Relative Dissociation Constants Research Articles

In Vivo HIV-1 Rev Multimerization in the Nucleolus and Cytoplasm Identified by Fluorescence Resonance Energy Transfer

Nuclear export of intron-containing human immunodeficiency virus type 1 RNA is mediated by the viral Rev protein. Rev is a nucleocytoplasmic transport protein that directly binds to its cis-acting Rev-responsive element RNA. Rev function depends on its ability to multimerize. The in vivo dynamics and the subcellular dependence of this process are still largely unexplored. To visualize and quantitatively analyze the mechanism of Rev multimeric assembly in live cells, we used high resolution in vivo fluorescence resonance energy transfer (FRET) and fluorescence recovery after photobleaching. By using two different dynamic FRET approaches (acceptor photobleaching and donor bleaching time measurements), we observed a strong Rev-Rev interaction in the nucleoli of living cells. Most interestingly, we could also detect Rev multimerization in the cytoplasm; however, FRET efficiency in the cytoplasm was significantly lower than in the nucleolus. By using fluorescence recovery after photobleaching, we investigated the mobility of Rev within the nucleolus. Mathematical modeling of the fluorescence recovery after photobleaching recoveries enabled us to extract relative association and dissociation constants and the diffusion coefficient of Rev in the nucleolus. Our results show that Rev multimerizes in the nucleolus of living cells, suggesting an important role of the nucleolus in nucleocytoplasmic transport.

Adeno-associated virus Rep78/Rep68 promotes localized melting of the rep binding element in the absence of adenosine triphosphate.

We have applied fluorescence anisotropy and molecular beacon fluorescence methods to study the interactions between the Adeno-associated virus Rep78/Rep68 protein and the 23-bp Rep binding element (RBE). Rep78/Rep68 stably interacted with both the single- and double-stranded conformations of the RBE, but the interaction mechanisms of single- and double-stranded DNA appeared to be fundamentally different. The stoichiometry of Rep78 association with both the separate top and bottom strands of the RBE was 1:1, and the relative dissociation constant (K(D)) values of these associations were calculated to be 2.3x10(-8) and 3.2x10(-8) M, respectively. In contrast, the stoichiometry of Rep78 association with the double-stranded RBE was 2:1, and the dissociation constant was determined to be 4.2x10(-15) M(2). Moreover, Rep78/Rep68 interaction with the 23-bp duplex RBE appeared to cause localized melting of the double-stranded DNA substrate in the absence of adenosine triphosphate (ATP). This melting activity showed slower kinetics than binding and may contribute to the initiation of ATP-dependent Rep78 helicase activity.

Characterization and molecular modeling of a highly stable anti-Hepatitis B surface antigen scFv

We raised a mouse monoclonal antibody (5S) against the ‘a’ epitope of the Hepatitis B surface antigen (HBsAg) by selecting for binding of the hybridoma supernatant in conditions that usually destabilize protein–protein interactions. This antibody, which was protective in an in vitro assay, had a high affinity with a relative dissociation constant in the nanomolar range. It also displayed stable binding to antigen in conditions that usually destabilize antigen–antibody interactions, like 30% DMSO, 8 M urea, 4 M NaCl, 1M guanidium HCl and extremes of pH. The variable regions of the antibody were cloned and expressed as an single chain variable fragment (scFv) (A5). A5 had a relative affinity comparable to the mouse monoclonal and showed antigen binding in presence of 20% DMSO, 8 M urea and 3 M NaCl. It bound the antigen in the pH range of 6–8, though its tolerance for guanidium HCl was reduced. Sequence analysis demonstrated a significant increase in the frequency of somatic replacement mutations in CDRs over framework regions in the light but not in the heavy chain. A comparison of the molecular models of the variable regions of the 5S antibody and its germ-line precurser revealed that critical mutations in the heavy and light chains interface resulted in better inter-chain packing and in the movement of CDR H3 and CDR L1 from their germline positions, which may be important for better antigen binding. In addition to providing a reagent for neutralizing for the virus, such an antibody provides a model for the evolution of stable high affinity interaction during antibody maturation.

Activation and inhibition of rubber transferases by metal cofactors and pyrophosphate substrates

Metal cofactors are necessary for the activity of alkylation by prenyl transfer in enzyme-catalyzed reactions. Rubber transferase (RuT, a cis-prenyl transferase) associated with purified rubber particles from Hevea brasiliensis, Parthenium argentatum and Ficus elastica can use magnesium and manganese interchangably to achieve maximum velocity. We define the concentration of activator required for maximum velocity as [A]max. The AmaxMg2+ in F. elastica (100 mM) is 10 times the AmaxMg2+ for either H. brasiliensis (10 mM) or P. argentatum (8 mM). The AmaxMn2+ in F. elastica (11 mM), H. brasiliensis (3.8 mM) and P. argentatum (6.8 mM) and the AmaxMg2+ in H. brasiliensis (10 mM) and P. argentatum (8 mM) are similar. The differences in AmaxMg2+ correlate with the actual endogenous Mg2+ concentrations in the latex of living plants. Extremely low Mn2+ levels in vivo indicate that Mg2+ is the RuT cofactor in living H. brasiliensis and F. elastica trees. Kinetic analyses demonstrate that FPP–Mg2+ and FPP–Mn2+ are active substrates for rubber molecule initiation, although free FPP and metal cations, Mg2+ and Mn2+, can interact independently at the active site with the following relative dissociation constants KdFPP <KdFPP–Metal <KdE–Metal. Similarly, IPP–Mg2+ and IPP–Mn2+ are active substrates for rubber molecule polymerization. Although metal cations can interact independently at the active site with the relative dissociation constant KdIPP–Metal <KdE–Metal, unlike FPP, IPP alone does not interact independently. All three RuTs have similar characteristics—indeterminate sized products, high KmIPP, high metal [A]max, metal cofactor requirements, and are membrane-bound enzymes.

Examination of the physical properties of polyphosphazene-silicate nanocomposites using novel synthetic strategies

Phosphazene-silicate nanocomposites were synthesized and their mechanical properties analyzed. Three distinct types of catalysts were employed to drive the ceramic condensation—acid, base and ionic salt species—resulting in a wide variety of mechanical properties. To validate the correlations between the physical properties observed and the ceramic morphologies formed, a survey of the extent of parent polymer degradation under these catalytic conditions was undertaken. Further, the effects of various ionic strengths of casting solutions resulting from relative dissociation constants, hence active catalyst availability, on salt-catalyzed silicate interpenetrating network (IPN) matrices were also investigated. The resulting information provides the appropriate synthetic control needed to produce nanocomposites with specifically tailored properties for a variety of applications.

Quantum mechanical prediction of the magnetic titration curve of a nitroxide `spin probe'

The variation of the magnetic properties of 2,2,5,5,tetrametyhl-4,methyl-imidazoline nitroxide with the pH of the embedding medium is investigated by means of quantum mechanical calculations. The hyperfine coupling constants of the nitroxide are determined by mixed QCISD/PBE0 calculations, while the geometry of the neutral and protonated nitroxide and the relative dissociation constants are calculated at the PBE0 level. Solvent effects are modelled both by including a few explicit solvent molecules (strongly bound to the solute) and by using the CPCM method. The agreement between the calculated and the experimental titration curve is quite good, confirming the reliability of our computational strategy.

Evaluation of chemiluminescent estradiol conjugates by using a surface plasmon resonance detector

A series of chemiluminescent 17β-estradiol probes were synthesized. Relative equilibrium dissociation constants ( K D) for the interaction of an anti-E 2 Fab fragment for the probes in solution were evaluated using a single E 2-analog biosensor surface on a BIAcore surface plasmon resonance instrument. The results show the antibody fragment binds all chemiluminescent conjugates tested with high affinity showing only minor preferences for site of substitution (C6 versus C7), stereochemistry (α versus β), or linker moiety.

Protein Domain Mapping by λ Phage Display: The Minimal Lactose-Binding Domain of Galectin-3

Mapping of protein domains having a distinct function is essential to understanding the protein's structure–function relationship. We used a bacteriophage λ surface expression vector, λfoo, in order to determine the minimal carbohydrate-binding domain of human galectin-3 (Gal-3). Gal-3 cDNA was randomly digested by DNase I and cloned into the phage vector. The library generated was screened by affinity selection using lactose immobilized on agarose beads. DNA sequence analysis of a set of isolated clones defined the minimal folding domain of Gal-3 required for lactose binding, which consisted of 136 amino-acid residues. Using the phage clones isolated, we also determined relative dissociation constants in solution between lactose and the minimal domain expressed on the phage surface. This technique does not require either purified or labeled proteins, and bacteriophage λ surface display may, therefore, be useful for protein domain mapping and in vitro studies of various macromolecular interactions.

Two distinct segments of the hepatitis B virus surface antigen contribute synergistically to its association with the viral core particles

The long surface antigen polypeptide (L-HBsAg) of hepatitis B virus (HBV) is believed to mediate contact between the virus envelope and nucleocapsid protein (HBcAg). The N and C termini of L-HBsAg were shortened progressively in order to define the minimum contiguous sequence of amino acids that contains the residues necessary for association with HBcAg. The resulting mutants were expressed in rabbit reticulocyte lysates and their interaction with HBcAg was examined with an immunoprecipitation assay and an equilibrium binding assay in solution to give relative dissociation constants. Binding of HBcAg particles by L-HBsAg displayed two widely differing dissociation constants, indicating two distinct binding sites between the molecules. The two distinct sites, one located between residues 24 and 191 and the other between residues 191 and 322 of L-HBsAg, contribute synergistically to high-affinity binding to HBcAg, but disruption of either of these segments resulted in a much weaker interaction showing only one dissociation constant. Inhibition of the interaction by peptides that bind to the tips of the nucleocapsid spikes differentiated contacts in HBcAg for the two binding domains in L-HBsAg and implied that the amino-terminal binding domain contacts the tips of the HBcAg spikes. Analysis of specific single amino acid mutants of L-HBsAg showed that Arg92 played an important role in the interaction.

Peptides that block hepatitis B virus assembly: analysis by cryomicroscopy, mutagenesis and transfection.

Peptides selected to bind to hepatitis B virus (HBV) core protein block interaction with the long viral surface antigen (L-HBsAg) in vitro. High resolution electron cryomicroscopy showed that one such peptide binds at the tips of the spikes of the core protein shell. The peptides contain two basic residues; changing either of two acidic residues at the spike tip to an alanine greatly reduced the binding affinity. Transfection of hepatoma cells with a replication-competent HBV plasmid gave significantly reduced production of virus in the presence of peptide, in a dose-dependent manner. These experiments show that the interaction of L-HBsAg with core particles is critical for HBV assembly, and give proof of principle for its disruption in vivo by small molecules.

Influence of lipid composition on pediocin PA-1 binding to phospholipid vesicles.

Pediocin PA-1 bound to anionic lipid vesicles with saturated or unsaturated fatty acid chains in a lipid concentration-dependent fashion. Little change in binding parameters was observed for zwitterionic lipid vesicles. Decreasing the anionic lipid content of the vesicles gave a higher relative dissociation constant for the peptide-lipid interactions and further supports the electrostatic interaction model of binding.

Functional interference of Sp1 and NF-kappaB through the same DNA binding site.

Gene activation by NF-kappaB/Rel transcription factors is modulated by synergistic or antagonistic interactions with other promoter-bound transcription factors. For example, Sp1 sites are often found in NF-kappaB-regulated genes, and Sp1 can activate certain promoters in synergism with NF-kappaB through nonoverlapping binding sites. Here we report that Sp1 acts directly through a subset of NF-kappaB binding sites. The DNA binding affinity of Sp1 to these NF-kappaB sites, as determined by their relative dissociation constants and their relative efficiencies as competitor DNAs or as binding site probes, is in the order of that for a consensus GC box Sp1 site. In contrast, NF-kappaB does not bind to a GC box Sp1 site. Sp1 can activate transcription through immunoglobulin kappa-chain enhancer or P-selectin promoter NF-kappaB sites. p50 homodimers replace Sp1 from the P-selectin promoter by binding site competition and thereby either inhibit basal Sp1-driven expression or, in concert with Bcl-3, stimulate expression. The interaction of Sp1 with NF-kappaB sites thus provides a means to keep an elevated basal expression of NF-kappaB-dependent genes in the absence of activated nuclear NF-kappaB/Rel.

Using altered specificity Oct-1 and Oct-2 mutants to analyze the regulation of immunoglobulin gene transcription.

Oct-1 and Oct-2 represent the prototypical example of related transcription factors with identical DNA recognition properties. They bind functionally critical octamer elements found in diverse regulatory sequences. It has not been possible to determine directly if these factors are functionally redundant or selective when interacting with different regulatory sequences in the appropriate cell type. An equivalent pair of altered DNA-binding specificity mutants of Oct-1 and Oct-2 are used to examine their function from varied regulatory contexts in B cells. These factors function as redundant activators of immunoglobulin (Ig) gene promoters (Vkappa and VH) and a histone H2B promoter. The structural basis of redundancy resides in the highly conserved DNA-binding POU domain, because this domain of either protein can activate transcription from both Ig and H2B promoters. We find that the nature of a distal enhancer dictates the relative potency of Oct-1 versus Oct-2 bound to a promoter. Oct-1 preferentially stimulates transcription from a VH or Vkappa promoter in combination with enhancers from the IgH or Igkappa locus, respectively. In this context, the more potent action of Oct-1 is dependent on a region external to the POU domain. These results suggest that Oct-1 may be the critical regulator of Ig gene transcription during B cell development and provide an explanation for selective Ig isotype expression defects in Oct-2 and OCA-B null mice.

Determination of acid dissociation constants of peptide side-chain functional groups by two-dimensional NMR.

An NMR method is described for determining residue-specific acid dissociation constants for peptides which contain more than one residue of the same acidic or basic amino acid. The method is based on using the differences in C alpha H proton chemical shifts which result from peptide sequence nearest-neighbor and possibly secondary structure effects to resolve resonances for carbon-bonded reporter protons adjacent to each side-chain acidic group in two-dimensional total correlation spectroscopy (TOC-SY) spectra. Acid dissociation constants were determined for each of the four lysine side-chain ammonium groups of the peptide Lys-Asn-Asn-Gln-Lys-Ser-Glu-Pro-Leu-Ile-Gly-Arg-Lys-Lys-Thr-NH2. Resonances for the C epsilon H2 protons adjacent to the four side-chain ammonium groups, which overlap in the one-dimensional spectrum, were resolved using the C alpha H-C epsilon H2 cross peaks in the TOCSY spectrum. Chemical shift-pH titration data were obtained for each lysine side-chain ammonium group from one-dimensional subspectra taken from two-dimensional TOCSY spectra measured as a function of pH. The pKAs of the Lys1, Lys5, Lys13, and Lys14 side-chain ammonium groups were determined to be 11.14 +/- 0.01, 10.95 +/- 0.01, 10.96 +/- 0.02, and 11.09 +/- 0.02, respectively. The chemical shift-pH titration data were also analyzed by a pH-independent procedure to obtain relative acid dissociation constants: KA(Lys1)/KA(Lys5) = 0.663 +/- 0.009, KA(Lys1)/KA(Lys13) = 0.703 +/- 0.014, and KA(Lys1)/KA(Lys14) = 0.910 +/- 0.009, which correspond to relative acidities for the side-chain ammonium groups of Lys1, Lys5, Lys13, and Lys14 of 1:1.508:1.422:1.099. To further demonstrate the utility of this method, acid dissociation constants were determined for the six acidic groups of the peptide Glu-Ala-Cys-Asn-Pro-Ala-Ala-Gly-Arg-His-Tyr-Ser-Cys-NH2. Chemical shift-pH titration curves were obtained for the C beta H2 protons adjacent to the two cysteine thiol groups using one-dimensional subspectra taken from TOCSY spectra measured as a function of pH. The pKAs of the CyS3 and Cys13 thiol groups were determined to be 9.21 +/- 0.07 and 8.60 +/- 0.06, respectively. The relative acid dissociation constants (KA(Cys3)/ (KA(Cys13)) were found to be 0.21 +/- 0.06 by the pH-independent calculation procedure.

The SRP9/14 subunit of the human signal recognition particle binds to a variety of Alu-like RNAs and with higher affinity than its mouse homolog.

The heterodimeric subunit, SRP9/14, of the signal recognition particle (SRP) has previously been found to bind to scAlu and scB1 RNAs in vitro and to exist in large excess over SRP in anthropoid cells. Here we show that human and mouse SRP9/14 bind with high affinities to other Alu-like RNAs of different evolutionary ages including the neuron-specific BC200 RNA. The relative dissociation constants of the different RNA-protein complexes are inversely proportional to the evolutionary distance between the Alu RNA species and 7SL RNA. In addition, the human SRP9/14 binds with higher affinity than mouse SRP9/14 to all RNAs analyzed and this difference is not explained by the additional C-terminal domain present in the anthropoid SRP14. The conservation of high affinity interactions between SRP9/14 and Alu-like RNAs strongly indicates that these Alu-like RNPs exist in vivo and that they have cellular functions. The observation that human SRP9/14 binds better than its mouse counterpart to distantly related Alu RNAs, such as recently transposed elements, suggests that the anthropoid-specific excess of SRP9/14 may have a role in controlling Alu amplification rather than in compensating a defect in SRP assembly and functions.

Structure-Function Relationships of Cellular Retinoic Acid-binding Proteins: QUANTITATIVE ANALYSIS OF THE LIGAND BINDING PROPERTIES OF THE WILD-TYPE PROTEINS AND SITE-DIRECTED MUTANTS

It has been suggested that electrostatic interactions are critical for binding of retinoic acid by cellular retinoic acid-binding proteins (CRABP-I and CRABP-II). However, the roles of two conserved arginine residues (Arg-111 and Arg-131 in CRABP-I; Arg-111 and Arg-132 in CRABP-II) that interact with the carboxyl group of retinoic acid have not been evaluated. A novel competitive binding assay has been developed for measuring the relative dissociation constants of the site-directed mutants of CRABPs. Arg-111 and Arg-132 of CRABP-II were replaced with methionine by site-directed mutagenesis. The relative dissociation constants of R111M and R132M (Kd (R111M)/Kd (CRABP-II) and Kd (R132M)/Kd(CRABP-II)) were determined to be 40-45 and 6-8, respectively. The ring protons of the aromatic residues of the wild-type CRABP-II and the two mutants were sequentially assigned by two-dimensional homonuclear NMR in conjunction with three-dimensional heteronuclear NMR. Detailed analysis of the nuclear Overhauser effect spectroscopy spectra of the proteins indicated that the conformations of the two mutants are highly similar to that of the wild-type CRABP-II. These results taken together showed that Arg-111 and Arg-132 are important for binding retinoic acid but contribute to the binding energy only by approximately 2.2 and 1.2 kcal/mol, respectively. In addition, the relative dissociation constant of CRABP-II and CRABP-I (Kd (CRABP-II)/Kd (CRABP-I)) was determined to be 2-3, in close agreement with that calculated using the apparent Kd values determined under the same conditions by fluorometric titrations.

Screening a monoclonal antibody with a fusion-phage display library shows a discontinuity in a linear epitope within pres1 of hepatitis B virus

The epitope recognized by the monoclonal antibody MA18/7, specific for the PreS1-domain of the hepatitis B virus surface antigen, has been defined precisely by means of a library of fusion-phage carrying random hexapeptides on the tip of filamentous phage fd particles. Phage, isolated after only one round of affinity selection, displayed hexapeptides showing strong conservation of the PreS1 primary sequence in the region 19-23 with three noncontiguous residues, DP (20 and 21) and F (23) appearing in phage that bound the antibody. The importance of these core residues was supported by comparing the antibody binding of individual phage in solution, which provided relative dissociation constants for these interactions. Replacement of F (23) by Y was the only substitution observed in the three core residues, and resulted in somewhat weaker binding. Synthetic tetra- and hexapeptides containing these key residues inhibited the reaction between the phage and the antibody.

Direct measurement via phage titre of the dissociation constants in solution of fusion phage-substrate complexes.

Studies of interactions between filamentous fusion phage particles and protein or nucleic acid molecules have gained increasing importance with recent successes of screening techniques based upon random phage display libraries (biopanning). Since a number of different phage are usually obtained by biopanning, it is useful to compare quantitatively the binding affinities of individual phage for the substrate used for selection. A procedure is described for determination of relative dissociation constants (KdRel) between filamentous phage carrying peptide fusions to the coat protein gpIII and substrates in solution. This novel method is based on the measurement of phage titres. Phage selected from a random fusion phage library for binding to a monoclonal antibody or a viral structural protein exhibited KdRel values in the nanomolar and micromolar ranges for their respective substrates, thus validating the method over a wide range of binding affinities.

The interaction of prothrombin with phospholipid membranes is independent of either kringle domain

Prothrombin contains two kringle domains, a structural motif common to other plasma proteins involved in hemostasis and fibrinolysis. To determine the role of the kringle domains of prothrombin, we prepared three recombinant human prothrombin forms lacking the first kringle domain (residues 63-144; PT/delta K1), the second kringle domain (residues 144-249; PT/delta K2), or both kringle domains (63-249; PT/delta K1,2). The isolated prothrombin proteins were greater than 95% pure by SDS-polyacrylamide gel electrophoresis and were well carboxylated. PT/delta K1 displayed 50% of the specific coagulant activity of plasma prothrombin, PT/delta K2 had 10% of the specific coagulant activity, and PT/delta K1,2 was inactive. Polyclonal antibodies directed against the Ca(II)-specific conformer of prothrombin bound PT/delta K1 and PT/delta K2 with the same affinity as prothrombin, indicating that the Ca(II)-induced conformational transition does not involve sites on the prothrombin kringle domains. Gel filtration studies demonstrated that radiolabeled plasma prothrombin and all of the prothrombin kringle deletion mutants bound to phospholipid vesicles in the presence of Ca(II) but not in the presence of Mg(II) or EDTA. Relative dissociation constants of 1.10 +/- 0.75 and 0.49 +/- 0.18 microM were obtained by quasielastic light scattering for the interaction of phospholipid vesicles with plasma prothrombin and PT/delta K1, respectively. These data indicate that neither the first nor the second kringle domain contain unique sites for the interaction of prothrombin with phospholipid vesicles and are not required for prothrombin-phospholipid binding.

Substrate-specific enhancement of the oxidative half-reaction of monoamine oxidase.

Monoamine oxidases A and B have identical flavin sites but different, although overlapping, amine substrate specificity. Reoxidation of ternary complexes containing substrate is much faster than of free enzyme, and the enhancement is greater in the A form than the B form. The oxidative half-reaction was studied with a variety of substrates to elucidate the specificity of the effect and to probe the different influences of substrate on the flavin reoxidation in the two forms of the enzyme. The second-order rate constant for the reoxidation was highest with monoamine oxidase A when kynuramine was the ligand (508 x 10(3) M-1 s-1) compared to 4 x 10(3) M-1 s-1 in its absence. MPTP (166 x 10(3) M-1 s-1) also enhanced reoxidation well, but indole substrates stimulated only poorly (e.g., tryptamine, 29 x 10(3) M-1 s-1; serotonin, 50 x 10(3) M-1 s-1). For the A form, the reduction of the flavin was rate-limiting in all cases. For the B form, reoxidation was rate-limiting for beta-phenylethylamine and contributed to the determination of the overall rate with several substrates. The ratio of the enhanced rate of oxidation to the rate of reduction correlated with the redox state of the enzyme in turnover experiments. All the observations are consistent with alternate paths of reoxidation, via either free enzyme or a reduced enzyme-substrate complex. The flux through each path is determined by the relative dissociation constants and rate constants.