Kinetics of binding of cyanide to hemin intercalated in micellar sodium lauryl sulfate.
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Animals↗
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Characterization of cell-binding properties of bovine herpesvirus 1 glycoproteins B, C, and D: identification of a dual cell-binding function of gB.
Previous studies have suggested that the attachment of bovine herpesvirus 1 (BHV-1) to permissive cells is mediated by its major glycoproteins B (gB), C (gC), and D (gD). In order to gain further insight into the mechanism of the BHV-1 attachment process, we purified authentic gB, gC, and gD from BHV-1-infected cells and membrane anchor-truncated, soluble gB, gC, and gD from stably transfected cell lines by affinity chromatography and examined their cell-binding properties on Madin-Darby bovine kidney cells. All of the glycoproteins tested exhibited saturable binding to Madin-Darby bovine kidney cells. All of the glycoproteins tested exhibited saturable binding to Madin-Darby bovine kidney cells. Addition of exogenous heparin or treatment of cells with heparinase to remove cellular heparan sulfate (HS) prevented both gC and gB from binding to cells but had no effect on gD binding. An assessment of competition between gB, gC, and gD for cell binding revealed that gC was able to inhibit gB binding, whereas other combinations showed no effect. Cell-bound gC could be dissociated by heparin or heparinase treatment. The response of bound gB to heparin and heparinase treatments differed for the authentic and soluble forms; while soluble gB was susceptible to the treatment, a significant portion of cell-bound authentic gB was resistant to the treatment. Binding affinity analysis showed that soluble gB and both forms of gC and gD each had single binding kinetics with comparable dissociation constants (Kds), ranging from 1.5 x 10(-7) to 5.1 x 10(-7) M, whereas authentic gB exhibited dual binding kinetics with Kd1 = 5.2 x 10(-7) M and Kd2 = 4.1 x 10(-9) M. These results demonstrate that BHV-1 gC binds only to cellular HS, gD binds to a non-HS component, and gB initially binds to HS and then binds with high affinity to a non-HS receptor. Furthermore, we found that while authentic gB was able to inhibit viral plaque formation, soluble gB, which retains the HS-binding property but lacks the high-affinity binding property, was defective in this respect. These results suggest that the interaction between gB and its high-affinity receptor may play a critical role in the virus entry process.
Amino Acid Sequence↗
pH-dependent binding of local anesthetics in single batrachotoxin-activated Na+ channels. Cocaine vs. quaternary compounds.
The effects of internal and external pH on the binding kinetics of local anesthetics (LAs) were studied in single batrachotoxin-activated Na+ channels incorporated into planar bilayers. With internal quaternary QX-314 and RAC421-II drugs, the binding interactions were little affected by either external or internal pH. With tertiary cocaine, the binding kinetics were drastically altered by pH. A decrease in the internal pH from 9.3 to 6.2 decreased the apparent equilibrium dissociation constant (Kd) of internal cocaine by more than 100-fold. This increase in the binding affinity was mostly accounted for by an increase in the apparent cocaine on-rate constant (kon) of approximately 80-fold. The cocaine off-rate constant (koff) was little changed (between 3-4 s-1). These results demonstrate quantitatively that the charged form of cocaine is the active form for BTX-activated Na+ channels. Surprisingly, the apparent pKa of cocaine near its binding site was estimated to be 1.4 units lower than that in bulk solution (7.1 vs. 8.5), indicating that the LA drug encounters a relatively hydrophobic environment. Opposite to the internal pH effect, a decrease of external pH from 8.4 to 6.2 increased the Kd value of internally and externally applied cocaine by approximately 8- and approximately 25-fold, respectively. External pH effect was primarily mediated by modulation of kon; koff was again relatively unaffected. Our findings support a model in which neutral cocaine can readily cross the membrane barrier, but needs to be protonated internally to bind to its binding site.
Anesthetics, Local↗
Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner.
The effect of two different DNA minor groove binding molecules, Hoechst 33258 and distamycin A, on the binding kinetics of NF-kappaB p50 to three different specific DNA sequences was studied at various salt concentrations. Distamycin A was shown to significantly increase the dissociation rate constant of p50 from the sequences PRDII (5'-GGGAAATTCC-3') and Ig-kappa B (5'-GGGACTTTCC-3') but had a negligible effect on the dissociation from the palindromic target-kappaB binding site (5'-GGGAATTCCC-3'). By comparison, the effect of Hoechst 33258 on binding of p50 to each sequence was found to be minimal. The dissociation rates for the protein--DNA complexes increased at higher potassium chloride concentrations for the PRDII and Ig-kappaB binding motifs and this effect was magnified by distamycin A. In contrast, p50 bound to the palindromic target-kappaB site with a much higher intrinsic affinity and exhibited a significantly reduced salt dependence of binding over the ionic strength range studied, retaining a K(D) of less than 10 pM at 150 mM KCl. Our results demonstrate that the DNA binding kinetics of p50 and their salt dependence is strongly sequence-dependent and, in addition, that the binding of p50 to DNA can be influenced by the addition of minor groove-binding drugs in a sequence-dependent manner.
Base Sequence↗
Catalytic roles of arginine residues 82 and 92 of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: site-directed mutagenesis and biochemical studies.
The roles of a pair of conserved positively charged residues R82 and R92 at a catalytic loop of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) have been investigated by site-directed mutagenesis and biochemical analysis. In the structure of HPPK in complex with ATP and a 6-hydroxymethyl-7,8-dihydropterin (HP) analogue, the guanidinium group of R82 forms two hydrogen bonds with the alpha-phosphate and that of R92 two hydrogen bonds with the beta-phosphate. In the structure of HPPK in complex with alpha,beta-methyleneadenosine triphosphate (AMPCPP, an ATP analogue) and HP, the guanidinium group of R82 has no direct interaction with AMPCPP and that of R92 forms two hydrogen bonds with the alpha-phosphate. Substitution of R82 with alanine caused a decrease in the rate constant for the chemical step by a factor of approximately 380, but there were no significant changes in the binding energy or binding kinetics of either substrate. Substitution of R92 with alanine caused a decrease in the rate constant for the chemical step by a factor of approximately 3.5 x 10(4). The mutation caused no significant changes in the binding energy or binding kinetics of MgATP. It did not cause a significant change in the binding energy of HP either but caused a decrease in the association rate constant for the binding of HP by a factor of approximately 4.5 and a decrease in the dissociation rate constant by a factor of approximately 10. The overall structures of the ternary complexes of both mutants were very similar to the corresponding structure of wild-type HPPK as described in the companion paper. The results suggest that R82 does not contribute to the binding of either substrate, and R92 is dispensable for the binding of MgATP but plays a role in facilitating the binding of HP. Both R82 and R92 are important for catalysis, and R92 plays a critical role in the transition state stabilization.
Amino Acid Substitution↗
Effects of temperature on 2-[125I]-iodomelatonin binding to melatonin receptors in the neural retina of the frog Rana perezi.
The present study analyzes the effect of temperature-dependent modifications on the binding of the analog 2-[125I]-melatonin to melatonin receptors in isolated neural retina membranes from the greenfrog Rana perezi. Association and dissociation rate constants (K+1, K-1) were exponentially increased by the assay temperature. At 15 degrees C, association and dissociation required several hours; meanwhile, at 35 degrees C, rate constants were 100- and 34-fold faster, respectively. However, the Kd constant calculated as K-1/K+1 was unmodified by the assay temperature. When frogs were acclimated at either 5 or 22 degrees C for 1 month, K+1, and K-1 constants determined at 15 and 25 degrees C were identical in both cold- and warm-acclimated groups. Thus, the binding kinetics of melatonin receptors in frog retinas did not shown any thermal compensation. Results from saturation curves and pharmacological profiles of melatonin binding sites support a lack of effect of assay temperature on the affinity of melatonin receptors in the frog retina. The inhibition of [125I]Mel binding by GTPgammaS showed clearly that the coupling of melatonin receptors to G proteins is temperature-dependent. Higher concentrations of the GTP analog were needed to inhibit specific binding when temperature decreased. The temperature effect on binding kinetics and on the G protein coupling to melatonin receptors suggests that the melatonin signal could be transduced distinctly depending on the temperature. Thus, temperature plays a major role, not only on melatonin synthesis, but also in the transduction of melatonin signal in ectotherms.
Acclimatization↗
Impairment of genomic DNA binding to a putative dysfunctional receptor on erythrocytes independent of complement and antibodies in systemic lupus erythematosus.
Systemic lupus erythematosus (SLE) is characterized by a variety of autoantibodies and other immune abnormalities indicative of an immunological hyperactivity. Antibodies against native DNA, however, are a disease-specific marker and play a major role in the pathogenesis of systemic or organ-specific disease manifestations. Nevertheless, the mechanisms causing the appearance of autoantibodies and immune complexes in SLE are not yet understood. Here, we report that chromosomal DNA and other forms of nucleic acids are usually cleared from circulation by binding to a yet unidentified receptor-like protein on the surface membrane of erythrocytes, independently from complement or antibodies. The binding kinetics of DNA and other nucleic acids to erythrocytes are significantly altered in SLE patients, showing an overall reduced binding capability and presaturated binding kinetics. Significant amounts of chromosomal DNA can be isolated from erythrocytes of SLE patients but not from normal controls. Electron microscopy shows electron-dense particles on the surface of SLE erythrocytes (approximate size 20-40 nm). Comparative genomic hybridization reveals that the nucleic acid isolated from erythrocytes of SLE patients is of genomic and random origin, leading to an accumulation of "free" nucleic acids in the periphery, which eventually induces a B-cell immune response.
Antibodies↗
Interaction of a signal peptide with phospholipid vesicles: the kinetics of binding, insertion and structural changes.
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Electron Transport Complex IV↗
Equilibrium binding analysis of estrogen agonists and antagonists: relation to the activation of the estrogen receptor.
The equilibrium binding kinetics of the interaction between the estrogen receptor and natural estrogens (estradiol, estriol and estrone), non-steroidal estrogen agonists (11 beta-chloromethyl-estradiol-17 beta, diethyl-stilbestrol, hexestrol) and non-steroidal antiestrogens (clomiphene, tamoxifen) have been characterized. It is proposed that positive cooperative binding of ligands by the estrogen receptor reflects conformational changes in the DNA binding domain of the receptor dimer which increase its affinity to estrogen responsive elements. Weak estrogens fail to induce maximal cooperativity and are less efficient in activating the receptor complex. Antiestrogens, that inhibit the [3H]estradiol-induced cooperative binding, suppress the activation of the receptor and inhibit its nuclear interactions. Another class of antiestrogens (e.g., 4-hydroxytamoxifen) interacts with the receptor in a manner that is indistinguishable from the cooperative interaction of estradiol, and the resulting complex may also exhibit increased affinity for estrogen responsive elements. However, these complexes cannot activate transcription, presumably due to an aberrant induction of transcription-activating domain in the receptor. We suggest that the positive cooperativity of the estrogen receptor results from conformational changes in the receptor that are transmitted also to the DNA binding domain. On the other hand, conformational changes in the transcription activating domain are not revealed by equilibrium binding kinetics. Thus, compounds that block the positive cooperative binding of [3H]estradiol by the receptor act as antiestrogens. Other compounds that interact cooperatively with the receptor can activate the receptor DNA binding domain, however, they may or may not induce the full array of conformational changes required for transactivation of transcription.
Clomiphene↗
Adjusting the binding thermodynamics, kinetics, and orientation of guests within large synthetic hydrophobic pockets.
Kinetic analysis of the host guest complexation of a large, open molecular basket and a highly complementary adamantoid guest reveals that for these types of systems a dissociative mechanism is in operation. Hence, the resident adamantyl guest must completely vacate the cavity before another guest molecule can move in to replace it. As a result of the rigid nature of the host, the energy barrier to this process is relatively high, about 16 kcal mol(-1) at room temperature. Modifying the cavity of the host by dangling either a methyl group or a hydroxyl group from the portal rim alters the thermodynamic binding profile of these hosts. (1)H NMR shift data analysis also reveals that these functional groups can adjust the orientation that monosubstituted guests adopt within the cavity. Additionally, (1)H NMR studies of the binding of (E)1,4-dibromoadamantane allow the observation of two energetically similar diastereomeric complexes. An examination of this guest binding to the three hosts reveals that the interchange between the isomers is much faster than the entry and egression rates, and that the functional groups at the rim of each cavity influence both the rates of reorientation and the equilibrium relating the isomers.
Binding Sites↗
Function of herpes simplex virus type 1 gD mutants with different receptor-binding affinities in virus entry and fusion.
We have studied the receptor-specific function of four linker-insertion mutants of herpes simplex virus type 1 glycoprotein D (gD) representing each of the functional regions of gD. We used biosensor analysis to measure binding of the gD mutants to the receptors HVEM (HveA) and nectin-1 (HveC). One of the mutants, gD(inverted Delta 34t), failed to bind HVEMt but showed essentially wild-type (WT) affinity for nectin-1t. The receptor-binding kinetics and affinities of the other three gD mutants varied over a 1,000-fold range, but each mutant had the same affinity for both receptors. All of the mutants were functionally impaired in virus entry and cell fusion, and the levels of activity were strikingly similar in these two assays. gD(inverted Delta 34)-containing virus was defective on HVEM-expressing cells but did enter nectin-1-expressing cells to about 60% of WT levels. This showed that the defect of this form of gD on HVEM-expressing cells was primarily one of binding and that this was separable from its later function in virus entry. gD(inverted Delta 243t) showed WT binding affinity for both receptors, but virus containing this form of gD had a markedly reduced rate of entry, suggesting that gD(inverted Delta 243) is impaired in a postbinding step in the entry process. There was no correlation between gD mutant activity in fusion or virus entry and receptor-binding affinity. We conclude that gD functions in virus entry and cell fusion regardless of its receptor-binding kinetics and that as long as binding to a functional receptor occurs, entry will progress.
Cell Line↗
Kinetics of binding of cyanide to sperm whale metmyoglobin.
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Acids↗
Nitric oxide binding and crystallization of recombinant nitrophorin I, a nitric oxide transport protein from the blood-sucking bug Rhodnius prolixus.
A nitric oxide transport protein (nitrophorin I) from the salivary glands of the blood-sucking bug Rhodnius prolixus has been expressed as an insoluble form in Escherichia coli, reconstituted with heme, and characterized with respect to NO binding kinetics and equilibria. NO binding and absorption spectra for recombinant nitrophorin I were indistinguishable from those of the insect-derived protein. The degree of NO binding, the rate of NO release, and the Soret absorption maxima for nitrophorin I were all pH dependent. The NO dissociation constant rose 9-fold over the pH range 5.0-8.3, from 0.19 x 10(-6) to 1.71 x 10(-6). The NO dissociation rate rose 2500-fold between pH 5.0 and pH 8.3, from 1.2 x 10(-3) to 3.0 s(-1). Thus, the NO association rate must also be pH dependent and reduced at pH 5.0 by approximately 280-fold. These factors are consistent with nitrophorin function: NO storage in the apparent low pH of insect salivary glands and NO release into the tissue of the insect's host, where vasodilation is induced. The reversible nature of NO binding, which does not occur with most other heme proteins, and the apparent kinetic control of NO release are discussed. We also report crystals of nitrophorin I that are suitable for structure determination by X-ray crystallography. The most promising crystal form contains two protein molecules in the asymmetric unit and diffracts beyond 2.0 A resolution.
Animals↗
Kinetic and binding effects of 1,N 6 -ethenoadenosine triphosphate to aspartate transcarbamylase.
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Adenosine Triphosphate↗
The kinetics for binding and catabolism of aggregated IgG by rat peritoneal macrophages.
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Animals↗
Association kinetics and binding constants of nucleoside triphosphates with G-actin.
The dissociation of the complex between 1:N6-ethenoadenosine, 5'-triphosphate (xiATP) and G-actin was initiated by dilution to concentrations between 1 micronM and 5 nM and monitored by the fluorescence change of xiATP. The results were quantitatively explained by a two-step mechanism: a reversible dissociation of the actin-nucleotide complex followed by a fast irreversible inactivation of nucleotide-free G-actin. Under normal conditions (0.8 mM CaCl2, pH 8.2,21 degrees C), the rate-limiting step was the dissociation of the nucleotide-G-actin complex. The half-time of the dissociation of xiATP from G-actin was 290 s as compared to only 13 s for the following denaturation step of nucleotide-free actin. 1 mM EDTA highly accelerated the dissociation step and, regardless of its concentration, the complex dissociated quantitatively within 1 min. Addition of Ca2+ within 20 s after EDTA addition induced a re-association of xiATP with nucleotide-free but still native G-actin. This reversal was kinetically resolved by means of a multimixing stopped-flow apparatus. The association rate constant was 6 X 10(6) M-1s-1. From the association and dissociation rate constant, a value of 2.5 X (10(9) M-1 was calculated for the binding constant of xiATP to G-actin. The binding constant of ATP (1.4 X 10(10) M-1) was derived from the relative binding constant of xiATP and ATP as determined by fluorescence titration of xiATP-G-actin with ATP. These binding constants are 10(3)-10(4) times higher than values reported earlier on the basis of more indirect data.
Actins↗
Evidence for catalytic cooperativity during ATP hydrolysis by beef heart F1-ATPase. Kinetics and binding studies with the photoaffinity label BzATP.
The photoaffinity analog of ATP, 3'-O-(4-benzoyl) benzoyl ATP (BzATP), was used to covalently modify the catalytic sites on the beef heart mitochondrial F1-ATPase. In the absence of actinic illumination, BzATP was a slow substrate for the enzyme (Vmax = 0.19 mumol min-1 mg-1; kcat/Km = 2.2 X 10(6) M-1s-1) and behaved as a classical competitive inhibitor versus ATP (Ki = 0.85 microM). Under photolytic conditions, BzATP inactivated F1 with pseudo first-order kinetics, and the photoinactivation reaction showed rate saturation suggesting specific, reversible binding of BzATP to F1 prior to covalent bond formation. ATP protected against F1 photoinactivation (Kprotect = 0.3 microM) and partially covalently modified F1 yielded the same Km for ATP as unmodified enzyme. These results strongly suggested that BzATP was bound to catalytic sites on the enzyme. In the absence of photolysis, BzATP saturated two binding sites on the F1 (KD = 1.6 microM), and under photolytic conditions, 1 mol of BzATP was shown to be covalently liganded to the beta subunit of the enzyme coincident with 100% loss in ATPase activity. Previous studies with the mitochondrial F1-ATPase have suggested a mechanism involving catalytic cooperativity during ATP hydrolysis. Our demonstration of a molar stoichiometry of 1 for photoinactivation is in accord with this mechanism. It is suggested that either F1 is unable to hydrolyze covalently bound BzATP, or that subsequent to hydrolysis, the BzADP product can not be released from the catalytic site. It is therefore inferred that F1 hydrolytic activity requires cooperativity between multiple, viable catalytic sites and that covalent modification of a single catalytic site is sufficient for complete enzyme inactivation.
Adenosine Diphosphate↗
Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism.
Dihydroxyacetone (Dha) kinases are a sequence-conserved family of enzymes, which utilize two different phosphoryldonors, ATP in animals, plants, and some bacteria, and a multiphosphoprotein of the phosphoenolpyruvate carbohydrate phosphotransferase system (PTS) in most bacteria. Here, we compare the PTS-dependent kinase of Escherichia coli and the ATP-dependent kinase of Citrobacter freundii. They display 30% sequence identity. The binding constants of the E. coli kinase for eleven short-chain carbonyl compounds were determined by acetone precipitation of the enzyme-substrate complexes. They are 3.4 microM for Dha, 780 microM for Dha-phosphate (DhaP), 50 microM for D,L-glyceraldehyde (GA), and 90 microM for D,L-glyceraldehyde-3-phosphate. The k(cat) for Dha of the PTS-dependent kinase is 290 min(-1), and that of the ATP-dependent kinase is 1050 min(-1). The Km for Dha of both kinases is <6 microM. The X-ray structures of the enzyme-GA and the enzyme-DhaP complex show that substrates as well as products are bound in hemiaminal linkage to an active-site histidine. Quantum-mechanical calculations offer no indication for activation of the reacting hydroxyl group by the formation of the hemiaminal. However, the formation of the hemiaminal bond allows selection for short-chain carbonyl compounds and discrimination against structurally similar polyols. The Dha kinase remains fully active in the presence of 2 M glycerol, and phosphorylates trace impurities of carbonyl compounds present in glycerol.
Acetone↗