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PubMed1994

Theory for measuring bivalent surface binding kinetics using total internal reflection with fluorescence photobleaching recovery.

Total internal reflection with fluorescence photobleaching recovery (TIR-FPR) is a method for experimentally examining coupled diffusion and reaction kinetics at surfaces. In a previous work (Thompson et al. 1981. Biophys. J. 33:435-454), a theoretical basis for interpreting TIR-FPR data was described for monovalent ligands that undergo a reversible reaction with monovalent surface sites in a single step. Here, the theory for TIR-FPR has been extended to two different surface binding mechanisms that involve sequential, bivalent surface attachment. Methods for obtaining the intrinsic surface association and dissociation kinetic rates from measured fluorescence photobleaching recovery curves are described. The new theory should be applicable to the association of bivalent protein ligands such as antibodies with supported planar model membranes.

Animals↗
PubMed1987

The immune response towards beta-adrenergic ligands and their receptors--VII. Equilibrium and kinetic binding studies of l-alprenolol to a monoclonal anti-alprenolol antibody.

Binding of the catecholamine beta-adrenergic antagonist, l-alprenolol, by the IgGl anti-alprenolol monoclonal antibody 37A4 was examined using the radioligand 3H-dihydroalprenolol as an extrinsic signal and the increase in antibody fluorescence upon l-alprenolol binding as intrinsic signal. Equilibrium binding studies based on both signals indicated that the binding process was exothermic with a positive entropy change. The difference in the affinity constants obtained by radioligand binding studies and by fluorescence analysis could be ascribed to the higher affinity of the hydrogenated tritiated l-dihydroalprenolol compared to the unsaturated l-alprenolol. The association rate constants determined by both signals were 10(4)-10(5)/M/sec and showed a high activation enthalpy (8-10 kcal/mol), thus excluding a diffusion controlled reaction. At low temp (7 degrees C), the fluorescence stopped-flow studies showed non-linear pseudo first order kinetics, indicating the existence of a fast pre-equilibrium of low affinity, followed by a conformational change leading to the tight binding of the ligand. The dissociation rate constants determined using both signals were very similar. Thus, the differences in affinity between the hydrogenated and non-saturated l-alprenolol could be ascribed to the association rate constants. Affinity constants and thermodynamic parameters calculated from the kinetic data were in close agreement with those determined by equilibrium binding. The mechanisms of ligand binding are discussed in terms of the interactions of idiotypes and anti-idiotypes in the anti-catecholamine immune response.

Alprenolol↗
PubMed1989

Kinetics, binding constant, and activation energy of the 48-kDa protein-rhodopsin complex by extra-metarhodopsin II.

We have found that the 48-kDa protein (or S-antigen 48k) of the rod photoreceptor enhances the light-induced formation of the photoproduct metarhodopsin II (MII) from prephosphorylated rhodopsin. The effect is analogous to the known enhancement of MII (extra-MII) that results from selective interaction of MII with G-protein. We have determined some parameters of the MII-48k interaction by measuring the extra-MII absorption change induced by the 48-kDa protein. The amplitude saturation yields a dissociation constant for the MII-48k complex on the order of 50 nM. At the technical limit of these measurements, 13.7 degrees C and 12 microM 48-kDa protein, we find a rate of 2.3 s-1 for formation of the 48k-MII complex. Extrapolation of these values to cellular conditions yields an occupation time of phosphorylated MII by 48k less than 200 ms. This is short compared to estimated rates of phosphorylation. The temperature dependence of the MII-48k formation rate is very high (Q10 for 5 degrees C/15 degrees C = 9-10). The related Arrhenius activation energy (165 kJ mol-1) is correspondingly high and indicates a considerable transient chemical change during the binding process.

Animals↗
PubMed2006

Structure and binding kinetics of three different human CD1d-alpha-galactosylceramide-specific T cell receptors.

Invariant human TCR Valpha24-Jalpha18+/Vbeta11+ NKT cells (iNKT) are restricted by CD1d-alpha-glycosylceramides. We analyzed crystal structures and binding characteristics for an iNKT TCR plus two CD1d-alpha-GalCer-specific Vbeta11+ TCRs that use different TCR Valpha chains. The results were similar to those previously reported for MHC-peptide-specific TCRs, illustrating the versatility of the TCR platform. Docking TCR and CD1d-alpha-GalCer structures provided plausible insights into their interaction. The model supports a diagonal orientation of TCR on CD1d and suggests that complementarity determining region (CDR)3alpha, CDR3beta, and CDR1beta interact with ligands presented by CD1d, whereas CDR2beta binds to the CD1d alpha1 helix. This docking provides an explanation for the dominant usage of Vbeta11 and Vbeta8.2 chains by human and mouse iNKT cells, respectively, for recognition of CD1d-alpha-GalCer.

Animals↗
PubMed2004

Quantifying the effects of molecular orientation and length on two-dimensional receptor-ligand binding kinetics.

Surface presentation of adhesion receptors influences cell adhesion, although the mechanisms underlying these effects are not well understood. We used a micropipette adhesion frequency assay to quantify how the molecular orientation and length of adhesion receptors on the cell membrane affected two-dimensional kinetic rates of interactions with surface ligands. Interactions of P-selectin, E-selectin, and CD16A with their respective ligands or antibody were used to demonstrate such effects. Randomizing the orientation of the adhesion receptor or lowering its ligand- and antibody-binding domain above the cell membrane lowered two-dimensional affinities of the molecular interactions by reducing the forward rates but not the reverse rates. In contrast, the soluble antibody bound with similar three-dimensional affinities to cell-bound P-selectin constructs regardless of their orientation and length. These results demonstrate that the orientation and length of an adhesion receptor influences its rate of encountering and binding a surface ligand but does not subsequently affect the stability of binding.

Animals↗
PubMed1999

A cyanobacterial hemoglobin with unusual ligand binding kinetics and stability properties.

The glbN gene of the cyanobacterium Nostoc commune UTEX 584 encodes a hemoprotein, named cyanoglobin, that has high oxygen affinity. The basis for the high oxygen affinity of cyanoglobin was investigated through kinetic studies that utilized stopped-flow spectrophotometry and flash photolysis. Association and dissociation rate constants were measured at 20 degrees C for oxygen, carbon monoxide, nitric oxide, and methyl and ethyl isocyanides. The association rate constants for the binding of these five ligands to cyanoglobin are the highest reported for any naturally occurring hemoglobin, suggesting an unhindered and apolar ligand binding pocket. Cyanoglobin also shows high rates of autoxidation and hemin loss, indicating that the prosthetic group is readily accessible to solvent. The ligand binding behavior of cyanoglobin was more similar to that of leghemoglobin a than to that of sperm whale myoglobin. Collectively, the data support the model of cyanoglobin function described by Hill et al. [(1996) J. Bacteriol. 178, 6587-6598], in which cyanoglobin sequesters oxygen, and presents it to, or is a part of, a terminal cytochrome oxidase complex in Nostoc commune UTEX 584 under microaerobic conditions, when nitrogen fixation, and thus ATP demand, is maximal.

Bacterial Proteins↗
PubMedDate not supplied

Single- and dual-fractal analysis of hybridization binding kinetics: biosensor applications.

The diffusion-limited hybridization kinetics of analyte in solution to a receptor immobilized on a biosensor or immunosensor surface is analyzed within a fractal framework. The data may be analyzed by a single- or a dual-fractal analysis. This was indicated by the regression analysis provided by Sigmaplot. It is of interest to note that the binding rate coefficient and the fractal dimension both exhibit changes in the same direction for both the single-fractal and the dual-fractal analysis examples presented. For example, for a single-fractal analysis and for the hybridization of 10 nM 16CFl (oligonucleotide) to 16B immobilized via sulfosuccinimidyl-6-(biotinamido)hexanoate and streptavidin using chemical and thermal regeneration (Abel, A. P.; Weller, M. G.; Duveneck, G. L.; Ehrat, M. Widmer, H. M. Anal. Chem. 1996, 68, 2905-2912), an increase in the fractal dimension, Df from 1.211 (chemical regeneration) to 1.394 (thermal regeneration), leads to an increase in the binding rate coefficient, k, from 86.53 (chemical regeneration) to 100.0 (thermal regeneration). An increase in the degree of heterogeneity on the biosensor surface leads to an increase in the binding rate coefficient. When a dual-fractal analysis was utilized, an increase in the fractal dimension value from Df1 to Df2 leads to an increase in the binding rate coefficient value from k1 to k2. The fractional order of dependence of the binding rate coefficient, k1, on (a) the analyte (rRNA) concentration in solution and (b) on the fractal dimension, Df1, for the hybridization kinetics to detect Listeria species (Fliss, R.; St-Laurent, M.; Emond, E.; Simard, R. E.; Lemieux, R.; Ettriki, A.; Pandian, S. Appl. Microbiol. Biotechnol. 1995, 43, 717-724.) further reinforces the fractal nature of the system. The binding rate coefficient(s) expressions developed as a function of the analyte concentration in solution and the fractal dimension are of particular value since they provide a means to better control of biosensor or immunosensor performance.

Biosensing Techniques↗
PubMed1990

Inhibition of chymotrypsin by peptidyl trifluoromethyl ketones: determinants of slow-binding kinetics.

A series of seven peptidyl trifluoromethyl ketone (TFK) inhibitors of chymotrypsin have been prepared which differ at the P1 and P2 subsites. Inhibition equilibria and kinetics of association and dissociation with chymotrypsin have been measured. The association rate of Ac-Phe-CF3 was measured at enzyme concentrations between 8 nM and 117 microM in order to examine the relation between the ketone/hydrate equilibrium of trifluoromethyl ketones and the "slow binding" by these inhibitors. The association rate decreases at high enzyme concentrations, indicating that TFK ketone is the reactive species and that conversion of TFK hydrate to ketone becomes rate limiting under these conditions. Inhibitors with hydrophobic side chains at P2 bind more tightly but more slowly to chymotrypsin, indicating that formation of van der Waals contacts between the P2 side chain and the His 57 and Ile 99 side chains of chymotrypsin is a relatively slow process. Inhibitor properties were compared to the Michaelis-Menten kinetic constants of a homologous series of peptide methyl ester and peptide amide substrates. Plots of log Ki vs log (kcat/Km) are linear with slopes of 0.65 +/- 0.2, indicating that these inhibitors are able to utilize 65% of the total binding energy between chymotrypsin and its hydrolytic transition state.

Acetylation↗
PubMed1989

Interaction of human rheumatoid synovial collagenase (matrix metalloproteinase 1) and stromelysin (matrix metalloproteinase 3) with human alpha 2-macroglobulin and chicken ovostatin. Binding kinetics and identification of matrix metalloproteinase cleavage sites.

The homologous proteinase inhibitors, human alpha 2-macroglobulin (alpha 2M) and chicken ovostatin, have been compared with respect to their "bait" region sequences and interactions with two human matrix metalloproteinases, collagenase and stromelysin. A stretch of 34 amino acid residues of the ovostatin bait region sequence was determined and the matrix metalloproteinase cleavage sites identified. Collagenase cleaved a X-Leu bond where X was unidentified, whereas the major cleavage site by stromelysin was at the Gly-Phe bond, 4 residues on the COOH-terminal side of the collagenase cleavage site. Collagenase cleaved the alpha 2M bait region at the Gly679-Leu680 bond, and stromelysin at Gly679-Leu680 and Phe684-Tyr685 bonds. Sequence similarity in the bait region of members of the alpha-macroglobulin family is strikingly low. The kinetic studies indicate that alpha 2M is a 150-fold better substrate for collagenase than type I collagen. Structural predictions based on the bait region sequences suggest that a collagen-like triple helical structure is not a prerequisite for the efficient binding of tissue collagenase to a substrate. The binding of stromelysin to alpha 2M is slower than that of collagenase. Stromelysin reacts with ovostatin even more slowly. Despite the preference of chicken ovostatin for metalloproteinases, human alpha 2M, a far less selective inhibitor, reacts more rapidly with collagenase and stromelysin. These results suggest that alpha 2M may play an important role in regulating the activities of matrix metalloproteinases in the extracellular space.

Amino Acid Sequence↗
PubMed2003

G100R mutation within 4070A murine leukemia virus Env increases virus receptor binding, kinetics of entry, and viral transduction efficiency.

Passage of 4070A murine leukemia virus (MuLV) in D17 cells resulted in a G-to-R change at position 100 within the VRA of the envelope protein (Env). Compared with 4070A MuLV, virus with the G100R Env displayed enhanced binding on target cells, internalized the virus more rapidly, and increased the overall viral titer in multiple cell types. This provides a direct correlation between binding strength and efficiency of viral entry. Deletion of a His residue at the SU N terminus eliminated the transduction efficiency by the G100R virus, suggesting that the G100R virus maintains the regulatory characteristics of 4070A viral entry. The improved transduction efficiency of G100R Env would be an asset for gene delivery systems.

3T3 Cells↗
PubMed1989

The effects of pressure on oxygen and carbon monoxide binding kinetics for myoglobin. A high pressure laser flash photolysis study.

The milli-, micro-, and nanosecond rebinding kinetics of oxygen and carbon monoxide with myoglobin (Mb) from sperm whale, horse, and dog were studied as a function of pressure up to 2 kbar by means of a high pressure laser photolysis apparatus. The results were analyzed quantitatively in terms of a three-step reaction scheme, and activation volumes (delta V not equal to) for each step were determined from the pressure dependence of the rate constants. In the case of CO binding to Mb, the overall reaction volume delta V not equal to was negative, resulting from the rate-determining bond formation step. Activation volumes for O2 to the iron binding step as well as for the O2 diffusion step within the protein matrix were quite different among three Mb species, and it was suggested that activation volumes are very sensitive to the amino acid constituents around the ligand path channel.

Animals↗
PubMed2002

Polydispersity of Bacillus thuringiensis Cry1 toxins in solution and its effect on receptor binding kinetics.

Dynamic light scattering and surface plasmon resonance techniques were used to investigate the influence of ionic strength, buffer composition and pH on the multimerization of trypsin-activated Cry1Ac and Cry1C toxins over time and the subsequent effects of the different multimers on receptor binding models. In carbonate buffer at pH 10.5, Cry1Ac and Cry1C assumed a monomeric state. After 24 h, a complete conversion of monomeric toxin to a dimeric or trimeric form was observed only for Cry1Ac under low ionic strength condition. Cry1C and Cry1Ac in high ionic strength buffer remained monomeric. Substitution of CAPS pH 11 for carbonate buffer suppressed this Cry1Ac oligomerization effect. Once Cry1Ac toxin was in an aggregated form, increases in ionic strength failed to revert the aggregated toxin back to a monomeric form. Monomeric Cry1Ac bound to a purified 115 kDa aminopeptidase N receptor from Manduca sexta in a 2:1 molar ratio thus confirming the existence of two binding sites on this receptor. Binding rates of dimeric or higher aggregated Cry1Ac toxin forms were different from those generated using the monomeric form and could not be fitted to existing binding models. In summary, our results confirm that the M. sexta 115 kDa aminopeptidase N receptor possesses two Cry1Ac binding sites. They further suggest that although high pH and low salt conditions promote Cry1Ac aggregation, this observation cannot be applied universally to other members of the Cry family.

Aminopeptidases↗
PubMed2004

Nucleotide-binding kinetics of Na,K-ATPase: cation dependence.

Correlation between the Na,K-ATPase affinity to ADP and the cation (its nature and concentration) present in the medium was investigated. In buffer with low ionic strength (I approximately 1 mM) high-affinity ADP binding was not observed, while a stepwise increase in the concentrations of added cation (Na(+), Tris(+), imidazole(+), N-methylglucamine(+), choline(+)) induced an increase in the ADP affinity. The effect was fully saturated at 30-50 mM for all of the cations tested. The maximal affinity for ADP was slightly higher in the presence of Na(+), Tris(+), or imidazole(+) than in the presence of N-methylglucamine(+) or choline(+) (equilibrium dissociation constant K(d) 0.2-0.3 vs 0.7 microM). The ADP dissociation rates from its complex with enzyme in the presence of Na(+) or Tris(+) were similar, implying identity of the nucleotide-binding enzyme conformations, which therefore are assigned to E(1). The ability to compete with K(+) clearly distinguished Na(+) from other cations, which speaks against the sole involvement of the transport sites in the induction of the ADP-binding E(1) conformation. Since the cations are similar in their mode of induction of the high ADP affinity but they demonstrate a pronounced difference in ability to compete with K(+), their effects cannot be combined within any scheme with only one type of cation-binding sites. We suggest that the high affinity toward nucleotide is induced by cation interactions within the protein or lipid and that these nucleotide-domain-related sites coexist with the transport sites, which bind only Na(+) or K(+).

Adenosine Diphosphate↗
PubMed1998

Selective alterations in binding kinetic parameters and allosteric regulation of N-methyl-D-aspartate receptors after prolonged seizures in the developing rat brain.

Among glutamate receptor subtypes, the N-methyl-D-aspartate (NMDA) receptor plays a key role in brain development and cognitive processes, and mediates excitotoxic injury. To test the hypothesis that prolonged seizures may affect NMDA receptor characteristics in the developing brain, a 30-min episode of generalized seizures was induced in rats at 5, 10, 15 and 25 d of age by i.p. administrations of bicuculline, NMDA receptors were analyzed using specific binding of [3H]-labeled (+)-5-methyl-10,11-dihydro-5H-dibenzo-[a,d]-cycloheptene-5,10-imin e maleate (MK-801) in brain membrane preparations, and allosteric regulation was studied by addition of glutamate (10 microM) and glycine (10 microM). In control pups, total number of binding sites increased between 5 and 25 d, Bmax values varying from 1032 +/- 93 to 2311 +/- 449 fmol/mg protein, whereas receptor affinity decreased with age, the affinity constant (Kd) changing from 20.9 +/- 2.0 to 29.1 +/- 2.0 nM. Activation of NMDA receptors by glutamate and glycine led to age-dependent decreases in Kd values, from 30% at 5 d to 72% at 25 d. Seizures altered receptor density only at 5 d (by 40%). Receptor affinity was increased after seizures at 5, 15 and 25 d (from 12 to 60%). The capacity of receptor activation by glutamate and glycine was significantly reduced by seizures at 5 d. There was no change either in density nor affinity of receptors at 10 d. Therefore, as previously shown for central adenosine and benzodiazepine receptors, sustained seizures are able to alter the characteristics of NMDA receptors in a specific way depending on the maturational stage, suggesting developmental changes in the mechanisms of brain response to seizures.

Allosteric Regulation↗
PubMed1992

Ligand binding kinetics of substance P and neurokinin A receptors stably expressed in Chinese hamster ovary cells and evidence for differential stimulation of inositol 1,4,5-trisphosphate and cyclic AMP second messenger responses.

Stably transfected Chinese hamster ovary cells expressing either the substance P receptor or neurokinin A receptor were constructed, isolated, and characterized. Equilibrium ligand binding studies performed on whole cells demonstrated that cell lines expressing either of these receptors contained a single class of high-affinity binding sites with an apparent KD of 0.16 nM for the substance P receptor and an apparent KD of 2.1 nM for the neurokinin A receptor. The higher affinity of substance P for its receptor was accounted for by both a greater association rate constant and a lesser dissociation rate constant. The time course and extent of ligand-stimulated inositol 1,4,5-trisphosphate mass increases in both cell lines were similar and displayed rapid and transient kinetics. Ligand-stimulated cyclic AMP accumulation was also apparent in the cell lines, although the time course and magnitude of the responses were substantially different, with the neurokinin A receptor mediating a greater and more prolonged response. These studies establish the presence of functional substance P receptors and neurokinin A receptors in the stably transfected cell lines and provide evidence for agonist-dependent differential stimulation of second messenger responses.

Animals↗
PubMed1997

Alteration of NF-kappa B p50 DNA binding kinetics by S-nitrosylation.

Nitric oxide (NO) regulates a wide variety of cellular functions, in part, by formation of S-NO bonds at critical active site thiol groups within proteins, including transcription factors. Previous studies have qualitatively demonstrated that S-nitrosothiol formation can alter transcription factor binding to the DNA recognition site. To more precisely define the effect of S-nitrosylation on transcription factor binding, the equilibrium binding constant was derived for S-nitrosylated NF-kappa B p50 (S-NO-p50) in a cell free system utilizing gel shift assays. Binding of NF-kappa B p50 subjected to the nitrosylation conditions in the absence of NaNO2 (C-p50-2) was not different from that of wild type NF-kappa B (C-p50-1). The extent of S-NO-p50 binding to its DNA target sequence was significantly decreased in comparison to that noted with C-p50-1 and C-p50-2. The binding constant was derived for each of the NF-kappa B variants: C-p50-1 = 1.01 x 10(10) M(-1); C-p50-2 = 0.92 x 10(10) M(-1); and S-NO-p50 = 0.28 x 10(10) M(-1). These data indicate that S-nitrosylation of p50 decreases its affinity for the target DNA sequence by four-fold.

Binding Sites↗