Evidence of heterogeneous 1-anilinonaphthalene-8-sulfonate binding to beta-lactoglobulin from fluorescence spectroscopy.

Steady-state and dynamic fluorescence titrations show that: (a) the complex between beta-lactoglobulin (BLG) and 1-anilinonaphthalene-8-sulfonate (ANS) displays a heterogeneous equilibrium with large changes in the binding strength vs. pH and ion concentration; and (b) the fluorescence response of bound ANS reveals two separate lifetimes that suggest two different sites (or binding modes). While steady-state fluorescence titrations yield effective values of the binding constant and of the bound ANS quantum efficiency, it is shown that, by combining steady-state fluorescence and lifetime decay of ANS, it is possible to give quantitative estimates of the association constants for each site. When heading from the acid (pH approximately 2) to the native state (pH approximately 6) the main result is a very large reduction of the effective binding constant. This and the results of titrations vs. ionic strength suggest that electrostatic interactions are a major contribution to ANS binding to BLG.     

Competitive binding of fatty acids and the fluorescent probe 1-8-anilinonaphthalene sulfonate to bovine beta-lactoglobulin

The use of spectroscopy in the study of fatty acids binding to bovine beta-lactoglobulin (BLG) appears to be a difficult task, as these acid compounds, assumed as the protein natural ligands, do not exhibit favorable optical response such as, for example, absorption or fluorescence. Therefore, the BLG fatty-acid equilibrium has been tackled by exploiting the competition between fatty acids and ANS, a widely used fluorescent hydrophobic probe, whose binding sites on the protein have been characterized recently. Two lifetime decays of the ANS-BLG complex have been found; the longer one has been attributed to the internal binding site and the shorter one to the external site. At increasing fatty acids concentration, the fractional weight associated with ANS bound to the internal site drops, in agreement with a model describing the competition of the dye with fatty acids, whereas the external site occupancy appears to be unaffected by the fatty acids binding to BLG. This model is supported by docking studies. An estimate of the acid-binding affinities for BLG has been obtained by implementing the fitting of the bound ANS intensities with a competitive binding model. A relevant dependence has been found upon the solution pH, in the range from 6 to 8, which correlates with the calyx accessibility modulated by the conformation of the EF loop. Fatty acids with longer aliphatic chains (palmitate and laurate) are found to display larger affinities for the protein and the interaction free energy nicely correlates with the number of contacts inside the protein calyx, in agreement with docking simulations.     

Location of a binding site for 1-anilinonaphthalene-8-sulfonate on calmodulin

The quenching by radiationless energy transfer of the ultraviolet fluorescence of Tyr-99 and Tyr-138 by bound 1-anilinonaphthalene-8-sulfonate (1,8-ANS) has been employed to determine the separation of a hydrophobic binding site of 1,8-ANS from each of the tyrosines. The results suggest that the dominant binding site is located in the N-terminal region of domain III.     

Oxidative phosphorylation in Azotobacter vinelandii. Energy-linked pH changes and fluorescence changes of atebrin and 1-anilinonaphthalene-8-sulphonate

1. Phosphorylating particles from Azotobacter vinelandii show a rapid, respiration-induced reversible increase in pH of the suspending medium; this is not found with non-phosphorylating particles.2. The observed pH response requires the presence of low concentrations of Mg²⁺ or of higher concentrations of Na⁺ or K⁺.3. Between 40 and 10 °C the rates of proton influx and efflux have similar temperature coefficients; below 10 °C the effect of temperature is greater on proton efflux.4. The kinetics of the energy-linked enhancement of fluorescence 1-anilinonaphthalene-8-sulphonate are slower than that of the quenching of the fluorescence of atebrin.     

The influence of diffusion potentials across liposomal membranes on the fluorescence intensity of 1-anilinonaphthalene-8-sulphonate

The influence of diffusion potentials across different phospholipid membranes on the fluorescence intensity of 1-anilinonaphthalene-8-sulphonate (ANS) was studied. With liposomes or chloroform spheres covered with a monolayer of egg lecithin, no specific effects were found. With liposomes of soy-bean phospholipids, generation of a diffusion potential leads to an enhancement or decrease, depending on the direction of the potential, of the intensity of ANS fluorescence. This effect is mainly due to a change in quantum yield of the bound ANS. These data support a mechanism according to which ANS molecules are pushed into or pulled out of the membrane by a potential, but not an electrophoretic one in which the potential causes movement of ANS across the membrane.     

Genome-wide identification of protein binding sites on RNAs in mammalian cells

RNA-binding proteins (RBPs) are proteins that bind to the RNA and participate in forming ribonucleoprotein complexes. They have crucial roles in various biological processes such as RNA splicing, editing, transport, maintenance, degradation, intracellular localization and translation. The RBPs bind RNA with different RNA-sequence specificities and affinities, thus, identification of protein binding sites on RNAs (R-PBSs) will deeper our understanding of RNA-protein interactions. Currently, high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP, also known as CLIP-Seq) is one of the most powerful methods to map RNA-protein binding sites or RNA modification sites. However, this method is only used for identification of single known RBPs and antibodies for RBPs are required. Here we developed a novel method, called capture of protein binding sites on RNAs (RPBS-Cap) to identify genome-wide protein binding sites on RNAs without using antibodies. Double click strategy is used for the RPBS-Cap assay. Proteins and RNAs are UV-crosslinked in vivo first, then the proteins are crosslinked to the magnetic beads. The RNA elements associated with proteins are captured, reverse transcribed and sequenced. Our approach has potential applications for studying genome-wide RNA-protein interactions.     

Characterization of cholecystokinin binding sites in rat cerebral cortex using a 125I-CCK-8 probe resistant to degradation

Specific binding sites for cholecystokinin (CCK) have been characterized in a particulate membrane fraction of rat cerebral cortex using a biologically active 125I-labeled derivative of the C-terminal octapeptide of CCK (CCK-8) prepared by reaction with the iodinated form of the imidoester (125IIE), methyl-p-hydroxybenzimidate. The time course of binding to cortical membranes was rapid, temperature dependent, and saturable. Half-maximal binding at 24 degrees C was reached in 30 min and full binding at 120 min. At 37 degrees C there was only a slight increase in 125IIE-CCK-8 bound after 15 min. The addition of a large excess of CCK-8 after 30 min of binding at 24 degrees C caused a prompt and rapid decline in radioligand bound showing that the interaction was reversible. There was a progressive decline in the amount of 125IIE-CCK-8 bound to membranes with increasing concentrations of CCK-8 and other structurally related peptides. CCK-8 displaced 50% of the radioligand at 4 nM, CCK-33 at 10 nM, and gastrin (desulfated CCK-8) at 60 nM. Secretin, a structurally unrelated peptide, was unable to displace the radioligand from cortical membranes at 1.0 microM. Finally, 125IIE-CCK-8 exposed to cortical membranes or to buffers that had previously contained such membranes for 60 min at 24 degrees C bound equally as well to fresh cortical membranes as control radioligand that had not been exposed to the same conditions. Thus the 125I-CCK-8 radioligand used in this study was highly resistant to degradative processes in rat brain tissue.     

Evidence for internal and external binding sites on human tear lipocalin

8-Anilino-1-naphthalenesulfonic acid (ANS) is widely used as a probe for locating binding sites of proteins. To characterize the binding sites of tear lipocalin (TL), we studied ANS binding to apoTL by steady-state and time-resolved fluorescence. Deconvolution of ANS binding revealed that two lifetime components, 16.99 ns and 2.76 ns at pH 7.3, have dissociation constants of 0.58 μM and 5.7 μM, respectively. At pH 3.0, the lifetime components show decreased affinities with dissociation constants of 2.42 μM and ∼21 μM, respectively. Selective displacement of ANS molecules from the ANS-apoTL complex by stearic acid discriminates the internal and external binding sites. Dependence of the binding affinity on ionic strength under various conditions provides strong evidence that an electrostatic interaction is involved. Time-resolved fluorescence is a promising tool to segregate multiple binding sites of proteins.     

Macrophage paraoxonase 1 (PON1) binding sites

Paraoxonase 1 (PON1), an HDL-associated esterase, is known to possess anti-oxidant and anti-atherogenic properties. PON1 was shown to protect macrophages from oxidative stress, to inhibit macrophage cholesterol biosynthesis, and to stimulate HDL-mediated cholesterol efflux from the cells. The aim of the present study was to characterize macrophage PON1 binding sites which could be responsible for the above anti-atherogenic activities.Incubation of FITC-labeled recombinant PON1 with J774 A.1 macrophage-like cell line at 37 °C, resulted in cellular binding and internalization of PON1, leading to PON1 localization in the cell’s cytoplasm compartment. In order to determine whether PON1 uptake is mediated via a specific binding to the macrophage, FITC-labeled recombinant PON1 was incubated with macrophages at 4 °C, followed by cell membranes separation. Macrophage membrane fluorescence was shown to be directly and dose-dependently related to the labeled PON1 concentration. Furthermore, binding assays performed at 4 and at 37 °C, using labeled and non-labeled recombinant PON1 (for competitive inhibition), demonstrated a dose-dependent significant 30% decrement in labeled PON1 binding to the macrophages, by the non-labeled PON1. Similarly, binding assays, using labeled PON1 and non-labeled HDL (the natural carrier of PON1 in the circulation) indicated that HDL decreased the binding of labeled PON1 to macrophages by 25%. Unlike HDL, LDL had no effect on labeled PON1 binding to macrophages. Finally, HDL were pre incubated without or with PON1 or apolipoprotein AI (apoAI) antibodies, in order to block PON1 or apoAI ability to bind to the cells. HDL incubation with antibody to PON1 or to apoAI significantly decreased HDL ability to inhibit macrophages-mediated LDL oxidation (by 32% or by 25%, respectively). A similar trend was also observed for HDL-mediated cholesterol efflux from macrophages, with an inhibitory effect of 35% or 19%, respectively. These results suggest that blocking HDL binding to macrophages through its apo A-I, and more so, via its PON1, results in the attenuation of HDL-PON1 biological activities.In conclusion, PON1 specifically binds to macrophage binding sites, leading to anti-atherogenic effects. Macrophage PON1 binding sites may thus be a target for future cardio protection therapy.     

Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation

We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 Å and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f′′ = 3.6 e⁻) of cadmium at 1.375 Å, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f′′ = 0.44 e⁻). Proteins 31:477–485, 1998. © 1998 Wiley-Liss, Inc.     

Unfolding kinetics of beta-lactoglobulin induced by surfactant and denaturant: a stopped-flow/fluorescence study

The beta-->alpha transition of beta-lactoglobulin, a globular protein abundant in the milk of several mammals, is investigated in this work. This transition, induced by the cationic surfactant dodecyltrimethylammonium chloride (DTAC), is accompanied by partial unfolding of the protein. In this work, unfolding of bovine beta-lactoglobulin in DTAC is compared with its unfolding induced by the chemical denaturant guanidine hydrochloride (GnHCl). The final protein states attained in the two media have quite different secondary structure: in DTAC the alpha-helical content increases, leading to the so-called alpha-state; in GnHCl the amount of ordered secondary-structure decreases, resulting in a random coil-rich final state (denatured, or D, state). To obtain information on both mechanistic routes, in DTAC and GnHCl, and to characterize intermediates, the kinetics of unfolding were investigated in the two media. Equilibrium and kinetic data show the partial accumulation of an on-pathway intermediate in each unfolding route: in DTAC, an intermediate (I(1)) with mostly native secondary structure but loose tertiary structure appears between the native (beta) and alpha-states; in GnHCl, another intermediate (I(2)) appears between states beta and D. Kinetic rate constants follow a linear Chevron-plot representation in GnHCl, but show a more complex mechanism in DTAC, which acts like a stronger binding species.     

Dissection of the critical binding determinants of cellular retinoic acid binding protein II by mutagenesis and fluorescence binding assay

The binding of retinoic acid to mutants of Cellular Retinoic Acid Binding Protein II (CRABPII) was evaluated to better understand the importance of the direct protein/ligand interactions. The important role of Arg111 for the correct structure and function of the protein was verified and other residues that directly affect retinoic acid binding have been identified. Furthermore, retinoic acid binding to CRABPII mutants that lack all previously identified interacting amino acids was rescued by providing a carboxylic acid dimer partner in the form of a Glu residue. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface

Continuum electrostatic methods are a powerful tool for the analysis and design of biomolecular complexes, with methodologies that allow for the detailed analysis of the electrostatic contributions to binding affinities and procedures for computing the properties of electrostatically optimal ligands. We have applied these methods to the design of improved inhibitors of HIV-1 cell entry. HIV infection of a cell requires viral-cell membrane fusion, an event partially driven by a large-scale conformational change in the viral membrane glycoprotein gp41. This transformation involves the docking of a helix from the C-terminal region of three gp41 chains against a pre-formed trimeric-coiled coil; several protein constructs that inhibit membrane fusion act by binding to an isolated C-terminal helix and blocking the formation of the fusogenic structure. A detailed analysis of the electrostatic contributions to the binding of one such inhibitor (5-Helix) to a C-terminal helix was performed using the X-ray crystal structure of the core of the HIV-1 gp41 ectodomain as a structural model, and several residues on 5-Helix that make substantial contributions to binding, both favorable and unfavorable, were identified. An electrostatic affinity optimization methodology was applied to the side chains of 5-Helix, with the results showing that significant improvements in binding affinity are possible if the electrostatic contributions to the binding free energy are optimized. Several mutations accessible by experimental methods are suggested, with calculated improvements in binding affinity of as much as 500-fold and greater.     

The essentiality of His-47 and the N-terminal region for the binding of 8-anilinonaphthalene-1-sulfonate with Taiwan cobra phospholipase A2

The binding of the apolar fluorescent dye 8-anilinonaphthalene-1-sulfonate (ANS) toNaja naja atra phospholipase A₂ (PLA₂) as well as the enhancement of ANS fluorescence of the PLA₂-ANS complex decreased with increasing pH in a pH range from 3 to 9. These pH-dependent curves can be well interpreted as the perturbation of an ionizable group with pK value of 5.8, which was assigned as His-47 in the active site of PLA₂. The ionizable group with pK 5.8 was no longer observed after methylation of His-47, supporting the idea that thepH dependence of ANS binding arose from an electrostatic interaction between His-47 and the bound ANS. Removal of the N-terminal octapeptide of PLA₂ caused a precipitous drop in the capability of PLA₂ for binding with ANS and enhancing ANS fluorescence, reflecting that the integrity of the N-terminal region was essential for maintaining the hydrophobic character of the ANS-binding site. However, the nonpolarity of the ANS-binding site in the N-terminus-removed derivative was still partially retained at lowpH, but was completely lost at highpH. Evidently, the N-terminal region plays a more crucial role in ANS binding at highpH than at lowpH. These results indicate that hydrophobic interaction as well as electrostatic interaction are involved in the binding of ANS to PLA₂, and that the relative contributions of both interactions in ANS fluorescence enhancement may be different under differentpH.     

A partially folded intermediate conformation is induced in pectate lyase C by the addition of 8-anilino-1-naphthalenesulfonate (ANS)

Addition of 8-anilino-1-naphthalenesulfonate (ANS) to acid-denatured pectate lyase C (pelC) leads to a large increase in the fluorescence quantum yield near 480 nm. The conventional interpretation of such an observation is that the ANS is binding to a partially folded intermediate such as a molten globule. Far-ultraviolet circular dichroism demonstrates that the enhanced fluorescence results from the induction of a partially folded protein species that adopts a large fraction of native-like secondary structure on binding ANS. Thus, ANS does not act as a probe to detect a partially folded species, but induces such a species. Near-ultraviolet circular dichroism suggests that ANS is bound to the protein in a specific conformation. The mechanism of ANS binding and structure induction was probed. The interaction of acid-unfolded pelC with several ANS analogs was investigated. The results strongly indicate that the combined effects of hydrophobic and electrostatic interactions account for the relatively high binding affinity of ANS for acid-unfolded pelC. These results demonstrate the need for caution in interpreting enhancement of ANS fluorescence as evidence for the presence of molten globule or other partially folded protein intermediates.     

Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora

Proteinase inhibitors are among the most promising candidates for expression by transgenic plants and consequent protection against insect predation. However, some insects can respond to the threat of the proteinase inhibitor by the production of enzymes insensitive to inhibition. Inhibitors combining more than one favorable activity are therefore strongly favored. Recently, a known small Kunitz trypsin inhibitor from Prosopis juliflora (PTPKI) has been shown to possess unexpected potent cysteine proteinase inhibitory activity. Here we show, by enzyme assay and gel filtration, that, unlike other Kunitz inhibitors with dual activities, this inhibitor is incapable of simultaneous inhibition of trypsin and papain. These data are most readily interpreted by proposing overlapping binding sites for the two enzymes. Molecular modeling and docking experiments favor an interaction mode in which the same inhibitor loop that interacts in a canonical fashion with trypsin can also bind into the papain catalytic site cleft. Unusual residue substitutions at the proposed interface can explain the relative rarity of twin trypsin/papain inhibition. Other changes seem responsible for the relative low affinity of PTPKI for trypsin. The predicted coincidence of trypsin and papain binding sites, once confirmed, would facilitate the search, by phage display for example, for mutants highly active against both proteinases.     

Computational predictions of common transcription factor binding sites on the genes of proline metabolism in plants

Proline, an imino acid, has been well documented to be associated with the stress response induced by abiotic factors such asdrought, cold and salinity in plants and biotic factors such as bacterial and fungal attacks. However, the regulatory mechanismscontrolling proline metabolism, intercellular and intracellular transport and connections of proline to other metabolic pathways arepoorly understood. F-MATCH analysis combined with composite module analysis (CMA) revealed that the binding sites matchingmatrices for O2 and OCSBF-1 were overrepresented in the promoters of differentially expressed proline metabolism genes. Thepresence of MYBAS1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promoters of genes of prolinebiosynthesis pathway and SBF1 and GT1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promotersof proline catabolic pathway genes suggest their involvement in modulation of proline metabolism and its accumulation in plants.     

Mapping the binding sites of peptide and non-peptide molecules to G protein-coupled receptors by fluorescence

Summary Novel fluorescence approaches to investigate ligand recognition and structure of G protein-coupled receptors in native membranes have been developed. These methods combine the biosynthetic incorporation of unnatural fluorescent amino acids at known sites in receptors with the technique of fluorescence energy transfer for distance measurement. This permits one to fix the ligand in space and to define the structure of the receptor in a model of ligand-receptor interactions. Subdomains of ligand binding sites on NK1 and NK2 receptors were also characterized using environment-sensitive fluorophores and the techniques of collisional quenching and anisotropy. Antagonists and agonists have different binding sites on NK1 and NK2.