Regression analysis of simulated radio-ligand equilibrium experiments using seven different mathematical models

Methods for measuring aptamer-protein equilibria: a review

Aptamers are single stranded DNA or RNA molecules that have been selected using in vitro techniques to bind target molecules with high affinity and selectivity, rivaling antibodies in many ways. In order to use aptamers in research and clinical applications, a thorough understanding of aptamer-target binding is necessary. In this article, we review methods for assessing aptamer-protein binding using separation based techniques such as dialysis, ultrafiltration, gel and capillary electrophoresis, and HPLC; as well as mixture based techniques such as fluorescence intensity and anisotropy, UV-vis absorption and circular dichroism, surface plasmon resonance, and isothermal titration calorimetry. For each method the principle, range of application and important features, such as sample consumption, experimental time and complexity, are summarized and compared.

Measurement of the affinity of anti-D in the serum of immunized mothers and in immunoglobulin preparations with unlabeled antibodies

BACKGROUND

Few data are available on the affinity of maternal anti-D responsible for hemolytic disease of the fetus and the newborn (HDN) and of anti-D used for the prophylaxis of that disease. A method was recently described to measure the affinity (K(a)) of untagged anti-D monoclonal antibodies (MoAbs). In this work, the same method was applied to determine the K(a) of polyclonal anti-D.

STUDY DESIGN AND METHODS

O R(1)r red blood cells (RBCs) were sensitized with increasing concentrations of native anti-D in serum samples from immunized mothers and donors and in RhIG preparations. At equilibrium, the amount of anti-D bound to RBCs was measured by enzyme-linked immunosorbent assay. Scatchard and Langmuir equations were used to determine Ka.

RESULTS

The experimental data fitted well with the Scatchard equation (mean r2=0.95) but a better correlation was observed with the Langmuir equation (mean r2=0.99). The mean Ka of anti-D in 11 maternal serum samples, in 6 immunized donors, and in 5 lots of RhIG were 5.6x10(8) per M (from 2.8x10(8) to 12x10(8)/M), 3.9x10(8) per M (from 1.5x10(8) to 6.8x10(8)/M), and 3.4x10(8) per M (from 3.1x10(8) to 4.2x10(8)/M), respectively. The comparison of anti-D affinity in 5 cases of HDN with fetal anemia and in 6 cases of HDN with postnatal anemia showed no significant difference.

CONCLUSION

The method previously described for anti-D MoAbs was applied to polyclonal anti-D present in the serum of immunized subjects and in immunoglobulin preparations. The experimental data fitted well with the Langmuir equation, and the affinity of polyclonal of anti-D was measured with accuracy.

Evaluation of the flow-dialysis technique for analysis of protein-ligand interactions: an experimental and a monte carlo study

Flow dialysis has found widespread use in determining the dissociation constant (KD) of a protein-ligand interaction or the amount of available binding sites (E0). This method has the potency to measure both these parameters in a single experiment and in this article a method to measure simultaneously the KD and E0 is presented, together with an extensive error analysis of the method. The flow-dialysis technique is experimentally simple to perform. However, a number of practical aspects of this method can have a large impact on the outcome of KD and E0. We have investigated all sources of significant systematic and random errors, using the interaction between mannitol and its transporter from Escherichia coli as a model. Monte Carlo simulations were found to be an excellent tool to assess the impact of these errors on the binding parameters and to define the experimental conditions that allow their most accurate estimation.

Measurement of anti-D intrinsic affinity with unlabeled antibodies

BACKGROUND

The method most commonly used for measuring the affinity of MoAbs specific for the D antigen is a binding assay using 125I-labeled MoAb. Although the method is relatively simple, there are several drawbacks that can lead to inaccurate results. The objective of the present work was to develop a method for the determination of the affinity of anti-D MoAb using unlabelled antibodies.

STUDY DESIGN AND METHODS

Rh-positive RBCs were sensitized with varying amounts of unlabeled anti-D MoAb, and, at equilibrium, the amount of anti-D bound to the RBCs was measured by ELISA. The affinity and the number of antigenic sites were determined with the Scatchard and Langmuir equations.

RESULTS

The method was applied to determine the affinity of several MoAbs specific for the D antigen on RBCs of different Rh-positive phenotypes. Similar results were observed with both equations. The affinity constant (Ka) for 3 MoAbs specific for the D antigen on group O R1r RBCs ranged from 1.3 to 7.4 108 M-1, depending on the antibody. When measured by a binding assay with 125I-labeled anti-D MoAbs, the Ka were significantly lower, indicating that 125I-labeling diminishes anti-D affinity, even when the labeling is at a low level.

CONCLUSION

A simple ELISA method was developed for the measurement of the affinity of anti-D MoAbs for the D antigen and for the number of antigenic sites per RBC. As a result, the affinity of anti-D can be estimated accurately, thus avoiding the drawbacks inherent in modification of the antibody by 125I-labeling.

Three Complement-Type Repeats of the Low-Density Lipoprotein Receptor-Related Protein Define a Common Binding Site for RAP, PAI-1, and Lactoferrin

The low-density lipoprotein receptor-related protein (LRP) is a 600-kD scavenger receptor that binds a number of protein ligands with high affinity. Although some ligands do not compete with each other, binding of all is uniformly blocked by the 39-kD receptor-associated protein (RAP). RAP is normally found in the endoplasmic reticulum and seems to function as a chaperone for LRP. To identify the binding sites for RAP, lactoferrin, and plasminogen activator inhibitor-1 (PAI-1), a bacterial expression system has been developed to produce soluble LRP fragments spanning residues 783-1399. These residues overlap most of the CNBr fragment containing the second cluster of complement-type repeats (C). Solid phase binding assays show that 125I-RAP binds to fragments containing three successive complement-type repeats: C5-C7. PAI-1 and lactoferrin bind to the same fragments. A fragment containing C5-C7 also blocks uptake and degradation of 125I-RAP by fibroblasts in a concentration-dependent manner. Binding competition experiments show that RAP, PAI-1, and lactoferrin each inhibit the binding of the others, suggesting that at this site in LRP, RAP acts as a competitive, rather than an allosteric, inhibitor of PAI-1 and lactoferrin binding.

© 1998 by The American Society of Hematology.

Three Complement-Type Repeats of the Low-Density Lipoprotein Receptor-Related Protein Define a Common Binding Site for RAP, PAI-1, and Lactoferrin

The low-density lipoprotein receptor-related protein (LRP) is a 600-kD scavenger receptor that binds a number of protein ligands with high affinity. Although some ligands do not compete with each other, binding of all is uniformly blocked by the 39-kD receptor-associated protein (RAP). RAP is normally found in the endoplasmic reticulum and seems to function as a chaperone for LRP. To identify the binding sites for RAP, lactoferrin, and plasminogen activator inhibitor-1 (PAI-1), a bacterial expression system has been developed to produce soluble LRP fragments spanning residues 783-1399. These residues overlap most of the CNBr fragment containing the second cluster of complement-type repeats (C). Solid phase binding assays show that 125I-RAP binds to fragments containing three successive complement-type repeats: C5-C7. PAI-1 and lactoferrin bind to the same fragments. A fragment containing C5-C7 also blocks uptake and degradation of 125I-RAP by fibroblasts in a concentration-dependent manner. Binding competition experiments show that RAP, PAI-1, and lactoferrin each inhibit the binding of the others, suggesting that at this site in LRP, RAP acts as a competitive, rather than an allosteric, inhibitor of PAI-1 and lactoferrin binding.

© 1998 by The American Society of Hematology.

Computational models in immunological methods: an historical review

The utilization of computational models in immunology dates from the birth of the science. From the description of antibody-antigen binding to the structural models of receptors, models are utilized to bring fundamental understandings of the processes together with laboratory measurements to uncover implications of these data. In this review, an historical view of the role of computational models in the immunology laboratory is presented, and short mathematical descriptions are given of fundamental assays. In addition, the range of current uses of models is explored -- especially as seen through papers which have appeared in the Journal of Immunological Methods from volume 1 (1971/1972) to volume 208 (1997). Each paper which introduced a new mathematical, statistical, or computer simulation model, or introduced an enhancement to an instrument through a model in those volumes is cited and the type of computational model noted.