Proceedings: Plasma protein binding and kinetics of diphenylhydantoin in uraemic patients.
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Humans↗
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Some aspects of dexamethasone binding in the old rat liver.
The maximal glucocorticoid responsiveness and the adaptation degree are reduced in old rat liver as demonstrated by cortisol stimulation of RNA polymerases. Nevertheless the concentration of unoccupied 3H-dexamethasone binding sites in molybdate-stabilized cytosol of adrenalectomized old animals is significantly increased in comparison with young adult rats. The KD constants showed an increasing tendency, but not a significant one. In the molybdate-free cytosol the results are similar. First studies of the binding kinetics in the molybdate-free system showed a sigmoidal saturation curve in the cytosol of young adult rats, but usual hyperbolic saturation kinetics in the cytosol of old animals. The Hill coefficient was 1.0 +/- 0.1 for old and 1.9 +/- 0.3 for young animals. The binding of activated 3H-dexamethasone receptor complexes to liver nuclei showed no significant age-dependent differences in binding kinetics, acceptor site concentration or affinity. Attention must be paid to altered glucocorticoid receptor binding in the cytosol and in nuclei as a potential cause of changes in hormone-induced gene expression at the pretranscriptional level.
Aging↗
Kinetic analysis of high affinity forms of interleukin (IL)-13 receptors: suppression of IL-13 binding by IL-2 receptor gamma chain.
Interleukin-13 (IL-13) is a pleiotropic cytokine that controls growth, differentiation, and apoptosis of immune and tumor cells. To understand the mechanisms of interaction between IL-13 and IL-13 receptors (IL-13R), and the role of the IL-2 receptor common gamma chain (gammac) in IL-13 binding and processing, we have examined IL-13 binding kinetics, dissociation/shedding, and internalization in renal cell carcinoma (RCC) cell lines. We observed a new phenomena in that the apparent rate of association, but not the dissociation, was strongly related to IL-13 concentration. We also observed cooperativity phenomena in IL-13 and IL-13R interaction in control RCC (MLneo) cells, but not in cells transfected with gammac chain (MLgammac). The number of IL-13 binding sites, the effective rate of ligand association, and the dissociation rate constants were reduced in gammac-transfected cells compared to control RCC cells. Two forms of IL-13R were detected in these cell lines, which differed in the kinetics of endocytosis and dissociation/exocytosis. Only a small fraction of bound receptors (14-24%) was rapidly internalized and the same fraction of the ligand-receptor complexes was shed and/or dissociated. The expression of gammac chain did not change any of these processes. A two independent high-affinity and moderate-affinity receptor model fit the kinetic observations in gammac-transfected cells. However, in control cells, the binding kinetics were more complicated. A mathematical model that fit a set of kinetic and steady state data in control cells was selected from a set of possible models. This best-fit model predicts that 1) two different IL-13R are expressed on the cell membrane, 2) a minor fraction of IL-13R exist as microclusters (homodimers and/or heterodimers) without exogenous IL-13, 3) high morphological complexity of the gammac-negative control cell membrane affects the cooperativity phenomena of IL-13 binding, and 4) a large number of co-receptor molecules is present, which helps keep the ligand on the cell surface for a long period of time after fast IL-13 binding and provides a negative control for ligand binding via production of the high affinity inhibitor bound to IL-13. Our data demonstrate that gammac exerts dramatic changes in the kinetic mechanisms of IL-13 binding.
Binding, Competitive↗
Correlating the kinetics of cytokine-induced E-selectin adhesion and expression on endothelial cells.
Many human diseases are mediated through the immune system. In chronic inflammatory disorders, the processes ordinarily involved in tissue healing become destructive. Endothelial cells normally recruit leukocytes to inflamed tissue using cytokine-induced adhesion receptors on the surfaces of interacting cells. Leukocyte capture depends on specialized characteristics of these receptors, particularly the binding kinetics. This study is designed to clarify the relationship between cytokine-induced changes in cell properties and binding kinetics. Here, we measure the kinetics of expression and monoclonal antibody binding for E-selectin in interleukin-1alpha-stimulated microvascular endothelium in vitro and incorporate the data into kinetic models. Quantitative flow cytometry is used to determine molecular density (expression), and micropipette assays are used to find the probability of adhesion (function). Within five hours of interleukin-1alpha stimulation, E-selectin density increases from 0 to 742 sites/microm(2), and antibody-E-selectin adhesion probability increases from a baseline of 6.3% to 64%. A kinetic model is applied to find an apparent association rate constant, k(f), of 3.7 x 10(-14) cm(2)/sec for antibody-E-selectin binding. Although the model successfully predicts experimental results, the rate constant is undervalued for a diffusion-limited process, suggesting that functional adhesion may be modified through cytokine-induced changes in microtopology and receptor localization.
Animals↗
Interaction of a synthetic mitochondrial presequence with isolated yeast mitochondria: mechanism of binding and kinetics of import.
The mechanism of interaction of a presequence with isolated yeast mitochondria was examined. A synthetic peptide corresponding to a matrix-targeting signal was covalently labeled with a fluorescent probe. Binding of the presequence to the surface of the mitochondria and translocation of the presequence into the interior of the mitochondria could then be monitored directly in solution by measuring changes in the steady-state fluorescence of the attached fluorophore. The binding step was rapid and reversible. Quantitation of the binding under equilibrium conditions suggested that the initial association of the presequence with the surface of the mitochondria occurred by partitioning of the presequence directly into the lipid bilayer of the outer membrane. Subsequent translocation of the bound presequence into the mitochondria was monitored by measuring the rate of disappearance of presequences sensitive to digestion by added trypsin. The efficiency of translocation was high, and the rate of the translocation was dependent on the electrical potential across the inner membrane. At physiological concentrations of presequence, the rate displayed first-order kinetics with respect to the concentration of bound presequence and had a rate constant of 0.19 min-1 at 20 degrees C. Several kinetic models for the translocation of the presequence are presented that are consistent with the experimental results.
Amino Acid Sequence↗
Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions.
BACKGROUND: A Nanopore Detector provides a means to transduce single molecule events into observable channel current changes. Nanopore-based detection can report directly, or indirectly, on single molecule kinetics. The nanopore-based detector can directly measure molecular characteristics in terms of the blockade properties of individual molecules--this is possible due to the kinetic information that is embedded in the blockade measurements, where the adsorption-desorption history of the molecule to the surrounding channel, and the configurational changes in the molecule itself, imprint on the ionic flow through the channel. This rich source of information offers prospects for DNA sequencing and single nucleotide polymorphism (SNP) analysis. A nanopore-based detector can also measure molecular characteristics indirectly, by using a reporter molecule that binds to certain molecules, with subsequent distinctive blockade by the bound-molecule complex. RESULTS: It is hypothesized that reaction histories of individual molecules can be observed on model DNA/DNA, DNA/Protein, and Protein/Protein systems. Preliminary results are all consistent with this hypothesis. Nanopore detection capabilities are also described for highly discriminatory biosensing, binding strength characterization, and rapid immunological screening. CONCLUSION: In essence, the heart of chemistry is now accessible to a new, single-molecule, observation method that can track both external molecular binding states, and internal conformation states.
Base Sequence↗
Photoaddition of thienocoumarin derivatives to DNA: stoichiometry and kinetics of binding.
Photoreaction of the 6,9-dimethyl-4-methoxymethyl-2H-thieno[3,2-g]-1-benzopyran-2-one (compound I) and 4-acetoxymethyl-6,9-dimethyl-2H-thieno[3,2-g]-1-benzopyran-2-one (compound II) to DNA was studied. The quantitative evaluation of the photobound molecules was performed by means of inductively coupled plasma atomic emission spectrometry (ICP-AES), exploiting the presence of the sulphur atom inside the tricyclic chromophore. The concurrent estimation of the phosphorus atom, present exclusively in the macromolecule, allowed possible intercalation sites to be identified and their involvement in the photoaddition reaction to be determined. The development of a kinetic model made it possible to discriminate and evaluate the single kinetic events that constitute the overall photoaddition process of I and II to DNA.
Animals↗
A model for substrate binding and kinetics of carboxypeptidase A.
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Binding Sites↗
Kinetics and binding sites for interaction of the prefoldin with a group II chaperonin: contiguous non-native substrate and chaperonin binding sites in the archaeal prefoldin.
Prefoldin is a jellyfish-shaped hexameric co-chaperone of the group II chaperonins. It captures a protein folding intermediate and transfers it to a group II chaperonin for completion of folding. The manner in which prefoldin interacts with its substrates and cooperates with the chaperonin is poorly understood. In this study, we have examined the interaction between a prefoldin and a chaperonin from hyperthermophilic archaea by immunoprecipitation, single molecule observation, and surface plasmon resonance. We demonstrate that Pyrococcus prefoldin interacts most tightly with its cognate chaperonin, and vice versa, suggesting species specificity in the interaction. Using truncation mutants, we uncovered by kinetic analyses that this interaction is multivalent in nature, consistent with multiple binding sites between the two chaperones. We present evidence that both N- and C-terminal regions of the prefoldin beta sub-unit are important for molecular chaperone activity and for the interaction with a chaperonin. Our data are consistent with substrate and chaperonin binding sites on prefoldin that are different but in close proximity, which suggests a possible handover mechanism of prefoldin substrates to the chaperonin.
Archaeal Proteins↗
Spatiotemporal dynamics of the COPI vesicle machinery.
Assembly of the coat protein I (COPI) vesicle coat is controlled by the small GTPase ADP ribosylation factor 1 (ARF1) and its GTPase-activating protein, ARFGAP1. Here, we investigate the diffusional behaviours of coatomer, the main component of the coat, and also those of ARF1 and ARFGAP1. Using fluorescence-correlation spectroscopy, we found that most ARF1 and ARFGAP1 molecules are highly mobile in the cytosol (diffusion constant D approximately equal to 15 microm(2) s(-1)), whereas coatomer diffuses 5-10 times more slowly than expected (D approximately equal to 1 microm(2) s(-1)). This slow diffusion causes diffusion-limited binding kinetics to Golgi membranes, which, in FRAP (fluorescence recovery after photobleaching) experiments, translates into a twofold slower binding rate. The addition of aluminium fluoride locks coatomer onto Golgi membranes and also decreases the binding kinetics of both ARF1 and ARFGAP1, suggesting that these proteins function in concert to mediate sorting and vesicle formation.
ADP-Ribosylation Factor 1↗
Receptor-binding properties of a soluble form of human cytomegalovirus glycoprotein B.
The human cytomegalovirus (HCMV) glycoprotein B (gB) (also known as gpUL55) homolog is an important mediator of virus entry and cell-to-cell dissemination of infection. To examine the potential ligand-binding properties of gB, a soluble form of gB (gB-S) was radiolabeled, purified, and tested in cell-binding experiments. Binding of gB-S to human fibroblast cells was found to occur in a dose-dependent, saturable, and specific manner. Scatchard analysis demonstrated a biphasic plot with the following estimated dissociation constants (Kd): Kd1, 4.96 x 10(-6) M; Kd2, 3.07 x 10(-7) M. Cell surface heparan sulfate proteoglycans (HSPGs) were determined to serve as one class of receptors able to facilitate gB-S binding. Both HSPG-deficient Chinese hamster ovary (CHO) cells and fibroblast cells with enzymatically removed HSPGs had 40% reductions in gB-S binding, whereas removal of chondroitin sulfate had no effect. However, a significant proportion of gB-S was able to associate with the cell surface in the absence of HSPGs via an undefined nonheparin component. Binding affinity analysis of gB-S binding to wild-type CHO-K1 cells demonstrated biphasic binding kinetics (Kd1, 9.85 x 10(-6) M; Kd2, 4.03 x 10(-8) M), whereas gB-S binding to HSPG-deficient CHO-677 cells exhibited single-component binding kinetics (Kd, 7.46 x 10(-6) M). Together, these data suggest that gB-S associates with two classes of cellular receptors. The interaction of gB with its receptors is physiologically relevant, as evidenced by an inhibitory effect on HCMV entry when cells were pretreated with purified gB-S. This inhibition was determined to be manifested at the level of virus attachment. We conclude that gB is a ligand for HCMV that mediates an interaction with a cellular receptor(s) during HCMV infection.
Animals↗
Discovery of new ligand binding pathways in myoglobin by random mutagenesis.
A random library of single amino acid mutants of myoglobin was generated using a highly efficient, single-base-misincorporation random mutagenesis method to discover new ligand-binding pathways in myoglobin. A surprisingly large fraction of the library exhibits ligand-binding kinetics that are substantially different from the wild-type protein. In addition to residues 45, 64 and 68, which comprise the best studied ligand-binding pathway single mutations of several other clusters of residues far away from that pathway are discovered which profoundly affect the ligand-binding kinetics. These results provide a new approach to explore the relationship between the fluctuations in protein structure and function.
Amino Acid Sequence↗
Thromboxane hypersensitivity in hypoxic pulmonary artery myocytes: altered TP receptor localization and kinetics.
Hypoxia-induced neonatal persistent pulmonary hypertension (PPHN) is characterized by sustained vasospasm and increased thromboxane (TxA2)-to-prostacyclin ratio. We previously demonstrated that moderate hypoxia induces myocyte TxA2 hypersensitivity. Here, we examined TxA2 prostanoid receptor (TP-R) localization and kinetics following hypoxia to determine the mechanism of hypoxia-induced TxA2 hypersensitivity. Primary cultured neonatal pulmonary artery myocytes were exposed to 10% O2 (hypoxic myocytes; HM) or 21% O2 (normoxic myocytes; NM) for 3 days. PPHN was induced in neonatal piglets by in vivo exposure to 10% FiO2 for 3 days. TP-R was studied in whole lung sections from pigs with hypoxic PPHN- and age-matched controls; intracellular localization was studied by immunocytochemistry. TP-R affinity was studied in cultured myocytes by saturation binding kinetics using 3H-SQ-29548 and competitive binding kinetics by coincubation with U-46619. Phosphorylation and coupling were examined in immunoprecipitated TP-R. We report distal propagation of TP-R expression in PPHN, extending to pulmonary arteries <50 microm. In HM, intracellular TP-R moves towards the perinuclear region, mirroring a change in endoplasmic reticulum (ER) morphology. TP-R kinetics also alter in HM membranes, with decreased Kd and Bmax (maximal binding sites). Additionally, in hypoxia, 3H-SQ-29548 is displaced at lower concentration of U-46619 than in normoxia, suggesting increased agonist affinity. Phosphorylation of serine residues on HM TP-R was significantly decreased compared with NM; this difference correlated with increased Galphaq coupling in hypoxia and was ablated by incubation with PKA. We conclude that the TP-R is normally desensitized in the neonatal pulmonary circuit by PKA-mediated regulatory phosphorylation, decreasing ligand affinity and coupling to Galphaq; this protection is lost following hypoxic exposure. Also, the appearance of TP-R in resistance arteries after development of hypoxic PPHN may contribute to increased pulmonary arterial pressure.
Animals↗
Time-resolved photolabeling of membrane proteins: application to the nicotinic acetylcholine receptor.
An apparatus has been developed that allows photoaffinity ligands to be crossed-linked to milligram quantities of membrane proteins with maximum attainable yield following contact times of approximately 1 ms. The apparatus consisted of three parts: a conventional rapid mixing unit, a novel freeze-quench unit, and a photolabeling unit. The freeze-quench unit consisted of a rapidly rotating metal disk which was precooled in liquid nitrogen. Correct alignment of the exit jet from the sample mixer allowed up to 2 ml of sample to be frozen in a thin film on the disk. Experiments with colorimetric reactions showed the combined dead time of mixing and freeze-quenching to be submillisecond. Photoincorporation was maximized by prolonged irradiation of the freeze-quenched sample. Using this apparatus we determine the binding kinetics of the resting state channel inhibitor 3-[125I](trifluoromethyl)-3-(m-iodophenyl) diazirine (TID) to nicotinic acetylcholine receptor-rich membranes from Torpedo. The binding kinetics for the 125I-labeled alpha and delta subunits were biphasic; about half the binding was complete by 2.4 ms, and the remainder could be resolved and occurred with a pseudo-first-order rate constant determined at 4 microM [125I]TID of 12.0 +/- 2.3 and 13.6 +/- 4.0 s-1, respectively. This compares well to the same constant determined for the inhibition of agonist-induced cation flux in Torpedo membranes.
Animals↗
Halothane modifies ischemia-associated injury to the voltage-sensitive calcium channels in canine heart sarcolemma.
BACKGROUND: Recent experimental data suggest that functional and metabolic changes in the myocardium caused during ischemia and subsequent reperfusion may be attenuated by the volatile anesthetics through the prevention of intracellular calcium accumulation. The main purpose of the current research is to identify a mechanism responsible for the alterations of ischemia-associated injury to the voltage-sensitive Ca2+ channels (VSCC) in the sarcolemma during halothane anesthesia. METHODS: The effect of 10 min myocardial ischemia in canine heart and 20 min reperfusion on the function of the VSCC in the sarcolemma was examined in the presence or absence of 1.6 vol% halothane administered in vivo. The membranes were isolated through differential centrifugation/filtration from the ischemic (left anterior descending territory) and normally perfused myocardium. Comparison of binding characteristics in the ischemic and nonischemic zones was made using equilibrium-binding studies of a dihydropyridine calcium channel blocker, [3H]isradipine (0.05-1.0 nM), to the VSCC in the sarcolemma. Control studies were performed on membranes prepared from the same perfusion zones, but from hearts who were not exposed to ischemia. RESULTS: The control studies (n = 5) showed no difference in binding kinetics between the different zones in the heart. After 10 min of ischemia, a 50 to 95% increase in specific [3H]isradipine binding to the sarcolemmal membranes was observed as compared to control membranes (P < 0.001). The maximal binding capacity (Bmax) increased by 85%, whereas the dissociation constant (Kd) remained unchanged. In the reperfusion experiments, a moderately increased binding (of 32%) was observed with a 40% increase in Bmax (P = NS). In the presence of 1.6% inhaled halothane, the effect of ischemia was attenuated. A decrease of 32.1% to 41.8% in equilibrium binding was observed (31% decrease in Bmax; P < 0.03 and 0.02, respectively). CONCLUSIONS: Even a brief period of myocardial ischemia produces a marked increase in the available high-affinity binding sites in the VSCC, a finding that is well correlated with previous experimental observation of increased calcium ion influx to the myocardial cell. On reperfusion, some recovery of the ischemic changes in the VSCC was evident. The binding kinetics which characterize this early phase of cell injury were reversed by halothane anesthesia, indicating a possible reduction in calcium entry, which may represent one of the beneficial effects of the anesthetic in the ischemic heart.
Animals↗
Measuring the assembly kinetics and binding properties of intermediate filament proteins.
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Amino Acid Sequence↗
Binding of estrogen and antiestrogen in uterine cell nuclei: in vivo autoradiographic studies.
The in vivo binding of antiestrogen in nuclei within the uterine stromal, epithelial and myometrial tissue compartments was compared to that of estrogen 2-48 h after injection. Tissue binding and retention of radioactivity was also studied. Immature rats were injected s.c. with 0.36 microgram [3H]hydroxytamoxifen [( 3H]TAM(OH] or 0.24 microgram [3H]estradiol [( 3H]E2) in oil. At 2, 4, 8, 12, 24 and 48 h after injection, uteri were processed for thaw-mount autoradiography and, along with other tissues, for liquid scintillation counting. After [3H]TAM(OH) injection total radioactivity in uterus, cervix, vagina and liver reached peak levels by 8 h then decreased slowly so that by 48 h radioactivity still remained in the tissues. At all time intervals, the levels of radioactivity in heart and muscle remained low. After [3H]E2 injection radioactivity in uterus, cervix and vagina reached peak levels between 2 and 4 h then decreased rapidly so that by 12 h radioactivity was low and essentially the same as in liver, heart and muscle. These results were paralleled by the time course of nuclear binding of [3H]TAM(OH) and [3H]E2 in the uterine cell types: peak levels occurred at 8 h and 4 h, respectively. Nuclear binding was still present 48 h after [3H]TAM(OH) injection but was absent by 24 h after [3H]E2 injection. Different uterine cell types bound different amounts of both the drug and the hormone. After [3H]TAM(OH) injection the decreasing order of labeling intensity in the tissue compartments was stroma, myometrium, epithelium; in contrast, that after [3H]E2 injection was stroma, epithelium, myometrium. The results indicate that the dissimilar nuclear binding kinetics of estrogen and antiestrogen are influenced by the pharmacokinetics but the uterine cell types may also influence binding kinetics.
Animals↗
Kinetics of binding of Hoechst dyes to DNA studied by stopped-flow fluorescence techniques.
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Base Sequence↗