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At least 955 records · Page 53Linked to original sources
PubMed2005

Capillary electrophoresis and fluorescence anisotropy for quantitative analysis of peptide-protein interactions using JAK2 and SH2-Bbeta as a model system.

Fluorescence anisotropy capillary electrophoresis (FACE) and affinity probe capillary electrophoresis (APCE) with laser-induced fluorescence detection were evaluated for analysis of peptide-protein interactions with rapid binding kinetics. The Src homology 2 domain of protein SH2-Bbeta (SH2-Bbeta (525-670)) and a tyrosine-phosphorylated peptide corresponding to the binding sequence of JAK2 were used as a model system. For peptide labeled with fluorescein, the K(d) = 82 +/- 7 nM as measured by fluorescence anisotropy (FA). APCE assays had a limit of detection (LOD) of 100 nM or 12 amol injected for SH2-Bbeta (525-670). The separation time of 4 s, achieved using an electric field of 2860 V/cm on 7-cm-long capillaries, was on the same time scale as complex dissociation allowing K(d) (101 +/- 12 nM in good agreement with FA measurements) and dissociation rate (k(off) = 0.95 +/- 0.02 s(-)(1) corresponding to a half-life of 0.73 s) to be determined. This measurement represents a 30-fold higher rate of complex dissociation than what had previously been measurable by nonequilibrium CE analysis of equilibrium mixtures. Using FACE, the protein was detected with an LOD of 300 nM or 7.5 fmol injected. FACE was not used for determining K(d) or k(off); however, this method provided better separation resolution for multiple forms of the protein than APCE. Both methods were found suitable for analysis of cell lysate. These results demonstrate that FACE and APCE may be useful complements to existing techniques for exploring binding interactions with rapid kinetics.

Adaptor Proteins, Signal Transducing↗
PubMed1989

L-glutamate binding sites of normal and atrophic human cerebellum.

The binding kinetics, pharmacologic properties, ontogeny and localization of L-glutamate binding sites were studied in membrane preparations and sections of normal and olivopontocerebellar atrophy (OPCA) human cerebellum. One binding component was found with a Kd value in the order of 150 x 10(-9) M. No significant changes of Kd values were observed with age, whereas the highest Bmax value was observed at the age of 1 year. L-Aspartate, ibotenate, quisqualate and L-homocysteic acid were potent inhibitors of L-[3H]glutamate binding. Quantitative densitometric measurements indicated the presence of L-glutamate sites in both the molecular and granule cell layer. In OPCA cerebella a very significant decrease of L-[3H]glutamate specific binding (Bmax) was observed, whereas Kd values were found unchanged. The pharmacologic properties of L-[3H]glutamate binding sites of OPCA cerebellar tissues were similar to those of normal cerebellum. [3H]quinuclidinyl benzylate binding, expressed in fmol/mg protein, did not show significant differences between normal and OPCA cerebella.

Adolescent↗
PubMed2002

Substrates modulate the rate-determining step for CO binding in cytochrome P450cam (CYP101). A high-pressure stopped-flow study.

The high-pressure stopped-flow technique is applied to study the CO binding in cytochrome P450cam (P450cam) bound with homologous substrates (1R-camphor, camphane, norcamphor and norbornane) and in the substrate-free protein. The activation volume DeltaV # of the CO on-rate is positive for P450cam bound with substrates that do not contain methyl groups. The kon rate constant for these substrate complexes is in the order of 3 x 10(6) M(-1) x s(-1). In contrast, P450cam complexed with substrates carrying methyl groups show a negative activation volume and a low kon rate constant of approximately 3 x 10(4) M(-1) x s(-1). By relating kon and DeltaV # with values for the compressibility and the influx rate of water for the heme pocket of the substrate complexes it is concluded that the positive activation volume is indicative for a loosely bound substrate that guarantees a high solvent accessibility for the heme pocket and a very compressible active site. In addition, subconformers have been found for the substrate-free and camphane-bound protein which show different CO binding kinetics.

Binding Sites↗
PubMed2006

Interaction mode of a symmetric Trp-rich undeca peptide PST11-RK with lipid bilayers.

To better understand the mode of action of the antimicrobial peptide PST11-RK, we investigated its (1) bactericidal kinetics, (2) ability to induce bacterial membrane depolarization, (3) ability to bind to liposomes, (4) cis/trans prolyl isomerization, (5) lipid binding kinetics and (6) translocation across lipid bilayers. Our findings suggest that PST11-RK acts mainly by collapsing the cytoplasmic membrane potential; it first attaches to the membrane via cationic C- and N-terminal residues and then inserts its central hydrophobic residues into the lipid interior. In addition, it seems likely that cis/trans isomerization facilitates the translocation of PST11-RK across the lipid bilayer, where it may interact with secondary intracellular targets.

Anti-Infective Agents↗
PubMed2001

The kinetics of inhibition of nicotinic acetylcholine receptors by (+)-tubocurarine and pancuronium.

Equilibrium conditions of neurotransmitter concentration and receptor binding are never achieved during synaptic transmission at the neuromuscular junction. Thus, it is important to determine the binding kinetics of drugs that act this synapse. Previous determinations of the dissociation rate of (+)-tubocurarine have produced inconsistent results ranging from 0.1 to 4000/s. Here, we used a direct approach to measure association (l(on)) and dissociation (l(on)) rates for two competitive antagonists (clinically used as nondepolarizing muscle relaxants), pancuronium and (+)-tubocurarine, at nicotinic acetylcholine receptors (nAChR). We made macroscopic current recordings from outside-out patches of BC3H-1 cells expressing embryonic mouse muscle nAChR. We used a three-tube rapid perfusion system to make timed applications of antagonists and acetylcholine to the patch. We made independent measurements of the equilibrium inhibition (IC(50)) and the kinetics of onset and recovery of antagonist inhibition at 20 to 23 degrees C. Rate constants were calculated from the predictions of a single (high-affinity) site model of competitive inhibition. For pancuronium: IC(50) = 5.5 +/- 0.5 nM (mean +/- S.D.), l(on) = 2.7 +/- 0.9 x 10(8) M(-1) s(-1), l(off) = 2.1 +/- 0.7/s [corrected] x 10(8)/s. For (+)-tubocurarine: IC(50) = 41 +/- 2 nM, l(on) = 1.2 +/- 0.2 x 10(8) M(-1) s(-1), l(off) = 5.9 +/- 1.3/s. The kinetic results are consistent with the equilibrium results in that l(off)/l(on) is in good agreement with the IC(50) values. All differences between the antagonists are significant at the p < 0.001 level. The higher affinity of pancuronium is caused by a faster association rate (2.2-fold) coupled with a slower dissociation rate (2.8-fold). The association rates of both antagonists are comparable with or greater than the association rate for acetylcholine binding to nAChR.

Animals↗
PubMed2004

Oligomerization-dependent changes in the thermodynamic properties of the TPR-MET receptor tyrosine kinase.

Although oligomerization of receptor tyrosine kinases (RTKs) is necessary for receptor activation and signaling, a quantitative understanding of how oligomerization mediates these critical processes does not exist. We present a comparative thermodynamic analysis of functionally active dimeric and functionally inactive monomeric soluble analogues of the c-MET RTK, which clearly reveal that oligomerization regulates the binding affinity and binding kinetics of the kinase toward ATP and tyrosine-containing peptide substrates. Thermodynamic binding data for oligomeric c-MET were obtained from the dimeric TPR-MET oncoprotein, a functionally active fusion derivative of the c-MET RTK. This naturally occurring oncoprotein contains the cytoplasmic domain of c-MET fused to a coiled coil dimerization domain from the nuclear pore complex. Comparative data were obtained from a soluble monomeric kinase compromising the c-MET cytoplasmic domain (cytoMET). Significantly, under equilibrium binding conditions, the oligomeric phosphorylated kinase showed a significantly lower dissociation constant (K(d,dimer) = 11 microM) for a tyrosine-containing peptide derived from the C-terminal tail of the c-MET RTK when compared to the phosphorylated monomeric kinase cytoMET (K(d,monomer) = 140 microM). Surprisingly, equilibrium dissociation constants measured for the kinase and ATP were independent of the oligomerization state of the kinase (approximately 10 microM). Stopped-flow analysis of peptide substrate binding showed that the association rate constants (k(2)) differed 2-fold and dissociation rate constants (k(-2)) differed 10-fold when phosphorylated TPR-MET was compared to phosphorylated cytoMET. ATP binding abrogated the differences in k(2) rates observed between the two oligomeric states of the c-MET cytoplasmic domain. These results clearly imply that oligomerization induces important thermodynamic and conformational changes in the substrate binding regions of the c-MET protein and provide quantitative mechanistic insights into the necessary role of oligomerization in RTK activation.

Adenosine Triphosphate↗
PubMed2001

DNA as the intracellular secondary target for antibacterial action of human neutrophil peptide-I against Mycobacterium tuberculosis H37Ra.

The secondary intracellular target of human neutrophil peptide-1 has been examined in M. tuberculosis H37Ra. Binding studies with radioiodinated HNP-1 revealed biphasic equilibrium binding kinetics with respect to time. The major site of HNP-1 binding was found to be plasma membrane/cell wall whereas the cytosol appears to be a secondary site. Among the different macromolecules examined, maximum inhibition (75%) was observed in DNA biosynthesis during treatment with HNP-1. The interaction of HNP-1 with mycobacterial genomic DNA on the basis of gel retardation assay revealed HNP-1 binding to DNA. These results indicate that HNP-1 has DNA as the secondary intracellular target for antibacterial action against mycobacteria.

Anti-Bacterial Agents↗
PubMed1992

Discrimination of multiple binding sites for antagonists of the calcium release channel complex of skeletal and cardiac sarcoplasmic reticulum.

The mechanisms by which ruthenium red (RR), neomycin and FLA 365 ([2,6-dichloro-4-aminophenyl]isopropylamine) inhibit calcium channels of skeletal and cardiac sarcoplasmic reticulum (SR) are characterized. Neomycin and FLA 365 inhibit ryanodine-enhanced calcium release from skeletal SR vesicles in a dose-dependent manner. The apparent affinity of [3H]ryanodine is reduced in a dose-dependent manner by each inhibitor indicative of competitive mechanisms. Displacement studies with skeletal and cardiac SR demonstrate that the order of inhibitory potency is RR greater than neomycin greater than FLA 365 and RR greater than FLA 365 greater than neomycin, respectively. Neomycin is 100-fold less potent in cardiac SR and inhibition of [3H]ryanodine binding is biphasic in both tissues. Neomycin induces a greater proportion of [3H]ryanodine binding states recalcitrant to inhibition in cardiac SR. The ability of neomycin to increase the apparent affinity of [3H]ryanodine for its binding sites is potentiated by RR and attenuated by FLA 365. Kinetic binding studies reveal that increasing neomycin concentrations decreases the association of [3H]ryanodine as predicted for competitive inhibition. However, high (much greater than Kn) neomycin increases [3H]ryanodine binding affinity by slowing dissociation of the radioligand demonstrating that, like micromolar ryanodine, neomycin induces allosterism. Studies with combinations of antagonists demonstrate the existence of two non-overlapping inhibitor recognition sites within the ryanoid site, one polycationic inhibitor site and one FLA 365 inhibitor site. These results suggest that aminoglycoside-induced muscle paralysis may be mediated by direct block of pre- and postsynaptic calcium release channels of endoplasmic reticulum.

Animals↗
PubMed2003

Direct measurement of equilibrium constants for high-affinity hemoglobins.

The biological functions of heme proteins are linked to their rate and affinity constants for ligand binding. Kinetic experiments are commonly used to measure equilibrium constants for traditional hemoglobins comprised of pentacoordinate ligand binding sites and simple bimolecular reaction schemes. However, kinetic methods do not always yield reliable equilibrium constants with more complex hemoglobins for which reaction mechanisms are not clearly understood. Furthermore, even where reaction mechanisms are clearly understood, it is very difficult to directly measure equilibrium constants for oxygen and carbon monoxide binding to high-affinity (K(D) << 1 micro M) hemoglobins. This work presents a method for direct measurement of equilibrium constants for high-affinity hemoglobins that utilizes a competition for ligands between the "target" protein and an array of "scavenger" hemoglobins with known affinities. This method is described for oxygen and carbon monoxide binding to two hexacoordinate hemoglobins: rice nonsymbiotic hemoglobin and Synechocystis hemoglobin. Our results demonstrate that although these proteins have different mechanisms for ligand binding, their affinities for oxygen and carbon monoxide are similar. Their large affinity constants for oxygen, 285 and approximately 100 micro M(-1) respectively, indicate that they are not capable of facilitating oxygen transport.

Binding, Competitive↗
PubMed2005

Kinetic characterization of novel pyrazole TGF-beta receptor I kinase inhibitors and their blockade of the epithelial-mesenchymal transition.

Transforming growth factor beta (TGF-beta) signaling pathways regulate a wide variety of cellular processes including cell proliferation, differentiation, extracellular matrix deposition, development, and apoptosis. TGF-beta type-I receptor (TbetaRI) is the major receptor that triggers several signaling events by activating downstream targets such as the Smad proteins. The intracellular kinase domain of TbetaRI is essential for its function. In this study, we have identified a short phospho-Smad peptide, pSmad3(-3), KVLTQMGSPSIRCSS(PO4)VS as a substrate of TbetaRI kinase for in vitro kinase assays. This peptide is uniquely phosphorylated by TbetaRI kinase at the C-terminal serine residue, the phosphorylation site of its parent Smad protein in vivo. Specificity analysis demonstrated that the peptide is phosphorylated by only TbetaRI and not TGF-beta type-II receptor kinase, indicating that the peptide is a physiologically relevant substrate suitable for kinetic analysis and screening of TbetaRI kinase inhibitors. Utilizing pSmad3(-3) as a substrate, we have shown that novel pyrazole compounds are potent inhibitors of TbetaRI kinase with K(i) value as low as 15 nM. Kinetic analysis revealed that these pyrazoles act through the ATP-binding site and are typical ATP competitive inhibitors with tight binding kinetics. More importantly, these compounds were shown to inhibit TGF-beta-induced Smad2 phosphorylation in vivo in NMuMg mammary epithelial cells with potency equivalent to the inhibitory activity in the in vitro kinase assay. Cellular selectivity analysis demonstrated that these pyrazoles are capable of inhibiting activin signaling but not bone morphogenic protein or platelet-derived growth factor signal transduction pathways. Further functional analysis revealed that pyrazoles are capable of blocking the TGF-beta-induced epithelial-mesenchymal transition in NMuMg cells, a process involved in the progression of cancer, fibrosis, and other human diseases. These pyrazoles provide a foundation for future development of potent and selective TbetaRI kinase inhibitors to treat human disease.

Adenosine Triphosphate↗
PubMed1987

Kinetic studies of recA protein binding to a fluorescent single-stranded polynucleotide.

Fluorescence spectroscopy was used to investigate the binding of Escherichia coli recA protein to a single-stranded polynucleotide. Poly(deoxy-1,N6-ethenoadenylic acid) was prepared by reaction of chloroacetaldehyde with poly(deoxyadenylic acid). The fluorescence of poly(deoxy-1,N6-ethenoadenylic acid) was enhanced upon recA protein binding. The kinetics of the binding process were studied as a function of several parameters: ionic concentration (KCl and MgCl2), pH, nature of the nucleoside triphosphate [adenosine 5'-triphosphate or adenosine 5'-O-(gamma-thiotriphosphate)], protein and polynucleotide concentrations, polynucleotide chain length, and order of sequential additions. The observed kinetic curves exhibited a lag phase followed by a slow binding process characteristic of a nucleation-elongation mechanism with an additional slow step governing the rate of the association process. The lag phase reflecting the nucleation step was not observed when the protein was first bound to the polynucleotide before addition of adenosine 5'-triphosphate. Adenosine 5'-triphosphate induced a dissociation of the recA protein, which was immediately followed by binding of the recA-adenosine 5'-triphosphate-Mg2+ ternary complex. The origin of this "mnemonic effect" and of the different kinetic steps is discussed with respect to protein conformational changes and aggregation phenomena.

Adenosine Triphosphate↗
PubMed2003

Binding of zona binding inhibitory factor-1 (ZIF-1) from human follicular fluid on spermatozoa.

Previous studies showed that zona binding inhibitory factor-1 (ZIF-1) was the glycoprotein mainly responsible for the spermatozoa zona binding inhibitory activity of human follicular fluid. ZIF-1 has a number of properties similar to glycodelin-A. A binding kinetics experiment in the present study demonstrated the presence of two binding sites of ZIF-1 on human spermatozoa. These binding sites were saturable, reversible, and bound to (125)I-ZIF-1 in a time-, concentration-, and temperature-dependent manner. Glycodelin-A shared one common binding site with ZIF-1 on spermatozoa, and it could displace only 70% of the (125)I-ZIF-1 bound on human spermatozoa. ZIF-1 and glycodelin-A formed complexes with the soluble extract of human spermatozoa. Coincubation of solubilized zona pellucida proteins reduced the binding of ZIF-1 to two complexes of the extract, suggesting that the ZIF-1 binding sites and zona pellucida protein receptors on human spermatozoa were closely related. ZIF-1, but not glycodelin-A, significantly suppressed progesterone-induced acrosome reaction of human spermatozoa. The carbohydrate moieties derived from ZIF-1 reduced the binding of native ZIF-1 on human spermatozoa as well as the zona binding inhibitory activity of the glycoprotein, although the intensity of the effects are lower when compared with the native protein. These effects are not due to the action of the molecules on the motility, viability, and acrosomal status of the treated spermatozoa. Deglycosylated ZIF-1 had no inhibitory effect on both ZIF-1 binding and zona binding capacity of spermatozoa. We concluded that the carbohydrate part of ZIF-1 was critical for the functioning of the glycoprotein.

Acrosome Reaction↗
PubMed1996

Mutants of single chain interleukin 5 show asymmetric recruitment of receptor alpha and betac subunits.

Dual asymmetric mutagenesis of single-chain interleukin 5 (scIL5) was used to obtain evidence that the normally homodimeric IL5 molecule, which contains two 4-helix bundle domains arranged symmetrically about a 2-fold axis, can recruit receptor alpha and betac subunits asymmetrically. Functionally active scIL5 was constructed using recombinant DNA methods by linking two IL5 monomers with a Gly-Gly linker. Mutants were constructed at residues Arg91, Glu110, and Trp111, previously shown to be involved in IL5 receptor alpha chain binding, and at residue Glu13, known to be involved in signal transduction presumably through interaction with the receptor betac chain. Mutants were examined for receptor alpha chain binding by an optical biosensor assay and for bioactivity using a cell proliferation assay. Substitution of the two binding site residues R91 and W111 in the same 4-helix bundle domain caused a 5-fold greater reduction in receptor binding affinity than when the two substitutions were distributed one in each domain. Substitution of E13 and R91 either in the same or in opposite domains gave comparable IL5Ralpha chain binding kinetics, essentially unchanged from those of scIL5. However, in contrast to the binding affinity pattern observed with R91A/W111A dual mutants, distributing the E13A/R91A mutations between the two 4-helix bundle domains caused a 5-6-fold greater loss of bioactivity than when the two changes were in the same domain, leaving the other domain unaltered. Taken with previous mutagenesis data, these results are consistent with a single shared-site model of IL5-IL5Ralpha chain recognition in which a single alpha chain can orientate in either of two modes, each one of which is stabilized preferentially by one of the two 4-helix bundles of IL5. Furthermore, the results suggest that a single betac molecule is activated for each IL5, through the Glu13 residue on the same helix bundle domain that dominates the IL5Ralpha interaction.

Animals↗
PubMed2006

Nature of the binding interaction for 50 structurally diverse chemicals with rat estrogen receptors.

This study was conducted to characterize the estrogen receptor (ER)-binding affinities of 50 chemicals selected from among the high production volume chemicals under the U.S. EPA's (U.S. Environmental Protection Agency's) Toxic Substances Control Act inventory. The chemicals were evaluated using the rat uterine cytosolic (RUC) ER-competitive binding assay, with secondary analysis using Lineweaver-Burk plots and slope replots to confirm true competitive inhibition and to determine an experimental K(i). Data from these ER-competitive binding assays represent the types of competitive binding curves that can be obtained when screening chemicals with broad structural diversity. True competitive inhibition was observed in 17 of 50 chemicals. Binding affinities were much lower than that of estradiol (E(2)) with K(i) concentrations ranging from 0.6 to 373 microM as compared with that of E(2) (0.77 nM). Other chemicals that appeared to displace radiolabeled E(2) binding to ER were, in fact, found not to be competitive inhibitors in the secondary K(i) experiments. These seven chemicals likely altered the stability of the assay by changing the buffer pH, denaturing ER, or disrupting the ER-binding kinetics. Thus, several conditions that may confound interpretation of RUC ER-binding assay data are illustrated. For another group of eight chemicals, neither an IC(50) nor K(i) could be determined due to solubility constraints. These chemicals exhibited slight (20-40%) inhibition at concentrations of 10-100 microM, suggesting that they could be competitors at very high concentrations, yet K(i) experiments were not possible as the limit of chemical solubility in the aqueous assay buffer was well above the IC(50). An additional 18 of the 50 chemicals were classified as nonbinders because in concentrations up to 100 microM they produced essentially no displacement of radiolabeled E(2). These results show that although the ER-competitive binding assay is a valuable tool for screening chemicals, secondary tests such as a double reciprocal Lineweaver-Burk experiment with slope replot should be used to confirm true competitive inhibition. This information will be useful for the ongoing validation of the RUC ER-competitive binding assay under the U.S. EPA's Endocrine Disruptor Screening Program, as well as to support research efforts to develop computational models designed to identify chemicals with the ability to bind to ER.

Animals↗
PubMed2002

Mutations in the extracellular amino-terminal domain of the NK2 neurokinin receptor abolish cAMP signaling but preserve intracellular calcium responses.

By combining real time measurements of agonist binding, by fluorescence resonance energy transfer, and of subsequent responses, we proposed previously that the neurokinin NK2 receptor preexists in equilibrium between three states: inactive, calcium-triggering, and cAMP-producing. Thr(24) and Phe(26) of the NK2 receptor extracellular domain are considered to interact with neuropeptide agonists based on the reduction of affinity when they are substituted by alanine. Using fluorescence resonance energy transfer, we now quantify the binding kinetics of two Texas Red-modified neurokinin A agonists to the fluorescent wild-type (Y-NK2wt) and the mutant (Y-NK2mut) receptor carrying Thr(24) --> Ala and Phe(26) --> Ala mutations. TR1-neurokinin A binds with a fast component and a slow component to the Y-NK2wt receptor and triggers both a calcium and a cAMP response. In contrast, on the mutant receptor, it binds in a single fast step with a lower apparent affinity and activates only the calcium response. Another agonist, TRC4-neurokinin A, binds to both wild-type and mutant receptors in a single fast step, with similar affinities and kinetics and promotes only calcium signaling. Kinetic modeling of ligand binding and receptor interconversions is carried out to analyze phenotypic changes in terms of binding alterations or changes in the transitions between conformational states. We show that the binding and response properties of the Y-NK2mut receptor are best described according to a phenotype where a reduction of the transition between the inactive and the active states occurs.

Calcium↗
PubMed1980

Kinetic analysis of calcium binding to concanavalin A.

The kinetics of calcium binding to concanavalin A was studied utilizing ultraviolet difference spectral measurements. The results show that calcium binds to the lectin in a biphasic process: a rapid and reversible phase, followed by a relaxation phase with a kobs of 0.012 sec-1. Kinetic measurements were used to calculate the association constant, Ka, for calcium binding to concanavalin A of 2.7 x 10(4) M-1, in reasonable agreement with values obtained by equilibrium methods.

Calcium↗
PubMed1992

Tightly-bound divalent cation of actin.

Actin is known to undergo reversible monomer-polymer transitions that coincide with various cell activities such as cell shape changes, locomotion, endocytosis and exocytosis. This dynamic state of actin filament self-assembly and disassembly is thought to be regulated by the properties of the monomeric actin molecule and in vivo by the influence of actin-associated proteins. Of major importance to the properties of the monomeric actin molecule are the presence of one tightly-bound ATP and one tightly-bound divalent cation per molecule. In vivo the divalent cation is thought to be Mg2+ (Mg-actin) but in vitro standard purification procedures result in the preparation of Ca-actin. The affinity of actin for a divalent cation at the tight binding site is in the nanomolar range, much higher than earlier thought. The binding kinetics of Mg2+ and Ca2+ at the high affinity site on actin are considered in terms of a simple competitive binding mechanism. This model adequately describes the published observations regarding divalent cation exchange on actin. The effects of the tightly-bound cation, Mg2+ or Ca2+, on nucleotide binding and exchange on actin, actin ATP hydrolysis activity and nucleation and polymerization of actin are discussed. From the characteristics that are reviewed, it is apparent that the nature of the bound divalent cation has a significant effect on the properties of actin.

Actins↗
PubMed1995

Determination of receptor-ligand kinetic and equilibrium binding constants using surface plasmon resonance: application to the lck SH2 domain and phosphotyrosyl peptides.

Experimental and computational methods were developed for surface plasmon resonance (SPR) measurements involving interactions between a solution-binding component and a surface-immobilized ligand. These protocols were used to distinguish differences in affinity between the SH2 domain of lck and phosphotyrosyl peptides. The surface-immobilized ligand was the phosphotyrosyl peptide EPQpYEEIPIA, which contains a consensus sequence (pYEEI) for binding lck SH2. In the kinetic experiment, SPR phenomena were measured during association and dissociation reactions for a series of glutathione-S-transferase (GST)-SH2 concentrations, generating a set of SPR curves. A global computational analysis using an A + B<==>AB model resulted in single set of parameter estimates and statistics. In an abbreviated format, an equilibrium experiment was designed so that equilibrium constants (Keq) could be determined rapidly and accurately. A competitive equilibrium assay was developed for GST-SH2 in which Keq values for a series of phosphotyrosyl peptides (derived from the pYEEI sequence) varied over 3 orders of magnitude. Interestingly, these results highlighted the significance of the +1 glutamate in providing high-affinity binding to the SH2 domain. For most drug discovery programs, these Keq determinations are a sufficient measure of potency for the primary screen, with koff and kon determined in a secondary assay. Thus, the application of these techniques to SPR binding phenomena should prove valuable in the discovery and design of receptor-ligand antagonists.

Amino Acid Sequence↗