Determination of antibody-hapten association kinetics: a simplified experimental approach.

A simplified method has been developed for the determination of antibody-hapten association kinetics that permits the study of high affinity interactions with second order forward rate constants of the order of 10-7 to 10-8 M-1 sec-1. Use of tritiated haptens of high specific activity and antibodies of high affinity allows reactions to be run at initial hapten and antibody concentrations of the order of 10-9 to 10-10M, well below the level at which mixing becomes the rate-limiting step. Separation of antibody-bound from free hapten by the use of dextran-coated charcoal can be carried out with sufficient rapidity (2 sec) that the systems under investigation are not appreciably disturbed. With this technique, the association of 3-H-ouabain with rabbit ouabain-specific antibody was found to occur with a rate constant of 0.8 times 10-7 M-1 sec-1, similar to association rates of dye haptens with antibodies of substantially lower affinity. The ratio of this association rate constant to the independently determined dissociation rate constant was 5.4 times 10-9 M-1, in satisfactory agreement with a ko value of 3.5 times 10-9 M-1 determined by Sips analysis of data obtained under equilibrium conditions. This approach should be applicable to the direct kinetic assessment of numerous high affinity antibody-hapten systems of current interest.     

Monoclonal antibody to rat apoC: multiple binding to apoC-I on lipoproteins increases its affinity constant

Using solid phase systems, the kinetics of binding of monoclonal antibody (LRB 45, IgG2b,kappa) to apoC-I and apoC-I on lipoproteins were investigated. At 25 degrees C, the association constant of LRB 45 antibody to apoC-I (3.56 X 10(6) M-1 X sec-1) was almost three times slower than the association constant LRB 45 antibody to lipoproteins (10.4 X 10(6) M-1 X sec-1). However, the dissociation constant of apoC-I from LRB 45 antibody (0.865 X 10(-4) sec-1) was also slower than the dissociation constant of lipoprotein from antibody (1.5 X 10(-4) sec-1). Thus, the calculated affinity constant (association constant/dissociation constant) of LRB 45 antibody for apoC-I was approximately half of that for lipoproteins (4.12 X 10(10) M-1 vs. 6.92 X 10(10) M-1). The intrinsic affinity constants for antibody binding to apoC-I and apoC-I on lipoproteins were determined by Scatchard analysis. The intrinsic affinity constant of antibody bound to apoC-I was estimated to be 5.49 X 10(10) M-1 whereas that of antibody binding to lipoproteins was 30 to 200 times less. Furthermore, ascites fluid from LRB 45 cell lines could immunoprecipitate serum lipoproteins. Thus, it is concluded that there is multiple binding of antibody to apoC-I on lipoproteins. This binding appears to increase the calculated affinity constant (avidity) for antibody-antigen interaction.     

Biointeraction analysis by high-performance affinity chromatography: Kinetic studies of immobilized antibodies

A system based on high-performance affinity chromatography was developed for characterizing the binding, elution and regeneration kinetics of immobilized antibodies and immunoaffinity supports. This information was provided by using a combination of frontal analysis, split-peak analysis and peak decay analysis to determine the rate constants for antibody–antigen interactions under typical sample application and elution conditions. This technique was tested using immunoaffinity supports that contained monoclonal antibodies for 2,4-dichlorophenoxyacetic acid (2,4-D). Association equilibrium constants measured by frontal analysis for 2,4-D and related compounds with the immobilized antibodies were 1.7–12 × 10⁶ M⁻¹ at pH 7.0 and 25 °C. Split-peak analysis gave association rate constants of 1.4–12 × 10⁵ M⁻¹ s⁻¹ and calculated dissociation rate constants of 0.01–0.4 s⁻¹ under the application conditions. Elution at pH 2.5 for the analytes from the antibodies was examined by peak decay analysis and gave dissociation rate constants of 0.056–0.17 s⁻¹. A comparison of frontal analysis results after various periods of column regeneration allowed the rate of antibody regeneration to be examined, with the results giving a first-order regeneration rate constant of 2.4 × 10⁻⁴ s⁻¹. This combined approach and the information it provides should be useful in the design and optimization of immunoaffinity chromatography and other analytical methods that employ immobilized antibodies. The methods described are not limited to the particular analytes and antibodies employed in this study but should be useful in characterizing other targets, ligands and supports.     

Interaction of trypsin with a trypsin inhibitor from bovine colostrum]

Kinetics of trypsin association with trypsin inhibitor from colostrum (IC) was studied. The association rate constant is 3-10-5 M- minus 1 sec- minus 1 at pH 7,8, 25 degrees C. The rate constant for the complex dissociation was determined from the kinetics of the IC displacement from the complex with trypsin by a specific substrate and was found to be 5-10- minus 6 sec- minus 1 (pH 7,8; 25 degrees C). The equilibrium constant (Ki) was measured in a special experiment and was equal to 4-10- minus 12 M (p H 7,8; 25 degrees C). The similarity of this reaction and the association of trypsin with other protein inhibitors was discussed.     

Kinetics of the reaction between testosterone and antitestosterone antiserum

In order to characterize from a kinetic viewpoint the antibody population mainly involved in the binding of testosterone by its homologous antiserum, the kinetics of the association reaction between [1,2,6,7-3H]-testosterone and rabbit antiserum anti-testosterone-3-(O-carboxymethyl)oxime-bovine serum albumin (Ab R2603-1) was followed at pH 7.4 and at constant ionic strength, at temperatures ranging from 2 degrees C to 37 degrees C and at concentration near to work conditions for testosterone radioimmunoassay; dextran coated charcoal suspension was used for the bound/free separation. In the examined concentration range, the observed kinetics trends can be explained by assuming the existence of two classes of antibody binding sites, Ab1 and Ab2. The kinetics of the dissociation reaction of the testosterone-antibody complex was also followed after the addition of a large excess of unlabeled testosterone. At 22.0 degrees C, association and dissociation rate constants are 2.1.10(7) s-1M-1 and 3.7.10(-3) s-1, respectively, for the Ab1 class of antibody binding sites, and 3.6.10(6) s-1M-1 and 7.0.10(-4) s-1 for the Ab2 class. Equilibrium constants obtained from kinetic data were very similar for both classes of antibody binding sites and in good agreement with the equilibrium values obtained from linear Scatchard plot. The order of magnitude of the second order rate constants and the high activation enthalpy for the forward and reverse reaction suggest a mechanism more complex than a simple second order.     

The kinetics of glucocorticoid binding to the soluble specific binding protein of mouse fibroblasts.

The kinetics of binding of glucocorticoids to the soluble, specific binding protein of mouse fibroblasts has been examined. The rate at which both potent and weak glucocorticoids achieve binding equilibrium is very slow. Second order rate constants of association range from 3 times 10-5 M- minus 1 min- minus 1 for cortisol to 6.7 times 10-5 M- minus 1 min- minus 1 for triamcinolone acetonide. Studies of the rates of binding at high steroid concentrations suggest that the slow rate of binding may be explained by a two-step mechanism. Active glucocorticoids, regardless of their potency, bind initially in a rapid manner to form a weak complex with the binding protein. The dissociation constant for the weak binding reaction is 0.87 times 10- minus 7 M for triamcinolone acetonide and 2.4 times 10- minus 7 M for cortisol. The weak binding complex becomes converted slowly to a tight complex. The first order rate constants for this conversion and the rate constants of dissociation from the tight complex have been determined for cortisol, dexamethasone and triamcinolone acetonide. The binding affinity of steroids of different biological potency is correlated with their rate of dissociation from this second tight binding state.     

Mandelate racemase from Pseudomonas putida. Magnetic resonance and kinetic studies of the mechanism of catalysis.

The interactions of mandelate racemase with divalent metal ion, substrate, and competitive inhibitors were investigated. The enzyme was found by electron paramagnetic resonance (EPR) to bind 0.9 Mn2+ ion per subunit with a dissociation constant of 8 muM, in agreement with its kinetically determined activator constant. Also, six additional Mn2+ ions were found to bind to the enzyme, much more weakly, with a dissociation constant of 1.5 mM. Binding to the enzyme at the tight site enhances the effect of Mn2+ on the longitudinal relaxation rate (1/T1p) of water protons by a factor of 11.9 at 24.3 MHz. From the frequency dependence of 1/T1p, it was determined that there are similar to 3 water ligands on enzyme-bound Mn2+ which exchange at a rate larger than or equal to 10-7 sec-1. The correlation time for enzyme-bound Mn2+-water interaction is frequency-dependent, indicating it to be dominated by the electron spin relaxation time of Mn2+. Formation of the ternary enzyme-Mn2+-mandelate complex decreases the number of fast exchanging water ligands by similar to 1, but does not affect tau-c, suggesting the displacement or occlusion of a water ligand. The competitive inhibitors D,L-alpha-phenylglycerate and salicylate produce little or no change in the enzyme-Mn2+-H2O interaction, but ternary complexes are detected indirectly by changes in the dissociation constant of the enzyme-Mn2+ complex and by mutual competition experiments. In all cases the dissociation constants of substrates and competitive inhibitors from ternary complexes determined by magnetic resonance titrations agree with K-M and K-i values determined kinetically and therefore reflect kinetically active complexes. From the paramagnetic effects of Mn2+ on 1/T1 and 1/T2 of the 13C-enriched carbons of 1-[13C]-D,L-mandelate and 2-[13C]-D,L-mandelate, Mn2+ to carboxylate carbon and Mn2+ to carbinol carbon distances of 2.93 plus or minus 0.04 and 2.71 plus or minus 0.04 A, respectively, were calculated, indicating bidentate chelation in the binary Mn2+-mandelate complex. In the active ternary complex of enzyme, Mn2+, and D,L-mandelate, these distances increase to 5.5 plus or minus 0.2 and 7.2 plus or minus 0.2 A, respectively, indicating the presence of at least 98.9% of a second sphere complex in which Mn2+, and C1 and C2 carbon atoms are in a linear array. The water relaxation data suggest that a water ligand is immobilized between the enzyme-bound Mn2+ and the carboxylate of the bound substrate. This intervening water ligand may polarize or protonate the carboxyl group. From 1/T2p the rate of dissociation of the substrate from this ternary complex (larger than or equal to 5.6 times 10-4 sec-1) is at least 52 times greater than the maximal turnover number of the enzyme (1070 sec-1), indicating that the complex detected by nuclear magnetic resonance (NMR) is kinetically competent to participate in catalysis. Relationships among the microscopic rate constants are considered.     

Binding of colchicine to purified microtubule protein.

The binding of colchicine to tubulin, purified by two cycles of assembly-disassembly, has been studied. Equilibrium studies indicated a dissociation constant which declined during incubation approaching a minimum value of approximately 0.30 times 10- minus 6 M after 13 hours of incubation. Because tubulin is unstable during prolonged incubation (t1/2 of 5.2 hours for free tubulin, t1/2 of 12.5 hours for tubulin bound to colchicine), the equilibrium Kd was felt to be an overestimation of the true Kd. The rate constant of dissociation (k-1 equal to 0.009 hour- minus 1 hour- minus 1) and the rate constant of association (k1 equal to 0.37 times 10-6 M-minus 1) were measured under conditions designed to circumvent or correct for tubulin instability. The dissociation constant determined by the ratio k-1/k1 was 0.024 times -minus 6 M. To determine whether the discrepancy between the "equilibrium" and "kinetic" determined dissociation constants could be accounted for on the basis of tubulin instability, the binding reaction was computer-simulated using the measured association and dissociation rate constants and the rate constants for decay of bound and free tubulin. Computer simulation was in close agreement with the experimentally determined behavior of the reaction during a 13-hour incubation. It is concluded that the Kd determined by equilibrium methodology results in a considerable overestimation due to the instability of tubulin, and that the best estimate for the Kd of the colchicine-tubulin equilibrium is the value determined by the ratio of the rate constants.     

The mechanism of binding of dihydropyridine calcium channel blockers to rat brain membranes

Detailed kinetic and equilibrium studies of the binding of two radiolabeled 1,4-dihydropyridine calcium antagonists to putative calcium channels in rat brain membranes were performed. (+/-)-[3H]Nitrendipine, a racemic ligand, and (+)-[3H]isopropyl 4-(2,1,3-benzoxadiazol-4-yl)-1, 4-dihydro-2,6-dimethyl-5-methoxycarbonylpyridine-3-carboxylate (PN200-110), a pure isomer, were used and their binding properties were quantitated and compared. Analysis of equilibrium binding revealed a single high affinity component for each radioligand with the same density of binding sites for both ligands. Association rates were determined over a 60-fold range of concentration of each radioligand. For both radioligands, the pseudo-first order association time courses were biphasic with the rate of the faster component dependent on radioligand concentration and the rate of the slower component independent of both the structure of the radioligand and the concentration of the radioligand. Dissociation rates were determined after various times of association. The dissociation of the optically pure radioligand, (+)-[3H]PN200-110, was monophasic at all association times, consistent with a single bound species being present throughout association. However, (+/-)-[3H]nitrendipine dissociation was biphasic after short association times (1-10 min). The biphasic dissociation observed with (+/-)-[3H]nitrendipine is consistent with the two optical isomers binding with approximately the same association rate but having different dissociation rates. These results appear to reflect the existence of two interconvertible binding states of the putative calcium channel in the membrane, one which binds the radioligands with high affinity in a simple bimolecular reaction and one which has no detectable affinity for the ligands. This mechanism of isomerization before ligand binding has been modeled by numerical solution of the differential equations of the scheme providing estimates of the rate constants for each reaction in the scheme.     

Inhibition of rabbit lung angiotensin-converting enzyme by N alpha-[(S)-1-carboxy-3-phenylpropyl]L-alanyl-L-proline and N alpha-[(S)-1-carboxy-3-phenylpropyl]L-lysyl-L-proline

Two novel peptide analogs, N alpha-[(S)-1-carboxy-3-phenylpropyl]L-alanyl-L-proline and the corresponding L-lysyl-L-proline derivative, have been demonstrated to be potent competitive inhibitors of purified rabbit lung angiotensin-converting enzyme: Ki = 2 and 1 X 10(-10) M, respectively, at pH 7.5, 25 degrees C, and 0.3 M chloride ion. Second-order rate constants for addition of these inhibitors to enzyme under the same conditions are in the range 1-2 X 10(6) M-1 s-1; first-order rate constants for dissociation of the EI complexes are in the range 1-4 X 10(-4) s-1. The association rate constants are similar to those measured for D-3-mercapto-2-methylpropanoyl-L-proline, captopril, but the dissociation rate constants are severalfold slower and account for the higher affinity of these inhibitors for the enzyme. The dissociation constant for the EI complex containing N alpha-[(S)-1-carboxy-3-phenylpropyl]L-alanyl-L-proline is pH-dependent, and reaches a minimum at approximately pH 6: Ki = 4 +/- 1 X 10(-11) M. The pH dependence is consistent either with a model for which the protonation state of the secondary nitrogen atom in the inhibitor determines binding affinity, or one for which ionizations on the enzyme alone influence affinity for these inhibitors. The affinity of this inhibitor for the zinc-free apoenzyme is 2 X 10(4) times less than for the zinc-free apoenzyme is 2 X 10(4) times less than that for the holoenzyme. If considered as a "collected product" inhibitor, N alpha-[(S)-1-carboxy-3-phenylpropyl]L-alanyl-L-proline appears to derive an additional factor of 375 M in its affinity for the enzyme compared to that of the two products of its hypothetical hydrolysis, a consequence of favorable entropy effects.     

His374 of wheat endoxylanase inhibitor TAXI-I stabilizes complex formation with glycoside hydrolase family 11 endoxylanases

Wheat endoxylanase inhibitor TAXI-I inhibits microbial glycoside hydrolase family 11 endoxylanases. Crystallographic data of an Aspergillus niger endoxylanase-TAXI-I complex showed His374 of TAXI-I to be a key residue in endoxylanase inhibition. Its role in enzyme-inhibitor interaction was further investigated by site-directed mutagenesis of His374 into alanine, glutamine or lysine. Binding kinetics and affinities of the molecular interactions between A. niger, Bacillus subtilis, Trichoderma longibrachiatumendoxylanases and wild-type TAXI-I and TAXI-I His374 mutants were determined by surface plasmon resonance analysis. Enzyme-inhibitor binding was in accordance with a simple 1 : 1 binding model. Association and dissociation rate constants of wild-type TAXI-I towards the endoxylanases were in the range between 1.96 and 36.1 x 10(4)m(-1) x s(-1) and 0.72-3.60 x 10(-4) x s(-1), respectively, resulting in equilibrium dissociation constants in the low nanomolar range. Mutation of TAXI-I His374 to a variable degree reduced the inhibition capacity of the inhibitor mainly due to higher complex dissociation rate constants (three- to 80-fold increase). The association rate constants were affected to a smaller extent (up to eightfold decrease). Substitution of TAXI-I His374 therefore strongly affects the affinity of the inhibitor for the enzymes. In addition, the results show that His374 plays a critical role in the stabilization of the endoxylanase-TAXI-I complex rather than in the docking of inhibitor onto enzyme.     

Characterization of tetramethylrhodaminyl-phalloidin binding to cellular F-actin.

Fluorescent derivatives of phalloidin are widely used to measure filamentous actin (F-actin) levels and to stabilize F-actin. We have characterized the kinetics and affinity of binding of tetramethylrhodaminyl (TRITC)-phalloidin to rabbit skeletal muscle F-actin and to F-actin in lysates of rabbit polymorphonuclear leukocytes (PMNs). We have defined conditions where TRITC-phalloidin can be used to inhibit F-actin depolymerization and to quantify F-actin without prior fixation. By equilibrium measurements, the affinity of TRITC-phalloidin binding to rabbit skeletal muscle F-actin (pyrene labeled) or to PMN lysate F-actin was 1-4 x 10(-7) M. In both cases, the stoichiometry of binding was approximately 1:1. Kinetic measurements of TRITC-phalloidin binding to PMN lysate F-actin resulted in an association rate constant of 420 +/- 120 M-1 sec-1 and a dissociation rate constant of 8.3 +/- 0.9 x 10(-5) sec-1. The affinity calculated from the kinetic measurements (2 +/- 1 x 10(-7) M) agreed well with that obtained by equilibrium measurements. The rate with which 0.6 microM TRITC-phalloidin inhibited 0.1 microM pyrenyl F-actin depolymerization (90% inhibition in 10 sec) was much faster than the rate of binding to pyrenyl F-actin (less than 1% bound in 10 sec), suggesting that phalloidin binds to filament ends more rapidly than to the rest of the filament. We show that TRITC-phalloidin can be used to measure F-actin levels in cell lysates when G-actin is also present (i.e., in cell lysates at high concentrations) if DNase I is included to prevent phalloidin-induced polymerization.     

The salt dependence of DNA recognition by NF-kappaB p50: a detailed kinetic analysis of the effects on affinityand specificity.

The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the dissociation constants. Under previously established high affinity buffer conditions, the k a for both sequences was in the order of 10(7) M-1s-1whilst the k d values varied 600-fold in a sequence-dependent manner between 10(-1) and 10(-4 )s-1, suggesting that the selectivity of p50 for different sequences is mediated primarily through sequence-dependent dissociation rates. The calculated K D value for the Ig-kappaB sequence was 16 pM, whilst the K D for the non-specific sequence was 9.9 nM. As the ionic strength increased to levels which are closer to that of the cellular environment, the binding of p50 to the non-specific sequence was abolished whilst the specific affinity dropped to nanomolar levels. From these results, a mechanism is proposed in which p50 binds specific sequences with high affinity whilst binding non-specific sequences weakly enough to allow efficient searching of the DNA.     

Multi-component system of estrogen binding proteins from the liver: characterization of binding properties of high molecular weight protein from rat liver similar to uterine estradiol receptors]

A comparative study of the hormonal specificity of the affinity, the equilibrium association constant (Ka) and the kinetics of [3H]-estradiol (3H-E2) interaction with high molecular weight specifically binding E2 proteins from liver cytosol of male and female rats and with uterine estrogen receptors was carried out. The hormonal specificity of the affinity for the E2-binding proteins from the three sources was found to be similar, i.e. only the compounds possessing the estrogen activity competed with 3H-E2 for the binding sites. The values of the apparent equilibrium constants (Ka) for the proteins from male rat liver and female rat liver and uterus were equal to (6,6 +/- 1,2) . 10(9) M-1, (7,4 +/- 0,9) . 10(9) M-1 and (11,2 +/- 2,3) . 10(9) M-1, respectively. The dissociation kinetics of the 3H-E2--protein complexes from the three tissues at 0--4 degrees were two-phase: during the first 8--12 hours the dissociation processes were characterized by the dissociation rate constants (k-1) equal to (4--5) . 10(-5) S-1; then the k-1 values were decreased approximately by one order of magnitude. The kinetics of 3H-E2 association with the three types of proteins are presumably two-phase as well. During the first 10--15 min the association process can be characterized by association rate constants equal to (8--27). .10(5 M-1 S-1; then these values decreased about 4-fold. The data obtained suggest that the high molecular weight estrogen--binding proteins from different tissues are similar in their E2-binding properties on the one hand, and may be interpreted as evidence for the heterogeneity of the populations of E2-binding proteins in various tissues, on the other.     

Metal binding to angiotensin converting enzyme: implications for the metal binding site

Angiotensin converting enzyme interacts with the chelator, 1,10-phenanthroline (OP) to form an OP-Zn-ACE ternary complex, which subsequently dissociates to OP-Zn and apoenzyme. The association and dissociation rate constants for the reaction OP + Zn-ACE in equilibrium OP-Zn-ACE have been determined and compared with those of known OP-metal complexes. Such constants were also used to calculate the rate constant for formation of the OP-Zn complex from OP-Zn-ACE. The rate of dissociation of zinc from ACE has been measured in the presence of EDTA (which acts only as a metal scavenger) as a function of chelator concentration, at different pH values, and with different buffers. The stability constant for the binding of zinc to apoACE log Kc = 8.2, determined by equilibrium dialysis using atomic absorption spectroscopy to assess metal concentration, is much smaller than that for Zn-carboxypeptidase A. Zn-thermolysin, or Zn-carbonic anhydrase. This weak binding is attributable to the zinc dissociation rate constant of ACE, 7.5 X 10(-3) sec-1 at pH 7.0, which is much greater than that of the other zinc metalloenzymes. These results lead to inferences regarding the metal binding site of ACE.     

Muscarinic binding to mouse brain receptor sites

In mouse brain the binding of [³H]-Atropine to the muscarinic receptor seems to be a simple mass-action determined process as gauged both by approach to equilibrium kinetics and binding at equilibrium. In contrast, using isotopic dilution technique, dissociation measurements indicate the existence of two receptor-ligand complexes. It would appear that association and dissociation rates of binding of the muscarinic antagonists atropine, scopolamine, N-methyl-4-piperidyl benzilate (4NMPB) and 3-quinuclidinyl benzilate (QNB) decrease with increasing affinity based on comparisons of kinetic binding data. The differences between the association rate constants are small whereas those between the dissociation rate constants differ markedly. This kinetic behavior is similar to the well-known time profile of antimuscarinic activity in isolated tissues. These phenomena are discussed in terms of possible isomerization of the receptor-ligand complex, as has been proposed recently for [³H]-scopolamine and [³H]-4NMPB binding.     

Kinetic and thermodynamic characterization of the interaction between Q beta-replicase and template RNA molecules

The specific binding of the RNA polymerase Q beta-replicase to some of its RNA template molecules, the single-stranded RNA variant MDV and also Q beta-RNA, was studied under various conditions by using a gel-retardation assay as well as filter retention. The dissociation of the replicase-RNA complex proceeds with first-order kinetics. The dependence of the dissociation rate constant on the concentration of monovalent ions suggests that there are three contacts between the midivariant (MDV) RNA and the replicase. Through analysis of the temperature dependence of the dissociation rate constant, values of 35 and 43 kJ/mol were obtained for the activation energies of complex dissociation between Q beta-replicase and the minus (-) and plus (+) strands of MDV, respectively. The bimolecular association is of second order with high rate constants that increase when the temperature is raised and decrease at higher salt concentrations. The equilibrium constants vary between 4.10(11) M-1 and 5.10(7) M-1, according to the reaction conditions. The temperature dependence of Ka gives delta H = -39 kJ/mol for MDV- and -47 kJ/mol for MDV+. Under nearly all conditions, distinct differences in the association and dissociation rates of plus and minus strands of MDV are observed. The binding of the small variant MDV to Q beta-replicase is three orders of magnitude stronger than the binding of the natural template Q beta-RNA.     

Kinetics of association of anti-lysozyme monoclonal antibody D44.1 and hen-egg lysozyme

Association rate constants for antigen/antibody associations have been computed by Brownian Dynamics simulations of D. L. Ermak and J. A. McCammon, J. Chem. Phys. 69:1352-1360, 1978. The model of monoclonal antibody (mAb) D44.1 is based on crystallographic data (B. C. Braden et al., J. Mol. Biol. 243:767-781, 1994). Electrostatic forces that steer the antigen to the antibody-combining site are computed by solving the linearized Poisson-Boltzmann equation. D44. 1-HEL complex displays very similar association motifs to a related anti-lysozyme antibody, HyHEL-5-HEL system. The computed association rate constants are comparable in the two systems, although the experimental affinity constants differ by three orders of magnitude (D. Tello et al., Biochem. Soc. Trans. 21:943-946, 1993; K. A. Hibbits et al., Biochemistry. 33:3584-3590, 1994). Simulations suggest that the origin of the differences in the affinity come from dissociation rate constants. We have also carried out simulation experiments on a number of mutant antibody fragment-HEL associations to address the role of electrostatics and, to a limited extent, the orientational aspects of association.     

Double and single exponential kinetics of microtubule assembly in vitro

The kinetics of the microtubule protein assembly were studied in Mes buffer, pH 6.6, at 28 degrees C. The assembly under above conditions follow a kinetic expression containing two exponential terms. The observed two rate constants depend on protein concentration, and are on the order of 10(-2) sec-1 and 10(-3) sec-1. When CaCl2 is added to the system in low concentration, the kinetic expression becomes single exponential. The observed rate constant is independent of protein concentration and its value is 5 X 10(-3) sec-1. It is concluded that the double exponential kinetics correspond to favorable assembly conditions, probably to a high extent of nucleation, whereas the single exponential kinetics correspond to favorable assembly conditions, probably to a high extent of nucleation, whereas the single exponential kinetics is a slower process which occur under hindered assembly conditions.     

Ion binding by X-537A. Rates of complexation of Ni2+ and Mn2+ in methanol.

The rates of complexation are studied through the effects of the paramagnetic ions upon the magnetic resonances of three of the proton species in X-537A = XH. For the dissociation of the complex MX+ leads to M2+ + X- at 25 degrees the rate is (2.4 plus or minus 0.4) x 10(2) sec-1 for Ni2+ and in the range from 2 x 10(4) to 1 x 10(6) sec-1 for Mn2+. For the Ni2+ complex the activation parameters are also determined and discussed in terms of the details of the process. The difference in rate constants found here is much greater than the difference in the dissociation constants.