Investigation toward multi-epitope vaccine candidates using native chemical ligation

We applied native chemical ligation (NCL) method to the synthesis of highly pure lipid-core peptide (LCP) vaccines to attach various peptide epitopes. In the case of the synthesis of LCP vaccine with two different peptide epitopes, LCP moieties having two free Cys and two protected Cys derivatives (S-acetamidemethyl-Cys, (Cys(Acm)), N-methylsulfonylethyloxycarbonyl-Cys (Msc-Cys), or 1,3-thiazolidine-4-carboxylic acid (Thz)) on oligolysine branches were prepared in order to couple two different epitopes by stepwise NCL. It was found that the difficulty in NCL of first two peptide antigen was associated with the steric hindrance. Using Thz instead of Cys(Acm) and Msc-Cys was important to reduce the steric hindrance and improve NCL yield.     

Conditions for the existence of critical points in scatchard plots of binding results

An equation is presented in Scatchard format which describes the binding of a ligand to a two-state acceptor system (either isomerizing or polymerizing). It is used to formulate a general set of conditions for the existence of critical points in Scatchard plots and this set is explored in detail for particular cases. Explicit relations between the thermodynamic parameters governing the binding are thereby obtained which permit discussion of the boundaries of domains within which critical points may exist. Moreover, several items of evidence are presented which show that there is an exact correspondence between the appearance of critical points in Scatchard plots and points of inflexion in associated binding curves examples are presented where zero, one or more critical points and points of inflexion are observed. Finally, the effects on preferential binding of the variation of the environmental parameters, temperature and pressure (and for acceptor polymerization, the total acceptor concentration) are discussed in terms of the derived conditions of existence of critical points in Scatchard plots and their equivalent domains of sigmoidality of binding curves.     

Membrane IgM-mediated signaling of human B cells. Effect of increased ligand binding site valency on the affinity and concentration requirements for inducing diverse stages of activation.

The potential for ligand-initiated signal transduction through B cell membrane IgM is assessed in terms of ligand concentration, binding site valency, and binding site affinity for membrane Ig. Estimates of the physicochemical requirements for achieving G0* enhancement of class II MHC expression, G1 entry, and S phase entry in human B cells were made by comparing the stimulatory effects of three affinity-diverse anti-Cmu2 mAb when in bivalent (unconjugated) form, or as mAb-dextran conjugates with low binding site valency (oligovalent ligands) or high binding site valency (multivalent ligands). An increase in binding site number (and concomitant molecular mass) caused a profound reduction in both the minimal concentration and affinity requisites for B cell activation. The enhancing effect of increased binding site valency was most evident for the signaling of those most distal stages in B cell activation, i.e., G1 and S phase, which were difficult to induce with bivalent ligands. The results suggest that highly multimeric TI-2 Ag may be good immunogens because they are able to elicit a full activation response not only from infrequent high affinity B cells, but also from a substantial proportion of the many lower affinity Ag-specific B cells in virgin B cell populations. Interestingly, the activation of B cells by ligands with binding sites of high intrinsic affinity (Ka = 5 x 10(8) M-1) was less influenced by increases in binding site valency than was B cell activation by ligands with intermediate binding site affinity (Ka = 2 x 10(7) M-1). This suggests that the minimal epitope valency requirement for T cell-independent B cell activation by mIg cross-linking Ag may be dependent on the intrinsic affinity with which membrane Ig molecules on a given B cell interact with the redundantly expressed epitopes.     

Interactions between micellar ligand systems and acceptors: Forms of binding curves

A previously formulated expression describing the competitive binding to an acceptor of two states of a ligand, monomeric and polymeric, coexisting in equilibrium is examined in terms of the different forms of Scatchard plots which may arise in cases of exclusive and of preferential binding of the ligand states. It is shown by differentiation of the binding equation written in Scatchard format, and by numerical examples, that exclusive binding of the monomeric form of ligand leads to Scatchard plots that are either sigmoidal or convex to the abscissa, whereas exclusive binding of the polymeric form results in plots concave to the abscissa and exhibiting a maximum. Particular attention is given to Scatchard plots which possess two critical points, a situation which is shown to be possible when the polymeric form of ligand binds preferentially (but not exclusively) to the acceptor. The two-state ligand concept is especially pertinent to solutes capable of globular micelle formation and several examples are cited of binding studies which have been conducted with such micellar systems. Of these, the chlorpromazine-brain tubulin system is given detailed consideration in order to illustrate the use of the present theory in describing the binding results which exhibit two critical points when plotted in Scatchard format.     

Ligand size as a determinant for catabolism by the low density lipoprotein (LDL) receptor pathway. A lattice model for LDL binding

Low density lipoproteins (LDL) are large (Mr = 2.5 x 10(6)) in comparison to LDL receptors (Mr = 115,000). Since most LDL receptors are clustered in coated pits, we tested the hypothesis that crowding of receptor-bound LDL particles would cause steric effects. The apparent affinity of LDL for receptors on cultured fibroblasts decreased near saturation causing concave-upward Scatchard plots. Both the higher and lower affinity components of binding were up-regulated by the cholesterol synthesis inhibitor, lovastatin, indicating that the entire binding curve was sterol-responsive. In contrast, neither component of LDL binding was present on lovastatin-treated or untreated null fibroblasts which are incapable of expressing LDL receptors. Therefore, the concave-upward Scatchard plots were entirely due to binding to LDL receptors. These results are consistent with a lattice model in which receptor-bound LDL are large enough to decrease binding to adjacent receptors. A lattice model implies that large LDL should produce steric effects at a lower receptor occupancy than should small LDL. This was tested using seven LDL fractions that differed in diameter from 20 to 27 nm. Fewer large than small LDL were bound to the cell surface at 4 degrees C and 37 degrees C, and fewer were internalized and degraded at 37 degrees C. Since large LDL bound via both apolipoprotein (apo) E and apoB100, receptor cross-linking could have caused fewer large LDL to be bound at saturation. However, when the potential for cross-linking was prevented by an apo-E-specific monoclonal antibody (1D7), the difference in binding by large versus small LDL was not eliminated; instead, it was exaggerated. Taken together, these results support a lattice model for LDL binding and indicate that steric hindrance associated with crowding of LDL particles on receptor lattices is a major determinant for catabolism by the LDL receptor pathway in vitro.     

An examination of the forms of scatchard plots of binding results outside domains of sigmoidality

General expressions are formulated for the first and second derivatives of the Scatchard function, r/[S], with respect to the binding function, r, from an equation that describes the binding of a ligand to a two-state acceptor system (either isomerizing or polymerizing). The expressions are utilized to determine the sign of the second derivative for particular systems under conditions where the first derivative is negative for all r. The work therefore correlates with previous studies, which stressed conditions of existence of critical points in Scatchard plots, by examining more fully possible forms of binding curves outside such domains of sigmoidality. Particular attention is given to the condition, d(r/[S])/dr < 0 and d²(r/[S])/dr² > 0 for all r (which defines a Scatchard plot convex to the r-axis). In agreement with previous findings it is proven that the isomerizing acceptor model cannot give rise to this form of plot and is therefore distinguished from negatively co-operative allosteric models. On the other hand, the polymerizing acceptor model may yield such a Scatchard plot, a feature demonstrated by formulating explicit conditions for its manifestation when ligand binding is exclusive to the polymeric state, and illustrated numerically for a system in which ligand binds to both oligomeric states. Distinction between such systems and those exhibiting negative co-operativity is possible on the basis of the Scatchard plots, which exhibit dependence on acceptor concentration in the case of a polymerizing acceptor; indeed, an example is provided where variation of acceptor concentration for a system characterized by fixed interaction parameters effects a conversion from sigmoidal binding behaviour to that typified by a Scatchard plot convex to the r-axis.     

Steric effects on multivalent ligand-receptor binding: exclusion of ligand sites by bound cell surface receptors.

Steric effects can influence the binding of a cell surface receptor to a multivalent ligand. To account for steric effects arising from the size of a receptor and from the spacing of binding sites on a ligand, we extend a standard mathematical model for ligand-receptor interactions by introducing a steric hindrance factor. This factor gives the fraction of unbound ligand sites that are accessible to receptors, and thus available for binding, as a function of ligand site occupancy. We derive expressions for the steric hindrance factor for various cases in which the receptor covers a compact region on the ligand surface and the ligand expresses sites that are distributed regularly or randomly in one or two dimensions. These expressions are relevant for ligands such as linear polymers, proteins, and viruses. We also present numerical algorithms that can be used to calculate steric hindrance factors for other cases. These theoretical results allow us to quantify the effects of steric hindrance on ligand-receptor kinetics and equilibria.     

A model of neutralization of Chlamydia trachomatis based on antibody and host cell aggregation on the elementary body surface

Humoral immunity is that aspect of specific immunity that is mediated by B lymphocytes and involves the neutralizing of pathogens by means of antibodies attaching to the pathogen's binding sites. Antibodies bind to and block ligand sites on the pathogen which prevents these sites from attaching to target cell receptors and so cell entry is inhibited. Many studies investigate the role of humoral immunity for protection against chlamydial challenge and they have shown that neutralization of the chlamydial body requires a large number of attached antibodies. Steric hindrance greatly influences the number of available sites that may be bound, reducing relative occupancy well below 100%. We model steric effects of antibody Fab fragment attachment indicating that they must be taken into consideration to accurately model valency, the number of available binding sites. We derive a partial differential equation for the number of antibody Fabs and host cell receptors that are aggregated to extracellular chlamydial elementary bodies. We consider steric effects in describing the size distribution of aggregates. Our theory is in good agreement with Monte Carlo simulations of binding. We use our theoretical prediction for the valency in a model for the in-host population dynamics of a chlamydial infection and we fit our model to experimental data.     

Studies on tautomeric forms of Guanine-Cytosine base pairs of nucleic acids and their interactions with water molecules

The relative stabilities of Guanine-Cytosine (G-C) DNA bare base pairs, its tautomeric forms and microhydrated base pairs are theoretically investigated with a focus on the keto-enol tautomerism as well as on the cis-trans isomerism using ab initio and density functional theory methods. The stabilities of the G-C bare base pairs, its tautomeric forms and microhydrated base pairs were affected by various factors including keto-enol tautomerization, cis-trans enol isomerization, and steric hindrance between the base pair and water molecules. The Atoms in Molecules theory (AIM) is employed to investigate H-bonding patterns both in bare and microhydrated base pairs. From the above topological results, an excellent linear correlation is shown between electron density [rho(r)], and its Laplacian [V2rho(r)] at the bond critical points. NBO analysis has been carried out to study the charge transfer between proton acceptor to the antibonding orbital of the X-H bond both in bare and microhydrated base pairs.     

Equilibrium theory for the binding of bivalent antibodies to regularly spaced sites on a DNA molecule

In the autoimmune disease, Systemic Lupus Erythematosus, an individual produces antibodies that bind to his or her own DNA. In this paper we consider a single, long DNA-like molecule in a solution containing bivalent antibodies that can bind to the DNA molecule at regularly spaced sites. The antibody can be attached to DNA by either one or two binding sites. We assume that, when an antibody molecule binds through both its sites, it spans a fixed number of free sites that remain accessible to antibody binding. In this model, antibody molecules can interdigitate along the DNA molecule. We allow steric hindrance within such interdigitating clusters of bound antibodies. We derive analytical expressions for the average number of free, monovalently bound and bivalently bound antibodies, and see how this distribution is influenced by steric hindrance and by the relative binding strengths of the singly and doubly bound antibody.     

Symmetry of binding sites of a mouse IgA myeloma protein (MOPC 315)

We have investigated the mechanism of monovalency of the 7S subunit of a mouse IgA myeloma protein (MOPC 315) against a large antigen. This subunit, although it clearly can bind two molecules of a small hapten, fails to precipitate or hemagglutinate the relevant multivalent antigen. In an equilibrium Farr assay, we have shown that the subunit has only one valence for a univalent 40,000 molecular weight antigen (dinitrophenyl-dextran). We have investigated how various levels of affinity labeling quantitatively affect (a) the valence observed in the equilibrium Farr assay against a large antigen, and (b) the binding of the MOPC 315 to an insoluble antigenic matrix. Our results indicate that the Fab regions of the 7S subunit are arranged symmetrically and that the inactivity of one of them toward a large antigen is probably due to steric hindrance caused by the antigen bound to the adjacent site.     

Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids

Sequence-specific DNA-binding molecules such as triple helix-forming oligonucleotides (TFOs) provide a means for inducing site-specific mutagenesis and recombination at chromosomal sites in mammalian cells. However, the utility of TFOs is limited by the requirement for homopurine stretches in the target duplex DNA. Here, we report the use of pseudo-complementary peptide nucleic acids (pcPNAs) for intracellular gene targeting at mixed sequence sites. Due to steric hindrance, pcPNAs are unable to form pcPNA–pcPNA duplexes but can bind to complementary DNA sequences by Watson–Crick pairing via double duplex-invasion complex formation. We show that psoralen-conjugated pcPNAs can deliver site-specific photoadducts and mediate targeted gene modification within both episomal and chromosomal DNA in mammalian cells without detectable off-target effects. Most of the induced psoralen-pcPNA mutations were single-base substitutions and deletions at the predicted pcPNA-binding sites. The pcPNA-directed mutagenesis was found to be dependent on PNA concentration and UVA dose and required matched pairs of pcPNAs. Neither of the individual pcPNAs alone had any effect nor did complementary PNA pairs of the same sequence. These results identify pcPNAs as new tools for site-specific gene modification in mammalian cells without purine sequence restriction, thereby providing a general strategy for designing gene targeting molecules.     

Alterations in monoclonal antibody affinity and antigenic receptor site expression on mycoplasma-infected human colorectal cancer cells

The affinity of MoAb CO 17-1A and expression of its antigenic target were studied on uninfected and mycoplasma-infected colorectal cancer cell lines SW 1116 and SW 948. Binding of 125I-labeled CO 17-1A to SW 1116 cells was quantified at 37 degrees C by determination of the affinity constant (Ka) and the number of antigenic receptor sites (r) per cell using Scatchard plots. When mycoplasma-free SW 1116 cells were used as targets, Ka was 0.92 +/- 0.06 x 10(8) M-1 and r = 1.32 +/- 0.14 x 10(6) at 37 degrees C. One batch of unspeciated, mycoplasma-infected SW 116 cells had reduced affinity and a decreased number of antigenic receptor sites per cell for 125I-labeled 17-1A, while another batch of infected SW 1116 cells had a 4- to 5-fold increase in r and diminished Ka for the antibody compared with uninfected cells. When unspeciated, mycoplasma-infected SW 948 cells were exposed to 125I-labeled 17-1A and the data subjected to Scatchard analysis, the affinity of the antibody deviated markedly from linearity and rendered analysis for Ka and r meaningless. These data indicate that mycoplasma infection can produce variable effects on the cellular expression of antigenic receptor sites and the affinity of antibody for its target, and emphasize the importance of using mycoplasma-free cell lines in studies of these parameters.     

Monoclonal antibodies against distinct determinants of histone H5 bind to chromatin

A series of monoclonal antibodies specific for distinguishable epitopes in chromosomal protein histone H5 were obtained from mice immunized with either free H5 or H5 . RNA complexes. The antibodies elicited by H5 could be distinguished from those elicited by H5 . RNA by their binding to native or acid-denatured H5, by their interaction with the globular region of H5, and by their cross-reactivity with H1o. The specificity of the antibodies was assessed by enzyme-linked immunosorbent assay (ELISA) and immunoblotting experiments. The antibodies could distinguish between H5 and the closely related histones H1 and H1o. The binding of some of the antibodies to the antigens was dependent on the type of assay used, suggesting nonrandom binding of the antigen to the solid supports used in ELISA and immunoblotting. Competitive ELISA experiments indicate that 8 of the 11 antibodies characterized bind to distinct epitopes. Three monoclonal antibodies bind to epitopes which are in close spatial proximity, causing mutual steric hindrance. The monoclonal antibodies bind to nuclei of fixed cells and to isolated chromatin, indicating that the epitopes are present both in the purified protein and in chromatin-complexed H5. These monoclonal antibodies can be used to study the organization of distinct regions of histones H5 and H1o in chromatin and chromosomes.     

Effect of temperature on the acidolysis of N-acyl-N,alpha,alpha-trialkyl glycine amides as related to the nature of substituents.

The C-terminal amide bond of N-acyl-N,alpha,alpha-trialkyl glycine amides is labile to acid and this has been currently assigned to steric crowding within the amino acid residue. However, our previous work has shown that in the acidolysis of some of these compounds steric hindrance seems to play a less important role than what one would expect. Thus, the cleavage of two sets of such compounds bearing different degrees of crowding was investigated at five different temperatures in order to clarify the effect of structure on reactivity in terms of enthalpy and entropy of activation. The compounds exhibited an Arrhenius-type behaviour, and both enthalpies and entropies of activation were calculated by taking advantage of the transition state theory. In addition, the kinetic data were analysed in terms of isokinetic relationships in order to find evidence to support that the compounds react under the same mechanism. The changes in the reaction rate are governed by the changes in both the enthalpy and the entropy of activation, which are related to bond energy and steric hindrance, respectively. In general, the entropies of activation are very negative for all compounds investigated, which reflects large steric constrictions associated with the formation of the transition state. In addition, they are very sensitive to the structure of the substrates.     

Binding capacity differences for antibodies and Fc-fusion proteins on protein A chromatographic materials

A range of studies were carried out to investigate the underlying reason for differences in dynamic binding capacities observed with various antibodies and Fc-fusion proteins during Protein A chromatography. Dynamic binding capacities were determined for these biomolecules using different protein A stationary phase materials. SEC was carried out to determine the relative sizes of the antibodies and fusion proteins. Pore diffusivities and static binding capacities were also determined on these Protein A resin materials. Trends in the dynamic binding capacities for these molecules did not correlate with differences in pore diffusion coefficients as might be expected for a mass transfer limited system. Instead, dynamic binding capacities were seen to follow the same trends as the static binding capacities and the apparent size of the molecules. Differences in static binding capacities were attributed to be due to differences in steric factor between the molecules. Solution binding stoichiometry studies were employed to estimate intra-Protein A steric effects while binding to the various domains within a Protein A ligand. In addition, steric hindrance was also found to exist between adjacent immobilized Protein A ligands on the chromatographic surface. The combination of intra and inter Protein A steric hindrances can explain differences in binding capacities observed between various antibody and Fc fusion proteins. The effect of Protein A ligand density on these supports was also examined and the results indicate that increasing Protein A ligand density leads to a situation of diminishing returns for binding capacity due to increased steric hindrance on the resin surface. The results presented in this paper show that steric hindrances can dominate over mass transfer effects in causing capacity variation between different molecules on the same stationary phase. This can lead to the development of more cost-efficient chromatographic stationary phases as well as provide information during the selection of Protein A media for preparative purification of monoclonal antibodies and Fc fusion proteins.     

Use of phycoerythrin and allophycocyanin for fluorescence resonance energy transfer analyzed by flow cytometry: advantages and limitations

BACKGROUND: This study validates the use of phycoerythrin (PE) and allophycocyanin (APC) for fluorescence energy transfer (FRET) analyzed by flow cytometry. METHODS: FRET was detected when a pair of antibody conjugates directed against two noncompetitive epitopes on the same CD8alpha chain was used. FRET was also detected between antibody conjugate pairs specific for the two chains of the heterodimeric alpha (4)beta(1) integrin. Similarly, the association of T-cell receptor (TCR) with a soluble antigen ligand was detected by FRET when anti-TCR antibody and MHC class I/peptide complexes () were used. RESULTS: FRET efficiency was always less than 10%, probably because of steric effects associated with the size and structure of PE and APC. Some suggestions are given to take into account this and other effects (e.g., donor and acceptor concentrations) for a better interpretation of FRET results obtained with this pair of fluorochromes. CONCLUSIONS: We conclude that FRET assays can be carried out easily with commercially available antibodies and flow cytometers to study arrays of multimolecular complexes.     

Further probes into quantitative aspects of competitive binding assays: allowance for effects of antigen multivalency in immunoassays

Effects of antigen multivalency on procedures for the analysis of immunoassays are examined on the basis of a theoretical expression developed in the context of quantitative affinity chromatography [Nichol, L. W., Ward, L. D., and Winzor, D. J. (1981) Biochemistry 20, 4856-4860] but which is also pertinent to antigen-antibody interactions that may be described in terms of a single intrinsic association constant. Quantitative relationships are generated which provide the basis for more rigorous logit-log analyses of radioimmunoassays in which the antigen is multivalent, and an additional, theoretically superior, linear transform of the basic expression is developed. Simulated binding data for a tetravalent antigen system are then used to demonstrate the curvilinearity of the conventional Scatchard plot for such a system despite the homogeneity of binding sites, and the application of the various linear transforms involving logarithmic functions. Of particular interest in that regard is the observation that the traditional logit-log analyses yield linear plots with the predicted slope of unity even though antigen univalence is an implicit assumption in their application. Results obtained in a solid-phase radioimmunoassay of triiodothyronine are then presented to provide, for that system at least, experimental justification of the above-mentioned assumption that the antibody-antigen interactions may be described in terms of a single intrinsic association constant. Finally, an enzyme-linked immunoassay of ferritin is used to illustrate the possibility that a linear Scatchard plot may be obtained with a multivalent antigen under conditions where steric factors restrict participation of an antigen molecule to a single interaction with immobilized antibody.     

Steric hindrance effects on surface reactions: applications to BIAcore

Because surface-volume reactions occur in many biological and industrial processes, understanding the rate of such reactions is important. The BIAcore surface plasmon resonance (SPR) biosensor for measuring rate constants has such a geometry. Though several models of the BIAcore have been presented, few take into account that large ligand molecules can block multiple receptor sites, thus skewing the sensogram data. In this paper some general mathematical principles are stated for handling this phenomenon, and a surface-reaction model is presented explicitly. An integro-partial differential equation results, which can be simplified greatly using perturbation techniques, yielding linear and nonlinear integrodifferential equations. Explicit and asymptotic solutions are constructed for cases motivated by experimental design. The general analysis can provide insight into surface-volume reactions occurring in various contexts. In particular, the steric hindrance effect can be quantified with a single dimensionless parameter. This work was supported in part by NIGMS Grant 1R01GM067244-01.