdomain IIA) of HSA is found to be largely hydrophobic while that of BSA is partially exposed to water. Larger shift in REE spectra and greater change in solvent reorganization energy of coumarin 343 (C343)-anion in HSA clearly reveals that binding pocket is relatively large and water molecules penetrate deeper into it unlike BSA. The individual response of proteins to perturbation by ligands is found to be way different. Although the subdomain IIA is primarily anion receptive (prefers anionic ligands), the present study suggests that HSA may also like to bind neutral guests due to its remarkable conformational features. Actually, HSA is capable of adopting favorable conformation like mechanical slide-wrench, when required, to accommodate neutral ligands [e.g., coumarin 314 (C314)], as well. But due to less flexible solution structure, BSA behaves like fixed mechanical spanners and hence is not very responsive to C314. Therefore, the generally speaking functional-structural similarities of homologous proteins can be apparent and needs to be analyzed exhaustively

Detailed Scenario of the Acid–Base Behavior of Prototropic Molecules in the Subdomain-IIA Pocket of Serum Albumin: Results and Prospects in Drug Delivery

The protein pocket performs magically in controlling, inhibiting, or optimizing various biochemical processes. The elegant 3D disposition of different side chains in the cavity is a key point in accommodating specific ligands. Anion receptors in the subdomain-IIA pocket of serum albumin (SA) prefer to home anionic ligands. Acid–base behavior is an important property that relates to bioavailability and action of prototropic molecules/drugs. The present study provides a comprehensive understanding of the effect of subdomain-IIA pocket-specific interaction on the acid–base equilibrium of housed guests. The p<i>K</i>_a of subdomain-IIA binder basic drugs decreases due to unfavorable interaction with the cationic drug species, while the decrease in the p<i>K</i>_a of acidic drugs is due to favored binding of the deprotonated species presumably via electrostatic interaction with anion receptors. Acidity-shifting efficacy of albumins is introduced for the first time using the p<i>K</i>_a-shifting index (α), a unique parameter for a given prototropic-drug-host pair to assess bioavailability. The acidic drug warfarin and the basic drug fuberidazole, showing a high α-value, should be efficient in drug-SA cocktail, and those with low α should be less efficient. Use of the p<i>K</i>_a-shifting index for prototropy-based drugs should enable the drug efficacy to be evaluated smartly for similar systems. Shifting of the p<i>K</i>_a of protein-encapsulated drugs stems the possibility of albumin-based delivery systems for extracting the therapeutically active species

Distilbene Derivative as a New Environment-Sensitive Bifunctional Ligand for the Possible Induction of Serum Protein Aggregation: A Spectroscopic Investigation and Potential Consequences

The photophysical properties of a new distilbene fluorophore, DPDB, belonging to the conjugated polyene family is found to be well modulated with the variation of the microenvironment. Compared to the ground state, the excited-state photophysical properties of the fluorophore have been altered to larger extents with the variation of polarity and the hydrogen-bonding nature of solvents. The change in the fluorescence intensity of DPDB shows a nice correlation with the aggregation behavior of different surfactants which have been utilized for the determination of the CMC of surfactants. The distribution of DPDB is found to be higher in nonionic micelles. On the other hand, DPDB specifically binds the subdomain IB cavity of serum albumin with a stronger binding ability with HSA compared to BSA. DPDB behaves like a bivalent (bifunctional) ligand and forms a complex of 2:1 stoichiometry with serum albumins. Dynamic light scattering and circular dichroism measurements indicate that DPDB favors the association of serum albumin molecules, promoting their preaggregation state. Aggregation is an important phenomenon and is known to be initiated by heat, extreme pH conditions, very high ionic strength, surfactants, metal ions, and so forth. This study explores a new avenue in bringing about association phenomena of serum albumins and points out that the binding of such a bifunctional ligand may also become an important factor in inducing the protein association

Correction to Modulation of Accessibility of Subdomain IB in the pH-Dependent Interaction of Bovine Serum Albumin with Cochineal Red A: A Combined View from Spectroscopy and Docking Simulations

Correction to Modulation of Accessibility of Subdomain IB in the pH-Dependent Interaction of Bovine Serum Albumin with Cochineal Red A: A Combined View from Spectroscopy and Docking Simulation

Exploration of pH-Dependent Behavior of the Anion Receptor Pocket of Subdomain IIA of HSA: Determination of Effective Pocket Charge Using the Debye–Hückel Limiting Law

Protein–ligand electrostatic interaction can be looked upon as ion receptor–ligand interaction, and the binding cavity of protein can be either an anion or cation receptor depending on the charge of the guest. Here we focus on the exploration of pH-modulated binding of a number of anionic ligands, specific to the subdomain IIA cavity of HSA, such as carmoisine, tartrazine, cochineal red, and warfarin. The logarithm of the binding constant is found to vary linearly with the square-root of ionic strength, indicating applicability of the Debye–Hückel limiting law to protein–ligand electrostatic binding equilibrium, and concludes that the subdomain IIA cavity is an anion receptor. The present approach is very unique that one can calculate the effective charge of the protein-based anion receptor pocket, and the calculated charge has been found to vary between +1 and +3 depending on the pH and ligand itself. The study also indicates that in such cases of specific ligand binding the pocket charge rather than the overall or surface charge of the macromolecule seems to have a paramount role in determining the strength of interaction. For the first time, it is demonstrated that the Debye–Hückel interionic interaction model can be successfully applied to understand the protein-based receptor–ligand electrostatic interaction in general

Modulation of Accessibility of Subdomain IB in the pH-Dependent Interaction of Bovine Serum Albumin with Cochineal Red A: A Combined View from Spectroscopy and Docking Simulations^#

Our recent report on the binding of Cochineal Red A, a food dye, with HSA and BSA at pH 7.4 has revealed that electrostatic forces is the principal cause of interaction. In that study issues relating to complications arising out of modulation of dye binding affinity of BSA with pH had not been explored. Here we have further explored the interaction of Cochineal Red A with BSA in pH range 4.8–7.8. Surprisingly, this system behaves differently in the texture of interaction pattern at two extremes of studied pH range, unlike HSA. Importantly, the charge on the amino acid side chains in the binding pocket is likely to play a significant role

Spectroscopic Investigation of the Effect of Salt on Binding of Tartrazine with Two Homologous Serum Albumins: Quantification by Use of the Debye–Hückel Limiting Law and Observation of Enthalpy–Entropy Compensation

Formation of ion pair between charged molecule and protein can lead to interesting biochemical phenomena. We report the evolution of thermodynamics of the binding of tartrazine, a negatively charged azo colorant, and serum albumins with salt. The dye binds predominantly electrostatically in low buffer strengths; however, on increasing salt concentration, affinity decreases considerably. The calculated thermodynamic parameters in high salt indicate manifestation of nonelectrostatic interactions, namely, van der Waals force and hydrogen bonding. Site-marker competitive binding studies and docking simulations indicate that the dye binds with HSA in the warfarin site and with BSA at the interface of warfarin and ibuprofen binding sites. The docked poses indicate nearby amino acid positive side chains, which are possibly responsible for electrostatic interaction. Using the Debye–Hückel interionic attraction theory for binding equilibria, it is shown that, for electrostatic binding the calculated free energy change increases linearly with square root of ionic strength. Also UV–vis, fluorescence, CD data indicate a decrease of interaction with salt concentration. This study quantitatively relates how ionic strength modulates the strength of the protein–ligand electrostatic interaction. The binding enthalpy and entropy have been found to compensate one another. The enthalpy–entropy compensation (EEC), general property of weak intermolecular interactions, has been discussed

Phosphorescence Kinetics of Singlet Oxygen Produced by Photosensitization in Spherical Nanoparticles. Part I. Theory

The singlet oxygen produced by energy transfer between an excited photosensitizer (pts) and ground-state oxygen molecules plays a key role in photodynamic therapy. Different nanocarrier systems are extensively studied to promote targeted pts delivery in a host body. The phosphorescence kinetics of the singlet oxygen produced by the short laser pulse photosensitization of pts inside nanoparticles is influenced by singlet oxygen diffusion from the particles to the surrounding medium. Two theoretical models are presented in this work: a more complex numerical one and a simple analytical one. Both the models predict the time course of singlet oxygen concentration inside and outside of the spherical particles following short-pulse excitation of pts. On the basis of the comparison of the numerical and analytical results, a semiempirical analytical formula is derived to calculate the characteristic diffusion time of singlet oxygen from the nanoparticles to the surrounding solvent. The phosphorescence intensity of singlet oxygen produced in pts-loaded nanocarrier systems can be calculated as a linear combination of the two concentrations (inside and outside the particles), taking the different phosphorescence emission rate constants into account

Phosphorescence Kinetics of Singlet Oxygen Produced by Photosensitization in Spherical Nanoparticles. Part II. The Case of Hypericin-Loaded Low-Density Lipoprotein Particles

The phosphorescence kinetics of singlet oxygen produced by photosensitized hypericin (Hyp) molecules inside low-density lipoprotein (LDL) particles was studied experimentally and by means of numerical and analytical modeling. The phosphorescence signal was measured after short laser pulse irradiation of aqueous Hyp/LDL solutions. The Hyp triplet state lifetime determined by a laser flash-photolysis measurement was 5.3 × 10^–6 s. The numerical and the analytical model described in part I of the present work (DOI: 10.1021/acs.jpcb.8b00658) were used to analyze the observed phosphorescence kinetics of singlet oxygen. It was shown that singlet oxygen diffuses out of LDL particles on a time scale shorter than 0.1 μs. The total (integrated) concentration of singlet oxygen inside LDL is more than an order of magnitude smaller than the total singlet oxygen concentration in the solvent. The time course of singlet oxygen concentrations inside and outside the particles was calculated using simplified representations of the LDL internal structure. The experimental phosphorescence data were fitted by a linear combination of these concentrations using the emission factor <i>E</i> (the ratio of the radiative singlet oxygen depopulation rate constants inside and outside LDL) as a fitting parameter. The emission factor was determined to be <i>E</i> = 6.7 ± 2.5. Control measurements were carried out by adding sodium azide, a strong singlet oxygen quencher, to the solution