Subdomain IIIB Research Articles

Biophysical studies of human serum albumin with cocaine and cocaethylene: Understanding the drug-protein interaction in simulated physiological conditions

In this study, HSA was used as a transport protein model to simulate the transport dynamics and availability of cocaine (COC) and its pharmacologically active metabolite, cocaethylene (CE). In the interaction studies between the alkaloids and HSA, the binding constant (Kb) values were higher for CE (2.92 to 8.33 × 104 M−1) than COC (1.15 to 3.77 × 104 M−1) at different temperatures. Thermodynamic parameter calculations indicate that COC preferentially interacts through van der Waals forces and hydrogen bonds, while CE interacts hydrophobically. Competition studies using the ANS probe confirmed the more hydrophobic characteristics of CE. Synchronized fluorescence indicated that both compounds preferentially interact in the microregion of the Trp214 residue. Based on 3D fluorescence, UV–vis, and circular dichroic results, changes in the secondary structure of the protein were confirmed. Studies to assess the HSA binding site were carried out using warfarin (site I), diazepam (site II), and digitoxin (subdomain IIIB) as markers, and it was verified that both compounds interact preferentially at the site I. Finally, based on the 1H NMR and theoretical studies, it was possible to propose the alkaloid epitope in the interaction with HSA. In conclusion, when compared to COC, CE presented greater HSA protein affinity, justifying its longer plasma lifetime and increasing the drug’s effects on the body.

Structural and dynamic properties of urinary human serum albumin fragments: a molecular dynamics study

A microalbuminuria level acts as a good index to screen and monitor diabetes and renal failure. However, the urinary albumin loss after sample preservation and storage is the major bottleneck to obtain the accurate microalbuminuria test. Such loss is due to the rapid albumin fragmentation by urinary proteases. Some fragments were suggested to be bioactive biomarkers of diabetes and renal disease, but no structural and dynamical properties of albumin fragments are available. Thus, in this work, the structural and dynamical properties of reported albumin fragments are revealed using molecular dynamics simulations. The properties of nine fragments (F1–F9) discovered recently were studied at the real pH conditions of urine samples (pH 4.5, 7 and 8). The complete loss of secondary structure is found in short fragments (F1–F6), while large-sized polypeptides (F7–F9) can somehow maintain their folds. Especially, F8 (subdomain IIIB) is the most stable fragment. The difference in histidine protonation states has no impact on the structural stability of albumin fragments. The ability of F8 (subdomain IIIB) to maintain its stability and folds suggests it as an alternative albumin biomarker in urine. An insight obtained here will become the fundamental importance for understanding clinical assays for albumin detection, sample stability and peptidomics analysis of urine. Communicated by Ramaswamy H. Sarma

Synthesis, Crystal Structure, Hirshfeld Surface Analysis, DNA/BSA Interaction and Molecular Docking Studies of 2-(6-(4-chlorophenyl)-1,2,4-triazin-3-yl)quinoline

We reported herein a new 1,2,4-triazine derivative, 2-(6-(4-chlorophenyl)-1,2,4-triazin-3-yl)quinoline, synthesized by cyclization of p‑chloro isonitrosophenylhydrazine with 2-quinolinecarboxaldehyde. Its structure was elucidated by FTIR, 1H NMR, 13C APT NMR, elemental analyses, and also its molecular and crystal structures were determined by single crystal X-ray analysis which revealed that the compound was crystallized in monoclinic system P 2/c space group with a = 17.2564 (6) Å, b = 6.0419 (3) Å, c = 14.4093 (5) Å, β = 103.469 (3)°, Z = 4 and V = 1461.01 (10) Å3. The Hirshfeld surface analysis of the crystal structure indicated that the most important contributions for the crystal packing were from H … H (29.2%), H … C/C … H (22.3%), H … N/CN … H (16.1%) and H … CI/CI … H (14.5%) interactions. Hydrogen bonding and van der Waals interactions were the dominant interactions in the crystal packing. The evaluation of the electrostatic, dispersion and total energy frameworks indicated that the stabilization was dominated via the dispersion energy contribution. The synthesized compound was investigated for CT-DNA and BSA binding activity using various in vitro and in silico techniques. Results were revealed that binding of the compound with CT-DNA via minor groove and with BSA via subdomain IIIB.

Lysine reactivity profiling reveals molecular insights into human serum albumin-small-molecule drug interactions.

Human serum albumin (HSA) is one of the most important serum carrier proteins that deliver small-molecule drugs to their specific targets. Clarifying the molecular mechanism of the interaction between natural HSA and drugs in an aqueous solution has been a hot topic in pharmaceutical chemistry, clinical medicine, and biochemistry in recent years, but it is still challenging. In this paper, the details of molecular interactions of HSA with a variety of therapeutic drugs including ibuprofen, indomethacin, phenylbutazone, and warfarin are systematically investigated using a mass spectrometry (MS)-based lysine reactivity profiling (LRP) strategy. The results reaffirm that the major ligand binding sites (including Sites I and II) of HSA are located in subdomains IIA and IIIA, while several potential drug-binding areas at subdomain IIIB and α helix IIB-IIIA are newly characterized. The MS-LRP strategy may have important application prospects in pharmacodynamics, pharmacokinetics, and safety evaluation of small-molecule drugs.

Probing the interaction between 7-geranyloxycoumarin and bovine serum albumin: Spectroscopic analyzing and molecular docking study

7-Geranyloxycoumarin (auraptene; AUR), as a potent phytochemical, is the naturally abundant prenyloxycoumarin found in many genera of the Rutaceae family. As the interaction with serum albumins may play a crucial role in identifying their pharmacological properties, we investigated AUR binding profile with bovine serum albumin (BSA) by experimental and computational methods. Binding constant, binding site, mode of binding, and the BSA structural change upon AUR addition, were studied. UV–vis spectroscopy results and fluorescence quenching analysis proposed that AUR can form the ground state complex with BSA. Meantime, thermodynamic parameters (negative ΔH and ΔS values) revealed that hydrogen bonds and van der Waals interactions play major role, as intermolecular forces, in the AUR–BSA complex formation. Synchronous fluorescence spectra and circular dichroism (CD) data showed that the secondary structure of BSA did not change significantly in the presence of AUR. Moreover, molecular docking results showed that AUR binds to the subdomain IIIB of BSA.

Characterization of the heterogeneous adsorption of three drugs on immobilized bovine serum albumin by adsorption energy distribution

Characterization of the heterogeneity of a protein surface is important for understanding the binding mechanism of a drug to the protein. A systematic methodology of integrated adsorption energy distribution (AED) calculation with the Scatchard plot was used to characterize the heterogeneous binding of drugs to bovine serum albumin (BSA). Frontal affinity chromatography (FAC) was applied to generate the adsorption data of three drugs on the immobilized BSA column. The concave Scatchard plots cannot distinguish the heterogeneous model between Toth and bi-Langmuir. The calculation of AED profiles allowed the accurate selection of adsorption models to reveal the physical sense of the drugs. Warfarin-BSA complex proved to be the bi-Langmuir model with association constants of 6.6 × 105 M−1 and 2.4 × 103 M−1, respectively. These results were highly consistent with traditional frontal analysis, ultrafiltration, and dynamic dialysis. Applying the AED related method, we achieved multiple and single kinds of binding sites for ephedrine-BSA and L-tryptophan-BSA complexes. Site-specific competitive studies exhibited non-competitive binding of ephedrine with warfarin or L-tryptophan on BSA, underlining that the location of ephedrine binding sites in the subdomain IIIB of BSA. This method permits an accurate heterogeneous characterization of drugs on a protein surface and has great potential in the reliable drug-protein interaction analysis.

HCV IRES Captures an Actively Translating 80S Ribosome.

Translation initiation of hepatitis C virus (HCV) genomic RNA is induced by an internal ribosome entry site (IRES). Our cryoelectron microscopy (cryo-EM) analysis revealed that the HCV IRES binds to the solvent side of the 40S platform of the cap-dependently translating 80S ribosome. Furthermore, we obtained the cryo-EM structures of the HCV IRES capturing the 40S subunit of the IRES-dependently translating 80S ribosome. In the elucidated structures, the HCV IRES "body," consisting of domain III except for subdomain IIIb, binds to the 40S subunit, while the "long arm," consisting of domain II, remains flexible and does not impede the ongoing translation. Biochemical experiments revealed that the cap-dependently translating ribosome becomes a better substrate for the HCV IRES than the free ribosome. Therefore, the HCV IRES is likely to efficiently induce the translation initiation of its downstream mRNA with the captured translating ribosome as soon as the ongoing translation terminates.

Fatty Acids Compete with Aβ in Binding to Serum Albumin by Quenching Its Conformational Flexibility

Human serum albumin (HSA) has been identified as an important regulator of amyloid-β (Aβ) fibrillization both in blood plasma and in cerebrospinal fluid. Fatty acids bind to HSA, and high serum levels of fatty acids increase the risk of Alzheimer’s disease. In vitro, fatty-acid-loaded HSA (FA·HSA) loses the protective effect against Aβ fibrillization, but the mechanism underlying the interference of fatty acids on Aβ-HSA interactions has been unclear. Here, we used molecular dynamics simulations to gain atomic-level insight on the weak binding of monomeric Aβ40 and Aβ42 peptides with apo and FA·HSA. Consistent with recent NMR data, C-terminal residues of the Aβ peptides have the highest propensities for interacting with apo HSA. Interestingly, the Aβ binding residues of apo and FA·HSA exhibit distinct patterns, which qualitatively correlate with backbone flexibility. In FA·HSA, both flexibilities and Aβ binding propensities are relatively even among the three domains. In contrast, in apo HSA, domain III shows the highest flexibility and is the primary target for Aβ binding. Specifically, deformation of apo HSA creates strong binding sites within subdomain IIIb, around the interface between subdomains IIIa and IIIb, and at the cleft between domains III and I. Therefore, much like disordered proteins, HSA can take advantage of flexibility in forming promiscuous interactions with partners, until the flexibility is quenched by fatty-acid binding. Our work explains the effect of fatty acids on Aβ-HSA binding and contributes to the understanding of HSA regulation of Aβ aggregation.

Characterization of the structural changes of human serum albumin upon interaction with single-walled and multi-walled carbon nanotubes: spectroscopic and molecular modeling approaches

Through the incorporation of spectorescopic and molecular methods of modeling, the researchers investigated the interaction between Carbon Nanotubes (CNTs) and Human Serum Albumin (HSA). Fluorescence spectroscopy revealed the ability in both single-wall and multi-wall CNTs to quench the spectrum through a static quenching procedure obtained from the Stern–Volmer quenching constant (Ksv) at three different temperatures. The Ksv values of HSA–CNTs complexes were 1.96 × 105 M−1 and 2.44 × 105 M−1 that showed two different behaviors of interaction between HSA and CNTs. The Van’t Hoff equation was used to calculate thermodynamic parameters of Gibbs free energy (ΔG°), entropy (ΔS°) and enthalpy changes (ΔH°). The binding distances (r) between the donor (Trp residue of HSA) and acceptor (CNTs) was measured through the Forster theory of non-radiative energy transfer, and it was found to be less than 7 nm. The conformational changes of protein in the presence of CNTs were revealed through synchronous fluorescence spectra and three-dimensional fluorescence spectra analysis. The experimental results were confirmed through molecular modeling technique. Circular dichroism technique showed the secondary structure changes of HSA upon interaction with CNTs. The complex formation of HSA and CNTs was determined by the measurement of the electric conductivity. The molecular modeling technique determined the binding site of CNTs that were embedded in the subdomain IIIB of HSA. These analyses play a major role in drug delivery and pharmacodynamics studies for better understanding of nanotechnology levels.

Clinical, Genetic, and Protein Structural Aspects of Familial Dysalbuminemic Hyperthyroxinemia and Hypertriiodothyroninemia.

Familial dysalbuminemic hyperthyroxinemia (FDH-T4) and hypertriiodothyroninemia (FDH-T3) are dominantly inherited syndromes characterized by a high concentration of thyroid hormone in the blood stream. The syndromes do not cause disease, because the concentration of free hormone is normal, but affected individuals are at risk of erroneous treatment. FDH-T4 is the most common cause of euthyroid hyperthyroxinemia in Caucasian populations in which its prevalence is about 1 in 10,000 individuals, but the prevalence can be much higher in some ethnic groups. The condition is caused by a genetic variant of human serum albumin (HSA); Arg218 is mutated to histidine, proline, or serine or Arg222 is changed to isoleucine. The disorder is characterized by greater elevation in serum l-thyroxine (T4) than in serum triiodothyronine (T3); T4 can be increased by a factor 8–15. The high serum concentration of T4 is due to modification of a binding site located in the N-terminal half of HSA (in subdomain IIA). Thus, mutating Arg218 or Arg222 for a smaller amino acid reduces the steric restrictions in the site and creates a high-affinity binding site. The mutations can also affect binding of other ligands and can perhaps cause modified pharmacokinetics of albumin-binding drugs. In normal HSA, the high-affinity site has another location (in subdomain IIIB). Different locations of these sites imply that persons with and without FDH-T4 can have different types of interactions, and thereby complications, when given albumin-binding drugs. FDH-T3 is caused by a leucine to proline mutation in position 66 of HSA, which results in a large increment of the binding affinity for T3 but not for T4. For avoiding unwanted treatment of euthyroid persons with hyperthyroxinemia or hypertriiodothyroninemia, protein sequencing and/or sequencing of the albumin gene should be performed.

A New Pathway for Protein Haptenation by β-Lactams.

The covalent binding of β-lactams to proteins upon photochemical activation has been demonstrated by using an integrated approach that combines photochemical, proteomic and computational studies, selecting human serum albumin (HSA) as a target protein and ezetimibe (1) as a probe. The results have revealed a novel protein haptenation pathway for this family of drugs that is an alternative to the known nucleophilic ring opening of β-lactams by the free amino group of lysine residues. Thus, photochemical ring splitting of the β-lactam ring, following a formal retro-Staudinger reaction, gives a highly reactive ketene intermediate that is trapped by the neighbouring lysine residues, leading to an amide adduct. For the investigated 1/HSA system, covalent modification of residues Lys414 and Lys525, which are located in sub-domains IIIA and IIIB, respectively, occurs. The observed photobinding may constitute the key step in the sequence of events leading to photoallergy. Docking and molecular dynamics simulation studies provide an insight into the molecular basis of the selectivity of 1 for these HSA sub-domains and the covalent modification mechanism. Computational studies also reveal positive cooperative binding of sub-domain IIIB that explains the experimentally observed modification of Lys414, which is located in a barely accessible pocket (sub-domain IIIA).

Ibuprofen and propofol cobinding effect on human serum albumin unfolding in urea.

The unfolding pathway of the defatted human serum albumin (HSA) binding ibuprofen and propofol has been studied by using small-angle X-ray scattering (SAXS) and the support of circular dichroism data. A set of HSA solutions with urea concentrations between 0.00 and 9.00 M was analyzed, and the singular value decomposition method applied to the complete SAXS data set allowed us to distinguish four different states in solution. Besides the native and unfolded forms, two intermediates I1 and I2 have been identified, and the low-resolution structures of these states were obtained by exploiting both ab initio and rigid body fitting methods. The I1 structure was characterized by only one open domain (domain I, which does not host a binding site for either of the ligands), whereas I2 presents only one closed domain (domain III). A direct comparison with the unfolding pathway of the HSA:Ibu complex (Galantini et al. Biophys. Chem. 2010, 147, 111-122) pointed out that the presence of propofol as a second ligand, located in subdomain IIIB, leads to the appearance of an intermediate with two closed domains (domains II and III), which are those that accommodate the ligands. Moreover, the equilibrium between I2 and the unfolded form is slightly shifted toward higher urea concentrations. These results suggest that the cobinding significantly hinders the unfolding process.

Determination of LMF Binding Site on a HSA-PPIX Complex in the Presence of Human Holo Transferrin from the Viewpoint of Drug Loading on Proteins

Holo transferrin (TF) and the natural complex of human serum albumin and protoporphyrin IX (HSA-PPIX) are two serum carrier proteins that can interact with each other. Such an interaction may alter their binding sites. In this study, fluorescence spectroscopy, as well as zeta potential and molecular modeling techniques, have been used to compare the complexes (HSA-PPIX)-LMF and [(HSA-PPIX)-TF]-LMF. The Ka1, Ka2, values of (HSA-PPIX)-LMF and [(HSA-PPIX)-TF]-LMF were 1.1×105 M−1, 9.7×106 M−1, and 2.0×104 M−1, 1.8×105 M−1, respectively, and the n1, n2 values were respectively 1.19, 1.53 and 1.17, 1.65. The second derivative of the Trp emission scan of (HSA-PPIX)-LMF exhibited one negative band at 310 nm, whereas for the [(HSA-PPIX)-TF]-LMF system, we observed one negative band at 316 nm indicating an increase in polarity around Trp. The effect of TF on the conformation of (HSA-PPIX)-TF was analyzed using three-dimensional fluorescence spectroscopy. The phase diagram indicated that the presence of a second binding site on HSA and TF was due to the existence of intermediate structures. Zeta potential analysis showed that the presence of TF increased the positive charges of the HSA-PPIX system. Site marker experiments revealed that the binding site of LMF to HSA-PPIX changed from Sudlow's site IIA to Sudlow's site IIIB in the presence of TF. Moreover, molecular modeling studies suggested the sub-domain IIIB in HSA as the candidate place for the formation of the binding site of LMF on the (HSA-PPIX)-TF complex.

The folding of the hepatitis C virus internal ribosome entry site depends on the 3′-end of the viral genome

Hepatitis C virus (HCV) translation initiation is directed by an internal ribosome entry site (IRES) and regulated by distant regions at the 3′-end of the viral genome. Through a combination of improved RNA chemical probing methods, SHAPE structural analysis and screening of RNA accessibility using antisense oligonucleotide microarrays, here, we show that HCV IRES folding is fine-tuned by the genomic 3′-end. The essential IRES subdomains IIIb and IIId, and domain IV, adopted a different conformation in the presence of the cis-acting replication element and/or the 3′-untranslatable region compared to that taken up in their absence. Importantly, many of the observed changes involved significant decreases in the dimethyl sulfate or N-methyl-isatoic anhydride reactivity profiles at subdomains IIIb and IIId, while domain IV appeared as a more flexible element. These observations were additionally confirmed in a replication-competent RNA molecule. Significantly, protein factors are not required for these conformational differences to be made manifest. Our results suggest that a complex, direct and long-distance RNA–RNA interaction network plays an important role in the regulation of HCV translation and replication, as well as in the switching between different steps of the viral cycle.

Identification of Anesthetic Binding Sites on Human Serum Albumin Using a Novel Etomidate Photolabel

We have synthesized a novel analog of the general anesthetic etomidate in which the ethoxy group has been replaced by an azide group, and which can be used as a photolabel to identify etomidate binding sites. This acyl azide analog is a potent general anesthetic in both rats and tadpoles and, as with etomidate, is stereoselective in its actions, with the R(+) enantiomer being significantly more potent than the S(-) enantiomer. Its effects on alpha1beta2gamma2s GABA(A) receptors expressed in HEK-293 cells are virtually indistinguishable from the parent compound etomidate, showing stereoselective potentiation of GABA-induced currents, as well as direct mimetic effects at higher concentrations. In addition, a point mutation (beta2 N265M), which is known to attenuate the potentiating actions of etomidate, also blocks the effects of the acyl azide analog. We have investigated the utility of the analog to identify etomidate binding sites by using it to photolabel human serum albumin, a protein that binds approximately 75% of etomidate in human plasma and which is thought to play a major role in its pharmacokinetics. Using HPLC/mass spectrometry we have identified two anesthetic binding sites on HSA. One site is the well-characterized drug binding site I, located in HSA subdomain IIA, and the second site is also an established drug binding site located in subdomain IIIB, which also binds propofol. The acyl azide etomidate may prove to be a useful new photolabel to identify anesthetic binding sites on the GABA(A) receptor or other putative targets.

Probing conformational changes of human serum albumin due to unsaturated fatty acid binding by chemical cross-linking and mass spectrometry

Mass spectrometry with chemical cross-linking was used to probe the conformational changes of HSA (human serum albumin) in solution on interaction with monounsaturated OA (oleic acid) or polyunsaturated AA (arachidonic acid) or DHA (docosahexaenoic acid). Fatty acid-free or -bound HSA was modified with lysine-specific cross-linkers and digested with trypsin. Cross-linked peptides were analysed by nano-electrospray ionization MS to localize the sites of cross-linking. Our data indicated that a local conformational change involving movement of the side chains of Lys-402 of subdomain IIIA or Lys-541 of subdomain IIIB occurred upon binding of all three fatty acids. Our data also indicated that the side chains of Lys-205 (IIA) and Lys-466 (IIIA) moved closer towards each other upon binding AA or DHA, but not OA, suggesting that the conformations of HSA when bound to mono- and poly-unsaturated fatty acids are distinctively different. While these observations agreed with previous X-ray crystallographic studies, the distances between epsilon-amino groups of most cross-linked lysine pairs were shorter than the crystal structure predicted, possibly reflecting a discrepancy between the solution and crystal structures. This method can serve as a useful complement to X-ray crystallography, particularly in probing the structure of a protein in solution.

Analysis of quasispecies in the viral 5? untranslated region of hepatitis C virus to evaluate ribavirin mutagenic effect in patients receiving ribavirin and interferon-alfa

In the study presented here the ribavirin mutagenic effect was investigated by analyzing quasispecies in the viral 5' untranslated region of hepatitis C virus in six patients with chronic infection who started interpheron-alpha and ribavirin therapy. A remarkable mutation rate during treatment was found in only one individual. This patient had a sustained response and harbored a type 3a virus strain. The different mutated clones in this patient demonstrated no apparent close relationship that could suggest lack of selection pressure by ribavirin. The mutations were located within the loops of subdomains IIIb and IIId of the internal ribosomal entry site. This is an interesting initial finding that needs to be substantiated in a larger trial.

The recombinant subdomain IIIB of human serum albumin displays activity of gonadotrophin surge-attenuating factor.

Gonadotrophin surge-attenuating factor (GnSAF) is an as yet unidentified ovarian factor that acts on the pituitary to attenuate the pre-ovulatory LH surge. In a previous study, GnSAF bioactivity was proposed to derive, at least in part, from a C-terminal domain (95peptide) of human serum albumin (HSA). We employ here the expression-secretion system of Pichia pastoris to produce and assay selected recombinant polypeptides of HSA for GnSAF activity. We show that the C-terminal 95peptide of HSA (residues 490-585; subdomain IIIB) can be expressed from P.pastoris in secreted form and supernatants from clones expressing this polypeptide reduce the GnRH-induced LH secretion of primary rat pituitary cultures by 50-82%. When expressed in the same system, HSA domain III (residues 381-585) or full-length HSA (residues 1-585) are inactive. The bioactive subdomain IIIB is also separable from either domain III or full-length HSA on Blue Sepharose chromatography. Taken together, the findings highlight the putative importance of HSA subdomain IIIB as a GnSAF-bioactive entity and introduce a unique experimental tool to engineer this molecule for structure-function analysis.