A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity

Structures of the multidrug-binding repressor protein QacR with monovalent and bivalent cationic drugs revealed that the carboxylate side-chains of E90 and E120 were proximal to the positively charged nitrogens of the ligands ethidium, malachite green and rhodamine 6G, and therefore may contribute to drug neutralization and binding affinity. Here, we report structural, biochemical and in vivo effects of substituting these glutamate residues. Unexpectedly, substitutions had little impact on ligand affinity or in vivo induction capabilities. Structures of QacR(E90Q) and QacR(E120Q) with ethidium or malachite green took similar global conformations that differed significantly from all previously described QacR-drug complexes but still prohibited binding to cognate DNA. Strikingly, the QacR(E90Q)-rhodamine 6G complex revealed two mutually exclusive rhodamine 6G binding sites. Despite multiple structural changes, all drug binding was essentially isoenergetic. Thus, these data strongly suggest that rather than contributing significantly to ligand binding affinity, the role of acidic residues lining the QacR multidrug-binding pocket is primarily to attract and guide cationic drugs to the "best available" positions within the pocket that elicit QacR induction.     

QacR-cation recognition is mediated by a redundancy of residues capable of charge neutralization

The Staphylococcus aureus multidrug binding protein QacR binds to a broad spectrum of structurally dissimilar cationic, lipophilic drugs. Our previous structural analyses suggested that five QacR glutamic acid residues are critical for charge neutralization and specification of certain drugs. For example, E57 and E58 interact with berberine and with one of the positively charged moieties of the bivalent drug dequalinium. Here we report the structural and biochemical effects of substituting E57 and E58 with alanine and glutamine. Unexpectedly, individual substitutions of these residues did not significantly affect QacR drug binding affinity. Structures of QacR(E57Q) and QacR(E58Q) bound to dequalinium indicated that E57 and E58 are redundant for charge neutralization. The most significant finding was that berberine was reoriented in the QacR multidrug binding pocket so that its positive charge was neutralized by side chain oxygen atoms and aromatic residues. Together, these data emphasize the remarkable versatility of the QacR multidrug binding pocket, illustrating that the capacity of QacR to bind myriad cationic drugs is largely governed by the presence in the pocket of a redundancy of polar, charged, and aromatic residues that are capable of electrostatic neutralization.     

Electron crystallography reveals plasticity within the drug binding site of the small multidrug transporter EmrE

EmrE is a Small Multidrug Resistance transporter (SMR) family member that mediates counter transport of protons and hydrophobic cationic drugs such as tetraphenylphosphonium (TPP⁺), ethidium, propidium and dequalinium. It is thought that the selectivity of the drug binding site in EmrE is defined by two negatively charged glutamate residues within a hydrophobic pocket formed from six of the α-helices, three from each monomer of the asymmetric EmrE homodimer. It is not apparent how such a binding pocket accommodates drugs of various sizes and shapes or whether the conformational changes that occur upon drug binding are identical for drugs of diverse chemical nature. Here, using electron cryomicroscopy of EmrE two-dimensional crystals we have determined projection structures of EmrE bound to three structurally different planar drugs, ethidium, propidium and dequalinium. Using image analysis and rigorous comparisons between these density maps and the density maps of the ligand-free and TPP⁺-bound forms of EmrE, we identify regions within the transporter that adapt differentially depending on the type of ligand bound. We show that all three planar drugs bind at the same pocket within the protein as TPP⁺. Furthermore, our analysis indicates that, while retaining the overall fold of the protein, binding of the planar drugs is accompanied by small rearrangements of the transmembrane domains that are different to those that occur when TPP⁺ binds. The regions in the EmrE dimer that are remodelled surround the drug binding site and include transmembrane domains from both monomers.     

Transition state P-glycoprotein binds drugs and modulators with unchanged affinity,suggesting a concerted transport mechanism

The P-glycoprotein multidrug transporter is a plasma membrane efflux pump for hydrophobic natural products, drugs, and peptides, driven by ATP hydrolysis. Determination of the details of the catalytic cycle of P-glycoprotein is critical if we are to understand the mechanism of drug transport and design ways to inhibit it. It has been proposed that the vanadate-trapped transition state of P-glycoprotein (Pgp x ADP x V(i) x M(2+), where M(2+) is a divalent metal ion) has a very low affinity for drugs compared to resting state protein, thus leading to binding of substrate on the cytoplasmic side of the membrane and release of substrate to the extracellular medium (or the extracellular membrane leaflet). We have used several different fluorescence spectroscopic approaches to show that isolated purified P-glycoprotein, when trapped in a stable transition state with vanadate and either Co(2+)or Mg(2+), binds drugs with high affinity. For vinblastine, colchicine, rhodamine 123, and doxorubicin, the affinity of the vanadate-trapped transition state for drugs was only very slightly (less than 2-fold) lower than the binding affinity of resting state Pgp, whereas for the modulators cyclosporin A and verapamil and the substrate Hoechst 33342, the binding affinity was very similar for the two states. The drug binding affinity of the ADP-bound form of the transporter was also comparable to that of the unoccupied transporter. These results suggest that release of drug from the transporter during the catalytic cycle precedes formation of the transition state.     

Domain movement of iron sulfur protein in cytochrome bc1 complex is facilitated by the electron transfer from cytochrome b(L) to b(H)

The key step of the "protonmotive Q-cycle" mechanism for cytochrome bc1 complex is the bifurcated oxidation of ubiquinol at the Qp site. ISP is reduced when its head domain is at the b-position and subsequent move to the c1 position, to reduce cytochrome c1, upon protein conformational changes caused by the electron transfer from cytochrome b(L) to b(H). Results of analyses of the inhibitory efficacy and the binding affinity, determined by isothermal titration calorimetry, of Pm and Pf, on different redox states of cytochrome bc1 complexes, confirm this speculation. Pm inhibitor has a higher affinity and better efficacy with the cytochrome b(H) reduced complex and Pf binds better and has a higher efficacy with the ISP reduced complex.     

Molecular analysis of the multidrug transporter, P-glycoprotein

Inherent or acquired resistance of tumor cells to cytotoxic drugs represents a major limitation to the successful chemotherapeutic treatment of cancer. During the past three decades dramatic progress has been made in the understanding of the molecular basis of this phenomenon. Analyses of drug-selected tumor cells which exhibit simultaneous resistance to structurally unrelated anti-cancer drugs have led to the discovery of the human MDR1 gene product, P-glycoprotein, as one of the mechanisms responsible for multidrug resistance. Overexpression of this 170 kDa N-glycosylated plasma membrane protein in mammalian cells has been associated with ATP-dependent reduced drug accumulation, suggesting that P-glycoprotein may act as an energy-dependent drug efflux pump. P-glycoprotein consists of two highly homologous halves each of which contains a transmembrane domain and an ATP binding fold. This overall architecture is characteristic for members of the ATP-binding cassette or ABC superfamily of transporters. Cell biological, molecular genetic and biochemical approaches have been used for structure-function studies of P-glycoprotein and analysis of its mechanism of action. This review summarizes the current status of knowledge on the domain organization, topology and higher order structure of P-glycoprotein, the location of drug- and ATP binding sites within P-glycoprotein, its ATPase and drug transport activities, its possible functions as an ion channel, ATP channel and lipid transporter, its potential role in cholesterol biosynthesis, and the effects of phosphorylation on P-glycoprotein activity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Investigation by fluorescence spectroscopy, resonance rayleigh scattering and zeta potential approaches of the separate and simultaneous binding effect of Paclitaxel and estradiol with human serum albumin

Separate and simultaneous binding effects of paclitaxel (a drug with anti-tumor activity) and estradiol (used for treating multiple maladies) with human serum albumin (HSA) were investigated by fluorescence quenching, UV absorption, circular dichroism, zeta potential and molecular dynamic techniques. An extensive fluorescence quenching was observed during the reaction of drugs and HSA and was rationalized in terms of a static quenching mechanism. The molecular distances between the donor (HSA) and acceptors (paclitaxel or estradiol) in binary and ternary systems were estimated according to F?rster's theory of dipole-dipole non-radiation energy transfer. The features of drug-induced structural disturbances of HSA have been studied in detail by synchronous fluorescence and circular dichroism (CD) analysis. The resonance Rayleigh scattering (RRS) intensities were proportional to the paclitaxel and estradiol concentrations in the range of respectively (0-8)×10(-6) and (0-1)×10(-4) mM in binary systems. The critical induced aggregation concentrations (C(CIAC)) of paclitaxel and estradiol for binary and ternary systems were determined by nonlinear relationships between the enhancement of the RRS intensities and the drug concentrations. A comparison between binary and ternary systems for two drugs allowed us to estimate the effect of a drug on the initial formation aggregation of the second drug. The zeta potential results were used to verify the existence of complexation and confirmed the C(CIAC) values obtained by the RRS technique. This phenomenon was supported by a progressive rise of the protein charge to a reversal point as a consequence of drug binding. The quantitative analysis data of circular dichroism (CD) spectra demonstrated that the binding of paclitaxel and/or estradiol to HSA induced conformational changes in HSA. Moreover, the α-helix content in HSA greatly decreased in the presence of paclitaxel as opposed when estradiol was present. Protein-ligand docking suggested that estradiol bound to residues situated in subdomain IIA of HSA. On the other hand, in the ternary system, the presence of the first drug decreased the binding affinity of the second drug to HSA. Therefore binding effects of paclitaxel and estradiol with HSA alone have different behavior than simultaneous interaction.     

Calcitonin gene-related peptide receptor independently stimulates 3′,5′-cyclic adenosine monophosphate and Ca2+ signaling pathways

The inhibition of ion transporting ATPases (Na⁺,K⁺-ATPase, Ca²⁺,Mg²⁺- and Ca²⁺-ATPase) by two amphiphilic drugs e.g. chlorpromazine (antipsychotic) and chloroquine (antimalarial) are found to be competitive in nature in vitro with respect to the substrate. Two binding sites - high and low affinity are found to exist on all the three ATPases toward these drugs as evident from the plot of F/F₀ vs. different drug concentrations of tryptophan fluorescence of the enzymes. Circular dichroism analysis suggest that binding of drugs to the high affinity site does not involve any change in conformation of ATPase molecules which occur only when drug binds to the low affinity sites. The drug binding sites and possible effect on conformational change of ATPase molecules of these two drugs have been described in this report.     

Systematic comparison of statistical analyses of electronic and vibrational circular dichroism for secondary structure prediction of selected proteins

The electronic (ultraviolet) circular dichroism (UVCD) and vibrational circular dichroism (VCD) of 20 proteins are systematically compared as to their relationship to the secondary structures of these proteins. The UVCD spectra are statistically treated by use of the same factor analysis methods used previously for VCD. The UVCD spectra can be reproduced as linear combinations of five subspectra. The first subspectrum reflected the expected alpha-helical UVCD shape, particularly at longer wavelengths, while the higher order ones had less obvious similarity to standard bandshapes. Cluster analysis on the UVCD factor analysis coefficients reflected the clustering on the basis of the fractional secondary structure parameters (from X-ray) but was less clear than VCD. Qualitative complementarity of protein VCD and UVCD spectra was demonstrated by combined cluster analysis of their respective factor analysis coefficients. Quantitative relationships between spectral coefficients and fractional secondary structure were determined by multiple regression analyses using only statistically important coefficients. These resulted in an ability to reproduce four of the structural parameters with errors for individual proteins comparable to the VCD result. In UVCD, the standard deviations of the regression fit for beta-sheet were worse and for the undefined part of the structure were better than in VCD. Parallel analyses using the partial least-squares method showed UVCD in that case to have more error than VCD in reproducing the training set structural parameters. Comparison of the regression and partial least-squares methods illustrated limitations of total back-transformation of the UVCD spectra into structural parameters.     

Reconstitution of the rat liver vasopressin receptor coupled to guanine nucleotide-binding proteins

The V1 vasopressin receptor has been solubilized from rat liver membranes with the zwitterionic detergent 3-[(3-cholamidopropyl)dimethylammoniol]-1-propanesulfonate (CHAPS) and reconstituted into phospholipid vesicles. There is essentially complete solubilization of the receptor by 3% CHAPS at a protein concentration of 15 mg/ml. Reconstitution into soybean phospholipid vesicles is readily achieved either by gel filtration chromatography or by membrane dialysis. The binding of [3H]vasopressin to proteoliposomes is specific, saturable, reversible, and magnesium-dependent. In contrast, the detergent-soluble vasopressin receptor does not display specific binding. The apparent affinity of the reconstituted receptor for [3H]vasopressin is approximately 4-fold lower than that of the receptor in native membranes. In addition, the binding of [3H]vasopressin to reconstituted vesicles is not sensitive to 100 microM guanosine 5'-O-thiotriphosphate (GTP gamma S) as it is in native membranes. However, the apparent affinity of the reconstituted receptor for ligand approximates that of native membranes when membranes are prebound with vasopressin prior to solubilization and reconstitution into vesicles. Furthermore, vesicles reconstituted from membranes prebound with vasopressin show GTP gamma S sensitivity of [3H] vasopressin binding. This finding strongly suggests that vasopressin stabilizes a receptor-G-protein complex during solubilization. The rat liver vasopressin receptor is a glycoprotein, as shown by its specific binding to the lectin "wheat germ agglutinin." The vasopressin receptor can be reconstituted from the N-acetylglucosamine-eluted peak of a wheat germ agglutinin-Sepharose column, and [3H] vasopressin binding activity is purified 5-6-fold from membranes by this chromatographic procedure. The functionality of the partially purified receptor is indicated by its ability to bind ligand with high affinity and by its ability to functionally interact with a G-protein when vasopressin is bound prior to solubilization.     

Role of structure and dynamics of DNA with cisplatin and oxaliplatin adducts in various sequence contexts on binding of HMGB1a

Anti-cancer drugs, such as cisplatin and oxaliplatin, covalently bind to adjacent guanine bases in DNA to form intra-strand adducts. Differential recognition of drug–DNA adducts by the protein HMGB1a has been related to the differences in efficacy of these drugs in tumours. Additionally, the bases flanking the adduct (the sequence context) also have a marked effect on HMGB1a binding affinity. We perform atomistic molecular dynamics simulations of DNA with cisplatin and oxaliplatin adducts in four sequence contexts (AGGC, CGGA, TGGA and TGGT) in the absence and presence of HMGB1a. The structure of HMGB1a-bound drug–DNA molecules is independent of sequence and drug identity, confirming that differential recognition cannot be explained by the protein-bound structure. The differences in the static and conformational dynamics of the drug–DNA structures in the absence of the protein explain some but not all trends in differential binding affinity of HMGB1a. Since the minor groove width and helical bend of all drug–DNA molecules in the unbound state are lower than the protein-bound state, HMGB1a must actively deform the DNA during binding. The thermodynamic pathway between the unbound and protein-bound states could be an additional factor in the binding affinity of HMGB1a for drug–DNA adducts in various sequence contexts.     

Probing the mechanism of drug/lipid membrane interactions using Biacore

Assay conditions were established to screen a panel of drugs for binding to liposome surfaces using a surface plasmon resonance (SPR) biosensor. Drugs were found to bind negligibly or reversibly or were retained on the liposome surface. Cationic amphiphilic drugs fell into the last class and correlated with drugs that induce phospholipidosis in vivo. To a first approximation, a single-site model yielded apparent binding affinities that adequately described a drug's dose-dependent binding to liposome surfaces. Affinities ranged at least 1000-fold within the drug panel. A liposome's drug-binding capacity and affinity depended on both the lipid headgroup and the drug's structure. Although a drug's charge state generally dominated whether or not it remained bound to the liposome, subtle structural differences between members of certain drug families led to them having widely differing binding affinities. A comparison between the dissociation of drugs from liposome surfaces by Biacore and the lipid retention measurements determined by a parallel artificial membrane permeability assay was drawn. The results from this study demonstrate the potential of using SPR-based assays to characterize drug/liposome-binding interactions.     

Allosteric and competitive displacement of drugs from human serum albumin by octanoic acid, as revealed by high-performance liquid affinity chromatography, on a human serum albumin-based stationary phase

A chiral stationary phase for high-performance liquid chromatography, based upon immobilized human serum albumin (HSA), was used to investigate the effect of octanoic acid on the simultaneous binding of a series of drugs to albumin. Octanoic acid was found to bind with high affinity to a primary binding site, which in turn induced an allosteric change in the region of drug binding Site II, resulting in the displacement of compounds binding there. Approximately 80% of the binding of suprofen and ketoprofen to HSA was accounted for by binding at Site II. Octanoic acid was found to also bind to a secondary site on HSA, with much lower affinity. This secondary site appeared to be the warfarin—azapropazone binding area (drug binding Site I), as both warfarin and phenylbutazone were displaced in a competitive manner by high levels of octanoic acid. The enantioselective binding to HSA exhibited by warfarin, suprofen and ketoprofen was found to be due to differential binding of the enantiomers at Site I; the primary binding site for suprofen and ketoprofen was not enantioselective.     

The Staphylococcal QacR Multidrug Regulator Binds a Correctly Spaced Operator as a Pair of Dimers

Expression of the Staphylococcus aureus plasmid-encoded QacA multidrug transporter is regulated by the divergently encoded QacR repressor protein. To circumvent the formation of disulfide-bonded degradation products, site-directed mutagenesis to replace the two cysteine residues in wild-type QacR was undertaken. Analysis of a resultant cysteineless QacR derivative indicated that it retained full DNA-binding activities in vivo and in vitro and continued to be fully proficient for the mediation of induction of qacA expression in response to a range of structurally dissimilar multidrug transporter substrates. The cysteineless QacR protein was used in cross-linking and dynamic light-scattering experiments to show that its native form was a dimer, whereas gel filtration indicated that four QacR molecules bound per DNA operator site. The addition of inducing compounds led to the dissociation of the four operator-bound QacR molecules from the DNA as dimers. Binding of QacR dimers to DNA was found to be dependent on the correct spacing of the operator half-sites. A revised model proposed for the regulation of qacA expression by QacR features the unusual characteristic of one dimer of the regulatory protein binding to each operator half-site by a process that does not appear to require the prior self-assembly of QacR into tetramers.