Mol Of Ligand Research Articles

Thermodynamics of the GTP-GDP-operated Conformational Switch of Selenocysteine-specific Translation Factor SelB

SelB is a specialized translation factor that binds GTP and GDP and delivers selenocysteyl-tRNA (Sec-tRNA(Sec)) to the ribosome. By analogy to elongation factor Tu (EF-Tu), SelB is expected to control the delivery and release of Sec-tRNA(Sec) to the ribosome by the structural switch between GTP- and GDP-bound conformations. However, crystal structures of SelB suggested a similar domain arrangement in the apo form and GDP- and GTP-bound forms of the factor, raising the question of how SelB can fulfill its delivery function. Here, we studied the thermodynamics of guanine nucleotide binding to SelB by isothermal titration calorimetry in the temperature range between 10 and 25 °C using GTP, GDP, and two nonhydrolyzable GTP analogs, guanosine 5'-O-(γ-thio)triphosphate (GTPγS) and guanosine 5'-(β,γ-imido)-triphosphate (GDPNP). The binding of SelB to either guanine nucleotide is characterized by a large heat capacity change (-621, -467, -235, and -275 cal × mol(-1) × K(-1), with GTP, GTPγS, GDPNP, and GDP, respectively), associated with compensatory changes in binding entropy and enthalpy. Changes in heat capacity indicate a large decrease of the solvent-accessible surface area in SelB, amounting to 43 or 32 amino acids buried upon binding of GTP or GTPγS, respectively, and 15-19 amino acids upon binding GDP or GDPNP. The similarity of the GTP and GDP forms in the crystal structures can be attributed to the use of GDPNP, which appears to induce a structure of SelB that is more similar to the GDP than to the GTP-bound form.

Binding of netropsin to several DNA constructs: Evidence for at least two different 1:1 complexes formed from an –AATT-containing ds-DNA construct and a single minor groove binding ligand

Isothermal titration calorimetry, ITC, has been used to determine the thermodynamics (Δ G, Δ H, and − TΔ S) for binding netropsin to a number of DNA constructs. The DNA constructs included: six different 20–22mer hairpin forming sequences and an 8-mer DNA forming a duplex dimer. All DNA constructs had a single –AT-rich netropsin binding with one of the following sequences, (A 2T 2) 2, (ATAT) 2, or (AAAA/TTTT). Binding energetics are less dependent on site sequence than on changes in the neighboring single stranded DNA (hairpin loop size and tail length). All of the 1:1 complexes exhibit an enthalpy change that is dependent on the fractional saturation of the binding site. Later binding ligands interact with a significantly more favorable enthalpy change (∂Δ H 1–2 from 2 to 6 kcal/mol) and a significantly less favorable entropy change (∂(− TΔ S 1–2)) from − 4 to − 9 kcal/mol). The ITC data could only be fit within expected experimental error by use of a thermodynamic model that includes two independent binding processes with a combined stoichiometry of 1 mol of ligand per 1 mol of oligonucleotide. Based on the biophysical evidence reported here, including theoretical calculations for the energetics of “trapping” or structuring of a single water molecule and molecular docking computations, it is proposed that there are two modes by which flexible ligands can bind in the minor groove of duplex DNA. The higher affinity binding mode is for netropsin to lay along the floor of the minor groove in a bent conformation and exclude all water from the groove. The slightly weaker binding mode is for the netropsin molecule to have a slightly more linear conformation and for the required curvature to be the result of a water molecule that bridges between the floor of the minor groove and two of the amidino nitrogens located at one end of the bound netropsin molecule.

Super Uranophile, Water-Soluble Calixarenes: Their Metal Complexes, Stability Constants and Selective Reactivity to Uranyl Ion

The complex-formation reaction of hydroxycalix[n]arene-p-sulfonates, Hj1nn–(n=4,8; j=n/2, n=6; j=2), with various metal ions were studied while focusing on the uranyl ion, UO22+, by the pH-titration method at 25ʰC and m=0.1. From the pH-titration data for Hj1nn–, the acid-dissociation constants were determined to be as follows: pKa1=3.25, pKa2=12.8 for H2144–, pKa1=3.28, pKa2=4.86 for H2166–, and pKa1=3.73, pKa2=4.39, pKa3=8.07, pKa4=10.1 for H4188–. These results indicate that the present ligands are relatively strong multi-protonic acids which release j mol of proton from one mol of ligand, Hj1nn–, having n mol of hydroxyl group in a weakly acidic-to-alkaline aqueous solution. The tetramer ligand, H2144– formed two unstable 1:2 (UO22+:ligand) complexes, [(UO22+)(146–)2(H+)]9– and [(UO22+)(146–)2]10–, and a hexamer ligand, H2166– formed four 1:1 complex species, such as [(UO22+)(168–)]6–, [(UO22+)(168–)(H+)–1]7–, [(UO22+)(168–)(H+)–2]8–, and [(UO22+)(168–)(H+)–3]9– with UO22+. Their selective reactivity to UO22+ over other various metal ions was evaluated based on their pKa values, stability constants and the compositions of the complexes including that for the octamer ligand, H4188–, for which the complex-formation reactions with various metal ions were already studied and found to form an extremely stable 2:1 complex, [(UO22+)2(1812–)(H+)–3]11–.

Immobilization of binding proteins on nonporous supports

Four different nonporous particulate materials, nylon, polystyrene, soda-lime silicate glass, and fused silica glass, have been evaluated for their appropriateness as immobilization supports for immunoglobulins. A method of protein quantitation that is usually applied to solutions, the bicinchoninic acid (BCA) assay, was used successfully to directly measure ng amounts of protein immobilized on the supports. Two proteins, a monoclonal antibody to theophylline and the biotin binding protein avidin, were studied. Radioactive theophylline and radioactive biotin were used to measure the activity of the immobilized protein. Ligand binding capacity per mm2 of support was measured as a function of amount of protein immobilized. By measuring both the amount of protein immobilized and its ligand binding capacity, we have determined that antitheophylline antibody adsorbed on polystyrene balls loses almost 90% of its binding activity after 65 h, although little protein is lost from the balls over this time. Avidin retains nearly full activity for biotin on polystyrene. The binding activity of biotinyl-antibody conjugate immobilized on avidin-adsorbed polystyrene is stable, even when stored for over 22 wk. Antibody covalently immobilized on soda-lime silicate glass beads retains its binding activity over long-term storage, although only 0.1 mol of 3H-theophylline bind per mol of immobilized antibody. Using fused silica glass particles as the solid support, the same antibody binds approx 0.6 mol of ligand per mol of immobilized antibody protein. The structural "softness" of the immunoglobulin requires that interaction with the surface be prevented in order to maintain activity.

Aluminum(3+) binding by adenosine 5'-phosphates: AMP, ADP, and ATP

To assess quantitatively the ability of Al 3+ to complete with Mg 2+ in many vital processes, we have determined the stability constants for Al 3+ binding to adenosine 5'-phosphates. With ATP, Al 3+ forms an equimolar complex 4000 times stronger than does Mg 2+ , and stronger than most metal ions including Cu 2+ . In addition to an equimolar complex, Al 3+ also forms a complex with 2 mol of ligand that dominates in slightly acidic and neutral solutions, from which a deprotonation occurs to form a mixed hydroxo complex. ADP forms only slightly weaker complexes than ATP

Characterization of putative cytoskeletal proteins from a trypanosomatid and their comparative binding to microtubules and soluble tubulin.

The corset of microtubules which encloses the cell body of Crithidia fasiculata displays cross-links joining tubules to each other and to plasma membrane. Two proteins, designated COP-33 and COP-61 on the basis of their subunit Mr values, have been considered putative components of this apparatus because of their abundance in isolated cytoskeleton and their ability to cross-link brain microtubules in vitro. The oligomeric structures of the native proteins have now been characterized, and they have been shown to be basic, rather symmetrical, and to require detergent for solubilization. Using monospecific antibodies, enzyme-linked immunoassays of subcellular fractions have shown that each is 5-fold enriched in the microtubule plasma membrane fraction and absent from flagellar and some internal membranes. The binding of each to soluble tubulin and to microtubules has been systematically studied and compared with that of two noncytoskeletal protein ligands (glycolytic enzymes). The observed positive cooperatively was unexpected for binding of these large ligands to microtubules. In each case the maximum number of mol of ligand bound per mol of tubulin (0.5-1.0) was identical whether the latter was dissociated or assembled and so were the dissociation constants (1.3-6.0 x 10(-7) M) for three of the ligand proteins.

Ligand interactions of the cation-independent mannose 6-phosphate receptor: The stoichiometry of mannose 6-phosphate binding

The interaction of the bovine cation-independent mannose 6-phosphate receptor with a variety of phosphorylated ligands has been studied using equilibrium dialysis and immobilized receptor to measure ligand binding. The dissociation constants for mannose 6-phosphate, pentamannose phosphate, bovine testes beta-galactosidase, and a high mannose oligosaccharide with two phosphomonoesters were 7 X 10(-6) M, 6 X 10(-6) M, 2 X 10(-8) M, and 2 X 10(-9) M, and the mol of ligand bound/mol of receptor monomer were 2.17, 1.85, 0.9, and 1.0, respectively. We conclude that the cation-independent mannose 6-phosphate receptor has two mannose 6-phosphate-binding sites/polypeptide chain.

Interaction of mono- and dianions with cyanase: evidence for apparent half-site binding.

Cyanase is an inducible enzyme in Escherichia coli that catalyzes bicarbonate-dependent hydrolysis of cyanate. The dianions oxalate, oxalacetate, and malonate are slow-binding inhibitors of cyanase, and some monoanions such as azide and chloride also inhibit cyanase activity [Anderson, P. M., & Little, R. M. (1986) Biochemistry 25, 1621-1626]. The purpose of this study was to investigate the interaction of selected dianions and monoanions by kinetic and equilibrium dialysis binding studies in an effort to obtain information about the active site and catalytic mechanism. Measurement of the effectiveness of 30 different dianions as inhibitors of cyanase showed a significant degree of structural and/or isomeric specificity and considerable variation with respect to the slow-binding nature of the inhibition. Oxalate and oxalacetate both show extreme slow-binding inhibition at very low concentrations. Kinetic studies of the rate of inhibition of cyanase by oxalate showed that the reaction is pseudo first order with respect to oxalate concentration and the results are consistent with a pathway in which oxalate forms a complex with the enzyme in a rapid initial reversible step followed by a slow isomerization step leading to a complex with a very low dissociation constant. The rate of inhibition is significantly reduced by the presence of relatively low concentrations of either azide (analogue of cyanate) or bicarbonate. Equilibrium dialysis binding studies showed that the stoichiometry of binding at saturation for oxalate, malonate, chloride, and bicarbonate is about 0.5 mol of ligand bound/mol of subunit for each compound.(ABSTRACT TRUNCATED AT 250 WORDS)

Thermal denaturation of the core protein of lac repressor.

The thermal denaturation of the core protein of lac repressor was studied alone and in the presence of the inducer isopropyl beta-D-thiogalactoside (IPTG) and the antiinducer o-nitrophenyl beta-D-fucoside (ONPF) by means of high-sensitivity differential scanning calorimetry. The denaturation that takes place at about 65 degrees C is apparently irreversible; i.e., a rescan of a previously scanned sample of protein solution shows no denaturational endotherm. Despite this irreversibility, the denaturation appeared to follow quantitatively the dictates of equilibrium thermodynamics as embodied in the van't Hoff equation. The results obtained indicate clearly that the tetrameric protein dissociates to monomers during denaturation and that the ligands are not dissociated until denaturation takes place. The enthalpy of denaturation of the protein is 4.57 +/- 0.25 cal g-1 and is independent of temperature. The enthalpies of dissociation of IPTG and ONPF at the denaturation temperature are very large, 37 and 42 kcal (mol of ligand)-1, respectively.

Species-specific irreversible inhibition of Neisseria gonorrhoeae dihydrofolate reductase by a substituted 2,4-diamino-5-benzylpyrimidine.

Neisseria gonorrhoeae dihydrofolate reductase undergoes a time-dependent, irreversible inactivation by 2,4-diamino-5-[3,5-dimethoxy-4-(p-bromoacetamidophenoxy)benzyl] pyrimidine. The kinetics of inactivation are consistent with the reversible formation of an enzyme-inhibitor complex followed by covalent binding to the enzyme. The reversible component is competitive with dihydrofolate and has an inhibitor binding constant of 10 nM. Irreversible inactivation proceeds as a pseudo first-order process with a minimum inactivation half-time of 20 min and a Ki of 28 nM. Using radiolabeled inhibitor, it was shown that approximately 1 mol of ligand was covalently bound to the enzyme/mol of methotrexate binding site when the enzyme was completely inhibited. Radiolabeled inhibitor remained associated with the enzyme following denaturation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Cyanogen bromide cleavage of the 14C-labeled enzyme-inhibitor complex yielded only one radioactive polypeptide, and sequence determinations showed that His-25 was modified by covalent attachment of the inhibitor. When dihydrofolate reductases from Lactobacillus casei, Streptococcus faecium, Escherichia coli, SR-1 rodent lymphoma, and chicken liver were tested with the affinity label, only the L. casei enzyme showed a time-dependent increase in inhibition. These data, along with comparisons of known amino acid sequences and x-ray crystal structures, were used to make predictions concerning the three-dimensional conformation of the gonococcal enzyme.

Affinity labeling of human serum thyroxine-binding globulin with N-bromoacetyl- l-thyroxine: Identification of the labeled amino acid residues

The l-thyroxine binding site in human serum thyroxine-binding globulin was investigated by affinity labeling with N-bromoacetyl- l-thyroxine (BrAcT 4). Competitive binding studies showed that, in the presence of 100 molar excess of BrAcT 4, binding of thyroxine to thyroxine-binding globulin was nearly totally abolished. The reaction of BrAcT 4 to form covalent binding was inhibited in the presence of thyroxine and the affinity-labeled thyroxinebinding globulin lost its ability to bind thyroxine. These results indicate BrAcT 4 and thyroxine competed for the same binding site. Affinity labeling with 2 mol of BrAcT 4/mol of thyroxine-binding globulin resulted in the covalent attachment of 0.7 mol of ligand. By amino acid analysis and high voltage paper electrophoresis, methionine was identified as the major residue labeled (75%). Lysine, tyrosine, and histidine were also found to be labeled to the extent of 8, 8, and 5%, respectively.

Interactions of small molecules with phospholipid bilayers. Binding to egg phosphatidylcholine of some uncharged molecules (2-acetylaminofluorene, 4-dimethylaminoazobenzene, oestrone and testosterone) that bind to ligandin and aminoazo-dye-binding protein A

1. To assess the possible involvement of ligandin and aminoazo-dye-binding protein A in intracellular transport it is necessary to know how their ligands, most of which are molecules with hydrophobic moieties, interact with cellular membranes. To obtain such information we have examined the interactions of 2-acetylaminofluorene, 4-dimethylaminoazobenzene, oestrone and testosterone with aqueous dispersions of egg phosphatidylcholine and egg phosphatidylcholine/cholesterol (1:1, molar ratio) by equilibrium dialysis and spectrophotometry. 2. At 25 degrees C and pH7.4, the partition coefficients for binding to phosphatidylcholine [expressed as (mol of ligand bound/mol of phosphatidylcholine)/unbound ligand concentration] were: for 2-acetylaminofluorene, 5.0x10(3) litre.mol(-1); for 4-dimethylaminoazobenzene, 2.1x10(4) litre.mol(-1); for oestrone, 3.1x10(3) litre.mol(-1); and for testosterone, 4.2x10(2) litre.mol(-1). In the ranges studied these values were independent of concentration. The results for the two steroids confirm those of Heap, Symons & Watkins [(1970) Biochim. Biophys. Acta218, 482-495]. 3. The introduction of cholesterol into the lipid bilayers caused large decreases in the partition coefficients of oestrone and testosterone, but had relatively little effect on the binding of 2-acetylaminofluorene and 4-dimethylaminoazobenzene. 4. By assuming that the interactions with egg phosphatidylcholine bilayers resemble those with the phospholipid components of mammalian intracellular membranes the phosphatidylcholine partition coefficients, together with data for binding to the intracellular proteins ligandin and aminoazo-dye-binding protein A, enable the subcellular distributions of the four compounds to be estimated. For the rat hepatocyte up to 98, 99, 89 and 58% of the total 2-acetylaminofluorene, 4-dimethylaminoazobenzene, oestrone and testosterone respectively may be membrane-bound.

Affinity labeling of human serum prealbumin with N-bromoacetyl-L-thyroxine.

Affinity labeling of human serum prealbumin with N-bromoacetyl-L-thyroxine (BrAcT4) was used to investigate the binding domain for L-thyroxine (T4) on prealbumin. Fluorescence titration with 8-anilinonaphthalene-1-sulfonate revealed a strong and a weak binding site for BrAcT4 (K1 = 1 X 10(8) M-1; K2 = 1 X 10(6) M-1). The reaction of BrAcT4 with prealbumin to form a covalent bond was inhibited in the presence of T4 and binding of T4 to prealbumin was nearly abolished after affinity labeling with BrAcT4. Affinity labeling with 2 mol of BrAcT4/mol of prealbumin resulted in covalent binding of 1 mol of ligand. Acid hydrolysis of affinity-labeled prealbumin gave Nepsilon-carboxymethyllysine and iminodiacetic acid, the latter being derived from the NH2-terminal glycine. A combination of analytical procedures, including tryptic digestion after maleylation, cyanogen bromide cleavage, digestion with yeast protease C, and sequential Edman degradations, revealed that the Nepsilon-carboxymethyllysine was derived from lysine-9 and lysine-15 and that the affinity label had distributed itself among glycine-1, lysine-9, and lysine-15 in a ratio of 29:63:8.