Measurement Of Dissociation Rate Constants Research Articles

In Situ Measurements of Metal Complex Exchange Kinetics in Freshwater

Trace metals were measured in situ in a freshwater river draining a peat catchment (DOC = 15 mg L(-1)) using diffusive gradients in thin-films (DGT) devices with a range of gel layer thicknesses (0.16-2.0 mm). The reciprocal of the accumulated mass of each metal varied linearly with the thickness of the diffusive layer. These plots allowed calculation of the thickness of an apparent diffusive boundary layer (ADBL). A constant value was obtained from the plots of Cd, Pb, and Zn. The observed increase in the ADBL for the other metals (Mn<Co<Ni<Cu<AI<Fe) was consistent with increasing kinetic limitation of metal supplied from complexes with humic substances. The results could be presented as a kinetic signature, which reflects the nature of the binding ligands available in the water. A theoretical basis for deriving kinetic constants from the DGT measurements was developed. The derived association rate constants for Ni, Mn, and Cu were consistent with values calculated by assuming that the Eigen mechanism holds and that the mean stability constants of the complexes are related to the binding constants of each metal with fulvic acid. These first in situ measurements of dissociation rate constants provided larger values than those obtained by different techniques in the laboratory, suggesting that trace metal complexes in natural waters may be more labile than previously thought.

Bacterial display using circularly permuted outer membrane protein OmpX yields high affinity peptide ligands

A bacterial display methodology was developed for N- and C-terminal display and demonstrated to enable rapid screening of very large peptide libraries with high precision and efficiency. To overcome limitations of insertional fusion display libraries, a new scaffold was developed through circular permutation of the Escherichia coli outer membrane protein OmpX that presents both N and C termini on the external cell surface. Circularly permuted OmpX (CPX) display was directly compared to insertional fusion display by screening comparable peptide libraries in each format using magnetic and fluorescence activated cell sorting. CPX display enabled in situ measurement of dissociation rate constants with improved accuracy and, consequently, improved affinity discrimination during screening and ranking of isolated clones. Using streptavidin as a model target, bacterial display yielded the well-characterized HP(Q)/(M) motif obtained previously using several alternative peptide display systems, as well as three additional motifs (L(I)/(V) CQNVCY, CGWMY(F)/(Y)xEC, ERCWYVMHWPCNA). Using CPX display, a very high affinity streptavidin-binding peptide was isolated having a dissociation rate constant k(off) = 0.002sec(-1) even after grafting to the C terminus of an unrelated protein. Comparison of individual clones obtained from insertional fusion and terminal fusion libraries suggests that the N-terminal display yields sequences with greater diversity, affinity, and modularity. CPX bacterial display thus provides a highly effective method for screening peptide libraries to rapidly generate ligands with high affinity and specificity.

Inhibition of tRNA aminoacylation by 2'-O-methyl oligonucleotides.

A 2'-O-methyl oligonucleotide complementary to 18 nucleotides in the dihydrouridine stemloop of Escherichia coli tRNA(Cys) has been shown to stably bind to the tRNA. The binding inhibits aminoacylation of the tRNA by cysteine tRNA synthetase. The same oligonucleotide sequence but with the DNA deoxy backbone does not bind to the tRNA. This provides the basis for the design and test of a series of 2'-O-methyl oligonucleotides for their ability to bind to E. coli tRNA(Cys) and inhibit aminoacylation. We show here that different regions of the tRNA have different sensitivities to oligonucleotides. A 10-mer that targets G15 forms a stable complex with the tRNA. The Kd of the complex is several orders of magnitude lower than that of the tRNA-synthetase complex. Measurements of dissociation rate constants indicate that the stronger affinity of the 10-mer to tRNA(Cys) is due to a significantly slower rate of dissociation (by a factor of 10(6)) than that of the synthetase from the tRNA. Only a stoichiometric amount of the 10-mer is necessary to completely inhibit aminoacylation. Because tRNA aminoacylation is fundamental to cell growth, these results provide the rationale for the 10-mer and its derivatives as pharmaceutical agents that target specific cell growth.

Kinetics of thapsigargin-Ca(2+)-ATPase (sarcoplasmic reticulum) interaction reveals a two-step binding mechanism and picomolar inhibition.

Thapsigargin is a high affinity inhibitor of sarco- and endoplasmic reticulum (SERCA) type ATPases. We have used kinetics to determine the dissociation constant of thapsigargin-sarcoplasmic reticulum Ca(2+)-ATPase interaction in the absence and presence of non-ionic detergent. The observed "off" rate constant was measured as 0.0052 s-1 at 26 degrees C by the kinetics of inhibition of ATPase activity following transfer from an inactivated thapsigargin-ATPase complex to native ATPase. Inactive ATPase was produced by cross-linking the active site with glutaraldehyde. The observed dissociation rate constant was increased 7-fold by 0.1% Triton X-100, indicating that perturbation of the transmembrane and stalk region by detergent altered the binding parameters of the inhibitor. In addition, thapsigargin stabilized the ATPase against inactivation caused by detergent in the absence of Ca2+. The observed "on" rate constant of thapsigargin was measured at 26 degrees C as 25 s-1 irrespective of thapsigargin concentration, by the kinetics of thapsigargin- induced change in intrinsic fluorescence. An Arrhenius plot showed a temperature dependence of this rate constant, indicative of a conformational change in the protein with an activation energy of 9.5 kcal/mol for thapsigargin binding. The affinity of the Ca(2+)-ATPase for thapsigargin was calculated to be greater than 2 pM at pH 7.0 and 26 degrees C.

Activation of DNA Binding by the Monomeric Form of the P1 Replication Initiator RepA by Heat Shock Proteins DnaJ and DnaK

RepA protein of plasmid P1 binds to arrays of 19 bp repeat sequences (iterons) and mediates initiation of replication and its control. Escherichia coli heat shock proteins DnaJ and DnaK can stimulate iteron binding activity of RepA in an ATP-dependent fashion. It has been proposed that RepA binds to DNA as monomers and that the stimulation in binding involves monomerization of RepA dimers which are inactive in the binding reaction. RepA-iteron and RepA-RepA interactions have been measured in this study to determine the equilibrium constants of the two reactions. The apparent K D value for RepA-iteron binding decreased from 10 nM to no more than 0·2 nM at increasing concentrations of the heat shock proteins. The stimulation of binding appears to be due to an increase in active RepA fraction and not to a change in the maximum binding capacity of the active species. This view was deduced from measurements of active RepA fraction, which increased in the presence of heat shock proteins, and from measurements of dissociation rate constants, which were independent of the heat shock protein concentrations. Accounting for the active fractions, the true K D value was estimated to be 0·10(±0·09) nM in 20 mM Tris·HCl (pH 8), 100 mM NaCl, 40 mM KCl, 10 mM MgCl 2, 1 mM dithiothreitol, 0·1 mM EDTA, ATP (50 μM), bovine serum albumin (50 μg/ml), calf thymus DNA (50 μg/ml) and glycerol (5%). The dissociation rate constant was 1·5 × 10 -2 s -1 and the calculated association rate constant was 1·5 × 10 8 M -1 s -1. Ultracentrifugation analyses of RepA at 15,000 r.p.m. in the above buffer but without ATP, bovine serum albumin, calf thymus DNA and glycerol, revealed that the protein was in monomer-direct equilibrium with a K D of 2·6(±0.2) μM at 5°C. Therefore, at protein concentrations used in the binding reactions, RepA is monomeric (>99·5%), in confirmation of the earlier result that RepA binds as a monomer. It follows that the species that is stimulated to bind by the heat shock proteins is also a monomeric form of RepA.

Binding Ca2+ to intracellular or to extracellular sites of dihydropyridine receptor of rabbit skeletal muscle discriminates between in vitro binding of Ca2+‐channel agonist and antagonist

Transverse tubule membrane vesicles contain dihydropyridine receptor of rabbit skeletal muscle in an insideout orientation. Digitonin-solubilized, purified dihydropyridine receptor is embedded in digitonin vesicles in an outside-out orientation. Ca2+ selectively stimulates binding of the Ca2+-channel antagonist [3H]PN200-110 to dihydropyridine receptor in the outside-out but not the inside-out orientation. The dissociation constant for binding Ca2+ to the extracellular Ca2+-specific binding site of dihydropyridine receptor is 2-3 microM. The data demonstrate that binding Ca2+ to the extracellular high-affinity Ca2+-binding site is required for binding dihydropyridines to dihydropyridine receptor. This binding is inhibited, however, by 1-10 mM concentrations of any divalent cation tested (Ba2+, Mn2+, Mg2+). Also, Ca2+ selectively stimulates binding of the Ca2+-channel agonist [3H]BayK8644 to dihydropyridine receptor in the inside-out orientation. The titration of this Ca2+ dependence indicates that the dissociation constant for binding Ca2+ to the intracellular Ca2+-specific binding site of dihydropyridine receptor is in the millimolar range. Thus, binding Ca2+-channel agonist or antagonist to dihydropyridine receptor is modulated by binding Ca2+ to different sites of the receptor. Measurements of dissociation rate constants for binding [3H]PN200-110 to dihydropyridine receptor in the presence of diltiazem, verapamil and/or Ca2+ indicate that Ca2+, like diltiazem or verapamil, is an allosteric effector of this receptor.

Peak-decay method for the measurement of dissociation rate constants by high-performance affinity chromatography

A new method was described for the measurement of dissociation rate constants of biological complexes by affinity chromatography. Theory and computer modeling were used to establish conditions such that each solute molecule would undergo only a single dissociation step during its passage through the column. As a result, the dissociation rate constant could easily be determined from the slope of the logarithm of the tailing porton of the peak. An experimental system, consisting of immobilized concanavalin A and a fluorescent sugar, was used to test the theory and to compare the peak-decay method with the conventional isocratic method.